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Web 2.0 e ricerca (Giovanni M. Dall'Olio – raduno molecularlab 2008)

Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

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Page 1: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Web 20 e ricerca

(Giovanni M DallOlio ndash raduno molecularlab 2008)

Cosa eacute Web 20

bull Blogs

bull Rss Feedsbull Wikis (wikipedia)

bull Social Bookmarking (delicious)bullMultimediashysharing systems (Youtube shygt videos

Flickr shygt photos lastfm shygt music )

These and others are called Web 20 Technologies[1]

The common point in all web 20 technologies is that they help people in sharing informations and opinions

Scientists also need to share and exchange their informations and opinions[2]

Lets see a few examples of some of the Web 20 applications actually used in the scientific community

What is Web 20

I - Blogs

I blog sono lequivalente di un diario personale reso pubblico su Internet

Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]

Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali

I - Blogs

The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla

genetica dei microrganismi unicellulari[5]

Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]

Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate

the fungalgenomeorg Blog

(httpwwwfungalgenomeorgblog)

programming4scientistscom

Blog di bioinformatica programmazione per scienziati

Lautore fornisce consigli e tutorial su come programmare per scienziati

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 2: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Cosa eacute Web 20

bull Blogs

bull Rss Feedsbull Wikis (wikipedia)

bull Social Bookmarking (delicious)bullMultimediashysharing systems (Youtube shygt videos

Flickr shygt photos lastfm shygt music )

These and others are called Web 20 Technologies[1]

The common point in all web 20 technologies is that they help people in sharing informations and opinions

Scientists also need to share and exchange their informations and opinions[2]

Lets see a few examples of some of the Web 20 applications actually used in the scientific community

What is Web 20

I - Blogs

I blog sono lequivalente di un diario personale reso pubblico su Internet

Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]

Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali

I - Blogs

The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla

genetica dei microrganismi unicellulari[5]

Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]

Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate

the fungalgenomeorg Blog

(httpwwwfungalgenomeorgblog)

programming4scientistscom

Blog di bioinformatica programmazione per scienziati

Lautore fornisce consigli e tutorial su come programmare per scienziati

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 3: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

The common point in all web 20 technologies is that they help people in sharing informations and opinions

Scientists also need to share and exchange their informations and opinions[2]

Lets see a few examples of some of the Web 20 applications actually used in the scientific community

What is Web 20

I - Blogs

I blog sono lequivalente di un diario personale reso pubblico su Internet

Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]

Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali

I - Blogs

The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla

genetica dei microrganismi unicellulari[5]

Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]

Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate

the fungalgenomeorg Blog

(httpwwwfungalgenomeorgblog)

programming4scientistscom

Blog di bioinformatica programmazione per scienziati

Lautore fornisce consigli e tutorial su come programmare per scienziati

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 4: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

I - Blogs

I blog sono lequivalente di un diario personale reso pubblico su Internet

Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]

Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali

I - Blogs

The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla

genetica dei microrganismi unicellulari[5]

Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]

Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate

the fungalgenomeorg Blog

(httpwwwfungalgenomeorgblog)

programming4scientistscom

Blog di bioinformatica programmazione per scienziati

Lautore fornisce consigli e tutorial su come programmare per scienziati

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 5: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

I blog sono lequivalente di un diario personale reso pubblico su Internet

Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]

Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali

I - Blogs

The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla

genetica dei microrganismi unicellulari[5]

Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]

Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate

the fungalgenomeorg Blog

(httpwwwfungalgenomeorgblog)

programming4scientistscom

Blog di bioinformatica programmazione per scienziati

Lautore fornisce consigli e tutorial su come programmare per scienziati

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 6: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla

genetica dei microrganismi unicellulari[5]

Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]

Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate

the fungalgenomeorg Blog

(httpwwwfungalgenomeorgblog)

programming4scientistscom

Blog di bioinformatica programmazione per scienziati

Lautore fornisce consigli e tutorial su come programmare per scienziati

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 7: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

the fungalgenomeorg Blog

(httpwwwfungalgenomeorgblog)

programming4scientistscom

Blog di bioinformatica programmazione per scienziati

Lautore fornisce consigli e tutorial su come programmare per scienziati

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 8: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

programming4scientistscom

Blog di bioinformatica programmazione per scienziati

Lautore fornisce consigli e tutorial su come programmare per scienziati

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 9: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Nature Blogs

Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 10: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Nascent

Blog sulla tecnologia web appartenente al circuito di Nature

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 11: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

II - Wikis

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 12: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

A wiki is a website that allows visitors to add remove and otherwise edit and change content

Like Wikipedia (httpenwikipediaorg)[7]

II - Wikis

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 13: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Wikipedia

(httpenwikipediaorg)

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 14: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Build your Labs Wiki

The software that run wikipedia is called MediaWiki and is released under a free license [8]

This means you can download it (the templates of the wiki without its contents) to use it for your own purposes

So you can create a website with the same functionalities and interface of wikipedia but with your own content

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 15: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Build your own wiki - examples(Alternative Splicing Wiki[9])

(This is a wiki I use on my laptop to organize my work about alternative splicing)

Alternative splicing analysis tools

Alternative splicing analysis tools

DatabasesArticles

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 16: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Build your own wiki - examples(appunti di bioinformatica libera[10])

(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

  • Pagina 1
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Page 17: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Wiki Technology in Bioinformatics Examples (I)

openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research

the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)

There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 18: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

OpenWetWare

(httpopenwetwareorg)

Protocols (How to make a PCR how to design primers etc)

Labs home pages

Resources (tutorials etc)

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

  • Pagina 1
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Page 19: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

AAAWiki (Annotation of 12 Drosophila spp genomes)

(httpranalblgovdrosophilawiki)

Announcements

DataPapers

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 20: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Wiki Technology in Bioinformatics Examples (II)

WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews

Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences

GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

  • Pagina 1
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Page 21: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

WikiOmics(wikipedia for bioinformaticists)

(httpwikiomicsorg)

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

  • Pagina 1
  • Pagina 2
  • Pagina 3
  • Pagina 4
  • Pagina 5
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Page 22: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Wiki Technology in Bioinformatics Examples (III)

GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms

EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network

The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation

The SynapticLeap (httpthesynapticleaporg) hosts some research communities

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 23: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Wiki Technology in Bioinformatics Examples (IV)

WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews

The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]

BioWiki (httpbiowikiorg) hosts other bioinformatics projects

WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 24: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

FungalGenome Wiki

(httpfungalgenomeorgwiki)

Projects - descriptions

Protocols

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

  • Pagina 1
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Page 25: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

III - Social-Bookmarking

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 26: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

III - Social-Bookmarking

Social Bookmarking meansndash When I find an interesting websitearticledocument I

share its address with other people ndash or with the other members of the lab(s)[13]

ndash Other people can add their comments and tags to it

ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 27: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Social Bookmarking in Science

The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 28: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

delicious

It is the most known Social Bookmarking Service

It is not designed to manage publications only bookmarks

Easy to configure and use (firefoxepiphany extension)

Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 29: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Social Bookmarking ndash how does it work

You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)

you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)

When you find an interesting article you click on that button and follow the instructions

Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 30: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Social Bookmarking in ScienceConnotea

Connotea is an online social bookmarking service for scientists created by Nature Publishing Group

It allows to post articles as well as web documents

It automatically recognizes metadata like title author abstract when posting an article

Slightly more difficult to configure and use (no firefox extension)[16]

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 31: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Connotea Screenshots (I)(main page)

(httpwwwconnoteaorg)

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 32: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Connotea Screenshots (II)(searching for tags)

(httpwwwconnoteaorgsearchq=22alternative+splicing22)

Search Interface

Search Results

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 33: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Connotea Screenshots (III)(posting an article)

(httpwwwconnoteaorg - note the automatic recognition of title and authors)

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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  • Pagina 53
  • Pagina 54
  • Pagina 55
Page 34: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Social Bookmarking in ScienceCiteULike

CiteULike is another social referencingbookmarking tool for scientists

Its not opensource but its not related to any publishing group (eg Nature)

Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc

CiteULike and Connotea have different databases and users[17]

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 35: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

CiteULike Screenshots (I)(searching between tags)

(httpwwwciteulikeorg)

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

  • Pagina 1
  • Pagina 2
  • Pagina 3
  • Pagina 4
  • Pagina 5
  • Pagina 6
  • Pagina 7
  • Pagina 8
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Page 36: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Connotea Screenshots (II)(posting an article)

(httpwwwciteulikeorg - note the automatic recognition of title and authors)

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 37: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

IV Scientific Communities

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 38: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Comunitagrave scientifiche

Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale

Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 39: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

myExperiment

Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici

Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 40: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Esempi di workflow da myExperiment

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 41: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Second Life

Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online

Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 42: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Molecularlab )

Non esistono molte comunitagraveforum scientifici attivi

Molti sono semishyabbandonati o con poca frequenza

A volte si preferiscono le mailing list

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 43: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Scivee

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 44: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

V - RSS Feed

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 45: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

V - RSS Feed

RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]

Imagine an online newspaper site users can use rss feeds to be notified when a new article appears

Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 46: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

how do I use Rss Feeds III

When you see this symbol

on a website it means it offers rss feeds You can click on it and follow the instructions to

subscribe to the sites rss feeed

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 47: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 48: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 49: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

how do I use Rss Feeds - examples

Rss Feeds Button(click on it to subscribe)

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 50: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

how do I use Rss Feeds IIII

Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have

builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash

they have a better interface they can show notifications on your desktop etc

ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)

How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

  • Pagina 1
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Page 51: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Rss Feeds instant notificationsof new articles on your desktop (I)

(liferea a rss reader)

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 52: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Liferea an RSS Reader

(This is liferea on my computer)

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 53: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

Rss Feeds instant notificationsof new articles on your desktop (II)

(mugshot another rss reader)

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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Page 54: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

References [1] Def Web 20 httpenwikipediaorgwikiWeb_20

httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020

[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )

[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog

[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)

[6] A few discussions about the topic blog and science

ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)

ndash httpwwwnodalpointorgnode1623 and others on nodalpoint

[7] Just in case httpenwikipediaorgwikiWikipedia

[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

  • Pagina 1
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Page 55: Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested

[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )

[11] Discussions and articles about using Wikis to improve genome annotation

ndash httpnodalpointorg20070212genome_wiki

ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation

ndash httpgenomebiologycom200781102

[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation

[13] Discussions about using Social Bookmarking in Science

ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint

[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental

[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics

[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide

[17] Connotea and CiteULike have different users

[18] Rss Feeds httpenwikipediaorgwikiRss_Feed

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