View
350
Download
3
Category
Preview:
DESCRIPTION
Astronomers are being drowned in data: facilities like ALMA currently provide datasets in the Gigabyte range, and increasing, while facilities like the LSST and the SKA will generate datasets large enough so that data download, even of the reduced datasets, will not be feasible. In this talk we will introduce the concept of Scientific Workflows, as software tools that allow for the easy exploration of both local and remote datasets and processing services, and of Research Objects, which encapsulate all relevant aspects of a scientific experiment, and allow for its quantitative and qualitative assessment, enable reuse with proper attribution, and linkage to publications, among others. The AstroTaverna plugin, with astronomy-specific for workflow creation, was also presented in this ALMA Weekly Seminar.
Citation preview
Wf4Ever: Scientific Workflows and Research Objects as tools for scientific insight and methodology curation
Juande Santander-Vela jdsant@iaa.esInstituto de Astrofísica de Andalucía-CSIC
Talk Outline
Introduction
Current challenges for radio astronomy and science
Potential e-Science solutions: Workflows and Research Objects
Final points
Introduction
Who am I?Member of the AMIGA international collaboration, based at IAA-CSIC
Ph.D. on bringing Radio Astronomical data archives and tools into the VO
Applied Scientist at ESO VLT archive, Software Engineer/Astronomy Specialist at ALMA archive (May 2009-Dec 2011)Back to IAA-CSIC as VIA-SKA Project Manager, Radio Astroinformatician
GROUP INTEREST IN TECH DEVELOPMENTS FOR BETTER SCIENCE
Why I’m here?
Collaboration with Stephane Leon and the ALMA Data Management Group
Helping bring the ALMA Science Archive to the VO ⬅ Modelling radio data cubesFinding use cases for workflow technology (see later)
AMIGAAnalysis of the interstellar Medium of Isolated GAlaxies
Multi-wavelength, multi-object study on isolated galaxies with strict isolation criteriaCareful curation of dataVery careful processing of new parameters from
Group’s own observation programs and data reductionLiterature table scanningVirtual Observatory table harvesting and parsing
Emphasis on marrying astronomy and computer science, and buy-in of the VO
E-SCIENCE USERS
AMIGAAnalysis of the interstellar Medium of Isolated GAlaxies
Multi-wavelength, multi-object study on isolated galaxies with strict isolation criteriaCareful curation of dataVery careful processing of new parameters from
Group’s own observation programs and data reductionLiterature table scanningVirtual Observatory table harvesting and parsing
Emphasis on marrying astronomy and computer science, and buy-in of the VO
E-SCIENCE DEVELOPERS!
AMIGA
Project goal: providing a baseline for galaxy properties to compare with other environments
Interaction-free sample, ideal for tracing HI infall: we can use CIG galaxies to detect the cosmic web
Need for very sensitive telescopes able to resolve faint HI ➡ Square Kilometre Array & pathfinders
PARTICIPATING IN SKA.TEL.SDP CONSORTIUMWE NEED TOOLS FOR OUR OWN SCIENCE ANALYSIS
⤷
Current challenges for radio astronomy
and science
Data over-abundanceMoore’s Law for Detectors ➡ Exponential increase of individual and accumulated data sets
We have more data than ever… but we can’t use it:Because we can’t:
Difficult to set up (for sharing)Difficult to find (for using)Difficult to document (both using and sharing)Difficult to deal with (because of size, formatting, purpose…)
Because it is not in our best interest
FULLY
?
Courtesy J.E. Ruiz (AMIGA, Wf4Ever)
Courtesy J.E. Ruiz (AMIGA, Wf4Ever)
Tools!
Data sharingSearch Go
Advanced search
Home News & Comment Research Careers & Jobs Current Issue Archive Audio & Video For Authors
SPECIALS See all specials
Editorial Feature Opinion Elsewhere in Nature
DATA SHARINGSharing data is good. But sharing your own data? That can get complicated. As two researchcommunities who held meetings in May on the issue report their proposals to promote data sharingin biology, a special issue of Nature examines the cultural and technical hurdles that can get in theway of good intentions.
Data SharingSpecials & supplements archiveArchive
DATA FLIRTING
DATA HOARDING
IRREPRODUCIBLE RESEARCH
?
Irreproducible researchSearch Go
Advanced search
Home News & Comment Research Careers & Jobs Current Issue Archive Audio & Video For Authors
SPECIAL See all specials
Editorial News and analysis Comment Perspectives and reviews
CHALLENGES IN IRREPRODUCIBLE RESEARCHNo research paper can ever be considered to be the final word, and the replication andcorroboration of research results is key to the scientific process. In studying complex entities,especially animals and human beings, the complexity of the system and of the techniques can alltoo easily lead to results that seem robust in the lab, and valid to editors and referees of journals,but which do not stand the test of further studies. Nature has published a series of articles aboutthe worrying extent to which research results have been found wanting in this respect. The editorsof Nature and the Nature life sciences research journals have also taken substantive steps to putour own houses in order, in improving the transparency and robustness of what we publish.Journals, research laboratories and institutions and funders all have an interest in tackling issuesof irreproducibility. We hope that the articles contained in this collection will help.
Free full access
Challenges in irreproducible researchSpecials & supplements archiveArchive
nature.com Sitemap Cart Login Register
Search GoAdvanced search
Home News & Comment Research Careers & Jobs Current Issue Audio & Video For Authors
SPECIAL See all specials
EDITORIAL
NEWS AND ANALYSIS
COMMENT
Editorial News and analysis Comment Perspectives and reviews
CHALLENGES IN IRREPRODUCIBLE RESEARCHNo research paper can ever be considered to be the final word, and the replication andcorroboration of research results is key to the scientific process. In studying complex entities,especially animals and human beings, the complexity of the system and of the techniques can alltoo easily lead to results that seem robust in the lab, and valid to editors and referees of journals,but which do not stand the test of further studies. Nature has published a series of articles aboutthe worrying extent to which research results have been found wanting in this respect. The editorsof Nature and the Nature life sciences research journals have also taken substantive steps to putour own houses in order, in improving the transparency and robustness of what we publish.Journals, research laboratories and institutions and funders all have an interest in tackling issuesof irreproducibility. We hope that the articles contained in this collection will help.
Free full access
Reducing our irreproducibilityNature 496, 398 ( 25 April 2013 )
Further confirmation neededA new mechanism for independently replicating research findings is one of several changes required toimprove the quality of the biomedical literature.Nature Biotechnology 30, 806 ( 10 September 2012 )
Error proneBiologists must realize the pitfalls of work on massive amounts of data.Nature 487, 406 ( 26 July 2012 )
Must try harderToo many sloppy mistakes are creeping into scientific papers. Lab heads must look more rigorously at thedata — and at themselves.Nature 483, 509 ( 29 March 2012 )
Independent labs to verify high-profile papersMonya BakerNature News ( 14 August 2012 )
Power failure: why small sample size undermines the reliability of neuroscienceKatherine S. Button, John P. A. Ioannidis et al.Nature Reviews Neuroscience 14, 365-376 ( 15 April 2013 )
Replication studies: Bad copyEd YongNature 485, 298-300 ( 17 May 2012 )
Why animal research needs to improveMalcolm MacleodNature 477, 511 ( 29 September 2011 )
Reliability of 'new drug target' claims called into questionAsher MullardNature Reviews Drug Discovery 10, 643-644 ( September 2011 )
If a job is worth doing, it is worth doing twiceJonathan F. RussellNature 496, 7 ( 04 April 2013 )
Challenges in irreproducible researchSpecials & supplements archiveArchive
Irreproducible researchSearch Go
Advanced search
Home News & Comment Research Careers & Jobs Current Issue Archive Audio & Video For Authors
SPECIAL See all specials
Editorial News and analysis Comment Perspectives and reviews
CHALLENGES IN IRREPRODUCIBLE RESEARCHNo research paper can ever be considered to be the final word, and the replication andcorroboration of research results is key to the scientific process. In studying complex entities,especially animals and human beings, the complexity of the system and of the techniques can alltoo easily lead to results that seem robust in the lab, and valid to editors and referees of journals,but which do not stand the test of further studies. Nature has published a series of articles aboutthe worrying extent to which research results have been found wanting in this respect. The editorsof Nature and the Nature life sciences research journals have also taken substantive steps to putour own houses in order, in improving the transparency and robustness of what we publish.Journals, research laboratories and institutions and funders all have an interest in tackling issuesof irreproducibility. We hope that the articles contained in this collection will help.
Free full access
Challenges in irreproducible researchSpecials & supplements archiveArchive
nature.com Sitemap Cart Login Register
Search GoAdvanced search
Home News & Comment Research Careers & Jobs Current Issue Audio & Video For Authors
SPECIAL See all specials
EDITORIAL
NEWS AND ANALYSIS
COMMENT
Editorial News and analysis Comment Perspectives and reviews
CHALLENGES IN IRREPRODUCIBLE RESEARCHNo research paper can ever be considered to be the final word, and the replication andcorroboration of research results is key to the scientific process. In studying complex entities,especially animals and human beings, the complexity of the system and of the techniques can alltoo easily lead to results that seem robust in the lab, and valid to editors and referees of journals,but which do not stand the test of further studies. Nature has published a series of articles aboutthe worrying extent to which research results have been found wanting in this respect. The editorsof Nature and the Nature life sciences research journals have also taken substantive steps to putour own houses in order, in improving the transparency and robustness of what we publish.Journals, research laboratories and institutions and funders all have an interest in tackling issuesof irreproducibility. We hope that the articles contained in this collection will help.
Free full access
Reducing our irreproducibilityNature 496, 398 ( 25 April 2013 )
Further confirmation neededA new mechanism for independently replicating research findings is one of several changes required toimprove the quality of the biomedical literature.Nature Biotechnology 30, 806 ( 10 September 2012 )
Error proneBiologists must realize the pitfalls of work on massive amounts of data.Nature 487, 406 ( 26 July 2012 )
Must try harderToo many sloppy mistakes are creeping into scientific papers. Lab heads must look more rigorously at thedata — and at themselves.Nature 483, 509 ( 29 March 2012 )
Independent labs to verify high-profile papersMonya BakerNature News ( 14 August 2012 )
Power failure: why small sample size undermines the reliability of neuroscienceKatherine S. Button, John P. A. Ioannidis et al.Nature Reviews Neuroscience 14, 365-376 ( 15 April 2013 )
Replication studies: Bad copyEd YongNature 485, 298-300 ( 17 May 2012 )
Why animal research needs to improveMalcolm MacleodNature 477, 511 ( 29 September 2011 )
Reliability of 'new drug target' claims called into questionAsher MullardNature Reviews Drug Discovery 10, 643-644 ( September 2011 )
If a job is worth doing, it is worth doing twiceJonathan F. RussellNature 496, 7 ( 04 April 2013 )
Challenges in irreproducible researchSpecials & supplements archiveArchive
Tool over-abundance
++
Starship Asterisk*APOD and General Astronomy Discussion Forum
Board index ‹ Learning & Resources ‹ The Engineering Deck: Astrophysics Source Code Library
FAQ Register Login
Search this forum… Search 671 topics • Page 1 of 7 • 1 2 3 4 5 ... 7
The Engineering Deck: Astrophysics Source Code Library
Search… SearchAdvanced search
Post a new topic
ANNOUNCEMENTS REPLIES VIEWS LAST POST
Welcome & Rules (please read before posting) by RJN » Mon Jan 18, 2010 7:40 pm 0 15666 by RJN
Mon Jan 18, 2010 7:40 pm
TOPICS REPLIES VIEWS LAST POST
Guide to the Astrophysics Source Code Library by RJN » Sat Jul 24, 2010 8:01 pm 13 17027 by owlice
Mon Jul 01, 2013 3:32 am
1 2Papers of Possible Interest to Astronomical Software Users by owlice » Tue Oct 12, 2010 7:02 am 27 7056 by owlice
Wed May 15, 2013 1:31 pm
1 2The Astrophysics Source Code Library: New codes welcome by RJN » Sat Jul 24, 2010 8:01 pm 26 5273 by Eran Ofek
Thu Dec 13, 2012 9:20 pm
*Web Resources and Tools for Astrophysicists/Astronomers* by owlice » Sat Jul 16, 2011 12:01 pm 22 2750 by owlice
Fri May 10, 2013 12:12 pm
2011 and 2012 Additions to the ASCL by owlice » Thu Feb 24, 2011 11:26 pm 23 1693 by owlice
Sat Dec 08, 2012 8:09 pm
21cmFAST: Simulation of the High-Redshift 21-cm Signal by owlice » Thu Feb 17, 2011 10:47 pm 0 3443 by owlice
Thu Feb 17, 2011 10:47 pm
2LPTIC: 2nd-order Lagrangian Perturbation Theory Initial Con by owlice » Tue Jan 03, 2012 5:27 am 0 855 by owlice
Tue Jan 03, 2012 5:27 am
2MASS Kit: 2MASS Catalog Server Kit by owlice » Sun Mar 17, 2013 5:16 pm 0 214 by owlice
Sun Mar 17, 2013 5:16 pm
3DEX: Fast Fourier-Bessel Decomposition of Spherical 3D Surv by owlice » Sat Nov 26, 2011 4:00 pm 0 741 by owlice
Sat Nov 26, 2011 4:00 pm
AAOGlimpse: Three-dimensional Data Viewer by owlice » Sat Oct 15, 2011 11:29 am 0 1034 by owlice
Sat Oct 15, 2011 11:29 am
ACORNS-ADI: Calibration, Registration and Nulling in Imaging by kcd » Sat Mar 30, 2013 7:40 am 0 177 by kcd
Sat Mar 30, 2013 7:40 am
ACS: ALMA Common Software by kcd » Sat Feb 09, 2013 3:44 am 0 269 by kcd
Sat Feb 09, 2013 3:44 am
AdaptaHOP: Subclump finder by kcd
671 topics • Page 1 of 7 •
Services too!
How to deal with all this?
++All of this compounds the problems of reproducibility, methodology assessment, result dissemination…
How to deal with all this?
AND THE CODE?
WHAT SOFTWARE DOES IT DEPEND ON?
WHICH CODE DID WHAT?
NOT
A GOOD
SOLUTION
TRADITIONALLY…
How to deal with all this?
++ORCHESTATION,ENCAPSULATION,DATA ACCESS,PROVENANCE,
ANNOTATION…
Why Workflows?SCIENTIFIC
Workflows define computationsEvents & ProcessesDependencies
ResourcesLocal & Remote ProcessesSequencesConcurrencesTriggers
FORMALLY,OR AT LEAST
MACHINE READABLE
➡
WORKFLOWDEFINITIONLANGUAGES
Workflows enable distributed computing
Distributed computing paradigmMove computation to the dataComputing services
Collaborative environments
Linked data }FOR SCIENTIFIC DISCUSSION &
SCIENCE EXTRACTION
➡ Science-computing
Workflows enable distributed computing
Data can be anywhere
Workflows can be constructed hierarchicaly
Each workflow does useful work on its own
The data flow can be easily followed
Workflows enable interactive computing
Each workflow run records it’s inputs, outputs, and intermediate results
You can build and run workflows incrementally
You can get (almost) immediate feedback on changes
Tools for workflow storage and discovery
About | Give us Feedback | Publications Juandesant
New Workflow GO Workflows Search
View
Download (v7)
Taverna 2
OriginalUploader
PaulFisher
View
Download (v4)
Taverna 1
OriginalUploader
MarcoRoos
View
Download (v3)
Taverna 1
OriginalUploader
HamishMcWilliam
View
Download (v4)
Taverna 1
OriginalUploader
MarkBorkum
View
Download (v4)
Taverna 1
OriginalUploader
PaulFisher
View
Download (v5)
Taverna 1
OriginalUploader
PaulFisher
View
Download (v4)
Taverna 1
OriginalUploader
AlanWilliams
View
Download (v1)
Taverna 1
OriginalUploader
M.B.Mon...
View
Download (v1)
Taverna 1
OriginalUploader
AlanWilliams
View
Download (v3)
Taverna 1
OriginalUploader
AndreaWiggins
Sort by: Rank« Previous 1 2 3 4 5 … 221 Next »
1111562243
43342624231813
223103102102
827775727167
268908268645345353533
1472339317
251310
9631
264776142322725222221
88432524241917161514
42302723191918171311
Search filter terms
Filter by type Taverna 2 Taverna 1 RapidMiner Kepler Bioclipse Scri… LONI Pipeline GWorkflowDL KNIME BioExtract Ser… Galaxy
Filter by tag example mygrid bioinformatics localworker cheminformatics benchmarks protein workflow votable ebi
Filter by user Alan Williams Paul Fisher Antoon Goderis Peter Li Anja Le Blanc Hamish McWil… Francois Belle… Rafael C. Jim… Stian Soiland-… Egon Willigha…
Filter by licence by-sa by-nd by BSD GPL Apache LGPL by-nc-sa CC0 MIT
Filter by group myGrid HELIO IST 600 SCAPE SabrOndexPr… AMIGA e-LICO BioSemantics MediGRID TextGrid
Filter by wsdl http://soap.ge… http://xml.nig.a… http://phoebus… http://eutils.nc… http://xml.nig.a… http://www.ebi… http://www.ebi… http://www.ch… http://cagnode… http://festung1…
Filter by curation Decommissio… Requires exa… Requires des… Runnable Obsolete - de… Test workflow Example data Not runnable Tutorial / exa… Whole solution
« Previous 1 2 3 4 5 … 221 Next »Sort by: Rank
Results per page: 10
Home Users Groups Workflows Files Packs Topics
Home > Workflows
Workflows
Showing 2207 results. Use the filters on the left and the search box below to refine the results.
Search
Pathways and Gene annotations for QTL region (7)
Created: 19/11/09 @ 18:18:52 | Last updated: 07/09/12 @ 18:23:36
Credits: Paul Fisher
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in themouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTLstart base pair position; QTL end base pair position. Data is then extracted from BioMart to annotateeach of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG toobtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways inthe KEGG path...
Rating: 4.6 / 5 (10 ratings) | Versions: 7 | Reviews: 1 | Comments: 7 | Citations: 1
Viewed: 7291 times | Downloaded: 1283 times
Tags (22):
adasd | chromosome | data-driven | disease | ensembl | entrez | gene | genes | genotype | kegg | mouse | nbiconworkflows | pathway |pathway-driven | pathways | phenotype | qtl | shim | subworkflow | uniprot
BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)
Created: 15/12/08 @ 20:46:09 | Last updated: 11/08/11 @ 09:22:23
Credits: Marco Roos AID
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow finds disease relevant to the query string via the following steps: 1. A user query:a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding
'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based onApa...
Rating: 4.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 3 | Citations: 0
Viewed: 4567 times | Downloaded: 749 times
Tags (9):
AIDA | BioAID | biorange_nl | disease | pkna | protein | text_mining | text_mining_network | VL-e
EBI_InterProScan (3)
Created: 26/10/08 @ 20:33:34 | Last updated: 01/04/11 @ 08:52:28
Credits: Hamish McWilliam
License: Creative Commons Attribution 3.0 Unported License
Note: the WSInterProScan web service used by this workflow is no longer available haveing beenreplaced by the EMBL-EBI's InterProScan (REST)(http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)(http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus theworkflow described here no longer works, see the alternative workflows for the InterProScan(SOAP) service for workflows which use the new services. Perform an InterProScan ...
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0
Viewed: 1680 times | Downloaded: 447 times
Tags (10):
bioinformatics | ebi | gff | go terms | interpro | interproscan | protein annotation | protein domain | protein family | protein motif
QR code (matrix code) generator (4)
Created: 07/10/07 @ 17:17:03 | Last updated: 15/08/12 @ 10:40:51
License: Creative Commons Attribution-Share Alike 3.0 Unported License
The latest (and greatest) version of the QR code generator workflow. This workflow uses theQR code service provided by the ChemTools project.
Rating: 1.5 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 1
Viewed: 1291 times | Downloaded: 445 times
Tags (4):
barcode | chemtools | qr | qrcode
HUMAN Microarray CEL file to candidate pat... (4)
Created: 03/10/07 @ 18:35:55 | Last updated: 26/11/09 @ 17:34:24
License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
This workflow takes in a CEL file and a normalisation method then returns a series ofimages/graphs which represent the same output obtained using the MADAT software package(MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Alsoreturned by this workflow are a list of the top differentialy expressed genes (size dependant onthe number specified as input - geneNumber), which are then used to find the candidatepathways which may be influencing the observed ...
Rating: 5.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 1692 times | Downloaded: 494 times
Tags (12):
affymetrix | cel | file | genotype | kegg | microarray | nbiconworkflows | pathway-driven | pathways | phenotype | shim
Entrez Gene to KEGG Pathway (5)
Created: 04/12/09 @ 16:04:38 | Last updated: 30/11/10 @ 12:18:53
Credits: Paul Fisher
License: Creative Commons Attribution 3.0 Unported License
This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id.These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to theKEGG pathway database and its relevant pathways returned.
Rating: 4.8 / 5 (4 ratings) | Versions: 5 | Reviews: 0 | Comments: 2 | Citations: 0
Viewed: 1452 times | Downloaded: 583 times
Tags (9):
entrez | genotype | kegg | ncbi | pathway | pathway-driven | pathways | phenotype | shim
BiomartAndEMBOSSAnalysis (4)
Created: 15/09/09 @ 15:11:11
License: Creative Commons Attribution 3.0 Unported License
Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequencesfrom 3 species: mouse, human, rat; align them, and returns a plot of the alignment result.Corresponding sequence ids are also returned.
Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 1378 times | Downloaded: 477 times
Tags (6):
bioinformatics | biomart | emboss | example | mygrid | taverna
Workflow for Protein Sequence Analysis (1)
Created: 09/01/08 @ 12:03:03 | Last updated: 09/01/08 @ 12:31:27
Credits: M.B.Monteiro
Attributions: BLAST using DDBJ service Simplify a BLAST text file conditional branch
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow performs a generic protein sequence analysis. In order to do that a novel proteinsequence enters into the software along with a list of known protein identifiers chosen by thebiologist to perform a homology search, followed by a multiple sequence alignment and finally aphylogenetic analysis.
Rating: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 1955 times | Downloaded: 525 times
Tags (10):
analysis | BLAST | homology | multiple sequence alignment | phylogenetic tree | protein | sequence | tree | wpsa
Example of a conditional execution workflow (1)
Created: 05/03/08 @ 13:55:45 | Last updated: 23/05/12 @ 11:18:50
Credits: Tomoinn
License: Creative Commons Attribution 3.0 Unported License
If the input is true then the string 'foo' is emited, if false then 'bar'. Just a simple example to show howthe monster works, so to speak. Note that this type of workflow is not suitable for Taverna 2. Analternative mechanism is recommended.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0
Viewed: 1875 times | Downloaded: 577 times
Tags (5):
condition | design pattern | example | mygrid | taverna
Success-Abandonment-Classification (3)
Created: 06/02/08 @ 14:35:41 | Last updated: 02/07/08 @ 17:15:25
Credits: Andrea Wiggins James Howison
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Retrieves data from FLOSSmole and from the Notre Dame SourceForge repository to computeproject statistics based on releases, downloads and project lifespan. Project statistics are thenused to classify projects according to the criteria set up in English & Schweik, but comparisoncriteria are parameterized so that a different set of criterion thresholds can be used to evaluatethe project characteristics.
Rating: 5.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0
Viewed: 2208 times | Downloaded: 6719 times
Tags (6):
classification | draft | floss | open source software | oss | social sciences
Copyright © 2007 - 2012 The University of Manchester and University of Southampton
Front PageHomeInvite people to myExperimentHelp pages
About UsNews and EventsMailing ListContact UsDevelopersPublications
Taverna Workflow WorkbenchmyGridBioCatalogueTridentGoogle Coop Search
EPSRCJISC
Microsoft
Powered by:
Icons: Silk icon set 1.3
Tools for workflow storage and discovery
About | Give us Feedback | Publications Juandesant
New Workflow GO Astrotaverna Workflows Search
View
Download (v3)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
View
Download (v2)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v2)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v3)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
View
Download (v2)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
Sort by: Relevance« Previous 1 2 3 4 5 Next »
44
4342402623
99955
2717
404
164
Search filter terms
Filter by type Taverna 2
Filter by tag astronomy astrotaverna votable virtual observ… starter pack local processes taverna workflow galfit sextractor
Filter by user Jose Enrique … Julian Garrido
Filter by licence by-sa BSD
Filter by group AMIGA Wf4Ever
« Previous 1 2 3 4 5 Next »Sort by: Relevance
Results per page: 10
Home Users Groups Workflows Files Packs Topics
Home > Workflows
Workflows
Showing 44 results. Use the filters on the left and the search box below to refine the results.
Astrotaverna Search
Remove search query
Cocatenates several VOTables into one (3)
Created: 30/08/12 @ 10:05:29 | Last updated: 22/04/13 @ 16:52:00
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The inputis four VOTables with the same number of columns. The result if using sample values providedwill be a four times vertically duplicated VOTable.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 26 times | Downloaded: 12 times
Tags (4):
astronomy | astrotaverna | cat | votable
Create configuration files from a template... (1)
Created: 26/07/12 @ 10:56:46 | Last updated: 04/09/12 @ 07:30:55
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow uses astrotaverna artifacts. It creates files by using a template whose keys arereplaced by data from a votable. A configuration file is created for every row in the votable. Thekeys must appear also in the vocabulary file and match column names in the votable. A columnin the votable must contain the name of the result configuration file.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 14 times | Downloaded: 15 times
Tags (4):
astronomy | astrotaverna | local processes | votable
Simulates the physical, dynamical, and che... (1)
Created: 17/05/13 @ 08:03:13
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Simulates the physical, dynamical, and chemical structure of a shocked layer of the ISM. Itcalls an asynchronous PDL service at Paris Server using a very simple loop condition (until
status is finished).
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 1 time | Downloaded: 0 times
Tags (4):
astrotaverna | ism | pdl service | simulation
Astronomical object name to equatorial coo... (1)
Created: 30/06/12 @ 17:06:50 | Last updated: 01/07/12 @ 11:51:11
Credits: Jose Enrique Ruiz
License: BSD License
Resolve equatorial coordinates of a list of objects (names) with AstroTaverna plugin
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 30 times | Downloaded: 10 times
Tags (5):
astronomy | astrotaverna | coordinates | virtual observatory | votable
Run scripts from a column in a votable (2)
Created: 07/08/12 @ 09:13:45 | Last updated: 07/09/12 @ 13:07:40
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
It runs scripts whose pathname are values of a column in a votable
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 31 times | Downloaded: 19 times
Tags (6):
astronomy | astrotaverna | ellipse | iraf | pyraf | votable
Create votable from ellipse results (2)
Created: 07/08/12 @ 09:21:19 | Last updated: 07/09/12 @ 13:20:03
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
The workflow takes from a votable the names of files where the ellipse result is stored. These filescontain data for several ellipses and the workflow takes the center from the inner ellipse and theellipticitiy from one of the outter ones. It uses astrotaverna plugin(http://wf4ever.github.com/astrotaverna/).
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 30 times | Downloaded: 12 times
Tags (7):
astronomy | astrotaverna | ellipse | iraf | pyraf | sextractor | votable
Add columns to a votable resulting from ex... (1)
Created: 30/08/12 @ 09:33:55
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Addcolumns that are needed to run galfit and ellipse. it requires columns coming fromsextractor and the astrotaverna plugin.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 19 times | Downloaded: 11 times
Tags (7):
astronomy | astrotaverna | galaxy | sextractor | taverna | votable | workflow
Extract a column from a VOTable into a List (3)
Created: 08/03/13 @ 12:18:11 | Last updated: 22/04/13 @ 11:40:01
Credits: Julian Garrido Susana
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for extracting a column from a VOTable into asingle List.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 26 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Discovery of Brown Dwarfs mining the 2MASS... (1)
Created: 12/04/13 @ 16:37:41
Credits: Jose Enrique Ruiz
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Brown dwarfs are objects occupying the gap between the least massive stars and the mostmassive planets. They are intrinsically faint objects so their detection is not straighforward and,in fact, was almost impossible until the advent of global surveys at deep optical and near-infrared bands like SDSS, 2MASS or DENIS among others. Here we propose to mine theSDSS and 2MASS databases to identify T-type brown dwarfs through an appropriate
combination of colours in the optical and the infra-red...
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 13 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Crossmatching VOTables (2)
Created: 12/04/13 @ 16:44:46 | Last updated: 22/04/13 @ 11:37:25
Credits: Jose Enrique Ruiz
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for crossmatching two VOTables VOTablesamples may be downloaded from MyExperimenthttp://www.myexperiment.org/files/911/versions/1/download/SDSS7.vot
http://www.myexperiment.org/files/910/versions/1/download/2MASS.vot
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 11 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Copyright © 2007 - 2012 The University of Manchester and University of Southampton
Front PageHomeInvite people to myExperimentHelp pages
About UsNews and EventsMailing ListContact UsDevelopersPublications
Taverna Workflow WorkbenchmyGridBioCatalogueTridentGoogle Coop Search
EPSRCJISC
Microsoft
Powered by:
Icons: Silk icon set 1.3
About | Give us Feedback | Publications Juandesant
New Workflow GO Astrotaverna Workflows Search
View
Download (v3)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
View
Download (v2)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v2)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v3)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
View
Download (v2)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
Sort by: Relevance« Previous 1 2 3 4 5 Next »
44
4342402623
99955
2717
404
164
Search filter terms
Filter by type Taverna 2
Filter by tag astronomy astrotaverna votable virtual observ… starter pack local processes taverna workflow galfit sextractor
Filter by user Jose Enrique … Julian Garrido
Filter by licence by-sa BSD
Filter by group AMIGA Wf4Ever
« Previous 1 2 3 4 5 Next »Sort by: Relevance
Results per page: 10
Home Users Groups Workflows Files Packs Topics
Home > Workflows
Workflows
Showing 44 results. Use the filters on the left and the search box below to refine the results.
Astrotaverna Search
Remove search query
Cocatenates several VOTables into one (3)
Created: 30/08/12 @ 10:05:29 | Last updated: 22/04/13 @ 16:52:00
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The inputis four VOTables with the same number of columns. The result if using sample values providedwill be a four times vertically duplicated VOTable.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 26 times | Downloaded: 12 times
Tags (4):
astronomy | astrotaverna | cat | votable
Create configuration files from a template... (1)
Created: 26/07/12 @ 10:56:46 | Last updated: 04/09/12 @ 07:30:55
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow uses astrotaverna artifacts. It creates files by using a template whose keys arereplaced by data from a votable. A configuration file is created for every row in the votable. Thekeys must appear also in the vocabulary file and match column names in the votable. A columnin the votable must contain the name of the result configuration file.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 14 times | Downloaded: 15 times
Tags (4):
astronomy | astrotaverna | local processes | votable
Simulates the physical, dynamical, and che... (1)
Created: 17/05/13 @ 08:03:13
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Simulates the physical, dynamical, and chemical structure of a shocked layer of the ISM. Itcalls an asynchronous PDL service at Paris Server using a very simple loop condition (until
status is finished).
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 1 time | Downloaded: 0 times
Tags (4):
astrotaverna | ism | pdl service | simulation
Astronomical object name to equatorial coo... (1)
Created: 30/06/12 @ 17:06:50 | Last updated: 01/07/12 @ 11:51:11
Credits: Jose Enrique Ruiz
License: BSD License
Resolve equatorial coordinates of a list of objects (names) with AstroTaverna plugin
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 30 times | Downloaded: 10 times
Tags (5):
astronomy | astrotaverna | coordinates | virtual observatory | votable
Run scripts from a column in a votable (2)
Created: 07/08/12 @ 09:13:45 | Last updated: 07/09/12 @ 13:07:40
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
It runs scripts whose pathname are values of a column in a votable
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 31 times | Downloaded: 19 times
Tags (6):
astronomy | astrotaverna | ellipse | iraf | pyraf | votable
Create votable from ellipse results (2)
Created: 07/08/12 @ 09:21:19 | Last updated: 07/09/12 @ 13:20:03
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
The workflow takes from a votable the names of files where the ellipse result is stored. These filescontain data for several ellipses and the workflow takes the center from the inner ellipse and theellipticitiy from one of the outter ones. It uses astrotaverna plugin(http://wf4ever.github.com/astrotaverna/).
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 30 times | Downloaded: 12 times
Tags (7):
astronomy | astrotaverna | ellipse | iraf | pyraf | sextractor | votable
Add columns to a votable resulting from ex... (1)
Created: 30/08/12 @ 09:33:55
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Addcolumns that are needed to run galfit and ellipse. it requires columns coming fromsextractor and the astrotaverna plugin.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 19 times | Downloaded: 11 times
Tags (7):
astronomy | astrotaverna | galaxy | sextractor | taverna | votable | workflow
Extract a column from a VOTable into a List (3)
Created: 08/03/13 @ 12:18:11 | Last updated: 22/04/13 @ 11:40:01
Credits: Julian Garrido Susana
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for extracting a column from a VOTable into asingle List.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 26 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Discovery of Brown Dwarfs mining the 2MASS... (1)
Created: 12/04/13 @ 16:37:41
Credits: Jose Enrique Ruiz
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Brown dwarfs are objects occupying the gap between the least massive stars and the mostmassive planets. They are intrinsically faint objects so their detection is not straighforward and,in fact, was almost impossible until the advent of global surveys at deep optical and near-infrared bands like SDSS, 2MASS or DENIS among others. Here we propose to mine theSDSS and 2MASS databases to identify T-type brown dwarfs through an appropriate
combination of colours in the optical and the infra-red...
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 13 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Crossmatching VOTables (2)
Created: 12/04/13 @ 16:44:46 | Last updated: 22/04/13 @ 11:37:25
Credits: Jose Enrique Ruiz
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for crossmatching two VOTables VOTablesamples may be downloaded from MyExperimenthttp://www.myexperiment.org/files/911/versions/1/download/SDSS7.vot
http://www.myexperiment.org/files/910/versions/1/download/2MASS.vot
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 11 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Copyright © 2007 - 2012 The University of Manchester and University of Southampton
Front PageHomeInvite people to myExperimentHelp pages
About UsNews and EventsMailing ListContact UsDevelopersPublications
Taverna Workflow WorkbenchmyGridBioCatalogueTridentGoogle Coop Search
EPSRCJISC
Microsoft
Powered by:
Icons: Silk icon set 1.3
About | Give us Feedback | Publications Juandesant
New Workflow GO Astrotaverna Workflows Search
View
Download (v3)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
View
Download (v2)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v2)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v3)
Taverna 2
OriginalUploader
JulianGarrido
View
Download (v1)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
View
Download (v2)
Taverna 2
OriginalUploader
JoseEnrique
Ruiz
Sort by: Relevance« Previous 1 2 3 4 5 Next »
44
4342402623
99955
2717
404
164
Search filter terms
Filter by type Taverna 2
Filter by tag astronomy astrotaverna votable virtual observ… starter pack local processes taverna workflow galfit sextractor
Filter by user Jose Enrique … Julian Garrido
Filter by licence by-sa BSD
Filter by group AMIGA Wf4Ever
« Previous 1 2 3 4 5 Next »Sort by: Relevance
Results per page: 10
Home Users Groups Workflows Files Packs Topics
Home > Workflows
Workflows
Showing 44 results. Use the filters on the left and the search box below to refine the results.
Astrotaverna Search
Remove search query
Cocatenates several VOTables into one (3)
Created: 30/08/12 @ 10:05:29 | Last updated: 22/04/13 @ 16:52:00
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The inputis four VOTables with the same number of columns. The result if using sample values providedwill be a four times vertically duplicated VOTable.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 26 times | Downloaded: 12 times
Tags (4):
astronomy | astrotaverna | cat | votable
Create configuration files from a template... (1)
Created: 26/07/12 @ 10:56:46 | Last updated: 04/09/12 @ 07:30:55
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow uses astrotaverna artifacts. It creates files by using a template whose keys arereplaced by data from a votable. A configuration file is created for every row in the votable. Thekeys must appear also in the vocabulary file and match column names in the votable. A columnin the votable must contain the name of the result configuration file.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 14 times | Downloaded: 15 times
Tags (4):
astronomy | astrotaverna | local processes | votable
Simulates the physical, dynamical, and che... (1)
Created: 17/05/13 @ 08:03:13
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Simulates the physical, dynamical, and chemical structure of a shocked layer of the ISM. Itcalls an asynchronous PDL service at Paris Server using a very simple loop condition (until
status is finished).
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 1 time | Downloaded: 0 times
Tags (4):
astrotaverna | ism | pdl service | simulation
Astronomical object name to equatorial coo... (1)
Created: 30/06/12 @ 17:06:50 | Last updated: 01/07/12 @ 11:51:11
Credits: Jose Enrique Ruiz
License: BSD License
Resolve equatorial coordinates of a list of objects (names) with AstroTaverna plugin
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 30 times | Downloaded: 10 times
Tags (5):
astronomy | astrotaverna | coordinates | virtual observatory | votable
Run scripts from a column in a votable (2)
Created: 07/08/12 @ 09:13:45 | Last updated: 07/09/12 @ 13:07:40
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
It runs scripts whose pathname are values of a column in a votable
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 31 times | Downloaded: 19 times
Tags (6):
astronomy | astrotaverna | ellipse | iraf | pyraf | votable
Create votable from ellipse results (2)
Created: 07/08/12 @ 09:21:19 | Last updated: 07/09/12 @ 13:20:03
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
The workflow takes from a votable the names of files where the ellipse result is stored. These filescontain data for several ellipses and the workflow takes the center from the inner ellipse and theellipticitiy from one of the outter ones. It uses astrotaverna plugin(http://wf4ever.github.com/astrotaverna/).
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 30 times | Downloaded: 12 times
Tags (7):
astronomy | astrotaverna | ellipse | iraf | pyraf | sextractor | votable
Add columns to a votable resulting from ex... (1)
Created: 30/08/12 @ 09:33:55
Credits: Julian Garrido
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Addcolumns that are needed to run galfit and ellipse. it requires columns coming fromsextractor and the astrotaverna plugin.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 19 times | Downloaded: 11 times
Tags (7):
astronomy | astrotaverna | galaxy | sextractor | taverna | votable | workflow
Extract a column from a VOTable into a List (3)
Created: 08/03/13 @ 12:18:11 | Last updated: 22/04/13 @ 11:40:01
Credits: Julian Garrido Susana
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for extracting a column from a VOTable into asingle List.
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 26 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Discovery of Brown Dwarfs mining the 2MASS... (1)
Created: 12/04/13 @ 16:37:41
Credits: Jose Enrique Ruiz
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Brown dwarfs are objects occupying the gap between the least massive stars and the mostmassive planets. They are intrinsically faint objects so their detection is not straighforward and,in fact, was almost impossible until the advent of global surveys at deep optical and near-infrared bands like SDSS, 2MASS or DENIS among others. Here we propose to mine theSDSS and 2MASS databases to identify T-type brown dwarfs through an appropriate
combination of colours in the optical and the infra-red...
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 13 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Crossmatching VOTables (2)
Created: 12/04/13 @ 16:44:46 | Last updated: 22/04/13 @ 11:37:25
Credits: Jose Enrique Ruiz
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Snippet showing how to use AstroTaverna tool for crossmatching two VOTables VOTablesamples may be downloaded from MyExperimenthttp://www.myexperiment.org/files/911/versions/1/download/SDSS7.vot
http://www.myexperiment.org/files/910/versions/1/download/2MASS.vot
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0
Viewed: 11 times | Downloaded: 1 time
Tags (5):
astronomy | astrotaverna | starter pack | virtual observatory | votable
Copyright © 2007 - 2012 The University of Manchester and University of Southampton
Front PageHomeInvite people to myExperimentHelp pages
About UsNews and EventsMailing ListContact UsDevelopersPublications
Taverna Workflow WorkbenchmyGridBioCatalogueTridentGoogle Coop Search
EPSRCJISC
Microsoft
Powered by:
Icons: Silk icon set 1.3
About | Give us Feedback | Publications Juandesant
New Workflow GO All Search
What is this?Linked Data
Version 3 (latest) (of 3) View version: 3 (latest)
Version created on: 22/04/13 @ 16:52:00 by: Julian Garrido
Title: Cocatenates several VOTables into oneType: Taverna 2
Preview
(Click on the image to get the full size)
Download Scalable Diagram (SVG)
Description
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The input is fourVOTables with the same number of columns. The result if using sample values provided will be a four timesvertically duplicated VOTable.
Download
Download Workflow File/Package (T2FLOW)
Download Workflow as a Galaxy tool
Run
Run this Workflow in the Taverna Workbench...
Option 1:
Copy and paste this link into File > 'Open workflow location...'http://www.myexperiment.org/workflows/3130/download?version=3
[ More Info ]
Workflow Components
Authors (1)
Titles (1)
Descriptions (1)
Dependencies (0)
Inputs (4)
Processors (1)
Beanshells (0)
Outputs (1)
Datalinks (5)
Coordinations (0)
Workflow TypeTaverna 2
Original Uploader
JulianGarrido
LicenseAll versions of this Workflow are licensed
under:
Credits (1)(People/Groups)
Julian Garrido
Attributions (0)(Workflows/Files)
None
Tags (4)
Original Uploader tags
astronomy | astrotaverna | cat |
votableAdd Tags
Shared with Groups (1)
AMIGA
Featured In Packs (1)
AstroTaverna Starter Pack
Ratings (0)Hover and click to rate
Current:
0.0 / 5(0 ratings)
You haven't rated yet
Breakdown
Attributed By (0)(Workflows/Files)
None
Favourited By (0)No one
Add to your Favourites
Statistics53 viewings
75 downloads[ see breakdown ]
More
Home Users Groups Workflows Files Packs Topics
Home > Workflows > Cocatenates several VOTables into one
Workflow Entry: Cocatenates several VOTables into oneCreated at: 30/08/12 @ 10:05:29 Last updated: 22/04/13 @ 16:52:00
| License | Credits (1) | Attributions (0) | Tags (4) | Featured in Packs (1) | Ratings (0) | Attributed By (0) | Favourited By (0) | | Citations (0) | Version History | Reviews (0) | Comments (0) |
Citations (0)
None
Version History
In chronological order:
1. Cat several votables into one
Created by Julian Garrido on Thursday 30 August 2012 @ 10:05:29 (UTC)
2. Cocatenates several VOTables into one
Created by Julian Garrido on Monday 15 April 2013 @ 08:52:18 (UTC)
Revision comment:
Addition of new metadata
3. Cocatenates several VOTables into one
Created by Julian Garrido on Monday 22 April 2013 @ 16:52:00 (UTC)
Reviews (0)
No reviews yet
Be the first to review!
Comments (0)
View Timeline
No comments yet
Make a Comment:
Submit Comment
Other workflows that use similar services (0)
There are no workflows in myExperiment that use similar services to this Workflow.
Non-Information Resource URI: http://www.myexperiment.org/workflows/3130
Alternative Formats
Copyright © 2007 - 2012 The University of Manchester and University of Southampton
Front PageHomeInvite people to myExperimentHelp pages
About UsNews and EventsMailing ListContact UsDevelopersPublications
Taverna Workflow WorkbenchmyGridBioCatalogueTridentGoogle Coop Search
EPSRCJISC
Microsoft
Powered by:
Icons: Silk icon set 1.3
About | Give us Feedback | Publications Juandesant
New Workflow GO All Search
What is this?Linked Data
Version 3 (latest) (of 3) View version: 3 (latest)
Version created on: 22/04/13 @ 16:52:00 by: Julian Garrido
Title: Cocatenates several VOTables into oneType: Taverna 2
Preview
(Click on the image to get the full size)
Download Scalable Diagram (SVG)
Description
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The input is fourVOTables with the same number of columns. The result if using sample values provided will be a four timesvertically duplicated VOTable.
Download
Download Workflow File/Package (T2FLOW)
Download Workflow as a Galaxy tool
Run
Run this Workflow in the Taverna Workbench...
Option 1:
Copy and paste this link into File > 'Open workflow location...'http://www.myexperiment.org/workflows/3130/download?version=3
[ More Info ]
Workflow Components
Authors (1)
Titles (1)
Descriptions (1)
Dependencies (0)
Inputs (4)
Processors (1)
Beanshells (0)
Outputs (1)
Datalinks (5)
Coordinations (0)
Workflow TypeTaverna 2
Original Uploader
JulianGarrido
LicenseAll versions of this Workflow are licensed
under:
Credits (1)(People/Groups)
Julian Garrido
Attributions (0)(Workflows/Files)
None
Tags (4)
Original Uploader tags
astronomy | astrotaverna | cat |
votableAdd Tags
Shared with Groups (1)
AMIGA
Featured In Packs (1)
AstroTaverna Starter Pack
Ratings (0)Hover and click to rate
Current:
0.0 / 5(0 ratings)
You haven't rated yet
Breakdown
Attributed By (0)(Workflows/Files)
None
Favourited By (0)No one
Add to your Favourites
Statistics53 viewings
75 downloads[ see breakdown ]
More
Home Users Groups Workflows Files Packs Topics
Home > Workflows > Cocatenates several VOTables into one
Workflow Entry: Cocatenates several VOTables into oneCreated at: 30/08/12 @ 10:05:29 Last updated: 22/04/13 @ 16:52:00
| License | Credits (1) | Attributions (0) | Tags (4) | Featured in Packs (1) | Ratings (0) | Attributed By (0) | Favourited By (0) | | Citations (0) | Version History | Reviews (0) | Comments (0) |
Citations (0)
None
Version History
In chronological order:
1. Cat several votables into one
Created by Julian Garrido on Thursday 30 August 2012 @ 10:05:29 (UTC)
2. Cocatenates several VOTables into one
Created by Julian Garrido on Monday 15 April 2013 @ 08:52:18 (UTC)
Revision comment:
Addition of new metadata
3. Cocatenates several VOTables into one
Created by Julian Garrido on Monday 22 April 2013 @ 16:52:00 (UTC)
Reviews (0)
No reviews yet
Be the first to review!
Comments (0)
View Timeline
No comments yet
Make a Comment:
Submit Comment
Other workflows that use similar services (0)
There are no workflows in myExperiment that use similar services to this Workflow.
Non-Information Resource URI: http://www.myexperiment.org/workflows/3130
Alternative Formats
Copyright © 2007 - 2012 The University of Manchester and University of Southampton
Front PageHomeInvite people to myExperimentHelp pages
About UsNews and EventsMailing ListContact UsDevelopersPublications
Taverna Workflow WorkbenchmyGridBioCatalogueTridentGoogle Coop Search
EPSRCJISC
Microsoft
Powered by:
Icons: Silk icon set 1.3
About | Give us Feedback | Publications Juandesant
New Workflow GO All Search
What is this?Linked Data
Version 3 (latest) (of 3) View version: 3 (latest)
Version created on: 22/04/13 @ 16:52:00 by: Julian Garrido
Title: Cocatenates several VOTables into oneType: Taverna 2
Preview
(Click on the image to get the full size)
Download Scalable Diagram (SVG)
Description
Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The input is fourVOTables with the same number of columns. The result if using sample values provided will be a four timesvertically duplicated VOTable.
Download
Download Workflow File/Package (T2FLOW)
Download Workflow as a Galaxy tool
Run
Run this Workflow in the Taverna Workbench...
Option 1:
Copy and paste this link into File > 'Open workflow location...'http://www.myexperiment.org/workflows/3130/download?version=3
[ More Info ]
Workflow Components
Authors (1)
Titles (1)
Descriptions (1)
Dependencies (0)
Inputs (4)
Processors (1)
Beanshells (0)
Outputs (1)
Datalinks (5)
Coordinations (0)
Workflow TypeTaverna 2
Original Uploader
JulianGarrido
LicenseAll versions of this Workflow are licensed
under:
Credits (1)(People/Groups)
Julian Garrido
Attributions (0)(Workflows/Files)
None
Tags (4)
Original Uploader tags
astronomy | astrotaverna | cat |
votableAdd Tags
Shared with Groups (1)
AMIGA
Featured In Packs (1)
AstroTaverna Starter Pack
Ratings (0)Hover and click to rate
Current:
0.0 / 5(0 ratings)
You haven't rated yet
Breakdown
Attributed By (0)(Workflows/Files)
None
Favourited By (0)No one
Add to your Favourites
Statistics53 viewings
75 downloads[ see breakdown ]
More
Home Users Groups Workflows Files Packs Topics
Home > Workflows > Cocatenates several VOTables into one
Workflow Entry: Cocatenates several VOTables into oneCreated at: 30/08/12 @ 10:05:29 Last updated: 22/04/13 @ 16:52:00
| License | Credits (1) | Attributions (0) | Tags (4) | Featured in Packs (1) | Ratings (0) | Attributed By (0) | Favourited By (0) | | Citations (0) | Version History | Reviews (0) | Comments (0) |
Citations (0)
None
Version History
In chronological order:
1. Cat several votables into one
Created by Julian Garrido on Thursday 30 August 2012 @ 10:05:29 (UTC)
2. Cocatenates several VOTables into one
Created by Julian Garrido on Monday 15 April 2013 @ 08:52:18 (UTC)
Revision comment:
Addition of new metadata
3. Cocatenates several VOTables into one
Created by Julian Garrido on Monday 22 April 2013 @ 16:52:00 (UTC)
Reviews (0)
No reviews yet
Be the first to review!
Comments (0)
View Timeline
No comments yet
Make a Comment:
Submit Comment
Other workflows that use similar services (0)
There are no workflows in myExperiment that use similar services to this Workflow.
Non-Information Resource URI: http://www.myexperiment.org/workflows/3130
Alternative Formats
Copyright © 2007 - 2012 The University of Manchester and University of Southampton
Front PageHomeInvite people to myExperimentHelp pages
About UsNews and EventsMailing ListContact UsDevelopersPublications
Taverna Workflow WorkbenchmyGridBioCatalogueTridentGoogle Coop Search
EPSRCJISC
Microsoft
Powered by:
Icons: Silk icon set 1.3
That’s not enough!
FOR ASTRONOMERS
FOR REPRODUCIBILITY AND REUSE
3
7 4
16
52
1. Intelligent Software Components (iSOCO, Spain)
2. University of Manchester (UNIMAN, UK)
3. Universidad Politécnica de Madrid (UPM, Spain)
4. Poznan Supercomputing and Networking Centre (PSNC, Poland)
5. University of Oxford (OXF, UK)6. Instituto de Astrofísica de Andalucía
(IAA, Spain)7. Leiden University Medical Centre
(LUMC, NL)
EU FUNDED FP7 STREP PROJECTDECEMBER 2010 – DECEMBER 2013
• Astronomy (IAA-CSIC)• Genome-wide Analysis and Biobanking
Case Studies
Archival, classification, and indexing of scientific workflows and their associated materials in scalable semantic repositories, providing advanced access and recommendation capabilities
Creation of scientific communities to collaboratively share, reuse, and evolve workflows and their parts, stimulating the development of new scientific knowledge
Goals
• Digital Libraries• Workflow Management • Semantic Web• Integrity & Authenticity• Provenance• Information Quality
Core Competencies (Tech)
• One SME• Six public organisations
Partners
Technological infrastructure for the preservation and efficient retrieval and reuse of scientific workflows in a range of disciplines
TARGETING ALREADY ESTABLISHED
COMMUNITIES: MYEXPERIMENT,
VIRTUAL OBSERVATORY
3
What is a Scientific Workflow? Workflows to Access and Massage VO Data
» A mechanism for coordinating the execution of services and codes, and linking together resources.
» The combination of data and processes into a configurable, modular, structured set of steps that implement semi-automated computational solutions in scientific problem-solving.
» The implementation of a scientific method.
COURTESY J.E. RUIZ
NOT A PIPELINE!
AMIGA4GAS3D KINEMATICAL MODELING
INPUT FILES
ROTCUR
12 RUNSPOSSIBLE COMBINATIONS
IN INPUT PARAMETERS
12 ASCII FILES
GALMOD
12 CUBES 4 APPROACHING
4 RECEEDING 4 BOTH COPY
8 CUBES 4 APPROACHING + RECEEDING
4 BOTH
MOMENTS
8 VELOCITY MAPS
1 DATACUBE1 VELOCITY MAP
1 CONFIG FILE ROTCUR 1 CONFIG FILE GALMOD
SUB
8 RESIDUAL CUBES8 RESIDUAL MAPS
SUB
MNMX 8 VALUES FOR PEAKS IN CUBES8 VALUES FOR PEAKS IN MAPS
VARIABLEPARAMS
INSETRADII, WIDTHS
WEIGHTTOLERANCE
DENSNVZ0
VDISP
How do we build workflows?
AstroTavernaTaverna plugin for retrieving and manipulating VO Data + Catalogs on HTML Pages
VO Services: ConeSearch, SIA, SSA, TAP coming soonTabular Data (VOTables, converters from other formats)
Crossmatching, Filtering, NameResolving, Coordinates and reference system transformation, Data massage.. (STILTS)Source catalog overplotting on Images and filtering, overplot circles, ellipses, etc. as a function of physical magnitude. Resampling, crops, blinks, mosaics, movies, blinks, RGBs, fusion, diff.. (through Aladin)VO Table rendering, SAMP for final inspection
Image support, Spectra not yet PLUS ADDITIONAL ANALYSIS USING
SCRIPTS
Service discovery
Data massaging
Data massagingX-Matching
Calculation
Additions
Filtering
Access
Data curation
X-Matching
Calculation
Additions
Filtering
Access
Data curation
X-Matching
Calculation
Additions
Filtering
Access
Data curation
X-Matching
Calculation
Additions
Filtering
Access
Aladin scripting
Interactive data inspection
Interactive data inspection
Learning examples
Not yet enough!FOR REPRODUCIBILITY
AND REUSE
Home RO at 5000 feet Examples Ontologies Tools Collaboration Publications History About
Search
Research Objects
Research ObjectsContent
Process (workflows), data, external resources and bibliographyExecution environment set-up and local software dependenciesExperimental protocol followedRoles, types and relationships among all digital componentsProvenance of intermediate and final resultsDecomposable attribution and authoringFine-grained access control and permissionsExample datasets for demonstration, reproducibility, monitoring, etc
TemplatesPlaceholders to ease the aggregation processCompleteness checking/quality assessment
Research ObjectsTarget Audiencies
Scientists [producers] who want to share their research outcomes so that they are more reusable and reproducible – ease of sharing and citation.Scientists [consumers] who want to understand, reuse, validate and further extend existing RO’s.Publishers can adopt the concept and principles of Research Object to enable the sharing of and access to the actual data and methods.Librarians who want to support research preservation.
Semantic annotationsAuthor of an annotation Author and co-authors of a workflow; reference link to a re-used workflow and its author Who has performed the execution of a workflow leading to the results provided in the RO Computing execution environment of the RO and local software dependencies Special access requirements to web services Datasets provider: person, webpage, survey, data release, etc. How much time does it take to run a workflow using the full data and the provided subsampleThe number of elements of the sample dataset where one workflow and/or RO iteratesPrevious and subsequent workflows to be executed, as in the experimental protocolResearch institution, country, and scientific domain of the RO The actual size of the RO and/or a folder
Semantic model
DataLink
MULTI DISCIPLINARY
RO data organisation
Recommended organisation provides automatic semantics for some items
It makes it easier for both people and machines to understand the RO
ROs in AstronomyADSLabs Research Objects
Authors
Publications
Journals
Objects SIMBAD
Tabular data behind the plots CDS
ASCL reference of used software
Observing time Proposals
Used facilities, surveys or missions
NOT JUST FROM WORKFLOWS
POTENTIAL FOR RESEARCH OBJECT INDEXING IN ADS
RO IncentivePAPERS WITH DATA LINKS ARE CITED MORE THAN THOSE WITHOUT
Effect of E-printing on Citation Rates in Astronomy and Physics2006. Edwin A. Henneken et al.
RO IncentivePAPERS WITH DATA LINKS ARE CITED MORE THAN THOSE WITHOUT
Effect of E-printing on Citation Rates in Astronomy and Physics2006. Edwin A. Henneken et al.
NOW YOU CAN CITE DATA AND
PROCESSES, TOO
RoadmapAstroTaverna, mostly ready: you can publish workflows and packs to myExperiment from Taverna
myExperiment, building support for ROs
ADS will populate myExperiment with literature-ROs
Taverna will be able to publish ROs to myExperiment
Final points
We need something like workflows to describe computations in a distributed environment
Workflows are not enough for supporting reuse and methodology preservation
Research Objects are meaningful associations of data, operations, provenance, which can also be cited CAN EMBED
COMPUTATIONS IN SCIENCE ARCHIVES
Useful Links
http://www.wf4ever-project.org
http://www.myexperiment.org
http://www.researchobject.org
http://wf4ever.github.io/astrotaverna/
http://amiga.iaa.es
Thank you!
Recommended