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Modern Tools & Rationales for 21st Century Research
Ross Mounce (@RMounce)Natural History Museum, London
European Phycological Congress, Student Symposium 2015-08-27
XKCD 1179 on ISO 8601
Slides available online: slideshare.net/rossmounce
Sharing is caring
If you wish, please do share, tweet, discuss, re-use this talk
I'm a firm believer that research should be open by default,
specifically including conference talks & posters!!!
Previous meetings to have got this wrong include: SVP '14 and ESA '15, as documented in Nature News recently… http://www.nature.com/news/conference-tweeting-rule-frustrates-ecologists-1.18207
#EPC6
Twitter & other social media are legitimate tools of great utility in academia. Tweet your talk slides & you'll get a much wider audience for your talk!
Open, online benefits you
I bet more people have read Seth's poster than any other poster here that hasn't been tweeted
Open, online benefits you
Nature Communications Open (blue) vs Paywalled (orange),
article views per day
Mean: Open
Mean: Paywalled
DOI: 10.1007/s11192-015-1547-0
Open, online benefits you
Piwowar HA, Vision TJ. (2013) Data reuse and the open data citation advantage. PeerJ 1:e175
“...open data citation benefit for this sample to be 9%”
relative to papers providing no public data, for gene expression microarray data
10.7717/peerj.175/fig-2See also previous work by Piwowar:10.1371/journal.pone.0000308
Open, online benefits you
Because the software is open source, online I could look at it and contribute suggested improvements
Users can easily report issues / bugs & feature requests
Demonstrate that people are interested in your software
Research tools are rapidly improving
Image credit:https://innoscholcomm.silk.co/
Analysis tools and their communities
These are my favourites, in no particular order.They are tools AND friendly communities. Important.
/
Supp. Data Needs to DieFrom the 1990s to 2010s, online supplementary data was used as a way of dumping data online in an ad hoc manner... It was available *shrugs*
Traditional, journal-hosted supplementary files bury data. Additional files are bunged online with little or no additional metadata describing them.
Thus typically, SI isn't searchable. That's a huge problem
Data should be FAIR:
Findable, Accessible, Interoperable, Re-usable
It should be findable independent of the research article
https://www.force11.org/group/fairgroup
Data sharing platforms
https://zenodo.org/http://figshare.com/http://datadryad.org/
Free-to-use but commercialFree-to-use, CERN backedNot-for-profit
Not-for-profit,Better curated
Charges to keep sustainable
Data Standards & Data File Formats
Adhere to existing standards! e.g. 2015-08-27 for dates
xkcd 927 on standards
ISO 8601
Intelligent data papers allow databases to automatically pull-in your data
Many publishers (e.g. Pensoft) intelligently markup data papers so that the data can be automatically ingested into appropriate db's on the day of publication!
Data
data
BiodiversityData Journal
Those who share data, do better science
Wicherts, J. M., Bakker, M. & Molenaar, D. (2011) Willingness to share research data is related to the strength of the evidence and the quality of reporting of statistical results. PLoS ONE 6, e26828+ URL http://dx.doi.org/10.1371/journal.pone.0026828
The authors examined psychological papers for the quality of statistical reporting & asked the authors of those papers for the full data underlying the reported results. Generally, those who shared, had more statistically robust, reproducible results.
“Email the author for data” - doesnt work
Wicherts JM, Borsboom D, Kats J, Molenaar D (2006) The poor availability of psychological research data for reanalysis. American Psychologist 61: 726–728 link
A well-known problem, which I myself have also faced many times!!!
Many legacy journals unfortunately still pretend that “email the author” is still acceptable.
Authoring Tools
Microsoft Word is crap.
Publishers have to spend significant time & effort (= $$$) converting MS Word documents into scholarly publications. Citation styling is stupid too.
Many problems could easily be avoided through use of better authoring tools:
http://biodiversitydatajournal.com/
https://paperpile.com/
+ ShareLatex, BlueLatex, FidusWriter, RVRite...
https://www.authorea.com/ https://www.overleaf.com/
Discovery Tools
Finding & obtaining access to research isn't easy. These tools can help
https://openaccessbutton.org/
Browser-plugin to help find you free access versions of paywalled research articles
http://www.sparrho.com/
https://www.pubchase.com/
Sparrho & PubChase provide personalised literature recommonedations, like Google Scholar but with more flexibility
Preprint platforms
A brilliant way of getting your article out there early & in a non-paywalled way
https://peerj.com/preprints/http://biorxiv.org/
http://arxiv.org/
Background reading: The Case for Open Preprints in Biology (2013) PLOS Biology
Open Access Journals
http://biodiversitydatajournal.com/https://peerj.com/
There are thousands out there. But these are my picks:
$99 per author, lifetime publishing
High-tech, integrated publishing from Pensoft
PeerJ is the epitome of modern, efficient publishing
A quick reminder of the cost of paywalls(per year, for 2014)
Institute Total Subscriptions (£)1: University of Manchester 3,205,7022: UCL 3,052,1703: University of Cambridge 2,963,8214: University of Nottingham 2,578,7165: Imperial College London 2,472,5306: University of Bristol 2,395,6547: University of Birmingham 2,178,5588: University of Oxford 2,153,8409: University of Glasgow 2,062,35310: Cardiff University 2,007,977
Source FOI requests, peer-reviewed here: http://f1000research.com/articles/3-274/v3
In Summary
There are a wealth of new, better tools out there. Use them!
Share: Data, Code, Presentations, Posters, Grant Proposals, Preprints, and Papers
Opening-up your work has benefits to you.
Thank you for your time!
