scott edmunds & rob davidson's talk at the metabolomics society 2014 meeting on beyond dead...
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Scott Edmunds & Rob Davidson's talk at the Metabolomics Society 2014 Meeting on Beyond Dead Trees: data & workflow publishing with GigaScience, Tsuruoka 23rd June 2014TRANSCRIPT
Beyond Dead Trees: data & workflow publishing with
Scott EdmundsRob Davidson
The problems with publishing
• Scholarly articles are merely advertisement of scholarship . The actual scholarly artefacts, i.e. the data and computational methods, which support the scholarship, remain largely inaccessible --- Jon B. Buckheit and David L. Donoho, WaveLab and reproducible research, 1995
• Lack of transparency, lack of credit for anything other than “regular” dead tree publication.
• Traditional publishing models, policies and practices holding things back
Why is this important?
…to publish protocols BEFORE analysis…better access to supporting data/code…more transparent & accountable review
…to publish replication studies
Need:
Consequences: increasing number of retractions>15X increase in last decade
1. Ioannidis et al., 2009. Repeatability of published microarray gene expression analyses. Nature Genetics 41: 142. Science publishing: The trouble with retractions http://www.nature.com/news/2011/111005/full/478026a.html3. Bjorn Brembs: Open Access and the looming crisis in science https://theconversation.com/open-access-and-the-looming-crisis-in-science-14950
At current % > by 2045 as many papers published as retracted
• Data• Software• Review• Re-use…
= Credit
}
Credit where credit is overdue:“One option would be to provide researchers who release data to public repositories with a means of accreditation.”“An ability to search the literature for all online papers that used a particular data set would enable appropriate attribution for those who share. “Nature Biotechnology 27, 579 (2009)
New incentives/credit
GigaSolution: deconstructing the paper
www.gigadb.orgwww.gigasciencejournal.com
Utilizes big-data infrastructure and expertise from:
Combines and integrates:Open-access journal
Data Publishing Platform
Data Analysis Platform
On top of regular papers…
Rewarding open data
http://gigadb.org/
• Multi Omics focus (not just genomics)• 10-100x faster download than FTP• Provide (ISA) curation & integration with other DBs
(e.g. MetaboLights, SRA, etc.)
For more see: http://database.oxfordjournals.org/content/2014/bau018.abstract
IRRI GALAXY
Democratization through data publishing
IRRI GALAXYRice 3K project: 3,000 rice genomes, 13.4TB public data
Democratization through data publishing
Two tools for reproducible research
Rob Davidson
RO:and
GigaSolution: deconstructing the paper
www.gigadb.orgwww.gigasciencejournal.com
Utilizes big-data infrastructure and expertise from:
Combines and integrates:Open-access journal
Data Publishing Platform
Data Analysis Platform
Visualizations & DOIs for workflows
galaxy.cbiit.cuhk.edu.hk
Implement workflows in a community-accepted format
http://galaxyproject.org
Over 36,000 main Galaxy server users
Over 1,000 papersciting Galaxy use
Over 55 Galaxyservers deployed
Open source
Rewarding and aiding reproducibility
Copyright NBAF-B 2013Tool list
Tool parameterisation Results panel
Rewarding and aiding reproducibilityImplement workflows in a community-accepted format
Birmingham Metabo-Galaxy Workflow
Birmingham Metabo-Galaxy
Tools wrapped in Python and XMLUser sees web form (easy!)Data stored centrally (secure!)Work done centrally (easy update)
First RAW -> stats Galaxy Pipe
SOAPdenovo2 S. aureus pipeline
NO
Handling of imaging (phenotype) dataCyber-centipedes & virtual worms
Aiding reproducibility
OMERO: providing access to imaging data
View, filter, measure raw images with direct links from journal article.
See all image data, not just cherry picked examples.
Download and reprocess.
JCB: Aiding reproducibility, adding value
The alternative...
...look but don't touch
In Summary
• Reproducibility is important!!– Currently not very common!
• Many tools appearing for data publishing and sharing (images, tools, workflows).
• Data publishing → more publications, more citations, more impact!
• Are you convinced? • What barriers? Code standards? Data
standards? Too much work?
Give us data, papers & pipelines*
Help us make it happen!
[email protected]@gigasciencejournal.com [email protected] [email protected]
Contact us:
* APC’s currently generously covered by BGI until 2015
www.gigasciencejournal.com
Ruibang Luo (BGI/HKU)Shaoguang Liang (BGI-SZ)Tin-Lap Lee (CUHK)Qiong Luo (HKUST)Senghong Wang (HKUST)Yan Zhou (HKUST)
Thanks to:
@gigasciencefacebook.com/GigaScienceblogs.biomedcentral.com/gigablog/
Peter LiHuayan Gao Chris HunterJesse Si ZheNicole NogoyLaurie GoodmanAmye Kenall (BMC)
Marco Roos (LUMC)Mark Thompson (LUMC)Jun Zhao (Lancaster)Susanna Sansone (Oxford)Philippe Rocca-Serra (Oxford) Alejandra Gonzalez-Beltran (Oxford)
www.gigadb.orggalaxy.cbiit.cuhk.edu.hk
www.gigasciencejournal.com
CBIITFunding from:
Our collaborators:team: