merging and sharing metabolomics analysis tools with galaxy: transparent, reproducible, open...
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Merging and sharingMetabolomics analysis tools with Galaxy:
transparent, reproducible, open 'omics
Robert L Davidson PhD. @bobbledavidson
#MMW2014
Merlion Metabolomics Workshop 2014
http://dx.doi.org/10.6084/m9.figshare.1243500http://bit.ly/1EPTbme
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Researcher bias Positive result bias
20 teams do studies, 1 publishes p<0.05 Poorly explained analyses
DOI: 10.1371/journal.pmed.0020124
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85% of research resources are wasted! We must ... favor ... unbiased, transparent, collaborative
research with greater standardization Share data, protocols, materials, software, other tools
DOI: 10.1371/journal.pmed.1001747
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Data sharing
Supported by gov policy: e.g. UK and NIH MetaboLights repository
www.ebi.ac.uk/metabolights/ NIH Metabolomics Data Repository
www.metabolomicsworkbench.org/data/index.php ISA-Tab for metadata
http://www.isa-tools.org/format.html
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What about methods?
http://reproducibility.cs.arizona.edu/
“The good news is that I was able to find some code. I am just hoping that it isa stable working version of the code... I have lost some data... The bad news is that the code is not commented and/or clean. So, I cannot really guarantee that you will enjoy playing with it.”
613 paperstested
123 successfulreproductions
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Problem
There is a reproducibility crisis Published results are untrustworthy Research is a waste of government money (85%)
What's the solution? Share data AND methods
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Galaxy
Over 36,000 main Galaxy server users
Over 1,000 papersciting Galaxy use
Over 55 Galaxyservers deployed
Open source
http://galaxyproject.org
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Galaxy – Toolshed
https://toolshed.g2.bx.psu.edu/
Many 'omics, stats,
visualisations
Metabolomics can pluginto this
2700+ tools!
Download;Run instantly
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Any tool in Galaxy<tool name=”myfunction”>
<command>
python myfunction input1
</command>
<inputs>
<param format=”txt” name=”input1”>
</inputs>
<outputs>
<data format=”csv” name=”output1”>
</outputs>
</tool>
Basic xml 'wrapper'Describe inputs and outputs
Calls command
Monitors for output
Logs/returns to 'history'
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Galaxy
Tool List Tool Parameters History/results
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Birmingham metabolomics workflow
SIM-Stitch DOI:10.1016/j.jasms.2009.02.001
XCMS DOI:10.1021/ac051437y
MI-Pack DOI:10.1016/j.chemolab.2010.04.010
KNN Impute DOI:10.1007/s11306-011-0366-4
PQ-Normalisation DOI:10.1021/ac051632c
G-Log transform DOI:10.1186/1471-2105-8-234
PCA (with statistical test of scores)
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Birmingham metabolomics workflow
Many tools
Many languages
Complex to learn
Many parameters
Complex to report
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Metabolomics workflow in Galaxy
User sees website (intuitive)
Centrally stored (secure)
Workflow is recorded
Methods shareable
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View, share, edit, rerun workflow
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Citable workflowAdd as supplemental files or publish with distinct DOI via GigaDB or FigShare
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Where to get our workflow
Coming soon! Galaxy Toolshed Github Submitted to GigaScience (gigasciencejournal.com)
VM/Code/TestData to be available on GigaDB.org Test server to be available at GigaGalaxy
http://galaxy.cbiit.cuhk.edu.hk/
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Summary
Share your data Share your software Share your workflow – in full Galaxy is not a new 'software', it's a flexible
sharing platform Add your tools to ours, in Galaxy Toolshed
Help make metabolomics: Trustworthy, meaningful, reproducible
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Acknowledgements
University of Birmingham Ralf Weber Mark Viant
GigaScience Pete Li
Funding NERC NE/K011294/1
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http://orcid.org/0000-0002-0311-9774
Me: Rob L. Davidson This presentation:
http://bit.ly/1EPTbmehttp://dx.doi.org/10.6084/m9.figshare.1243500