1. Merging and sharing Metabolomics 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.1243500 http://bit.ly/1EPTbme

2. Researcher bias Positive result bias  20 teams do studies, 1 publishes p<0.05 Poorly explained analyses DOI: 10.1371/journal.pmed.0020124

3. 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

4. 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

5. 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 is a 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 papers tested 123 successful reproductions

6. 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

7. Galaxy Over 36,000 main Galaxy server users Over 1,000 papers citing Galaxy use Over 55 Galaxy servers deployed Open source http://galaxyproject.org

8. Galaxy – Toolshed https://toolshed.g2.bx.psu.edu/ Many 'omics, stats, visualisations Metabolomics can plug into this 2700+ tools! Download; Run instantly

9. Any tool in Galaxy python myfunction input1 Basic xml 'wrapper' Describe inputs and outputs Calls command Monitors for output Logs/returns to 'history'

10. Galaxy Tool ListTool ParametersHistory/results

11. 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)

12. Birmingham metabolomics workflow Many tools Many languages Complex to learn Many parameters Complex to report

13. Metabolomics workflow in Galaxy User sees website (intuitive) Centrally stored (secure) Workflow is recorded Methods shareable

14. View, share, edit, rerun workflow

15. Citable workflow Add as supplemental files or publish with distinct DOI via GigaDB or FigShare

16. 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/

17. 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

18. Acknowledgements University of Birmingham  Ralf Weber  Mark Viant GigaScience  Pete Li Funding  NERC NE/K011294/1

19. http://orcid.org/0000-0002-0311-9774 Me: Rob L. DavidsonThis presentation: http://bit.ly/1EPTbme http://dx.doi.org/10.6084/m9.figshare.1243500