1. HEALTH & E-SCIENCE IN WESTERN FRANCE : USE CASES Yvan Le Bras Cyril Monjeaud Olivier Collin & the GenOuest team CNRS UMR 6074 IRISA-INRIA

2. Context Kahn. On the future of genomic data. Science (2011) vol. 331 (6018) pp. 728-9  Now : Genomics : Next Generation Sequencing  Now : Proteomics  Next : Bio-imaging  Digital data  Huge amount  Heterogenous  Critical situation for some laboratories

3. E-BIOGENOUEST An innovative VRE: A system of open source systems

4. E-Biogenouest Started in May 2012 for 3 years Funded by Brittany and Pays de la Loire E-science initiative for the Biogenouest network Test an e-Science approach Roadmap preparation

5. E-Biogenouest A success! Started in May 2012 for 3 years Funded by Brittany and Pays de la Loire E-science initiative for the Biogenouest network Test an e-Science approach Roadmap preparation An innovative VRE concept More than 150 scientists trained! More than 200 users! 1669 meetings ;) -Mission interdisciplinarité CNRS -PIA -IFB -IFB -Fce Génomique -Fce Génomique -Rapsodyn -Rapsodyn -Sciences citoyennes -Sciences citoyennes -UEB C@mpus -CPER-FRM-INCa-H2020 Health IT Agro Environment 7 articles Peer review

6. VRE: a tool for e-Science application Virtual Research Environment Web portal Data softwares Processing resources User Community Collaboration

7. An innovative VRE approach Research Lifecycle Open source solutions Don’t reinvente the wheel http://www.jisc.ac.uk/whatwedo/campaigns/res3/jischelp.aspx#simulate Mutualise win win Break down silos

8. Communauté HubZero GalaxyEMME Continuum Continuum data management & analysis Collaborative environment Collaboration

9. EMME Experimental Metadata Management Environment

10. ISAtools : Experimental data management EMME ISAtools suite to store data & metadata Fonctionalities -based on biomed ontologies -bridge between biomed standards -format publication submission -Pydio to upload data -biological investigation repository (data + metadata) Oxford eResearch Centre P. Rocca-Serra et al. Bioinformatics, 26;254(6), 2010 Open source

11. Pydio : File sharing platform Pydio by GenOuest To store & share data as links Informations -Galaxy workspace -EMME workspace Share - data via URI - control - safety - privacy Abstrium SAS Charles du jeu, David Gillard et al. Open source

12. GALAXY Analyze, share and visualize data, create workflows through the web

13. Galaxy : Data analysis web platform GALAXY by GenOuest To analyse & share data as processes and tools Informations 40276 jobs 152 users More than 800 tools Share - data - histories - workflows - tools Penn state university J. Goecks, A. Nekrutenko, J. Taylor, et al. Genome Biol, 25;11(8):R86, 2010 Open source

14. Galaxy : GUGGO Working group Galaxy User Group Grand Ouest 5 sites - Plouzané : Ifremer CAPArmor - Roscoff : IFB-GO ABiMS - Rennes : IFB-GO GenOuest + INRA BIPAA - Nantes : IFB-GO BIRD - Angers : Bioinformatics IRHS team Actions - Meetings (tools dev / admin / users) - A dedicated Tool Shed - Training (Galaxy Training Network) - A group on eBGO HUB

15. HUBZERO Collaboration platform dedicated to scientifics collaboration

16. HUBzero : Scientifique collaborative platform eBGO HUB HUBzero to share knowledge and manage groups and projects Informations 260 users 127 projects 58 groups 796 resources > 800 unique users by month … Purdue University M. McLennan, R. Kennell. Comput Sci Eng, 12:48-53, 2010. Open source

17. For society Open Science and open data For end users scientists communities Data management plan Preserve, access, share & visualise (data & analytics porocesses) Help for project management … For ICT Facilitate the use of tools Research Service Accelerate switch between dev to production state Optimise infrastructures use (storage, computing & network…) Infrastructure for data infastructure of data What are our goals ? Datamanagement Reproducibility Accessibility OPEN DATA LINKED DATA

18. HEALTH USE CASE 1 National INCa project NGS use in diagnostic

19. A dedicated group

20. A dedicated group: wiki

21. A dedicated group: resources sharing

22. A dedicated group: related Projects

23. Data storage & share

25. A Project: Files

26. A Project: To-Do

27. A Project: Notes

28. HEALTH USE CASE 2 Collaboration with Alexis Bouin from Reims Dilated cardiomyopathy, NGS & Enterovirus

29. A dedicated project

30. Data analysis

31. HEALTH USE CASE 3 Collaboration with Rennes INSERM research team Reproductive research using NGS & Proteomics

32. The ReproGenomics Viewer (RGV)

33. Data visualization

34. Data analysis

35. Merci de votre attention eBGO HUB (collaboration) http://www.e-biogenouest.org/http://www.e-biogenouest.org/ EMME portal (data management) http://emme.genouest.org/http://emme.genouest.org/ Galaxy instance (data analysis) http://galaxy.genouest.org/http://galaxy.genouest.org/ La plate-forme Bio-informatique GenOuest CHU Rennes Olivier Collin Yvan Le Bras Cyril Monjeaud Marie de Tayrac Jean Mosser Wilfried Carré Marc Aubry Alexandra Lespagnol IRSET Rennes Frédéric ChalmelThomas Darde CHU & University Reims Alexis Bouin