1. E-SCIENCE IN WESTERN FRANCE : BEGINS… 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. 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

4. Context Facilitate data analysis Skills transfer by Training Accessibility : More usable tools Reproducibility : Peer review / re-analysis / Portability Transparency : Public funding / citizens & society “people with the skills to analyse data are scarce & will become scarcer” Ludwig Siegele Welcome to the yotta world The economist, 2012

5. Context Exchange from one domain to another From ICT / IT to scientific domains Between scientific domains Life science integratorse-Science integrators « …comprehensible to everyone »

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

7. 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

8. 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

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

10. 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

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

12. EMME Experimental Metadata Management Environment

13. ISAtools : Experimental data management EMME ISAtools suite to store data & metadata Fonctionalities -based on biomed ontologies -bridge between existing 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

14. 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

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

16. 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

17. 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

18. HUBZERO Collaboration platform dedicated to scientifics collaboration

19. HUBzero : Scientifique collaborative platform eBGO HUB HUBzero to share knowledge and manage groups and projects Informations 218 users 127 projects 57 groups 796 resources > 400 unique users by month … Purdue University M. McLennan, R. Kennell. Comput Sci Eng, 12:48-53, 2010. Open source

20. 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 ?

21. CESGO: A FIRST FRENCH E-SCIENCE CENTER Horizon & Challenge

22. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Log in using Google or LinkedIn Account New joujou

23. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Import / export citations New joujou

24. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Subscribe to newsletter / mailing lists New joujou

25. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : e-learning / catalog New joujou

26. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : e-learning / a course

27. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : e-learning / a course module

28. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : e-learning / embedded youtube video

29. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Syncing with Google drive New joujou

30. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Collaborative editing with Google drive New joujou

31. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Collaborative editing with Google drive

32. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Collaborative editing with Google drive

33. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Collaborative editing with Google drive

34. CeSGO : Western France e-Science VRE in production : Welcome to CeSGO HUB ! New functionalities : Collaborative editing with Google drive

35. CeSGO : Western France e-Science New Friends… or more friends! In Western France Brittany & Pays de la Loire regions! Biogenouest UEB In France IFB INRIA In Europe H2020 VRE call : project submitted! Integration in PLANe, the platform for European eScience centers In the rest of the universe CeSGO as the HUBzero european contact point Galaxy team support Icelandic & Swiss collaboration for MMOS Support

36. CeSGO : An e-Science center Discipline 4 Discipline 1 Discipline 2 Discipline 3 Integrator 2 Integrator 3 Integrator 4 Integrator 1 Collaboration ConnectCoordinate Translate e-Science center center

37. CeSGO : An e-Science center Models Algorithms Technics Concepts e-Science center center Developpement ShareSimplify Standardise

38. CeSGO : An e-Science center Cloud computing Grid Clusters Storage Resources MonitorConnect Train e-Science center center

39. VRE AS A STARTING BLOCK Horizon & Challenge

40. CeSGO : Western France e-Science Datamanagement Life sciences protocols metadata URI

41. CeSGO : Western France e-Science Reproducibility cloud docker Galaxy versioning

42. Accessibility wiki Public resources Analytics processes Publications Experiments

43. CeSGO : Western France e-Science New VREs! Open Data

44. CeSGO : Western France e-Science New VREs! Connected using semantic web approaches Thanks to DOI attribution Linked Data

45. CeSGO : Western France e-Science New methods to make science! Scitizen A web platform + a smartphone app Create your dedicated citizen science project web page MMOS A new method for citizen science A first Biogenouest call in december 2014 Citizen science

46. Imagine… Cyril Monjeaud Olivier Collin Olivier Sallou 1 idée 1 projet Principalement 4 poilus 1 environnement propice ~10 To / 512 Go Ram Peu d’infra garantie

47. Imagine…& take part! CeSGO … Enhance Science using e-Science

48. Merci de votre attention eBGO HUB (collaboration) http://www.e-biogenouest.org/http://www.e-biogenouest.org/ Scitizen portal (citizen science) http://scitizen.genouest.orghttp://scitizen.genouest.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/ GO4Bioinformatics (education ) https://www.e-biogenouest.org/einfrastructure/educationhttps://www.e-biogenouest.org/einfrastructure/education La plate-forme Bio-informatique GenOuest Le groupe Symbiose IRISA/INRIA GenOuest-Dyliss-Genscale

49. Imagine…& take part! Preliminary roadmap! Data Management Platform Data Management Plan DOI attribution Valorize research data VRE hosting Coordination Linked data Infrastructure set-up Up to 1 Po storage Cloud