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

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

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

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

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 -CPER-FRM-INCa-H2020 Health IT Agro Environment 7 articles Peer review

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

An innovative VRE approach Research Lifecycle Open source solutions Don’t reinvente the wheel Mutualise win win Break down silos

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

EMME Experimental Metadata Management Environment

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

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

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

Galaxy : Data analysis web platform GALAXY by GenOuest To analyse & share data as processes and tools Informations 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

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

HUBZERO Collaboration platform dedicated to scientifics collaboration

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, Open source

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

HEALTH USE CASE 1 National INCa project NGS use in diagnostic

A dedicated group

A dedicated group: wiki

A dedicated group: resources sharing

A dedicated group: related Projects

Data storage & share

A Project: Files

A Project: To-Do

A Project: Notes

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

A dedicated project

Data analysis

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

The ReproGenomics Viewer (RGV)

Data visualization

Data analysis

Merci de votre attention eBGO HUB (collaboration) EMME portal (data management) Galaxy instance (data analysis) 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