health & e-science in western france : use cases yvan le bras cyril monjeaud olivier collin...
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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. 728-9
Now : Genomics : Next Generation Sequencing
Now : Proteomics
Next : Bio-imaging
Digital data Huge amount Heterogenous
Critical situation for some laboratories
E-BIOGENOUESTAn 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 succ
ess!
• 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 -Fce Génomique -Rapsodyn -Sciences citoyennes
-UEB C@mpus-CPER-FRM-INCa-H2020
HealthIT
Agro
Environment
7 articles
Peer r
eview
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
http://www.jisc.ac.uk/whatwedo/campaigns/res3/jischelp.aspx#simulate
Mutualis
e
win win
Break d
own silos
Communauté
HubZero
Galaxy EMME
Continuum
Continuum data management & analysis
Collaborative environment Collaboration
EMMEExperimental Metadata Management Environment
ISAtools : Experimental data management
EMMEISAtools 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 CentreP. Rocca-Serra et al. Bioinformatics, 26;254(6), 2010
Open source
Pydio : File sharing platform
Pydio by GenOuestTo store & share data as links
Informations-Galaxy workspace-EMME workspace
Share - data via URI - control - safety - privacy
Abstrium SASCharles du jeu, David Gillard et al.
Open source
GALAXYAnalyze, share and visualize data, create workflows through the web
Galaxy : Data analysis web platform
GALAXY by GenOuestTo analyse & share data as
processes and toolsInformations40276 jobs152 usersMore than 800 tools
Share - data - histories - workflows - tools
Penn state universityJ. 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
HUBZEROCollaboration platform dedicated to scientifics collaboration
HUBzero : Scientifique collaborative platform
eBGO HUBHUBzero to share knowledge
and manage groups and projects
Informations260 users127 projects58 groups796 resources> 800 unique users by month…
Purdue UniversityM. McLennan, R. Kennell. Comput Sci Eng, 12:48-53, 2010.
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 ?Data
management
Reproducibility
Accessibility
OPEN DATA
LINKED DATA
HEALTH USE CASE 1National 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
Data storage & share
A Project: Files
A Project: To-Do
A Project: Notes
HEALTH USE CASE 2Collaboration with Alexis Bouin from Reims
Dilated cardiomyopathy, NGS & Enterovirus
A dedicated project
Data analysis
HEALTH USE CASE 3Collaboration 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) http://www.e-biogenouest.org/
EMME portal (data management) http://emme.genouest.org/
Galaxy instance (data analysis) 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 Chalmel Thomas Darde
CHU & University Reims
Alexis Bouin