health & e-science in western france : use cases yvan le bras cyril monjeaud olivier collin...

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