E-SCIENCE IN WESTERN FRANCE : BEGINS… 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

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

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

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

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 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

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 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, 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 ?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

VRE AS A STARTING BLOCK Horizon & Challenge

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

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

Accessibility wiki Public resources Analytics processes Publications Experiments

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

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

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

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

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

Merci de votre attention eBGO HUB (collaboration) Scitizen portal (citizen science) EMME portal (data management) Galaxy instance (data analysis) GO4Bioinformatics (education ) La plate-forme Bio-informatique GenOuest Le groupe Symbiose IRISA/INRIA GenOuest-Dyliss-Genscale

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