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. 728-9

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. 728-9

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 SiegeleWelcome to the yotta worldThe economist, 2012

Context

• Exchange from one domain to another• From ICT / IT to scientific domains• Between scientific domains

Life science integrators e-Science integrators

« …comprehensible to everyone »

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 existing 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

Informations218 users127 projects57 groups796 resources> 400 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 ?

CESGO: A FIRST FRENCH E-SCIENCE CENTERHorizon & 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

Inte

grat

or 3

Integrator 4

Integrator 1

Collaboration

Connect Coordinate

Translate

e-Science center

CeSGO : An e-Science center

Models

Algorithms

Technics

Concepts

e-Science center

Developpement

Share Simplify

Standardise

CeSGO : An e-Science center

Cloud computing

Grid

Clusters

Storage

Resources

Monitor Connect

Train

e-Science center

VRE AS A STARTING BLOCKHorizon & Challenge

CeSGO : Western France e-Science

Datamanagement

Life sciences protocols

metadata

URI

CeSGO : Western France e-Science

Reproducibilitycloud

docker

Galaxy

versioning

CeSGO : Western France e-Science

Accessibilitywiki

Public resources

Analytics processes

PublicationsExperiments

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 sc

ience

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) http://www.e-biogenouest.org/

Scitizen portal (citizen science) http://scitizen.genouest.org

EMME portal (data management) http://emme.genouest.org/

Galaxy instance (data analysis) http://galaxy.genouest.org/

GO4Bioinformatics (education ) https://www.e-biogenouest.org/einfrastructure/education

La plate-forme Bio-informatique GenOuestLe 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