Upload
gwenda-price
View
219
Download
1
Tags:
Embed Size (px)
Citation preview
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