Ins$tut Français de Bioinforma$que Current situa+on and prospect. IFB General Assembly Gif- sur- Yve=e, January

Transcription

1 Ins$tut Français de Bioinforma$que Current situa+on and prospect IFB General Assembly Gif- sur- Yve=e, January

2 Background 2010: Na+onal Infrastructures in Biology and Health call from the Investment for the Future program 2011: France Génomique proposal accepted Apr. 2012: ReNaBi- IFB project accepted July 2013: agreement gran+ng subsidy signed with ANR Official start of the project: January 1 st 2013 Sept. 2013: first mee+ng of the IFB steering commi=ee Dec. 2013: IFB kick- off mee+ng

3 IFB mission To offer core bioinforma+cs resources and services to the life science community To provide support for life science research programs: projects bolstering users training To provide an IT infrastructure devoted to management and analysis of biological data (high throughput data): Material resources (CPUs, storage, network, etc.) Availability of biological data collec+ons Deployment of bioinforma+cs tools To act as a middleman between the life science community and the bioinforma+cs/computer science research community To be the ELIXIR French node

4 IFB structure IFB consists of: A network of 6 regional centers (29 PFs) A na+onal hub: IFB- core

5 IFB endowment 20 M grant from Investments for the Future program (un+l 2020) 10 M expendible endowment 10 M loan interests (1.25 M /year) Project divided into two phases Investment phase (16.16 M ) Opera+on phase (3.84 M ) Four items of expenditure: Equipment: 6.8 M Hired manpower: 6 M Opera+ng costs: 3.8 M French contribu+on to ELIXIR: 3.4 M (actually 3.8 M up to 2018)

6 IFB schedule of payments

7 IFB consolidated budget (2014) Spending (k ) Available funds in 2015 (k ) IFB- core T1 Equipment T1 Staff T1 ELIXIR contribu+on T2 Opera+ons T2 IDRIS hos+ng Regional PFs T1 Equipment T1 Staff T2 Opera+ons

8 Summary of ac+vi+es in 2014 Sekng up the na+onal hub Defining IFB scien+fic policy: steering commi=ee Communica+on: crea+ng the web site (Q. Barbier) Training (C. Thermes, C. Blanchet) Na+onal e- infrastructure and Cloud deployment (C. Blanchet) Task forces (C. Caron, O. Collin) Bioinforma+cs work packages (C. Medigue, M. Ruiz, P Tuffery, G Perrières) Collabora+ons with other na+onal infrastructures (P. Le Ber, V. Loux, C. Bruley, E Thévenot) ELIXIR (N. Blomberg)

9 IFB na+onal hub: IFB- core UMS 3601 created in 2013 by CNRS, on Gif campus Supervisory authori+es : CNRS, CEA, INRA, INRIA, INSERM So far, IFB- core is officially recognized by CNRS, INRA and INSERM. Equipment of the UMS premises, February 2014 Mee+ng with CNRS DR4 staff Agreement for establishment of UMS not yet signed IFB has no legal personality

10 IFB- core: permanent staff Director: J- F Gibrat, DR1 INRA Administra+ve staff: P. Laplagne, TR INRA Head of Communica+on, Forma+on et Valorisa+on team Engineer in charge of Web site E- learning plarorm Head of the e- infrastructure team: C. Blanchet, IR1 CNRS Engineer system administrator Engineer Cloud deployment Two engineers data integra+on and tools interoperability

11 IFB- core: permanent staff Director: J- F Gibrat, DR1 INRA Administra+ve staff: P. Laplagne, TR INRA Head of Communica+on, Forma+on et Valorisa+on team Engineer in charge of Web site E- learning plarorm: Q. Barbier Head of the e- infrastructure team: C. Blanchet, IR1 CNRS Engineer system administrator : F. Ben Ali Engineer Cloud deployment : M. Bedri 2 engineers data integra+on and tools interoperability : M. Grosjean

12 IFB web site Important for communica+on and as a collabora+ve tool Crea+on of the web site has been very slow Impaired by absence of head of CFV team Lack of staff to create the web site (un+l hiring of Q. Barbier in Oct.) June 2014: contract web site development to a company November 2014: local installa+on of the web site Site is s+ll in development! PFs must fill the informa+on form and check the web site PFs are responsible for upda+ng their data

13 IFB steering commi=ee Defines IFB scien+fic policy Meets every two weeks 25 mee+ngs so far (mee+ng minutes are available to PF staff members) Steering commi=ee composi+on: IFB director: J- F Gibrat, INRA / C. Blanchet, CNRS Representa+ves of the 6 regional centers IFB- NE (M. Pupin, Lille 1 Univ. / J. Thompson, CNRS) IFB- SO (M. Nikolski, CNRS / C. Gaspin, INRA) IFB- GO (C. Caron, CNRS, E. Corre, CNRS) IFB- GS (O. Gascuel, CNRS, V. Lefort CNRS) PRABI (G. Perrière, CNRS, P. Veber CNRS) APLIBIO (P. Tuffery, INSERM / D. Gautheret Paris Sud Univ) IDRIS director : D. Girou, CNRS France Génomique director: P. Le Ber, CEA

14 Task forces Foster structuring, pooling of resources and know- how dissemina+on Dedicated to specific areas of interest for several PFs Galaxy Virtual Research Environments (VRE) IT infrastructure, Cloud federa+on (GRISBI: PF system administrators) Infrastructure economic model Strengthening of IFB PFs organiza+on/interac+ons Local organiza+on, I.e., the six regional centers Na+onal organiza+on, i.e., by topics/areas of interest ELIXIR work streams

15 e- infrastructure & Cloud To provide an IT infrastructure dedicated to life science data management and analysis. Infrastructure accessible via an academic Cloud Federa+on of Clouds with regional PFs Crea+on of VMs (appliances) dedicated to a bioinforma+cs domain (e.g., proteomics) or specific tasks (e.g., RNA- seq analyses) (see work packages) Pre- installed, on demand, ready to use environment Referenced in a marketplace (catalog of VMs)

16 Federa+on of Clouds

17 Bioinforma+cs work packages Improvement/development of services in selected areas 17 FTC (18 months) engineers Evolu+onary bioinforma+cs Structural bioinforma+cs Plant bioinforma+cs Microbial bioinforma+cs Na+onal hub opera+ons 24 FTC (2x18 months) engineers (France Génomique) Development of NGS sequencing data analysis tools/services

18 Bioinforma+cs services Access to specialized databases with added value coming from the scien+fic exper+se of the laboratory: e.g., IMGT, ProDom, GiantVirus, etc. Provision of tools and on line services corresponding to the scien+fic exper+se of the laboratory: e.g., PhyML, Phylogeny.fr, MicroScope, etc. Access to an IT infrastructure (equipment, data, tools) Support to life science scien+fic projects and hos+ng on the infrastructure Training Others?

19 IFB call of proposals Publica+on of the call by the end of January 2015 Open call for development of services All thema+c areas are eligible, focus on usefulness of services offered All laboratories (not only IFB s PFs) are en+tled to submit a proposal, but if the service offered is selected, the laboratory will be requested to join IFB Projects evaluated by external reviewers Call provides funds for 2 years FTC engineer + opera+ons

20 Collabora+ons with other 22 NIBSs Infrastructure for biological informa+on as a key role in life science Collabora+ons with Na+onal Infrastructures in Biology & Health France Génomique (sequencing) - P Le Ber, V Loux Profi (proteomics) - C. Bruley MetaboHub (metabolomics) E. Thévenot IFB governance: Users Community Commi=ee Alliances : AVIESAN, ALLENVI (D. Joly) Other na+onal infrastructures (biomedical community) What is the best way for sekng up fruirul collabora+ons with other NIs?

21 Structuring the community Organiza+on of scien+fic challenges (SFBI, GdR BIM) Analysis of 3 rd genera+on sequencing technology data (long reads - - PacBio, Oxford Nanopore) Unresolved issues in specific domains proposed by biologists Involvement in high- visibility ins+tu+onal projects seedencode, FR- AgENCODE (plants and farm animals) TARA Help for organizing workshops, schools, bootcamps, hackathons

22 ELIXIR France signed MoU in Oct Presenta+on of the French node applica+on to SAB Dec ELIXIR kick- off mee+ng Dec During 2014 several mee+ngs of HoNs/technical coordinators ELIXIR program, work streams Pilot ac+vi+es Proposals to H2020 calls EMBRIC (INFRADEV ) several ESFRIs: ELIXIR, EMBRC, MIRRI, etc. EXCELERATE (INFRADEV ) France has not signed the ECA (required to be a full member) French contribu+on to ELIXIR: 2014 : 0.46 M ; 2015 : 0.68 M ; 2016 : 0.72 M ; 2017 : M ; 2018 : 1.15 M

23 Thank you for your a=en+on Ques+ons?