InsJtut Français de BioinformaJque Current situagon and prospect

Ins$tut Français de Bioinforma$que Current situa+on and prospect IFB General Assembly Gif-­‐sur-­‐Yve=e, January 9 2015 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 1st 2013 •  Sept. 2013: first mee+ng of the IFB steering commi=ee •  Dec. 2013: IFB kick-­‐off mee+ng 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 IFB structure IFB consists of: •  A network of 6 regional centers (29 PFs) •  A na+onal hub: IFB-­‐core 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: – 
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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) IFB schedule of payments IFB consolidated budget (2014) Spending 2013-­‐2014 (k€) Available funds in 2015 (k€) IFB-­‐core T1 Equipment 101 1899 T1 Staff 300 300 T1 ELIXIR contribu+on 460 678 T2 Opera+ons 121 167 T2 IDRIS hos+ng 0 1038 Regional PFs T1 Equipment 1080 490 T1 Staff 1011 1889 T2 Opera+ons 168 54 3242 6515 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) 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 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” 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 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 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 • 
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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 Task forces •  Foster structuring, pooling of resources and know-­‐how dissemina+on •  Dedicated to specific areas of interest for several PFs – 
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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 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) Federa+on of Clouds Bioinforma+cs work packages •  Improvement/development of services in selected areas •  17 FTC (18 months) engineers – 
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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 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? 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 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 ? Structuring the community •  Organiza+on of scien+fic challenges (SFBI, GdR BIM) –  Analysis of 3rd 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 ELIXIR • 
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France signed MoU in Oct. 2013 Presenta+on of the French node applica+on to SAB Dec. 2013 ELIXIR kick-­‐off mee+ng Dec. 2013 During 2014 several mee+ngs of HoNs/technical coordinators –  ELIXIR program, work streams –  Pilot ac+vi+es –  Proposals to H2020 calls •  EMBRIC (INFRADEV-­‐4-­‐2014) several ESFRIs: ELIXIR, EMBRC, MIRRI, etc. •  EXCELERATE (INFRADEV-­‐3-­‐2015) •  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 : 0.845 M€ ; 2018 : 1.15 M€ Thank you for your a=en+on Ques+ons ?