Coordination of ELIXIR with the ESFRI BMS RI & the European e-Infrastructures Projects

1. Coordination of ELIXIR with the ESFRI BMS RI & the European e-Infrastructures Projects Presented at ELIXIR Funders Meeting Hinxton, October 2010 Andrew Lyall www.elixir-europe.org @emblebi

2. ELIXIR Mission To construct and operate a sustainable infrastructure for biological information in Europe, to support life science research and its translation to medicine and the environment, the bio-industries and society.

3. Contention The scale of the ELIXIR Mission is such that we need to explore ways of achieving it through wider coordination with other European Projects, in particular… • Interactions with the ESFRI BMS Projects in order to support life-sciences research and its translation… • Interactions with the e-Infrastructures to produce a sustainable infrastructure…

4. Life sciences Medicine Agriculture Pharmaceuticals Biotechnology Environment Bio-fuels Cosmaceuticals Neutraceuticals Consumer products Personal genomes Etc… Literature and ontologies Literature and ontologies CitExplore , GO CitExplore , GO Genomes Genomes Nucleotide sequence Nucleotide sequence Ensembl , Ensembl Ensembl , Ensembl EMBL - Bank EMBL - Bank Genomes, EGA Genomes, EGA Proteomes Proteomes UniProt , PRIDE Gene expression UniProt , PRIDE Gene expression ArrayExpress ArrayExpress Protein structure Protein structure PDBe PDBe Protein families, Protein families, motifs and domains motifs and domains Chemical entities Chemical entities InterPro InterPro ChEBI , ChEMBL ChEBI , ChEMBL Protein interactions Protein interactions IntAct IntAct Pathways Pathways Reactome Reactome Systems Systems BioModels BioModels Comprehensive, universal, integrated… 4

5. Who/What are the ESFRI BMS PP Projects.

6. Where did ESFRI come from? European Council Strasbourg Conference on RI “…need new arrangements to support policies related to research infrastructures” Lisbon Strategy Innovation Strategy European Research Area European Parliament European Commission Council of the EU • Timeline • 2000 Strasbourg Conference on RI • 2000 Lisbon strategy • 2000 European Research Area • 2002 Competitiveness Council • 2002 ESFRI • 2006 Innovation Strategy • 2006 Roadmap for RIs • 2007 Framework 7 • 2008 RI Preparatory Phases • 2011 RI Implementations Competitiveness Council Framework Seven European Strategic Forum on RI (ESFRI) € Roadmap for Research Infrastructures RIs 6

7. Cost of 35 Mature ESFRI RI Projects Computing €300M Social Science Environment € 1,300 Physics € 3,600 Biomedical € 1,600 Energy € 2,200 Materials € 4,500 Total Capital Cost = €13,696 Million

8. ELIXIR Support of the European Grand Challenges ELIXIR supports the European Grand Challenges by providing Infrastructure for the other ESFRI Biology Projects.

9. European Grand Challenges • Healthcare for an aging population • A sustainable food supply • An internationally competitive life-sciences industrial sector • Protection of the environment. • A sustainable energy supply

10. Recent new activities at EBI for ESFRI RIs • Recovery of biomolecular data based on a specific sample identifier • BBMRI, EATRIS, ECRIN • Recovery of biomolecular data based on a geographical location • LIFEWATCH, EMBRC • Organism specific genome browsers • Infrafontier • Chemoinformatics • EUOpenScreen

11. Who/what are the e-Infrastructures GÉANT is the pan-European network created in association with National Research & Education Networks that connects 40 million users in over 8,000 institutions across 40 countries DANTE (Delivery of Advanced Network Technology to Europe) plans, builds and operates advanced networks for research and education PRACE (Partnership for Advanced Computing in Europe) is a unique persistent pan-European Research Infrastructure for High Performance Computing DEISA (Distributed European Infrastructure for Supercomputing Applications) is a consortium of leading national Supercomputing centres that aims at fostering the pan-European world-leading computational science research EGI (European Grid Initiative) is a pan-European Grid Infrastructure created in collaboration with National Grid Initiatives (NGI) EUDAT Emerging proposal to build a high-quality, cost-efficient and sustainable pan-European Data Ecosystem, with Europe-wide sharing of resources, services and competence

12. Growth of disk storage at EMBL-EBI Ten petabytes at May 2010. 12

13. Very large user community One Million unique users in 2009 13

14. Data growth exceeds growth in IT capability CPU Power doubles <> 24 months (Moores Law) Disk capacity doubles <> 18 months 1000 800 600 400 No. of Racks 200 0 2018 2009 Network bandwidth doubles <> 20 months Racks in EBI machine room double <> 12 months 14

15. Disruptive technologies. “A technology becomes disruptive when the rate at which it improves exceeds the rate at which users can adapt to the new performance.” The Innovator's Dilemma. Clayton M. Christensen. Harvard Press. 1997 15

16. Disruptive technologies in biology Next-generation DNA sequencing Data will be 1,000 <> 1,000,000 times cheaper to produce Data production rates will be 1,000 <> 1,000,000 more by the end of the ESFRI period. Imaging (including video) at all scales from molecules to whole organisms Protein sequencing by Mass Spectrometry may also be disruptive There will probably be others Macromolecular structure determination by Electron Microscopy etc 16

17. Exponential growth in data… Cannot equate to exponential growth in funding, so Link budgets for data generation and data processing Only produce as much data as you can deal with Take steps to control staff growth Automation of annotation and curation Implement distributed annotation (DAS) Use web services and distributed resources Support for metadata deposition Take steps to control IT resource requirements. Develop policies for which data are to be kept (& which not) Develop data compression techniques 17

18. Capability t Biology e-Infrastructure Requirements e-Infrastructure available in Europe e-Infrastructure required by biology Now

19. e-Infrastructure Challenges Summary • Europe is facing unprecedented (grand) challenges. • The solutions are (mainly) biological • There are emerging (disruptive) technologies that offer ways forward • These are very demanding of IT (e-Infrastructure) • Biology has not been here before • It will be necessary to move quickly to arrange the necessary funding streams • Action is needed at every level (scientific, technical, funding, political, ...).

20. Contention revisited The scale of the ELIXIR Mission is such that we need to explore ways of achieving it through wider coordination with other European Projects, in particular… • Interactions with the ESFRI BMS Projects in order to support life-sciences research and its translation… • Interactions with the e-Infrastructures to produce a sustainable infrastructure…

21. Contention Part 2 This is achieved by • Attending relevant European Committees and Working Groups • Creating consortia to implement the interactions • Applying for funding to fund the consortia

22. The ESFRI BMS RI Coordinators BBMRI – Prof. Kurt Zatloukal, Institute of Pathology, Medical University of Graz EATRIS – Prof. Rudi Balling, Helmholtz Centre for Infection Research, Braunschweig ECRIN – Prof. Jacques Demote-Mainard, INSERM ELIXIR – Prof. Janet Thornton, European Bioinformatics Institute EMBRC – Prof. Roberto Di Lauro, Stazione Zoologica Anton Dorn, Naples EUOpenScreen – Dr. Ronald Frank Leibniz, Institute for Molecular Pharmacology, Berlin EUROBioImaging (Scientific) – Dr. Jan Ellenberg, EMBL, Heidelberg EUROBioImaging (Medical) – Prof. Dr Stefan, Schoenberg University, Mannheim ERINHA – Hervé Raoul, LABORATOIRE P4, Inserm, Lyon Infrafrontier – Prof. Martin Hrabe de Angelis, GSF, Munich INSTRUCT – Prof. David Stuart, University of Oxford

23. ESFRI Thematic Working Groups • Monitor scientific development & need for RIs in the thematic areas • Consultation with existing relevant scientific organisations • Follow implementation of projects on ESFRI Roadmap • Give feedback to ESFRI on relevant issues • Advise ESFRI on whether projects should remain on the Roadmap • Evaluate possible proposals for the update of the Roadmap. • Advising ESFRI on potential improvement in the pan-European availability and management of existing RIs • Coordinate interdisciplinary activities with the other TWGs • ELIXIR & all of the other ESFRI BMS Projects attend the BMS TWG

24. European Grid Initiative • A foundation established under Dutch law • To create and maintain a pan-European Grid Infrastructure • Works collaboratively with National Grid Initiatives (NGIs) • European Research Organisations are members • Seeks to guarantee the long-term availability of a generic e-infrastructure for all European research communities and their international collaborators • EMBL is a member

25. e-Infrastructure Reflection Group • To support the creation of a political, technological & administrative framework for an easy and cost-effective shared use of distributed electronic resources across Europe • Particular attention on grid computing, storage, and networking. • Defines and recommends best practices for pan-European efforts • Consists of official government delegates from all the EU countries. • Produces white papers, roadmaps and recommendations, and analyses the future foundations of the European Knowledge Society. • Current first priority is e-Infrastructure under Framework Seven • ELIXIR is a member of the e-Infrastructure Reflection Group where it represents the ESFRI BMS Projects

26. FP7 INFRASTRUCTURE-2011 Call 8, INFRA-2011-1, is managed by Research Call 9, INFRA-2011-2, is managed by INFSO They are coordinated Previous INFSO calls were technology-led This call is intended to “redress the balance” – M.Campolargo The emphasis should be on Data and “Expert” Communities They are seeking proposals that are user-led

27. ELIXIR-led FP7 consortia Consortium 1 • Members are the ESFRI BMS Projects • Topic is INFRA-2011 2.3.2 (Implementation of common solutions for a cluster of ESFRI infrastructures in the field of "Life sciences”) • Short Name BMSBRIDGES Consortium 2 • Members are several e-Infrastructures and several BMS Projects • Topic is INFRA-2011 1.2.1 (e-Science Environments) • Short Name e-BioMedSci

28. Thank you for your attention...