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European Life Sciences Infrastructure for Biological Informationwww.elixir‐europe.org
Introduction to ELIXIR
Andy Smith, ELIXIR Hub 18 March 2015 ‐Wageningen
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medicine
agriculture
bioindustries
environment
ELIXIR connects national bioinformatics centres and EMBL‐EBI into a sustainable European infrastructure for biological research data
ELIXIR underpins life science research – across academia and industry
www.elixir-europe.org
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N Databases
Gig
abyt
esThe data challenge: Volume
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The data challenge: Geographically disperse
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• Data production sites increasing across Europe
• European Illuminasales up 20% 2o14
Source: http://omicsmaps.com
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databasesdatabases
Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2012. MY Galperin, GR Cochrane – Nucleic Acids Research, 2011
The data challenge: diversity
• Diverse• Plentiful• Disperse
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An international distributed infrastructure for
• Data
• Standards
• Tools
• Compute
• Training
• Industry
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A distributed infrastructure scales with the challenges
• ELIXIR deliver services through national ELIXIR Nodes
• ELIXIR Nodes build local bioinformatics capacity throughout Europe
• ELIXIR Nodes build on national strengths and priorities
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ELIXIR funding
Hub funded jointly by
ELIXIR member states
Joint applications
to EU funding
Nodes funded by national agencies
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ELIXIR Nodes
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• Over 100 institutes involved in ELIXIR Nodes
• Collaboration Agreements to be signed between Hub and Nodes
• Nodes that are national networks are developing own internal Node agreements
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ELIXIR Core Data Resources
• Small subset of ELIXIR data resources and archives
• Fundamental importance to life science
• Long term preservation and reuse of biological data
Focal point of ELIXIR’s technical and science policy actions for data sustainability
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ELIXIR Named Services
• Quality indicator of the Service or Tool • have clearly outlined terms of usage,
• declared service levels and monitoring
• vetted by the ELIXIR SAB as part of Node application
• Sustainability & Commitment to Service• Described in Service Delivery Plans annexed to the Hub‐
Node Collaboration Agreements
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ELIXIR tools and data registry
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Integration and interoperability of resources
• Formats, Ontologies, Guidelines, …
• Professional skills for managing and exploiting data
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“… typically 40% of our effort in biomarker discovery is data integration”J. Wojcik, CEO, Quartz Bio
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Data interoperability – Human Protein Atlas
The Human Protein Atlas portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in 46 different normal human tissues and 20 different cancer types, as well as 47 different human cell lines.
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ELIXIR pilots to address key challenges in biomedical research:
1. Cloud computing“Embassy cloud”: Access reference data in a virtual environment – work as though you are at EMBL-EBI or SIB, Switzerland
3. High-Performance Computing“Lightpath”: Connections for on-demand reference data to remote HPC centres at EMBL-EBI and CSC Finland
2. Authentication & AuthorisationImproved methods and processes for access to clinical data
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ELIXIR prioritised by ESFRI and Council of EU
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ELIXIR‐EXCELERATE
• ELIXIR’s application following ESFRI Prioritisation in 2014
• Results expected in Spring; project start Summer
• Eur 19 million 4 year project
• Focus on accelerating the implementation of ELIXIR
• Use case on Plant Sciences: Integrating Genomic and Phenotypic Data for Crop and Forest Plants
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ELIXIR Industry Advisory Committee
• Philippe Sanseau, GlaxoSmithKline, UK
• Wendy Filsell, Unilever R&D, UK (Vice Chair)
• Angel Pizarro, Amazon Web Services, USA
• Jakob de Vlieg, Bayer CropSciences Innovation Center, Belgium
• Martin Ebeling, Hoffmann‐La Roche, Switzerland
• Anita Eliasson, Biocomputing Platforms Ltd, Finland
• Mark Forster, Syngenta, UK (Chair)
• Montserrat Vendrell, Biocat, Spain
• Natalia Jiménez Lozano, Bull and Atos, Spain
• Iain Hrynaszkiewicz, Nature Publishing Group ‐Macmillan, UK
• Claus Stie Kallesøe, Gritsystems A/S, Denmark
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Industry Advisory Committee
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Public data: a foundation for innovation
• Supporting Europe’s SMEs that build services on top of the public bioinformatics resources – understanding impact
• ELIXIR Core Resources and Named Services• Facilitating integration through Pilot Actions
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Innovation and SME programme
Copenhagen, 24‐25 November 2014
• Focussed on pharma and ELIXIR resources for drug discovery
Wageningen, 18‐19 March 2015
• Data‐driven growth in the agri‐food industries
Basel, 9 June 2015
• Pharma and biotech
Future events?
• Marine informatics
• HPC suppliers
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Benefit of ELIXIR to industry ‐ supplier
• The life science sector as a consumer of HPC is already high and set to increase further
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ELIXIR industry distribution channel
• Mailing list of around 200 companies and SME Associations
• Events, news and industry/academia funding opportunities from across ELIXIR
• Content, reach and frequency to expand through 2015
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ELIXIR webinars
• Regular series of updates from ELIXIR
• Typically 3rd Wednesday of month
• 30 minute talk: 30 min questions
• Future webinars:
• Data and Software carpentry ‐ Aleksandra Pawlik
• Marine metagenimics: towards user centric services –Nils Peder Willassen
• Run using WebEx ‐ for live or recorded viewing
• Full programme: elixir‐europe.org/webinar
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www.elixir‐europe.org
Thank you