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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
N Databases
Gig
abyt
esThe data challenge: Volume
The data challenge: Geographically disperse
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• Data production sites increasing across Europe
• European Illuminasales up 20% 2o14
Source: http://omicsmaps.com
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
An international distributed infrastructure for
• Data
• Standards
• Tools
• Compute
• Training
• Industry
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
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
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
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
ELIXIR tools and data registry
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
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.
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
ELIXIR prioritised by ESFRI and Council of EU
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
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
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
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
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
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