EMBL-EBI Industry Support
Dominic Clark, Industry Programme Manager
An overview of how EMBL-EBI works with industry
stakeholders.
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We support larger companies through the “Industry
Programme”
• Since its foundation in 1996, the Industry Programme has
been an integral part of the EMBL-EBI.
• It provides on-going and regular contact with key
stakeholder groups.
• The Industry Programme is now well established as a
subscription-funded service for larger companies.
• Through the Industry Programme, EMBL-EBI provides
specialist workshops, standards-based activities and pre-
competitive research and development opportunities of
particularly relevance to the industry programme
members.
Potentially many areas of industry
Forestry
Biotech
Fisheries
Big Pharma
Computing Biofuels
Medical
devices
Agri-food
Environmental
protection
Cosmetics
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There are currently 20 members (Dec 2011)
• Pharmaceuticals
• Astellas Pharma
• AstraZeneca
• Bayer Schering
Pharma
• Boehringer
Ingelheim
• Eli Lilly and
Company
• F. Hoffmann-La
Roche
• Galderma
• GlaxoSmithKline
• Janssen (J&J)
• Merck Serono
• Novartis Pharma
• Novo Nordisk
• Orion Pharma
• Pfizer Ltd
• Sanofi-Aventis
• UCB Pharma
“The Industry
Programme’s
regular meetings
foster inter-
company
interactions as we
collaborate on
special projects and
liaise on other
industry initiatives”
Bertram Weiss,
Principle Scientist,
Target Discovery, Bayer
Schering Pharma
• Nestlé
• Unilever
• Syngenta
Philips Research
Diagnostics
Agri-food
Pharmaceuticals
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Scope of Industry Programme
• 1. Forum for interaction between EBI and our users in industry
• 2. Provide training for our commercial users
• 3. Inform „industrial users‟ of EBI‟s status and future plans
• 4. Feed industry requirements into the EBI‟s planning (influencing)
• 5. Provide a neutral meeting place for inter-company interactions
on bioinformatics
• 6. Coordinate workshops on topics decided by programme –
gathering expert speakers (industrial and academic)
• 7. To initiate „precompetitive projects‟ at EBI with targeted
collaborative funding
• 8. External liaison as appropriate with other industry initiatives
Knowledge Exchange Workshops
• The Industry Programme organises high quality
workshops and symposia, providing expert level
presentations and strategic discussion opportunities for
members and other key opinion leaders.
• Workshops:
• Prioritised by the IP members based on proposals
• Organised through a planning team,
• Include key opinion leaders as speakers
• Include appropriate stakeholders
• By individual/collective invitation only.
• Facilitated
• Take a significant amount of planning
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Workshops during 2011
Workshop Title Dates
Public-Private Data challenges Jan 2011
Foundations for Biomedical Data and Model
Interoperability
Mar 2011
Bio-therapeutics Apr 2011
Semantic Web for Industry May 2011
Literature Services June 2011
Molecular Informatics and Open Source
Software
Jul 2011
Chemical Registry Systems Oct 2011
Systems Biology for Drug Discovery &
Development
Nov 2011
Patent Informatics (EPO, The Hague) Dec 2011
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Workshops for 2012
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Workshop Title Date
Using electronic health records (EHRs) for
translational bioinformatics
Feb 2012
Chemogenomics Mar 2012
1000 Genomes Apr 2012
R & Bioconductor training workshop May 2012
Metabolomics May 2012
Antibody Informatics June 2012
Systems Biology for Toxicology Pathways Sept 2012
1000 Genomes and NGS data Analysis * Nov 2012
Pre-clinical Safety Data ** Nov 2012
Plus other joint workshops
Workshops for 2013
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Workshop Title Date
Nutrigenomics Feb 2013
Cancer genomics Mar 2013
EMBL-EBI Industry Programme workshop
17th-18th April 2012
1000 Genomes Workshop
Agenda: 17th April 2012
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Tuesday 17th April 2012 (James Watson Room, WTCC)
12.00 Lunch (buffet lunch in WTCC cloisters outside James Watson Room)
13.30 Welcome and Overview (Dominic Clark & Paul Flicek)
13.45 Paul Flicek (EMBL-EBI) Overview of the 1000 Genomes Project and
update on progress
14.30 Discussion
14.45 Jan Korbel (EMBL) Structural Variation in the 1000 Genomes project
15.30 Tea/Coffee
16.00 Anders Malarstig (Director Human Genetics, Pfizer
Pharmaceuticals)“Drug development in the 1000 genomes era –the
Pfizer road map to improve confidence in target mechanism and safety”
16.30 Mark A. DePristo (Broad Institute) Tools for the analysis of NGS data
and their application to the 1000 Genomes project
17.30 Discussion
18.00 Close of day
Agenda: 18th April 2012
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Wednesday 18th April 2012 (James Watson Room, WTCC)
09.00 Tea/Coffee
09.15 Matt Nelson (Director of Statistical Genetics, GSK) “Industry use cases”
09.45 James Holzwarth (Nestle) Exploration of 1000 genomes pilot data release
using genomic context
10.15 Elizabeth Worthey (Medical College of Wisconsin) Diagnoses of rare
diseases. 11.00 Tea/Coffee
11.20 Ele Zeggini (WT Sanger Institute) Next generation association studies:
searching for low frequency and rare variants in complex traits.
12.00 Laura Clarke (EMBL-EBI) - Tools for access and analysis of 1000
Genomes Data
12.45 Discussion and Close of Workshop
13.00 Lunch (Hinxton Hall Restaurant)
Industry Programme Workshop:
Antibody Informatics
July 10nd-11th 2012
Speakers
• Hiroki Shirai (Astellas Pharma Inc)
Workshop Overview
• Bojana Popovic (MedImmune)
Applications of structural bioinformatics
in MedImmune
• Shinji Soga (Astellas) Antibody
engineering collaboration in Japan,
antibody druggability
• Paolo Marcatili (La Sapienza
University, Rome) The DIGIT
Database and Analysis tools
• Roland Dunbrack (Institute for
Cancer Research) Clustering of
antibody CDR loop conformations
• Randi Vita (La Jolla Institute for
Allergy and Immunology) Therapeutic
Antibody Data in the IEDB and The
Antibody Registry Project
• Marie-Paule Lefranc (Univ.
Montpellier, CNRS) IMGT®, the
international ImMunoGeneTics
information system®
• Jianqing Xu (Johns Hopkins
University) A Rosetta-based
computational pipeline for antibody
engineering.
• Annemarie Honegger (University of
Zurich) Recent applications of
bioinformatics to antibody engineering.
• Oda Stoevesandt (Babraham
Institute) The AFFINOMICS project.
• Discussant
• Mathew Woodwark, Director of R&D
Informatics, MedImmune
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What happens after workshops?
• Where appropriate EMBL-EBI will act as a coordinator or
broker in establishing pre-competitive
collaborations/initiatives between Industry programme
members (and third parties – academic groups, funding
organisations, other commercial companies)
• Examples from 2011
• Completion of the SESL Pilot Demonstrator
• MIABE paper in NRDD
• Tox ontology roadmap papers
Published Sept. 2011, PMID: 21878981
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Quarterly meetings
• The principal forum for prioritisation of projects/workshops
• Inform industry participants on status of EMBL-EBI & future plans
• Receive feedback from industry partners
• Typically includes the directors of EMBL-EBI
Retreat September 2011
• In addition to the quarterly meeting we held an off-site
retreat (at ATC building in Heidelberg).
• Eight major topics were identified that will be discussed
further during the quarterly meetings.
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Eight major topics were identified that will be discussed further
during the 2012 quarterly meetings:
• Computing Infrastructure and Services
• Collaborative Research with EMBL-EBI
• New Data & Tools: Pharma
• New Data & Tools: non-Pharma
• Pre-competitive collaborations
• Mechanistic and systems modelling, translational bioinformatics and
biomarkers
• Data Integration, Semantics, Standards & Ontologies
• Training, Workflows and Applications
Industry Programme Retreat
Heidelberg, September 2011
Pre-competitive projects
• In addition to:
• 1) ESFRI Projects: ELIXIR and EU-Openscreen
• 2) IMI projects (e.g. eTox, EMTRAIN, DDMoRe and
EHR4CR, OpenPhacts),
• 3) Collaborations with the Pistoia Alliance (e.g. SESL
Pilot project),
• We have a number of pre-competitive industry funded
projects.
• These are funded by industry, but EMBL retains the IP
and the results are integrated into our services for the
benefit of all stakeholders.
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Training for Industry
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Training for Industry
• On site training
• Tutorials by WebEx
• Specially designed courses
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In Summary
• EMBL-EBI is committed to supporting industry
• For larger companies we have the EMBL-EBI Industry
Programme. This facilitates discussion with industry,
organised expert workshops on topics prioritised by
members and promotes pre-competitive initiatives and
projects that ultimately benefit all our stakeholders.
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