EMBL-EBI Industry Support

Dominic Clark, Industry Programme Manager

clark@ebi.ac.uk

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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