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EBIIndustry Support at the EBIThe EBI Industry ProgrammeWorkshopsProteomic Strategies Workshop

Biological Networks: Reconstruction, Analysis,and Modelling Workshop

5-6 May 2009

Dear Associates,

We would like to invite you to the EBI Industry Programme workshop on Biological Networks: Reconstruction, Analysis and Modelling, May 5th to 6th 2009 at the European Bioinformatics Institute, Hinxton, Cambridge, on May 5th to 6th 2009. The venue will be the EBI IT Training room.

Motivation

Reductionist approaches in molecular biology combined with the development of high throughput platforms have led to several large information resources documenting structures, functions and experimental data relating to sub cellular components. What is important now is to infer and understand how molecules function within systems in ways that are not predictable from their individual properties. Network based approaches are an important element of this analysis and modelling.

This workshop will bring together experts and key opinion leaders from the academic and industrial research groups to identify key challenges, opportunities and bottlenecks in the process of network reconstruction, network analysis and network based modelling.

The workshop is sponsored by the EMBL-EBI Industry programme and is positioned as one of a number of pre-competitive initiatives supported by the programme.

The workshop is dividing into three sections focussed on

  • Reconstructing networks (afternoon of 5th May)
  • Analysing Networks (morning of 6th May)
  • Modelling networks (afternoon of 6th May)
The workshop will include presentations by industry partners on what are seen as challenges and opportunities in this area and close with a discussion around these themes. A short report will be written on the workshop and presentations will be made available in PDF format to all participants.

Agenda:

Time Agenda
Tuesday 5 May 2009
12.30 Registration and buffet lunch
13.30 Welcome and Introductions - Dominic Clark & Representative of the Industry Programme members
13.40 Overview of the Agenda - Nicolas Le Novère
  Session 1:Reconstructing Networks
14.00
  • 14.00 Short presentations by members of the industry program involved in the analysis of biological networks, or needing to invest efforts in that direction
  • 14.30 Modelling and reconstruction of gene networks from expression data. Thomas Schlitt (King's College London)
  • 15.15 Primary data resource – IntAct. How to retrieve, download and process protein interaction data in a form suitable to reconstruct protein networks. Sam Kerrien (EMBL-EBI)
  • 15.45 Discussion
16.00 Tea/Coffee break
16.30
  • 16.30 Analysis of Gene Networks using Array Express Atas.“ Misha Kapushesky –(EMBL-EBI)
  • 17.00 Intergrating protein-protein interactions and text mining for protein function prediction,Samira Jaeger (Humboldt‐Universität zu Berlin)
  • 17.30 Discussion: Which kind of data is missing in the current public repositories. Where should be the emphasis of ELIXIR? What sofware is missing in a usable form?
18.00 Close of first day
18.30 Drinks Reception, Hinxton Hall Foyer and Lounges
19.00 Dinner, Tickell Arms
Wednesday 6 May 2009
08.45 Tea and Coffee
09.15 Welcome and summary of Day 1 - Dominic Clark & Nicolas Le Novere
  Session 2: Analysing Networks
09.30
  • 09.30 Introduction
  • 09.45 Analysing transcriptional and metabolic networks - Nick Luscombe (EMBL-EBI, invited)
  • 10.15 Data integration with Cytoscape  - Benno Schwikowski (Pasteur Institute, Paris, invited)
  • 10.45 Discussion
11.00 Tea/Coffee
11.30 Tutorial: Linking Cytoscape and CellDesigner with BiNoM: from networks to models  Laurence Calzone (Curie Institute, Paris, invited)
12.30 Lunch
  Session 3: Modelling Networks
14.00
  • 14.00 Introduction (Nicolas Le Novere)
  • 14.15 Encoding and annotating models with SBML - Lukas Endler (EMBL-EBI)
  • 14.45 Annotating and merging models with SBMLsemantics - Wolfram Liebermeister (Max Planck Institute for Molecular Genetics, Berlin, invited)
15.15 Tea and Coffee
15.45 Qualitative models of influence networks - Ioannis Xenarios (SIB, Geneva)
16.30 Wrap up discussion (chair Dominic Clark, discussant: Nicolas Le Novere)
17.00 Close of meeting
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