First Systems Biology Symposium/Workshop

21-22 June 2006

Dear Associates,

The EBI will host the Industry Programme's First Systems Biology Symposium/Workshop on the 21st - 22nd June 2006 in Hinxton, Cambridge. The Scientific Coordinators are: Kah-Tong Seow - Merck KGaA, and Nicolas Le Novère - EMBL-EBI.

Aim:
To bring together experts from both academia and industry to discuss and identify rapidly evolving systems biology methodology and thinking that will lead, or has let, to deliverables within biomedical industry.

Objectives:
Systems biology represents fast emerging technology that complements the conventional experimental design methods, instead of a more reductionistic approach, it applies a holistic thinking where a biological problem is studied potentially without the preferred views defined by domain experts, but by an unbiased representation supported by available observations and knowledge consistent with OMIC-scale experiments. To follow this rapidly evolving and exciting field of research, it would be productive to combine our efforts through a panel of international academic experts and industry scientists active in systems biology research and development through a series presentations and round-table discussions to identify the latest trends of systems biology that are likely to add value and deliver tangible results for biomedical industry.

Programme:
Day one: We will hear from academic experts on non-standard ODE ways to perform modeling and simulation as well as network properties that are critical to the analysis and understanding of a systems behaviour, such as robustness. This will be followed by a hands-on workshop, where building and analysis of simple models will be performed by attendees. The rational behind different modelling approaches will be discussed, and the sensitivity to initial conditions and parameter values will be studied. A tutorial on BioModels Database usage will also be provided.

Day two: We will hear from industry scientists representing Physiomics, GSK, J&J, Unilever, GeneGo, GNS and Physiomics, through a series of presentations and round-table discussions, discussing about the heterogeneous systems biology methods that have been proven to add value to the health-care industry. We shall also be learning from case studies how to initiate systems biology projecta in an industry setting.

Day1: Academic speakers:
· Darren Wilkinson (Univ Newcastle): Modelling in Ageing (stochastic)
· Denis Thieffry (Univ Marseille): Modelling in Development (logical)
· Joerg Stelling (ETH, Zurich): Robustness in biological networks
· Michael Rebhan (FMI, Basel)
·

Day 1: Workshop (Instructor: Nicolas Le Novère)
How to select apporaches, tools and algorithms when developing a model of biological process. Hopefully with the academic speakers, we
will discuss the constraints to take into account before to start
developing a model (size of the system, accuracy of the experimental
measures etc.), and their consequences when it comes to choose between
continuous and discrete approaches, kinetic or steady-state, or between
specific simulation tools.

Quick tutorial on BioModels Database: How to retrieve models, how to
understand them, how to download them and run simulations.

Practical assignments: attendees will choose between some simple but
interesting process we will provide, and try to write down the models,
run the simulations and perform quick analysis of their
properties. We will use the following tools:

CellDesigner: http://www.celldesigner.org/
COPASI: http://www.copasi.org/
SBMLeditor: http://www.ebi.ac.uk/compneur-srv/SBMLeditor.html

Day 2: Industry speakers:
· Andrew Finney (Physiomics, Oxford, UK): Modelling in cancer research
·(ODE)
· · Andrew Stubbs (Johnson & Johnson, Belgium)
· Yuri Nikolsky CEO GeneGO
· Colin Hill CEO Gene Network Sciences

Day2: Round-table discussion session

Topic 1: How to scout/evaluate systems biology companies, issues
concerning contract, measurable milestones, cost considerations,
Chair (Guy Warmer, Unilever)
Participating companies: GeneGO, GNS, Physiomics

Topic 2: What are the heterogeneous computational/mathematical-based
models/methods that constitute the systems biology methodologies? How to match these methods to systems biology problems in drug industry?
Chair (Andrew Stubbs, J&J)
Participating companies: GeneGO, GNS, Physiomics