Writer's museum

Public lecture

  • Rule-based Modeling of Cellular Signalling
  • Vincent Danos
  • Thursday 20th September 2007, 5pm
  • e-Science Institute, 13-15 South College Street, Edinburgh
Public lecture during CMSB 2007

The CMSB conference is pleased to host a public lecture on behalf of the School of Informatics, University of Edinburgh. Entry to this lecture is free to all members of the School of Informatics.

Vincent Danos (Directeur de Recherches CNRS, Université Denis Diderot, Paris, France)
Title: Rule-based Modeling of Cellular Signalling
Abstract: Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of reasoning. Yet, this same combinatorial explosion makes the traditional modelling paradigm based on systems of differential equations impractical. In contrast, agent-based or concurrent languages, such as kappa describe biological interactions in terms of rules, thereby avoiding the combinatorial explosion besetting differential equations. Rules are expressed in an intuitive graphical form that transparently represents biological knowledge. In this way, rules become a natural unit of model building, modification, and discussion. We illustrate this with a sizeable example obtained from refactoring two models of EGF receptor signalling that are based on differential equations. An exciting aspect of the agent-based approach is that it naturally lends itself to the identification and analysis of the causal structures that deeply shape the dynamical, and perhaps even evolutionary, characteristics of complex distributed biological systems. In particular, one can adapt the notions of causality and conflict, familiar from concurrency theory, to kappa, our representation language of choice. Using the EGF receptor model as an example, we show how causality enables the formalization of the colloquial concept of pathway and, perhaps more surprisingly, how conflict can be used to dissect the signalling dynamics to obtain a qualitative handle on the range of system behaviours. By taming the combinatorial explosion, and exposing the causal structures and key kinetic junctures in a model, agent- and rule-based representations hold promise for making modelling more powerful, more perspicuous, and of appeal to a wider audience.
Date: Thursday 20th September 2007, 5pm
Venue: e-Science Institute, 13-15 South College Street, Edinburgh
CMSB conference news

CMSB 2008 will be held in Rostock, Germany.

The conference is scheduled to take place 12th-15th October. Please send your best paper to CMSB 2008.

Abstract submission deadline: 05/05/2008 at 23:55.
Paper submission deadline: 12/05/2008 at 23:55.


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