Rule-Based Modelling 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, agentbased or concurrent languages, such as κ [1,2,3] or the closely related BioNetGen language [4,5,6,7,8,9,10], 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 [11,12]. An exciting aspect of the agent-based approac...

• Type: Conference
• Year: 2007
• Where: CONCUR
• Authors: Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine
• Keywords: Biological, Combinatorial Explosion, CONCUR 2007, Differential Equations