The Continuous π-Calculus: A Process Algebra for Biochemical Modelling

Ian Stark

Date - 20 March 2009 04:00 PM

Location - IF-4.31/33

Abstract
Systems biology is the study of dynamic processes within living organisms, in particular addressing the behaviour that emerges from interactions between components. One potential contribution to this from theoretical computer science lies in the range of existing languages and techniques for working with concurrent systems. Several groups are pursuing this, with biological applications for various process algebras. In this talk I present joint work with Marek Kwiatkowski on a continuous π-calculus, intended to model protein-protein intracellular reactions and in particular issues around the evolution of biochemical pathways. The calculus is succinct and expressive, supporting the modular description of biochemical systems as networks of interacting processes. Process behaviour is given by a compositional semantics in ordinary differential equations, already widely used for modelling biological systems and amenable to standard numerical analysis. This gives us a continuous space of processes, within which we can explore the effect of variation in the original system, looking at questions of robustness, neutrality and evolvability. To illustrate this, I shall describe a model of a circadian clock in the blue-green algae Synechococcus Elongatus; this is a simple oscillatory pathway whose detailed mechanism is the subject of current research.

Extra notes

Marek Kwiatkowski and Ian Stark. The Continuous π-Calculus: a Process Algebra for Biochemical Modelling. In Computational Methods in Systems Biology: Proc. CMSB 2008. Lecture notes in Computer Science 5307, pp. 103–122. Springer-Verlag, 2008.