The Continuous π-Calculus: A Process Algebra for Biochemical Modelling
- 11:30 26th November 2008 ( week 7, Michaelmas Term 2008 )Room 441, Oxford University Computing Laboratory
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.�
Marek Kwiatkowski and Ian Stark.� The Continuous pi-Calculus: a Process�Algebra for Biochemical Modelling.� LNCS 5307:103-122.�http://dx.doi.org/10.1007/978-3-540-88562-7_11