Ian Stark

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

Marek Kwiatkowski and Ian Stark

In Computational Methods in Systems Biology: Proceedings of 6th International Conference CMSB 2008, Rostock, Germany, October 12–15, 2008. Lecture Notes in Computer Science 5307, pages 103–122. Springer-Verlag, 2008.

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We introduce the continuous π-calculus, a process algebra for modelling behaviour and variation in molecular systems. Key features of the language are: its expressive succinctness; support for diverse interaction between agents via a flexible network of molecular affinities; and operational semantics for a continuous space of processes. This compositional semantics also gives a modular way to generate conventional differential equations for system behaviour over time. We illustrate these features with a model of an existing biological system, a simple oscillatory pathway in cyanobacteria. We then discuss future research directions, in particular routes to applying the calculus in the study of evolutionary properties of biochemical pathways.

  author =       {Marek Kwiatkowski and Ian Stark},
  title =        {The Continuous $\pi$-Calculus: A Process Algebra for
                  Biochemical Modelling},
  booktitle =    {Computational Methods in Systems Biology: Process of the
                  Sixth International Conference CMSB~2008},
  pages =        {103--122},
  year =         2008,
  series =       {Lecture Notes in Computer Science},
  number =       5307,
  publisher =    {Springer-Verlag},
  url =          {http://homepages.ed.ac.uk/stark/continuous-pi.html},
  pdf =          {http://homepages.ed.ac.uk/stark/continuous-pi.pdf},
  doi =          {10.1007/978-3-540-88562-7_11}

This research was supported by an EPSRC studentship, the Laboratory for Foundations of Computer Science, and The University of Edinburgh School of Informatics.

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