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Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, and Jean Krivine.
Rule-based modelling, symmetries, refinements.

In Proceedings of the First International Workshop, Formal Methods in Systems Biology, FMSB'08. Cambridge, UK, June 4 -- 5, 2008, J. Fisher(Ed.), Lecture Notes in Computer Science 5054, © Springer, Berlin, Germany, pp 103--122.
© Springer, Berlin, Germany.

Abstract: Rule-based modelling is particularly effective for handling the highly combinatorial aspects of cellular signalling. The dynamics is described in terms of interactions between partial complexes, and the ability to write rules with such partial complexes -i.e., not to have to specify all the traits of the entitities partaking in a reaction but just those that matter- is the key to obtaining compact descriptions of what otherwise could be nearly infinite dimensional dynamical systems. This also makes these descriptions easier to read, write and modify. In the course of modelling a particular signalling system it will often happen that more traits matter in a given interaction than previously thought, and one will need to strengthen the conditions under which that interaction may happen. This is a process that we call rule refinement and which we set out in this paper to study. Specifically we present a method to refine rule sets in a way that preserves the implied stochastic semantics. This stochastic semantics is dictated by the number of different ways in which a given rule can be applied to a system (obeying the mass action principle). The refinement formula we obtain explains how to refine rules and which choice of refined rates will lead to a neutral refinement, i.e., one that has the same global activity as the original rule had (and therefore leaves the dynamics unchanged). It has a pleasing mathematical simplicity, and is reusable with little modification across many variants of stochastic graph rewriting. A particular case of the above is the derivation of a maximal refinement which is equivalent to a (possibly infinite) Petri net and can be useful to get a quick approximation of the dynamics and to calibrate models. As we show with examples, refinement is also useful to understand how different subpopulations contribute to the activity of a rule, and to modulate differentially their impact on that activity.

   author =    {Vincent Danos and J\'er\^ome Feret and Walter Fontana and Russell Harmer and Jean Krivine},
   title =     {Rule-based modelling, symmetries, refinements.},
   editor =    {Jasmin Fisher},
   booktitle = {Proceedings of the First International Workshop, Formal Methods in Systems Biology, FMSB$\,$'2008},
   address =   {Cambridge, UK},
   series =    {Lecture Notes in BioInformatics},
   volume =    {5054},
   publisher = {Springer, Berlin, Germany},
   pages =     {103--122},
   month =     {4--5 June},
   year =      {2008},