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Translating Stochastic CLS into Maude

Authors
Journal
Electronic Notes in Theoretical Computer Science
1571-0661
Publisher
Elsevier
Publication Date
Volume
227
Identifiers
DOI: 10.1016/j.entcs.2008.12.103
Keywords
  • Calculus Of Looping Sequences
  • Maude
  • Model-Checking
  • Biological System
Disciplines
  • Chemistry
  • Computer Science
  • Mathematics

Abstract

Abstract This paper describes preliminary results on the application of statistical model-checking to systems described with Stochastic CLS. Stochastic CLS is a formalism based on term rewriting that allows biomolecular systems to be described by taking into account their structure and by allowing very general events to be modelled. Statistical model-checking is an analysis technique that permits properties of a system to be studied on the results of a number of stochastic simulations. We choose Real-Time Maude as a tool that supports the modelling and analysis of systems with real-time properties. We adapt Gillespie's algorithm for simulating chemical systems into our approach. The resulting method is applied to analyse some simple examples and a model of the lactose operon regulation in E.coli.

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