Type Disciplines for Analysing Biologically Relevant Properties
Electronic Notes in Theoretical Computer Science (ENTCS)
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
Transactions on Computational Systems Biology IX
Equivalence and Discretisation in Bio-PEPA
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
The calculus of looping sequences
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
A semantic equivalence for Bio-PEPA based on discretisation of continuous values
Theoretical Computer Science
Spatial Calculus of Looping Sequences
Theoretical Computer Science
Equivalences for a biological process algebra
Theoretical Computer Science
Modeling dependencies and simultaneity in membrane system computations
Theoretical Computer Science
Measurable stochastics for Brane Calculus
Theoretical Computer Science
Typed stochastic semantics for the calculus of looping sequences
Theoretical Computer Science
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Bisimulations are well-established behavioural equivalences that are widely used to study properties of computer science systems. Bisimulations assume the behaviour of systems to be described as labelled transition systems, and properties of a system can be verified by assessing its bisimilarity with a system one knows to enjoy those properties. In this paper we show how semantics based on labelled transition systems and bisimulations can be defined for two formalisms for the description of biological systems, both capable of describing membrane interactions. These two formalisms are the Calculus of Looping Sequences (CLS) and Brane Calculi, and since they stem from two different approaches (rewrite systems and process calculi) bisimulation appears to be a good candidate as a general verification method. We introduce CLS and define a labelled semantics and bisimulations for which we prove some congruence results. We show how bisimulations can be used to verify properties by way of two examples: the description of the regulation of lactose degradation in Escherichia coli and the description of the EGF signalling pathway. We recall the PEP calculus (the simplest of Brane Calculi) and its translation into CLS, we define a labelled semantics and some bisimulation congruences for PEP processes, and we prove that bisimilar PEP processes are translated into bisimilar CLS terms.