Information Processing Letters
PI-Calculus: A Theory of Mobile Processes
PI-Calculus: A Theory of Mobile Processes
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Modelling and simulation of biological processes in BlenX
ACM SIGMETRICS Performance Evaluation Review
A Language for Biochemical Systems
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
An Abstract Machine for the Stochastic Bioambient calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
Exploiting non-Markovian Bio-Processes
Electronic Notes in Theoretical Computer Science (ENTCS)
Efficient, correct simulation of biological processes in the stochastic pi-calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
A graphical representation for biological processes in the stochastic pi-calculus
Transactions on Computational Systems Biology VII
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Modelling, simulating and verifying turing-powerful strand displacement systems
DNA'11 Proceedings of the 17th international conference on DNA computing and molecular programming
Bio-PEPAd: A non-Markovian extension of Bio-PEPA
Theoretical Computer Science
Stochastic simulation of multiple process calculi for biology
Theoretical Computer Science
Measurable stochastics for Brane Calculus
Theoretical Computer Science
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This paper presents a generic abstract machine for simulating a broad range of process calculi with an arbitrary reaction-based simulation algorithm. The abstract machine is instantiated to a particular calculus by defining two functions: one for transforming a process of the calculus to a set of species, and another for computing the set of possible reactions between species. Unlike existing simulation algorithms for chemical reactions, the abstract machine can simulate process calculi that generate potentially unbounded numbers of species and reactions. This is achieved by means of a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. As a proof of concept, the generic abstract machine is instantiated for the stochastic pi-calculus, and the instantiation is implemented as part of the SPiM stochastic simulator. The structure of the abstract machine facilitates a significant optimisation by allowing channel restrictions to be stored as species complexes. We also present a novel algorithm for simulating chemical reactions with general distributions, based on the Next Reaction Method of Gibson and Bruck. We use our generic framework to simulate a stochastic pi-calculus model of plasmid co-transfection, where plasmids can form aggregates of arbitrary size and where rates of mRNA degradation are non-exponential. The example illustrates the flexibility of our framework, which allows an appropriate high-level language to be paired with the required simulation algorithm, based on the biological system under consideration.