Paper Info
Title
A generic abstract machine for stochastic process calculi
Abstract
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.
Year
DOI
Venue
2010
10.1145/1839764.1839771
CMSB
Keywords
Field
DocType
required simulation algorithm,spim stochastic simulator,arbitrary reaction-based simulation algorithm,generic framework,possible reaction,species complex,process calculus,stochastic process calculus,novel algorithm,abstract machine,generic abstract machine,stochastic process,stochastic simulation,high level language,just in time compiler,proof of concept,implementation,process calculi,chemical reaction,biological systems
MRNA degradation,Discrete mathematics,Computer science,Algorithm,Communication channel,Stochastic process,Compiler,Theoretical computer science,Proof of concept,Process calculus,Simulation algorithm,Abstract machine
Conference
Citations 
PageRank 
References 
10
0.69
13
Authors
4
Name
Order
Citations
PageRank
Loïc Paulevé120418.68
Simon Youssef2231.59
Matthew R. Lakin37910.99
Andrew Phillips422717.50