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  1. Proceedings of the 8th International Conference on Computational Methods in Systems Biology (CMSB '10)
  2. A generic abstract machine for stochastic process calculi
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From species to pathway and tissue as process
Building cell-like structures from the bottom-up
Discrete causal model view of biological networks
Steady-state solution of biochemical systems, beyond S-systems via T-invariants
On verifying Bio-PEPA models
Target driven biochemical network reconstruction based on petri nets and simulated annealing
A generic abstract machine for stochastic process calculi
Hybrid numerical solution of the chemical master equation
Action-based analysis of discrete regulatory networks with short-term stimuli
Stochasticity in reactions: a probabilistic Boolean modeling approach
Understanding signalling networks as collections of signal transduction pathways
A comparative study of stochastic analysis techniques
Structural identification of GMA models: algorithm and model comparison

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A generic abstract machine for stochastic process calculi

Content Provider ACM Digital Library
Author Phillips, Andrew Youssef, Simon Lakin, Matthew R. Paulevé, Loïc
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.
Starting Page 43
Ending Page 54
Page Count 12
File Format PDF
ISBN 9781450300681
DOI 10.1145/1839764.1839771
Language English
Publisher Association for Computing Machinery (ACM)
Publisher Date 2010-09-29
Publisher Place New York
Access Restriction Subscribed
Subject Keyword Generic abstract machine Stochastic pi-calculus Non-markovian simulation Bioambient calculus Implementation
Content Type Text
Resource Type Article
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