Journal
THEORETICAL COMPUTER SCIENCE
Volume 410, Issue 33-34, Pages 3065-3084Publisher
ELSEVIER
DOI: 10.1016/j.tcs.2009.02.037
Keywords
Process algebras; Biochemical networks; Modelling; Analysis
Categories
Funding
- BBSRC [BB/D019621/1] Funding Source: UKRI
- EPSRC [EP/C54370X/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/D019621/1] Funding Source: researchfish
- Engineering and Physical Sciences Research Council [EP/C543696/1, EP/C54370X/1] Funding Source: researchfish
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In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performance analysis of computer systems, in order to handle some features of biological models, such as stoichiometry and the use of general kinetic laws. Bio-PEPA maybe seen as an intermediate, formal, compositional representation of biological systems, on which different kinds of analyses can be carried out. Bio-PEPA is enriched with some notions of equivalence. Specifically, the isomorphism and strong bisimulation for PEPA have been considered and extended to our language. Finally, we show the translation of a biological model into the new language and we report some analysis results. (C) 2009 Elsevier B.V. All rights reserved.
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