Bio-PEPA: A framework for the modelling and analysis of biological systems

被引：181

作者：

Ciocchetta, Federica ^{[1
]}

Hillston, Jane ^{[1
]}

机构：

[1] Univ Edinburgh, Lab Fdn Comp Sci, Edinburgh EH8 9AB, Midlothian, Scotland

来源：

THEORETICAL COMPUTER SCIENCE | 2009年 / 410卷 / 33-34期

基金：

英国生物技术与生命科学研究理事会; 英国工程与自然科学研究理事会;

关键词：

Process algebras; Biochemical networks; Modelling; Analysis; SIMULATION; CHECKING; CALCULUS; DATABASE;

D O I：

10.1016/j.tcs.2009.02.037

中图分类号：

TP301 [理论、方法];

学科分类号：

080201 [机械制造及其自动化];

摘要：

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.

引用

页码：3065 / 3084

页数：20

共 48 条

[1]

Aziz Adnan, 1996, Computer Aided Verification (Lecture Notes in Computer Science, P269, DOI [DOI 10.1007/3-540-61474-5, 10.1007/3-540-61474-575, DOI 10.1007/3-540-61474-575, 10.1007/3-540-61474-5_75, DOI 10.1007/3-540-61474-5_75]

[2]

Baier C, 1999, LECT NOTES COMPUT SC, V1664, P146

[3]

BORNSTEIN BJ, 2004, SYSTEMS BIOL, V1, P41

[4]

BORTOLUSSI L, 2007, ENTCS

[5]

BORTOLUSSI L, 2007, U UDINE PH D THESIS

[6]

BORTOLUSSI L, 2008, LNCS, V5015, P424

[7]

Modeling biological systems in stochastic concurrent constraint programming [J].

Bortolussi, Luca ;

Policriti, Alberto .

CONSTRAINTS, 2008, 13 (1-2) :66-90

[8]

Fluctuations and slow variables in genetic networks [J].

Bundschuh, R ;

Hayot, F ;

Jayaprakash, C .

BIOPHYSICAL JOURNAL, 2003, 84 (03) :1606-1615

[9]

Calder M., 2005, Computational Methods in Systems Biology, P204

[10]

Calder M, 2006, LECT NOTES COMPUT SC, V4230, P1

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