Some investigations concerning the CTMC and the ODE model derived from bio-PEPA

DOI10.1016/J.ENTCS.2009.02.010MaRDI QIDQ5404080zbMATH OpenOpenAlexWikidataFDO

Authors Federica Ciocchetta, A. Degasperi, Jane Hillston, M. Calder

Publication date 21 March 2014

Published in Electronic Notes in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.entcs.2009.02.010

zbMATH Keywords

Markov chainsordinary differential equationssystems biologyprocess algebrasanalysis

Mathematics Subject Classification ID

Systems biology, networks (92C42) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85)

Recommendations

• Relating continuous and discrete PEPA models of signalling pathways
• Bio-PEPA: A framework for the modelling and analysis of biological systems
• Bio-PEPA: an extension of the process algebra PEPA for biochemical networks
• A semantic equivalence for Bio-PEPA based on discretisation of continuous values
• Equivalences for a biological process algebra

Cites work

• Application of a stochastic name-passing calculus to representation and simulation of molecular processes
• Bio-PEPA: A framework for the modelling and analysis of biological systems
• Bio-PEPA: an extension of the process algebra PEPA for biochemical networks
• Computational Methods in Systems Biology
• Limit theorems for sequences of jump Markov processes approximating ordinary differential processes
• Modeling biological systems in stochastic concurrent constraint programming
• Relating continuous and discrete PEPA models of signalling pathways
• Solutions of ordinary differential equations as limits of pure jump markov processes

Cited in

(14)

• Bio-PEPA: A framework for the modelling and analysis of biological systems
• Improved continuous approximation of PEPA models through epidemiological examples
• Relating PDEs in cylindrical coordinates and CTMCs with levels of concentration
• Probabilistic approximations of ODEs based bio-pathway dynamics
• Modular modelling of signalling pathways and their cross-talk
• A semantic equivalence for Bio-PEPA based on discretisation of continuous values
• Unwinding biological systems
• Jump longer to jump less: improving dynamic boundary projection with \(h\)-scaling
• Modelling biological compartments in bio-PEPA
• Approximate analysis of biological systems by hybrid switching jump diffusion
• A model and analysis of the AKAP scaffold
• Bio-PEPA: an extension of the process algebra PEPA for biochemical networks
• Product form approximation of transient probabilities in stochastic reaction networks
• A process algebra framework for multi-scale modelling of biological systems

Describes a project that uses

Uses Software

• PEPA
• Bio-PEPA
• PRISM

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