Hybrid semantics for Bio-PEPA

DOI10.1016/J.IC.2014.01.016MaRDI QIDQ2453221zbMATH OpenOpenAlexFDO

Authors Vashti Galpin

Publication date 6 June 2014

Published in Information and Computation (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.ic.2014.01.016

zbMATH Keywords

biological modelingcontinuous modelingdeterministic simulationdiscrete behavioreventshybrid modelinginstantaneous simulationprocess algebrastochastic modeling

Mathematics Subject Classification ID

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

Recommendations

• HYPE Applied to the Modelling of Hybrid Biological Systems
• Bio-PEPA: A framework for the modelling and analysis of biological systems
• HYPE with stochastic events
• Equivalences for a biological process algebra
• Bio-PEPA: an extension of the process algebra PEPA for biochemical networks

Cites work

• (Hybrid) automata and (stochastic) programs. The hybrid automata lattice of a stochastic program
• A delay-differential equation model of HIV infection of \(\text{CD}4^+\) T-cells
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• Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems
• Amplified biochemical oscillations in cellular systems
• An Introduction to Delay Differential Equations with Applications to the Life Sciences
• Application of a stochastic name-passing calculus to representation and simulation of molecular processes
• Bio-PEPA with Events
• Bio-PEPA: A framework for the modelling and analysis of biological systems
• Bio-PEPAd: a non-Markovian extension of Bio-PEPA
• BioAmbients: an abstraction for biological compartments
• Computational Methods in Systems Biology
• Delay stochastic simulation of biological systems: a purely delayed approach
• Distributed delays in a hybrid model of tumor-immune system interplay
• Equivalences for a biological process algebra
• Fifty years of stiffness
• Formal molecular biology
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• scientific article; zbMATH DE number 3994822 (Why is no real title available?)
• Hybrid dynamics of stochastic programs
• Hybrid performance modelling of opportunistic networks
• Hybrid representation and simulation of stiff biochemical networks
• Hybrid stochastic simulations of intracellular reaction-diffusion systems
• HYPE with stochastic events
• HYPE: A Process Algebra for Compositional Flows and Emergent Behaviour
• HYPE: hybrid modelling by composition of flows
• Integration of Stiff Equations
• Transactions on Computational Systems Biology IV

Cited in

(6)

• Hybrid behaviour of Markov population models
• Modeling and Simulation of Biochemical Processes Using Stochastic Hybrid Systems: The Sugar Cataract Development Process
• Bio-PEPA with Events
• HYPE with stochastic events
• Process calculi for biological processes
• Bio-PEPAd: a non-Markovian extension of Bio-PEPA

Describes a project that uses

Uses Software

• PRISM
• LBS
• Bio-PEPA
• Bio-PEPAd

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