A process algebra framework for multi-scale modelling of biological systems

DOI10.1016/J.TCS.2013.03.018MaRDI QIDQ388145zbMATH OpenOpenAlexWikidataFDO

Authors A. Degasperi, M. Calder

Publication date 19 December 2013

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

Full work available at URL https://doi.org/10.1016/j.tcs.2013.03.018

zbMATH Keywords

biological systemsfunctional ratesmulti-scale modelingprocess algebra

Mathematics Subject Classification ID

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

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Cites work

• A process algebra framework for multi-scale modelling of biological systems
• An introduction to systems biology. Design principles of biological circuits.
• 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
• Brane Calculi
• Computational Methods in Systems Biology
• Extended Markovian Process Algebra
• Foundational aspects of multiscale modeling of biological systems with process algebras
• scientific article; zbMATH DE number 4039251 (Why is no real title available?)
• scientific article; zbMATH DE number 42752 (Why is no real title available?)
• Modeling biological systems in stochastic concurrent constraint programming
• Multistationarity, the basis of cell differentiation and memory. II: Logical analysis of regulatory networks in terms of feedback circuits
• Non-expansive \(\varepsilon\)-bisimulations for probabilistic processes
• Process algebra with hooks for models of pattern formation
• Refining dynamics of gene regulatory networks in a stochastic -calculus framework
• Rule-Based Modelling of Cellular Signalling
• Simulating the impact of a molecular `decision-process' on cellular phenotype and multicellular patterns in brain tumors
• Some investigations concerning the CTMC and the ODE model derived from bio-PEPA
• State-Aware Performance Analysis with eXtended Stochastic Probes
• Testing equivalences for processes

Cited in

(7)

• Bio-PEPA: A framework for the modelling and analysis of biological systems
• Process Algebra Models of Population Dynamics
• A process algebra framework for multi-scale modelling of biological systems
• Foundational aspects of multiscale modeling of biological systems with process algebras
• Design of a biomolecular device that executes process algebra
• Process algebra with hooks for models of pattern formation
• Relating PDEs in cylindrical coordinates and CTMCs with levels of concentration

Describes a project that uses

Uses Software

• Bio-PEPA
• BioNetGen
• BIOCHAM
• PEPA
• LBS

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