Communicating sequential processes
Communicating sequential processes
Communication and Concurrency
Extended Markovian Process Algebra
CONCUR '96 Proceedings of the 7th International Conference on Concurrency Theory
Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
Process Algebra with Hooks for Models of Pattern Formation
Electronic Notes in Theoretical Computer Science (ENTCS)
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Transactions on Computational Systems Biology VII
Foundational aspects of multiscale modeling of biological systems with process algebras
Theoretical Computer Science
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We present a stochastic process algebra designed for modelling biological systems at multiple scales, called process algebra with hooks (PAH). In PAH, processes represent different scales, e.g. biochemistry, cells or tissue. There are two synchronisation operators, distinguishing interactions within and between scales; composed actions represent events that occur at multiple scales. A stochastic semantics is provided, based on functional rates derived from kinetic laws. A parametric version of the algebra ensures that a model description is compact. An example illustrates how the algebra can be used to model and simulate multi-scale tissue growth, where growth and death of tissue depend on the local concentration of chemicals.