Comput. Biol. Med. - Modelling and simulating reaction-diffusion systems using coloured Petri nets.

Tópicos

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Resumo

Reaction-diffusion systems often play an important role in systems biology when developmental processes are involved. Traditional methods of modelling and simulating such systems require substantial prior knowledge of mathematics and/or simulation algorithms. Such skills may impose a challenge for biologists, when they are not equally well-trained in mathematics and computer science. Coloured Petri nets as a high-level and graphical language offer an attractive alternative, which is easily approachable. In this paper, we investigate a coloured Petri net framework integrating deterministic, stochastic and hybrid modelling formalisms and corresponding simulation algorithms for the modelling and simulation of reaction-diffusion processes that may be closely coupled with signalling pathways, metabolic reactions and/or gene expression. Such systems often manifest multiscaleness in time, space and/or concentration. We introduce our approach by means of some basic diffusion scenarios, and test it against an established case study, the Brusselator model.

Resumo Limpo

reactiondiffus system often play import role system biolog development process involv tradit method model simul system requir substanti prior knowledg mathemat andor simul algorithm skill may impos challeng biologist equal welltrain mathemat comput scienc colour petri net highlevel graphic languag offer attract altern easili approach paper investig colour petri net framework integr determinist stochast hybrid model formal correspond simul algorithm model simul reactiondiffus process may close coupl signal pathway metabol reaction andor gene express system often manifest multiscal time space andor concentr introduc approach mean basic diffus scenario test establish case studi brussel model

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