Simulating Signalling Pathways With BioWayS | Zendy

Davide Chiarugi | Zendy; Moreno Falaschi | Zendy; Diana Hermith | Zendy; Michell Guzmán | Zendy; Carlos Olarte | Zendy

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Simulating Signalling Pathways With BioWayS

Author(s) -

Davide Chiarugi,

Moreno Falaschi,

Diana Hermith,

Michell Guzmán,

Carlos Olarte

Publication year - 2013

Publication title -

electronic notes in theoretical computer science

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.242

H-Index - 60

ISSN - 1571-0661

DOI - 10.1016/j.entcs.2013.02.016

Subject(s) - concurrency , computer science , context (archaeology) , model checking , process calculus , biological pathway , theoretical computer science , programming language , biological network , distributed computing , computational biology , biology , paleontology , biochemistry , gene expression , gene

We report on a technique for modelling biological systems based on the ntcc calculus, a model of concurrency where systems are specified by means of constraints (i.e., formulae in logic). We show that the ability of ntcc to express partial information, concurrency, non-determinism and timed behaviour makes it well-suited model and simulate biochemical reactions networks. Based on this technique, we introduce BioWayS (BIOchemical pathWAY Simulator), a software tool for the quantitative modelling and analysis of biological systems. We show the applicability of BioWayS in the context of two well-studied biological systems: the glycogen breakdown pathway and the life cycle of the human immunodeficiency virus

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