Modelling Self-assembly in BlenX

Larcher, Roberto; Priami, Corrado; Romanel, Alessandro

doi:10.1007/978-3-642-11712-1_5

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2013

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Cited by 2 publications

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“…EMs are typically specified through formal languages based either on process algebras (e.g. [10,12,11,25,3]) or other formalisms such as logic [9] or rewriting logic [14], constraint programming [21,13] or Petri nets [6]. These models can be used for analyzing either static, qualitative properties of biological systems [7] or their quantitative, dynamical behaviour.…”

Section: Introductionmentioning

confidence: 99%

Simulating Signalling Pathways With BioWayS

Chiarugi

Falaschi

Hermith

et al. 2013

Electronic Notes in Theoretical Computer Science

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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 wellsuited 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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