Simulating Signalling Pathways With BioWayS

Authors:
Davide Chiarugi;Moreno Falaschi;Diana Hermith;Michell Guzman;Carlos Olarte
Affiliations:
Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universití degli Studi di Siena, Italy;Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universití degli Studi di Siena, Italy;Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universití degli Studi di Siena, Italy;Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle Cali, Colombia;Departamento de Electrónica y Ciencias de la Computación, Universidad Javeriana Cali, Colombia
Venue:
Electronic Notes in Theoretical Computer Science (ENTCS)
Year:
2013

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Abstract

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.