Simulating signalling pathways with BioWayS
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Falaschi, M
Hermith, D
Guzman, M
Olarte, C
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Stockholm, Sweden
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. © 2013 Elsevier B.V. All rights reserved.
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Electronic Notes in Theoretical Computer Science
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293
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© The Author(s) 2013. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) License, which permits unrestricted, non-commercial use, distribution and reproduction in any medium, providing that the work is properly cited.
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Theory of computation
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Chiarugi, D; Falaschi, M; Hermith, D; Guzman, M; Olarte, C, Simulating signalling pathways with BioWayS, Electronic Notes in Theoretical Computer Science, 2013, 293, pp. 17-34