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 allows us to neatly 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 HIV life cycle.
Chiarugi, D., Falaschi, M., Guzman, M., HERMITH RAMIREZ, D.P., Olarte, C. (2013). Simulating Signalling Pathways With BioWayS. ELECTRONIC NOTES IN THEORETICAL COMPUTER SCIENCE, 293, 17-34 [10.1016/j.entcs.2013.02.016].
Simulating Signalling Pathways With BioWayS
FALASCHI, MORENO
;
2013-01-01
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 allows us to neatly 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 HIV life cycle.File | Dimensione | Formato | |
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https://hdl.handle.net/11365/40029