Abstractions of Biochemical Reaction Networks

MABSys includes three main parts: modeling of biochemical reaction networks by means of ODEs, sim- plification of these dynamical systems and symbolic qualitative analysis tools

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The application of mathematical programming methodologies to biochemical systems is demonstrated with the presentation of a linear programming (LP) algorithm for calculating minimal

Starting from a network of elementary reactions and assuming time scale separation, we derive a thermodynamics for the network obtained after coarse graining the fast evolving

As the surface concentration of the adsorbed species is reflected by the low frequency limit of the adsorption capacitance C 0 , a sensor of the actual AChCl bulk concentration

Such datasets can contain (a) data from several replicates of an experiment performed on a biological system; (b) data measured from a biochemical network subjected to

We have shown that in the Biochemical Abstract Machine BIOCHAM, the rule-based language for modeling bio- molecular interactions, and the temporal logics used for formalizing

In order to model resource storage, we introduce a novel technique of reparametrization of deterministic models of Biochemical Reaction Networks, which allows one to tune the