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  7. Analysis of Biochemical Mechanisms using Mathematica with Applications

Analysis of Biochemical Mechanisms using Mathematica with Applications

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Authors: Kyurkchiev, NikolayMarkov, SvetoslavMincheva, Maya
Issue Date: 2016
Citation: Serdica Journal of Computing, Vol. 10, No 1, (2016), 063p-078p Copy to clipboard
ISSN: 1312-6555
URI: http://hdl.handle.net/10525/2915 Copy to clipboard
Abstract: Biochemical mechanisms with mass action kinetics are usually modeled as systems of ordinary differential equations (ODE) or bipartite graphs. We present a software module for the numerical analysis of ODE models of biochemical mechanisms of chemical species and elementary reactions (BMCSER) within the programming environment of CAS Mathematica. The module BMCSER also visualizes the bipartite graph of biochemical mechanisms. Numerical examples, including a double phosphorylation model, are presented demonstrating the scientific applications and the visualization properties of the module. ACM Computing Classification System (1998): G.4.
Language: en
Publisher: Institute of Mathematics and Informatics, Bulgarian Academy of SciencesSubject: Biochemical MechanismMass-Action KineticsStoichiometric MatrixRate FunctionsConservation RelationsBipartite GraphDouble Phosphorylation
Type: Article