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Title: Analysis of Biochemical Mechanisms using Mathematica with Applications
Authors: Kyurkchiev, Nikolay
Markov, Svetoslav
Mincheva, Maya
Keywords: Biochemical Mechanism
Mass-Action Kinetics
Stoichiometric Matrix
Rate Functions
Conservation Relations
Bipartite Graph
Double Phosphorylation
Issue Date: 2016
Publisher: Institute of Mathematics and Informatics Bulgarian Academy of Sciences
Citation: Serdica Journal of Computing, Vol. 10, No 1, (2016), 063p-078p
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.
ISSN: 1312-6555
Appears in Collections:Volume 10 Number 1

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