Geodesic
Analysis of Biochemical Mechanisms using Mathematica with Applications
Serdica Journal of Computing, Tome 10 (2016) no. 1, pp. 063-078.

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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.
Keywords: Biochemical Mechanism, Mass-Action Kinetics, Stoichiometric Matrix, Rate Functions, Conservation Relations, Bipartite Graph, Double Phosphorylation 
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Kyurkchiev, Nikolay; Markov, Svetoslav; Mincheva, Maya. Analysis of Biochemical Mechanisms using Mathematica with Applications. Serdica Journal of Computing, Tome 10 (2016) no. 1, pp. 063-078. http://geodesic.mathdoc.fr/item/SJC_2016_10_1_a4/