swMATH ID: 29888
Software Authors: Kyurkchiev, Nikolay; Markov, Svetoslav; Mincheva, Maya
Description: Analysis of biochemical mechanisms using Mathematica with applications. 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.
Homepage: https://core.ac.uk/download/pdf/156902172.pdf
Dependencies: Mathematica
Keywords: biochemical mechanism; mass-action kinetics; stoichiometric matrix; rate functions; conservation relations; bipartite graph; double phosphorylation
Related Software: Mathematica
Cited in: 1 Publication

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