BMCSER 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 Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year Analysis of biochemical mechanisms using Mathematica with applications. Zbl 1387.92006Kyurkchiev, Nikolay; Markov, Svetoslav; Mincheva, Maya 2016 Cited by 3 Authors 1 Kyurkchiev, Nikolaĭ Veselinov 1 Markov, Svetoslav Marinovich 1 Mincheva, Maya Cited in 1 Serial 1 Serdica Journal of Computing Cited in 3 Fields 1 Combinatorics (05-XX) 1 Ordinary differential equations (34-XX) 1 Biology and other natural sciences (92-XX) Citations by Year