Institute of Mathematics and Informatics Bulgarian Academy of Sciences
Serdica Journal of Computing, Vol. 10, No 1, (2016), 063p-078p
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.