Analysis of Biochemical Mechanisms using Mathematica with Applications

Kyurkchiev, Nikolay, Markov, Svetoslav, and Mincheva, Maya. "Analysis of Biochemical Mechanisms using Mathematica with Applications." Serdica Journal of Computing 10.1 (2016): 063-078. <http://eudml.org/doc/289538>.

@article{Kyurkchiev2016,
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.},
author = {Kyurkchiev, Nikolay, Markov, Svetoslav, Mincheva, Maya},
journal = {Serdica Journal of Computing},
keywords = {Biochemical Mechanism; Mass-Action Kinetics; Stoichiometric Matrix; Rate Functions; Conservation Relations; Bipartite Graph; Double Phosphorylation},
language = {eng},
number = {1},
pages = {063-078},
publisher = {Institute of Mathematics and Informatics Bulgarian Academy of Sciences},
title = {Analysis of Biochemical Mechanisms using Mathematica with Applications},
url = {http://eudml.org/doc/289538},
volume = {10},
year = {2016},
}

TY - JOUR
AU - Kyurkchiev, Nikolay
AU - Markov, Svetoslav
AU - Mincheva, Maya
TI - Analysis of Biochemical Mechanisms using Mathematica with Applications
JO - Serdica Journal of Computing
PY - 2016
PB - Institute of Mathematics and Informatics Bulgarian Academy of Sciences
VL - 10
IS - 1
SP - 063
EP - 078
AB - 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.
LA - eng
KW - Biochemical Mechanism; Mass-Action Kinetics; Stoichiometric Matrix; Rate Functions; Conservation Relations; Bipartite Graph; Double Phosphorylation
UR - http://eudml.org/doc/289538
ER -