Hynne, Dano, Sorensen, 2001
This model runs in both OpenCell and COR to replicate the published results (figure 6). The units have been checked and they are consistent. This CellML model translation is based on the curated SBML model in the BioModels database (BIOMD0000000061.xml). Note that in order to replicate figure 6 the model has to be run for at least 100 seconds first to allow all the oscillations to stabilise.
ABSTRACT: We present a powerful, general method of fitting a model of a biochemical pathway to experimental substrate concentrations and dynamical properties measured at a stationary state, when the mechanism is largely known but kinetic parameters are lacking. Rate constants and maximum velocities are calculated from the experimental data by simple algebra without integration of kinetic equations. Using this direct approach, we fit a comprehensive model of glycolysis and glycolytic oscillations in intact yeast cells to data measured on a suspension of living cells of Saccharomyces cerevisiae near a Hopf bifurcation, and to a large set of stationary concentrations and other data estimated from comparable batch experiments. The resulting model agrees with almost all experimentally known stationary concentrations and metabolic fluxes, with the frequency of oscillation and with the majority of other experimentally known kinetic and dynamical variables. The functional forms of the rate equations have not been optimized.
The original paper reference is cited below:
Full-scale model of glycolysis in Saccharomyces cerevisiae, F. Hynne, S. Dano, and P. G. Sorensen , 2001, Biophysical Chemistry , 94, 121-163. PubMed ID: 11744196
|The glycolysis pathway described by the mathematical model.|