Optimisation Benchmarks

The purpose of this section is to collect models and studies on optimisation algorithms and parameter estimation.

Benchmark models

KinMMfit

This benchmark consists of parameter estimation of a couple of rate constants of the Michaelis-Menten mechanism from 5 progress curves.

File	purpose
KinMMfit.cps	Copasi file
KinMMfit.gps	Gepasi file
mmspec.txt	Data file

Linear-3

This benchmark is a parameter estimation for a network consisting of three metabolic reactions catalysed by enzymes that are also target of transcriptional control. The problem is described in a chapter by Mendes in the 2001 Foundations of Systems Biology book. The problem consisted of identifying 36 parameter values by fitting a single time course trajectory. In the original publication Gepasi was used to obtain the best fit through a combination of algorithms (evolutionary programming, followed by Hooke-Jeeves, followed by Levenberg-Marquardt).

File	purpose
FoundationSysBioFit.cps	Copasi file
FoundationSysBioFit.gps	Gepasi file
linear3.perturbations.dyn	Data file

Comparison of Gepasi and COPASI