SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system.


BACKGROUND
http://sysbio.molgen.mpg.de/SBML-PET/. The website also contains detailed documentation for SBML-PET.
Zi
Zhike
Z
Max Planck Institute for Molecular Genetics, Ihnestr. 73 14195 Berlin, Germany. zhike_zi@molgen.mpg.de
Klipp
Edda
E
D000465:Algorithms; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D016247:Information Storage and Retrieval / Q000379:methods; D008954:Models, Biological; D011381:Programming Languages; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014584:User-Computer Interface