SBML-PET: a Systems Biology Markup Language-based parameter estimation tool

Bioinformatics. 2006 Nov 1;22(21):2704-5. doi: 10.1093/bioinformatics/btl443. Epub 2006 Aug 22.

Abstract

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.

Availability: http://sysbio.molgen.mpg.de/SBML-PET/. The website also contains detailed documentation for SBML-PET.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cell Physiological Phenomena*
  • Computer Simulation
  • Information Storage and Retrieval / methods
  • Models, Biological*
  • Programming Languages*
  • Signal Transduction / physiology*
  • Software*
  • Systems Biology / methods*
  • User-Computer Interface*