SBML-PET: A systems biology markup language-based parameter estimation tool

被引：53

作者：

Zi, Zhike ^{[1
]}

Klipp, Edda ^{[1
]}

机构：

[1] Max Planck Inst Mol Genet, D-14195 Berlin, Germany

来源：

BIOINFORMATICS | 2006年 / 22卷 / 21期

关键词：

D O I：

10.1093/bioinformatics/btl443

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2704 / 2705

页数：2

共 17 条

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