Dataset Information

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

ABSTRACT: BACKGROUND: It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. RESULTS: This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. CONCLUSION: SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes.

SUBMITTER: Zi Z

PROVIDER: S-EPMC2529325 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

Zi Zhike Z Zheng Yanan Y Rundell Ann E AE Klipp Edda E

BMC bioinformatics 20080815

<h4>Background</h4>It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models.<h4>Results</h4>This work introduces a freely downloadable, software package, SBML ...[more]

PMID: 18706080

Similar Datasets

Project description:BACKGROUND:The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. RESULTS:In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. CONCLUSIONS:With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

Dataset Information

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

Publications

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets