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

Zi Z, Zheng Y, Rundell AE, Klipp E - BMC Bioinformatics (2008)

Bottom Line: 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.SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computational Systems Biology, Max Planck Institute for Molecular Genetics, Ihnestr, 73, 14195 Berlin, Germany. zhike_zi@molgen.mpg.de

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.

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Local sensitivity analysis in SBML-SAT. Local sensitivity analysis of the integrated response of MAPK cascade model [43] (BioModels ID: BIOMD0000000010) with respect to variation of initial conditions.
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Figure 4: Local sensitivity analysis in SBML-SAT. Local sensitivity analysis of the integrated response of MAPK cascade model [43] (BioModels ID: BIOMD0000000010) with respect to variation of initial conditions.

Mentions: The result of a SBML-SAT normalized local sensitivity analysis on the MAPK cascade model (BioModels ID: BIOMD0000000010) is shown in Figure 4. For this analysis, the objects of the sensitivity analysis were the state variables associated with the various phosphorylated forms of the MAPK cascade elements and the model output analyzed were the integrated responses. The parameters perturbed were the initial concentrations of each form with the default perturbation coefficient. These results indicate that the integrated response of the MAPK concentration was the most sensitive to the initial concentration of MAPK.


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

Zi Z, Zheng Y, Rundell AE, Klipp E - BMC Bioinformatics (2008)

Local sensitivity analysis in SBML-SAT. Local sensitivity analysis of the integrated response of MAPK cascade model [43] (BioModels ID: BIOMD0000000010) with respect to variation of initial conditions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2529325&req=5

Figure 4: Local sensitivity analysis in SBML-SAT. Local sensitivity analysis of the integrated response of MAPK cascade model [43] (BioModels ID: BIOMD0000000010) with respect to variation of initial conditions.
Mentions: The result of a SBML-SAT normalized local sensitivity analysis on the MAPK cascade model (BioModels ID: BIOMD0000000010) is shown in Figure 4. For this analysis, the objects of the sensitivity analysis were the state variables associated with the various phosphorylated forms of the MAPK cascade elements and the model output analyzed were the integrated responses. The parameters perturbed were the initial concentrations of each form with the default perturbation coefficient. These results indicate that the integrated response of the MAPK concentration was the most sensitive to the initial concentration of MAPK.

Bottom Line: 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.SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computational Systems Biology, Max Planck Institute for Molecular Genetics, Ihnestr, 73, 14195 Berlin, Germany. zhike_zi@molgen.mpg.de

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.

Show MeSH