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Literature DB >> 16574696

SBMLToolbox: an SBML toolbox for MATLAB users.

Sarah M Keating¹, Benjamin J Bornstein, Andrew Finney, Michael Hucka.

Abstract

SUMMARY: We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML. AVAILABILITY: SBMLToolbox is freely available from http://sbml.org/software/sbmltoolbox

Mesh：

Year: 2006 PMID： 16574696 DOI： 10.1093/bioinformatics/btl111

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

49 in total

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Review 3. Network integration and graph analysis in mammalian molecular systems biology.

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4. Identification of alterations in the Jacobian of biochemical reaction networks from steady state covariance data at two conditions.

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5. SBML and CellML translation in antimony and JSim.

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6. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

Authors: Jan Schellenberger; Richard Que; Ronan M T Fleming; Ines Thiele; Jeffrey D Orth; Adam M Feist; Daniel C Zielinski; Aarash Bordbar; Nathan E Lewis; Sorena Rahmanian; Joseph Kang; Daniel R Hyduke; Bernhard Ø Palsson
Journal: Nat Protoc Date: 2011-08-04 Impact factor: 13.491

SBMLToolbox: an SBML toolbox for MATLAB users.

1. Simulating physiological interactions in a hybrid system of mathematical models.

Review 2. Systems biology of pro-angiogenic therapies targeting the VEGF system.

Review 3. Network integration and graph analysis in mammalian molecular systems biology.

4. Identification of alterations in the Jacobian of biochemical reaction networks from steady state covariance data at two conditions.

5. SBML and CellML translation in antimony and JSim.

6. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

7. Synthetic biology: a foundation for multi-scale molecular biology.

8. Elimination of thermodynamically infeasible loops in steady-state metabolic models.

9. Statistical Analysis of Discrete Dynamical System Models for Biological Networks.

10. DOTcvpSB, a software toolbox for dynamic optimization in systems biology.