SBMLToolbox

Use SBML models in Matlab
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SBMLToolbox Ranking & Summary

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  • Rating:
  • License:
  • Freeware
  • Price:
  • FREE
  • Publisher Name:
  • SBML Team
  • Publisher web site:
  • http://sbml.org/Main_Page
  • Operating Systems:
  • Mac OS X
  • File Size:
  • 1.5 MB

SBMLToolbox Tags


SBMLToolbox Description

Use SBML models in Matlab SBMLToolbox is built on top of libSBML and provides a free and open source set of basic functions allowing SBML models to be used in MATLAB. SBMLToolbox provides functions for reading, writing, and validating SBML models; viewing model structures in a simple GUI; converting models into a symbolic form suitable for use with MATLAB's Symbolic Math Toolbox; and simulate models using MATLAB's ordinary differential equation solvers.SBMLToolbox works by translating SBML models to/from a MATLAB structure called MATLAB_SBML. It provides facilities for manipulating this and its substructures within MATLAB, as well as functions for saving and loading MATLAB_SBML structures to/from MATLAB data files.The toolbox is not intended to be a complete Systems Biology toolbox for MATLAB, but rather a platform facilitating getting SBML in and out of MATLAB and serving as a starting point from which users can develop their own functionality. NOTE: SBMLToolbox is licensed and distributed under the terms of the GNU Library or Lesser General Public License (LGPL). Requirements: · Matlab What's New in This Release: · added the GetStoichiometrySparse function contributed by Arsen Batagov. This returns the stoichiometry matrix as a sparse matrix and is much quicker for larger models. · The TranslateSBML function has a second optional argument that indicates whether the model is to be validated prior to import. The default value is 0; indicating no validation. In the case of no argument to the function; which opens a browse window to locate the file to import; the user is prompted to indicate whether validation should be done. In the case of validation errors these are displayed to the user, who will be prompted as to whether to import the model regardless. · removed the ReadAndValidate function as this was essentially a version of TranslateSBML that performed validation. · added support for SBML Level 2 Version 2 and Level 2 Version 3. This support does not extend to the GUI's that could be used to view individual components of a model. · fixed bug in DetermineSpeciesRoleInReaction which failed for a level 1 model


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