SBML2Scilab Outdated XSL

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Conversion from SBML to Scilab

About SBML

SBML is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. An example of this is a network of biochemical reactions. SBML's framework is suitable for representing models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. If you want to know more, you can read the Basic Introduction on SBML


About Scilab

Scilab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.


Documentation

This converter is not maintained any more, last updates are from 2007.

However, this converter should work on simple SBML L2V1 models.

The conversion is performed in one XSLT pass, but using four stylesheets.


SBML elements not supported

  • event
  • constraint
  • initialAssignment
  • stoichiometryMath
  • complex units
  • SBML Level 3 packages


Information lost in the conversion

  • sboTerm
  • notes
  • most annotations

Quick Setup

   To generate a Scilab file from an SBML model, run:

      Xalan MyModel_sbml.xml sbml_to_scilab.xsl > MyModel.sci

   You can download the XSL stylesheets in the section below.


Download

You have to download these four XSL stylesheets and put them in the same folder


Getting Help and Support

In case you discover a bug within SBFC or request new features, please let us know. There are two dedicated trackers:

For general discussions about SBFC, please use the forum:

sbfc-forum [at] googlegroups.com.

If you need further support or you wish to develop new modules in SBFC you can contact the team using the following e-mail address:

sbfc-devel [at] googlegroups.com.

Other known converters

  • no other known converters. SBML2Octave could be used if the matlab syntax is supported by the mfile2sci function in scilab.