CellML2SBML Outdated XSL

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Conversion from CellML to SBML

About CellML

CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.


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


Documentation

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

However, this converter should work on cellml 1.0 models. It generate SBML level 2 version 1 models.

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

Most of the cellml 1.0 elements are converted and conserved in the resulting SBML file as long as the mathML elements used are part of the subset defined in the SBML specifications.



Quick Setup

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

      Xalan MyModel_cellml.xml cellml_sbml.xsl > MyModel_sbml.xml

   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

  • Antimony written in C++, using libSBML contain a much more up to date converter that support the SBML L3 comp package (Hierarchical Model Composition). It allow to support cellml-1.1 and to create a SBML file that follow the structure into modules of the CellML file.