SBML2Dot Outdated XSL

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Conversion from SBML to DOT

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 DOT

DOT is the language used to encode the graphics processed by GraphViz.

DOT is a plain text graph description language. It is a simple way of describing graphs that both humans and computer programs can use.

Various programs can process DOT files. Some, like OmniGraffle, dot, neato, twopi, circo, fdp, and sfdp, will read a DOT file and render it in graphical form. Others, like gvpr, gc, accyclic, ccomps, sccmap, and tred, will read a DOT file and perform calculations on the represented graph. Finally, others, like GVedit, KGraphEditor, lefty, dotty, and grappa, provide an interactive interface. Most programs are part of the Graphviz package or use it internally. (definition from the DOT Article on wikipedia)


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.

The converter will first generate a dot file from a SBML file and then will use the dot program from graphviz to generate either an svg or png file. All the SBML species will be transformed into a dot node. Then all the reactions will be transformed as well into a dot node. To finish, we use the list of reactants, products and modifers of each reactions to create some edges from the reaction nodes to the species nodes.


Quick Setup

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

      Xalan MyModel_sbml.xml sbml_dot.xsl > MyModel.dot

   To generate an initial svg file from the dot file with the program GraphViz, run:

      dot -Tsvg MyModel.dot -o MyModel_initial.svg

   To generate an improved svg file from the initial svg file, run:

      Xalan -p model_name "'MyModel_SBML.xml'" MyModel_initial.svg svg2svg.xsl > MyModel.svg

   The -p option sets a global parameter, here the name of the file containing the model, model_name to the value MyModel_SBML.xml. This syntax can vary according to the    version of Xalan.
   Furthermore, if you want to enjoy some interactive effects, please download biomd.js and put it in the same directory with the generated svg file.

   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