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layout.m plugin


This package implements (most of) the proposed layout extenson for SBML, version of April 25, 2005. It does not support the rendering extension. For more details on the specification of this extenstion see http://projects.villa-bosch.de/bcb/sbml.

layoutShow[filename] reads an SBML file that includes layout information already in it and displays the layout on the screen. The returned graphic item can be converted to any desired graphics format that Mathematica supports.

layoutGenerate[filename] reads an SBML file and generates a graphical visualization from the model using Mathematica's built-in graph visualization tools. Any layout information already in the model is ignored.

layoutGenerate[filename, "output"->new filename] will also generate a new sbml model file with the new layout information include as an annotation. Any old layout information will be removed. The level and version of the new file will be the same as the old file.

New in version 2.6.1; GraphPlot requires Mathematica 5.1


Limitations

Example

Download a layout example xml file from EML. Here is the output of layoutShow:

Download Biomodels Database model 10 SBML file

Here is the graphical output of layoutGenerate on model 10:

Download Biomodels Database model 10 SBML file with layout generated by layoutGenerate

Download Biomodels Database model 10 SBML file with layout generated by the SBML Layout Viewer/Manipulator at sys-bio.org

For comparison, here is the graphics generated by layoutShow for the layout generated using the SBML Layout Viewer/Manipulator:

See also

visualizeSBMLModel