SBML glyph/graph/layout

Question

Do you know how to generate a draw or graph that I can convert or export in SVG from my SBML models. Or maybe directly generate SVG from SBML model wrote in XML?

I read documentation baut it doesn't help me for this projet.

Answer 1

There are ways to achieve that, but how useful these graphs depend on the content of the SBML file. Suppose the SBML file contains layout information in the SBML layout package. In that case, it is possible to convert it to such an image using tools such as the following:

• EscherConverter
• SBML Layout Viewer

If the SBML file does not contain layout information, automated layout tools can generate such graphs, e.g.,

• Cytoscape with the Cy3SBML app
• The online Systems Biology Format Converter (SBFC)
• CellDesigner
• Another option could be the MINERVA platform that generates layouts similar to that of CellDesigner and provides many options to work with SBML, e.g., via web services.

Please note:

1. The Systems Biology Format Converter (SBFC) creates GraphViz files for further processing. You can compile them using GraphViz and obtain SVGs based on automated layout.
2. CellDesigner directly supports exporting SVG. From File > Export Image… > Select SVG files and then Save. Currently, CellDesigner only supports SBML up to Level 2 Version 4. Its Layouts are often handy and can be easily manually adjusted. However, it may be necessary to downconvert the model first using SBFC. There are also importers and converters for CellDesigner that can deal with the SBML Layout package if needed, such as the CellDesigner Parser.

Answer 2

I would contact the Sauro lab, they have a number of tools in development that should be able to do this (including PDF). They also support the SBML layout/render extension. They are also developing a pydot to SBML converter.