Gepasi and SBML

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From version 3.30, Gepasi has added support for the SBML format (level 1). Gepasi imports and exports SBML level 1 files.

What is SBML?

It is a common, model-based description language for systems biology simulation software. SBML is defined as a XML markup language. It is mostly useful for exchange of models between different software. SBML was developed by the Caltech unit of the ERATO Kitano project, with frequent input from the community (including ours).

The SBML specification was described in a manuscript to appear soon in the journal Bioinformatics.

Some SBML files generated with Gepasi

These are supplied with the purpose of allowing developers of other SBML supporting software to test if Gepasi-generated SBML will import into their programs. They are also useful for Gepasi users to try the SBML import functionality.

SBML files produced by Gepasi
Brusselator The Henri-Michaelis-Menten model Sequential feedback
Signal transduction cascade Yeast glycolysis Minimal chemical Hopf bifurcation
5-step linear pathway
(exports the link as a rule)
100 Yeast cells (2Mb)
(VERY LARGE SBML file, 2000 reactions!)
Logistic growth
(has a dummy metabolite)

Issues with Gepasi SBML export

Gepasi forms valid SBML level 1 files. SBML level 1 is a compromise on features that most software can import/export. Gepasi models contains several elements that are not translatable to SBML:

Issues with Gepasi SBML import

Gepasi does not interpret the full specification of SBML level 1. At this time, it cannot deal with a number of features and ignores them if they are present in SBML files. These ignored features are:

Because SBML does not support the concept of a normalized database of kinetic functions, Gepasi imports all kinetic functions as user-defined. This has the undesirable effect of proliferation of kinetic types that may be the same but have different names. To make matters worse, SBML does not allow for naming kinetic types, so the imported kinetic functions are named in Gepasi’s kinetic type database with uninformative names (e.g. “1-1 SBML3”). Users are advised to change the kinetic types of imported SBML models to existing kinetic types in their local databases whenever possible.


Gepasi's SBML functionality is achieved using the sbml11.dll software kindly supplied by Herbert Sauro.

Last modified: September 3, 2002 Copyright © 2002 Pedro Mendes
Gepasi - biochemical simulation