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.
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:
- Gepasi is not able to properly export kinetic functions that include
rand(), gauss(), or boltz() functions. In such cases,
Gepasi will export a different function, where the arguments of those functions
appear alone. For example, the function k*S-0.1*gauss(S) will be exported
as k*S-0.1*(S).
- Only a few links can be exported, namely those that set the values of kinetic
constants and compartment volumes, and only if they are linked to other parameters
or compartment volumes. In particular no links setting initial concentrations can
be exported, nor links that include user-defined functions in the right hand side.
- SBML defines a very restrictive alphabet for names (identifiers), which makes
many names in Gepasi models to be illegal in SBML. To circumvent this, Gepasi adds
the underscore to the beginning of any names that require it to become legal SBML.
Any character that is not representable in SBML (such as the hyphen!) is substituted
by an underscore. This has the effect that many names are exported differently
from what they are in Gepasi.
- SBML does not allow representing reactions without substrates or products, which
are legal in Gepasi. To circumvent this SBML limitation, Gepasi creates a dummy
chemical species named _void_.
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:
- rules
- units (Gepasi assumes all numbers are in consistent units)
- Annotations (though model notes are imported to Gepasi's comments)
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.
Acknowledgement
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 |
 |
