SBML-shorthand mod2sbml.py and sbml2mod.py
This page archives all versions of SBML-shorthand specifications and translation tools.
SBML-shorthand specification
- SBML-shorthand specification, version 1.2.1 (PDF) - targeted at SBML Level 1, Version 2.
- SBML-shorthand specification, version 2.1.1 (PDF) - targeted at SBML Level 2, Version 1.
- SBML-shorthand specification, version 2.1.2 (PDF) - targeted at SBML Level 2, Version 1.
- SBML-shorthand specification, version 2.1.3 (PDF) - targeted at SBML Level 2, Version 1.
- SBML-shorthand specification, version 2.3.1 (PDF) - targeted at SBML Level 2, Version 3.
- SBML-shorthand specification, version 2.4.1 (PDF) - targeted at SBML Level 2, Version 4.
- SBML-shorthand specification, version 3.1.1 (PDF) - targeted at SBML Level 3, Version 1.
mod2sbml.py model translation tool
Note about libSBML version dependencies! Most of these converters
require installation of libSBML and the libsbml python bindings. The
libSBML API is currently undergoing a period of rapid change, and so it is
vital that you use a version of the scripts that is suitable for the
version of libSBML that you have installed. That may mean that you need to
use an old version of the conversion scripts. I am trying to keep scripts
up to date with current libSBML releases, and I am hoping to get SBML
Level 3 support implemented during the SBML Hackathon taking place early
May 2010.
Python-only
- mod2sbml.py code and documentation (PDF) (version 1.2.1.4), which is targeted at
SBML-shorthand version 1.2.1.
Python+libsbml < 3.0.0
- mod2sbml.py code and documentation (PDF) (version 2.1.1.2), which is targeted at
SBML-shorthand version 2.1.1.
- mod2sbml.py code and documentation (PDF) (version 2.1.2.3), which is targeted at
SBML-shorthand version 2.1.2.
- mod2sbml.py code and documentation
(PDF) (version 2.1.3.1), which is targeted at
SBML-shorthand version 2.1.3, and all previous versions.
Python+libsbml >= 3.0.0 (and < 4.0.0)
- mod2sbml.py code and documentation
(PDF) (version 2.3.1.1), which is targeted at
SBML-shorthand version 2.3.1, and all previous versions.
- mod2sbml.py code and documentation
(PDF) (version 2.4.1.1), which is targeted at
SBML-shorthand version 2.4.1, and all previous versions.
Python+libsbml >= 4.1.0 (and < 5.0.0)
- mod2sbml.py code and documentation
(PDF) (version 2.4.1.2), which is targeted
at
SBML-shorthand version 2.4.1, and all previous versions.
- mod2sbml.py code and documentation
(PDF) (version 3.1.1.1), which is targeted
at
SBML-shorthand version 3.1.1, and all previous versions.
Note that this translator is written in Python, so you need a working Python
environment in order to use it. Most of the scripts also require libSBML and the libSBML
Python bindings. The latest version of the code is
strongly recommended. The old code is not being maintained.
sbml2mod.py
Python-only
- sbml2mod.py (version 1.2.1.3)
works exactly like mod2sbml.py (for spec 1.2.1), except the translation is the other way
around. It requires Python XML support (specifically, the
xml.sax package), but that comes as standard with most Python
installations.
Python+libsbml < 3.0.0
- sbml2mod.py (version 2.1.1.1) is
the reverse translation tool for Level 2. It requires libsbml
(and the libsbml python bindings).
- sbml2mod.py (version 2.1.2.1) is
the reverse translation tool for Level 2. It requires libsbml
(and the libsbml python bindings).
- sbml2mod.py (version 2.1.3.1) is
the reverse translation tool for Level 2, version 1 and all
previous versions. It requires libsbml
(and the libsbml python bindings).
Python+libsbml >= 3.0.0 (and < 4.0.0)
- sbml2mod.py (version 2.3.1.1) is
the reverse translation tool for Level 2, version 3 and all
previous versions. It requires libsbml
(and the libsbml python bindings).
- sbml2mod.py (version 2.4.1.1) is
the reverse translation tool for Level 2, version 4 and all
previous versions. It requires libsbml
(and the libsbml python bindings).
Python+libsbml >= 4.1.0 (and < 5.0.0)
- sbml2mod.py (version 2.4.1.2) is
the reverse translation tool for Level 2, version 4 and all
previous versions. It requires libsbml
(and the libsbml python bindings).
- sbml2mod.py (version 3.1.1.1) is
the reverse translation tool for Level 3, version 1 and all
previous versions. It requires libsbml
(and the libsbml python bindings).
