You can use neuro-sbml using command:
$ python neurord-sbml -r <path/to/Reactions.xml> -ic <path/to/IC_singlecompartment.xml> -o </path/to/output_SBML_file.xml>
To turn on file validation, use the argument -v. To also add unit-checking, use -u:
$ python neurord-sbml -v -u -r <path/to/Reactions.xml> -ic <path/to/IC_singlecompartment.xml> -o </path/to/output_SBML_file.xml>
More information can be found by python neurord-sbml help
This package converts combines NeuroRD files into SBML files. NeuroRD divides the model up into several sections in the form of XML files: Reacting species, Reactions and rate parameters, initital conditions and morphology files. Here, we take these files and use the simple0sbml package to construct a corresponding SBML file with appropriate units.
- You need to install libsbml and simplesbml::
- $ pip install python-libsbml simplesbml