Re: [Neuroml-python] How 2 convert SBML to neuron using python

[Padraig G. <p.g...@uc...>]

Hi Robert,

Yes, that seems to be the best way to do it via Python. It does of 
course require that Java is set up correctly in the system, but that's 
required for getting most of the jNeuroML specific functionality in 
pyNeuroML.

Regards,

Padraig



On 13/10/17 12:42, Robert Lindroos wrote:
> Hi again.
> I solved it using the pynml.py description:
>
> https://github.com/NeuroML/pyNeuroML/blob/master/pyneuroml/pynml.py
>
> For reference it was the run_jneuroml() function that should be used 
> for this task.
>
> Here's an example script:
>
> from pyneuroml import pynml
> pynml.run_jneuroml('-sbml-import', 'SBML_file_name.xml', '1 1' )      
>      # creates a LEMS file called SBML_file_name_LEMS.xml
> pynml.run_jneuroml('', 'SBML_file_name_LEMS.xml', '-neuron')          
>    # creates a NEURON .mod file
>
>
> Best,
> R
>
> 2017-10-12 22:02 GMT+02:00 Robert Lindroos <rob...@gm... 
> <mailto:rob...@gm...>>:
>
>     Hi,
>     I am able to export an SBML file to NEURON readable mod file using
>     jnml in the following way.
>
>     Import;
>     ./jnml -sbml-import SBML.xlm 1 1
>
>     Export;
>     ./jnml SBML.xlm_LEMS.xml -neuron
>
>     But how can I do this with the python version?
>
>     Preferably the names of the substrates in the SBML file would be
>     used in the mod file as well if possible (instead of the ID that
>     seems to be the standard). Ultimately I would need this to work in
>     a jupyter notebook.
>
>
>     Thanks and regards,
>     Robert
>
>
>
>
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Padraig Gleeson
Room 321, Anatomy Building
Department of Neuroscience, Physiology&  Pharmacology
University College London
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United Kingdom

+44 207 679 3214
p.g...@uc...
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