Convert Python to Hoc

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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vogdb
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Joined: Sun Aug 13, 2017 9:51 am

Convert Python to Hoc

Post by vogdb » Wed Aug 14, 2019 2:24 pm

Hello! There is a model https://senselab.med.yale.edu/ModelDB/s ... del=184187. It exists in NeuroML2 and standalone Python versions. Is it possible to convert any of these into Hoc? What would you suggest? Would it be simpler just to recreate Hoc file from scratch? My circumstances are that I need Hoc exactly.
I tried to convert NeuroML2 with CellBuilder->import but NeuroML2 seems to be unsupported yet.

vogdb
Posts: 25
Joined: Sun Aug 13, 2017 9:51 am

Re: Convert Python to Hoc

Post by vogdb » Thu Aug 15, 2019 6:45 am

Seems that https://github.com/NeuroML/jNeuroML is a way to go.

ted
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Re: Convert Python to Hoc

Post by ted » Thu Aug 15, 2019 9:54 am

It will be interesting to know if the translated version of the model produces results identical to the original, and if not, what fixes are necessary to resolve the problem.

vogdb
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Re: Convert Python to Hoc

Post by vogdb » Thu Aug 15, 2019 1:43 pm

For now I couldn't do it. Currently jNeuroML does not support json files. I have to make it by hands unfortunately, can't waste time on this anymore.

ted
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Re: Convert Python to Hoc

Post by ted » Thu Aug 15, 2019 3:41 pm

It should be possible to use NEURON's Import3d tool to convert the swc file to a hoc file. Adding an axon and assigning biophysical properties will be easy. Easier yet would be to have the Import3d tool export to a CellBuilder, then use the CellBuilder to set up Subsets, spatial discretization, and assignment of biophysical properties to the members of the subsets. Then export from that CellBuilder to a hoc file, and append to the end of that hoc file a statement that attaches an axon.

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