Easy way to 'import' a NEURON model to Jaxley?

[briandepasquale]

I'm quite new to jaxley, and it's been well over a decade since I used NEURON. There's a NEURON model from ModelDB (https://modeldb.science/118662) that I'd like to translate over to jaxley. Is there an easy/obvious way to do this, or to do it for some part of the model (e.g., just the morphology from .hoc files)? Thanks!

[michaeldeistler]

Hi there,

thanks for reaching out! Unfortunately, we do not yet support automated translation of NEURON models.

• for morphologies, Jaxley supports SWC files. Thus, you would have to export your morphology .hoc file (e.g. dm1_morph_1.hoc) to an .swc file. There are conversion tools available (e.g. here) but I have not tried them myself.
• for channels (or other mechanisms), @r-makarov built an automated tool to convert .mod files here. Please post feedback here.

Please let us know if you need any more input or if anything is not working as expected!

All the best
Michael

[michaeldeistler]

Cool! Keep us updated, I would be curious to hear if this works!

[briandepasquale]

Thanks! I gave it a shot and hit an error almost immediately. I opened an issue issue with the developers but if you have any insight I'd welcome it!

[michaeldeistler]

Ah, too bad! I don't think I have any direct insights on why it's crashing unfortunately. Let's see what the devs say!

[kirkw-1]

Wow this would be a super useful tool, was there any progress on this?

"for channels (or other mechanisms), we are working on an automated tool that directly translates .nmodl files to Jaxley compatible channels"

[michaeldeistler]

Yes, there is an update! @r-makarov built such a tool for his DendroTweaks toolbox. See here for a tutorial on how to use it.

I have to admit that I have not tried it myself---any reports (both positive and negative) on how it works would be greatly appreciated! Please post feedback here.

Michael

[michaeldeistler]

Update:

@r-makarov built a tool to convert .mod files to Jaxley channels for his DendroTweaks toolbox. See here for a tutorial on how to use it.

Any reports (both positive and negative) on how it works would be greatly appreciated! Please post feedback here.

Michael