Learning by recreating the HH model

The basics of how to develop, test, and use models.
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careBearStare
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Joined: Tue May 11, 2021 12:17 pm

Learning by recreating the HH model

Post by careBearStare »

I'm new to NEURON, trying to work my way through the book, and starting off by recreating the Hodgkin-Huxley model. This includes setting up a set of new mechanisms, getting the setting right and everything as much from scratch as I can.

1. sometimes things I build don't always match the output of NEURON's stock HH mechanism. How do I "lift the hood" and see what those built-in HH settings are?
2. How is temperature a part of model building in NEURON? I found the Celsius variable (and later the Temperature panel), and can enable resetting with ion_style()...but should I be adjusting temp through changing the rate constants instead instead of this seemingly global temp variable?
ted
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Re: Learning by recreating the HH model

Post by ted »

How do I "lift the hood" and see what those built-in HH settings are?
Examine the NMODL code for the hh mechanism. It's in hh.mod. I don't think you'll find hh.mod on your machine if you used one of NEURON's binary installers; if that's the case, download NEURON's source code

https://github.com/neuronsimulator/nrn/ ... master.zip

expand it, and look in nrn/src/nrnoc for hh.mod.
How is temperature a part of model building in NEURON? I found the Celsius variable
The name of the parameter is celsius, not Celsius. Don't tinker with rate constants directly. Instead, rely on whatever celsius-involving code might exist in the NMODL files you're using. Before you do anything, go to

Board index / Making and using models with NEURON / Hot tips

and look for the thread titled celsius and temperature-dependent mechanisms (this will be in the second page of Hot tips), where you will find some links to useful information.
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