How to configure reversal potentials in `ModFileConverter`

[bgmeulem]

Hiya

Thanks again for the nice work, and quick responses.

I was wondering where ModFileConverter gets its default values for reversal potentials from.
I noticed that Dendrotweaks automatically sets the following reversal potentials upon reading READ e{ion} in the NEURON block

• $E_{Na}=60mV$
• $E_K = -80mV$
• $E_{Ca}=140mV$

This however collides with the default values NEURON uses. I think they're default at least, otherwise I'm not sure where they come from on our end. Perhaps they are rescaled for our temperature, since we run at $T=34^\circ C$, but then I'd be surprised that they are nice round numbers:

• $E_{Na}=50mV$
• $E_K = -85mV$
• $E_{Ca}\approx 131mV$

I was wondering:

1. Where do these values come from for ModFileConverter
2. Can these be re-configured before running the conversion?
3. Can you configure custom reversal potentials, e.g. for the $I_{HCN}$ current

It's not a huge deal to manually adapt these afterwards, and dendrotweaks already gives a great starting point. I'm mainly reporting hiccups as I encounter them to smooth out the experience as much as possible :)

Update: these are not default NEURON values, I've since figured out where we get them from

[r-makarov]

Hi, thank you for bringing it up!

This was a temporary workaround that hasn't been fixed yet. The root of the problem is that in NEURON, reversal potentials are shared across all channels, while in Jaxley, they need to be explicitly set for each channel, e.g.:

https://github.com/jaxleyverse/jaxley/blob/c222cae7e46f1a7fe7f8ef9e923b38db2a29967b/jaxley/channels/pospischil.py#L78-L82

I'd like to find a solution that will make them shared as well, i.e., something like E = params.get("E_na", 60).

The values you are referring to come from a dictionary:

DendroTweaks/src/dendrotweaks/biophys/io/code_generators.py

Lines 19 to 23 in 10976f4

	EQUILIBRIUM_POTENTIALS = {
	'na': 60,
	'k': -80,
	'ca': 140
	}

These values are somewhat arbitrary and were taken from a model I used for testing the conversion. Using NEURON defaults might make more sense, but still not optimal, as these values are only used for Jaxley templates. The solution for now, as you mentioned, is to manually set the value afterward.

Elsewhere, DendroTweaks' defaults for reversal potentials match those from NEURON:

DendroTweaks/src/dendrotweaks/model.py

Lines 605 to 613 in 10976f4

	def _add_equilibrium_potentials_on_mech_insert(self, ion: str) -> None:
	"""
	"""
	if ion == 'na' and not self.params.get('ena'):
	self.params['ena'] = {'all': Distribution('constant', value=50)}
	elif ion == 'k' and not self.params.get('ek'):
	self.params['ek'] = {'all': Distribution('constant', value=-77)}
	elif ion == 'ca' and not self.params.get('eca'):
	self.params['eca'] = {'all': Distribution('constant', value=140)}

I'll revisit this later and work on a proper fix.
Thanks again for your feedback!