Changing reversal potentials in NetPyNE

A Python package that facilitates development and use of models of biological neural networks

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lblood
Posts: 2
Joined: Wed Jul 10, 2019 7:59 pm

Changing reversal potentials in NetPyNE

Post by lblood » Thu Jul 11, 2019 1:16 pm

When using NetPyNE, how do you change the reversal potential of k, na, and ca ions?

For example, we are trying to change ek in NetPyNE tutorial 2 (http://netpyne.org/tutorial.html#networ ... tutorial-2).

We’ve tried the following:

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cellRule['secs']['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70, 'ek': -95}
This gives the error 'nrn.Mechanism' object has no attribute 'ek'

We also tried

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cellRule['secs']['soma']['mechs']['k_ion']={'ek': -95}
And this gave the same error.

We have also attempted:

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cellRule['secs']['soma']['mechs']['ion']['k']={'ek': -95}
and this produced an error.

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cellRule['secs']['soma']={'ek': -95}
creates a new dictionary, but h.psection() reveals it does not actually change ek.

Thanks in advance for the help.

salvadord
Posts: 80
Joined: Tue Aug 18, 2015 3:49 pm

Re: Changing reversal potentials in NetPyNE

Post by salvadord » Tue Jul 23, 2019 6:13 pm

Sorry for the delay responding. To change the reversal potential of ions, you can use eg.

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cellRule['secs']['soma']['ions']['na'] = {'e': 60}
similarly for the internal and external concentrations of the ion you can use:

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cellRule['secs']['soma']['ions']['na'] = {'i': 15, 'o': 150 }
Apologies, this is one of the things that we still need to update in the documentation. Please let us know if you have any other questions.

lblood
Posts: 2
Joined: Wed Jul 10, 2019 7:59 pm

Re: Changing reversal potentials in NetPyNE

Post by lblood » Wed Jul 24, 2019 1:30 pm

That worked. Thank you for your response.

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