Old tutorial of NEURON

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2015shanbhvi

Old tutorial of NEURON

Post by 2015shanbhvi » Wed Jun 01, 2016 10:43 am

Hello All,

I'm still pretty new to using Neuron, and I am trying to follow this tutorial:

http://www.neuron.yale.edu/neuron/stati ... tline.html

but it seems to be pretty outdated. Some of the buttons that show up in the pictures for the tutorial don't show up at all in my Neruon-7.4.
For example, for artificial cells, there are four defaults: NetStim, IntFire1, IntFire2, IntFire3.
I am confused as to which one of these corresponds to the single IntFire that is the default for the older version in the tutorial.

Thanks,

Vinay

ted
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Re: Old tutorial of NEURON

Post by ted » Wed Jun 01, 2016 11:14 pm

Thanks for pointing that out. This It is an old tutorial, unlikely to be revised until after the upcoming NEURON Summer Course. Some terminology has changed, but surely it's not as difficult as reading Shakespeare.

Regarding the figures, most differences are not related to the exercise, and most of the remainder are in the "doesn't matter" category.
For example, for artificial cells, there are four defaults: NetStim, IntFire1, IntFire2, IntFire3.
I am confused as to which one of these corresponds to the single IntFire that is the default for the older version in the tutorial.
This falls into the "doesn't matter" category, except for NetStim which clearly isn't the right choice. IntFire1 is the contemporary name for the class that what was formerly called IntFire, but any of the three that begin with "IntFire" will "work", although simulation results may be different. The Programmer's Reference explains what they're about.

The two substantive differences are related to the VariableTimeStep tool. First, in recent NEURON versions, the "Local dt" button is on the Numerical Method Selection panel, which is brought up by clicking on a button labeled "Details" in the VariableTimeStep tool. Second, in recent NEURON versions with this model you can't activate the local time step option--all you can do is turn adaptive integration on or off, either by toggling it on or off with the "Use variable dt" button in the VariableTimeStep tool, or in the Numerical Method Selection panel by clicking on Cvode or Daspk or Local step to turn it on, or on Implicit Fixed Step or C-N Fixed Step to turn it off.

Second, given the inability to specify local variable time step integration with this very simple model, the final sentence in the exercise no longer makes sense, and should be replaced with something like
"The speedup with adaptive integration ON reflects the performance difference between continuous time and discrete event simulations."

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