www.neuron.yale.edu

Yes, ModelDB would be a good place to start looking. Also, do you know of one or more published articles that provides a mathematical description of the exact phenomenon you want to represent in your model?

I've been trying to insert normally distributed noise onto my cells via IClamp . . . I have a vector of say 1x1000 (1 per ms) that I want to set as the amp value. Your code was heading in the right direction. Just a few changes and it will work. Here's a toy example (just a single cell) that might ...

I'm trying to connect multiple neuron cells . . . I need to take into account the connection probabilities between the cells. So I was thinking of multiplying the connection probability by the number of dendrites in the post synaptic cell. Why would that be useful? Is the number of dendrites presen...

gladonias wrote: ↑Mon Sep 14, 2020 7:36 am Let's say you instantiated a model of a neuron into a variable named cell, you can get the total number of dendritic compartments with len(cell.dend).

Interesting. Can you provide a working example?

Great question. hoc and Python keep track of how many variables reference each object instance. An object instance persists as long as there is at least one variable that references it. If an object instance's "reference count" drops to 0, the object is destroyed and the memory that it used is freed...

Trapezoidal integration has nothing to do with it. If a section's geometry is specified using the stylized method (specification of L and diam), each segment is treated as if it is cylindrical and its surface area is calculated from its diameter. If geometry is specified with the 3d (AKA pt3d) metho...

The original implementation of NMDA_Mg_T did not initialize Mg binding to ion channels correctly. Instead, initialization set channels to "unbound" (i.e. "completely free of Mg") state. Consequently, depending on parameter values, it was necessary to delay synaptic activation for t == 50 ms or more ...

Never apologize for using the GUI--the GUI has many tools that are powerful and easy to use. A quick way to learn a lot of useful information is to go straight to the Documentation page at NEURON's web site https://neuron.yale.edu/neuron/docs and check out the links under For NEURON beginners and es...

Actually the "step 4" code isn't doing what you think it is. Examine the time course of each segment's e_extracellular and you will see that only the last segment's e_extracellular is being driven by the sine wave. Why? The first pass through the loop for seg in axon1: y = h.Vector(np.sin(t)) y.play...

That code runs on neurons, but it doesn't run when I import it in the other simulation tool What "other simulation tool" do you mean? I want to fix the morpologies in the txt file so that hoc coding is possible. I guess you want to convert the Neurolucida text file to a hoc file. 1. Use the Import3...

Great, you are off to a good start! My first suggestion is that you approach the problem in the same way that an experimentalist would explore the properties of a real neuron. If you already have some wet lab experience, some this may be obvious to you in retrospect. An experimentalist would have th...

Suggest you uninstall whatever version of NEURON is currently on your PC and get 7.8.1 which is now available from www.neuron.yale.edu and is likely to include a fix for the problem you encountered.

Instead of

import neuron
import hoc

try this:
from neuron import h

What happens?

modeldb.yale.edu/140828's NMDA_Mg_T.mod should be revised so that it is driven by events, instead of using a POINTER to a variable controlled by some other mod file (release_BMK.mod in this case). The changes required are minimal and I will be glad to implement them so you can get on with your proje...

A good place to start looking for answers to your question: ModelDB.