Search found 5785 matches

by ted
Mon Sep 14, 2020 3:17 pm
Forum: NEURON + Python
Topic: Frequency dependent activation of g protein models
Replies: 2
Views: 2049

Re: Frequency dependent activation of g protein models

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?
by ted
Mon Sep 14, 2020 3:10 pm
Forum: NEURON + Python
Topic: injecting continuous normally distributed noise in python
Replies: 2
Views: 1093

Re: injecting continuous normally distributed noise in python

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 ...
by ted
Mon Sep 14, 2020 1:47 pm
Forum: NEURON + Python
Topic: Connect multiple cells using connection probabilities
Replies: 4
Views: 3235

Re: Connect multiple cells using connection probabilities

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...
by ted
Mon Sep 14, 2020 1:46 pm
Forum: NEURON + Python
Topic: Connect multiple cells using connection probabilities
Replies: 4
Views: 3235

Re: Connect multiple cells using connection probabilities

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?
by ted
Mon Sep 14, 2020 12:03 pm
Forum: NEURON + Python
Topic: Netstim in automated repeating simulations
Replies: 2
Views: 73

Re: Netstim in automated repeating simulations

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...
by ted
Thu Sep 10, 2020 12:29 am
Forum: Anatomically detailed models
Topic: Questions about geometry & area(x)
Replies: 3
Views: 5964

Re: Questions about geometry & area(x)

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...
by ted
Tue Sep 08, 2020 5:07 pm
Forum: NEURON + Python
Topic: Multiple stimulation of POINT_PROCESS per run
Replies: 3
Views: 248

Re: Multiple stimulation of POINT_PROCESS per run

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 ...
by ted
Tue Sep 08, 2020 11:25 am
Forum: Other questions
Topic: Regarding diameter of geometry
Replies: 1
Views: 118

Re: Regarding diameter of geometry

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...
by ted
Wed Aug 26, 2020 9:14 am
Forum: Other questions
Topic: trouble with e_extracellular and play
Replies: 3
Views: 254

Re: trouble with e_extracellular and play

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...
by ted
Tue Aug 25, 2020 8:13 am
Forum: Other questions
Topic: Change list of morphology file into hoc code
Replies: 2
Views: 141

Re: Change list of morphology file into hoc code

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...
by ted
Sat Aug 22, 2020 12:03 pm
Forum: Modeling networks
Topic: Synaptic input model for dopaminergic neuron to examine pacemaking mechanism
Replies: 4
Views: 344

Re: Synaptic input model for dopaminergic neuron to examine pacemaking mechanism

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...
by ted
Mon Aug 17, 2020 11:14 am
Forum: MSWin
Topic: DLL LOAD FAILED importing python packages from anaconda into neuron
Replies: 1
Views: 213

Re: DLL LOAD FAILED importing python packages from anaconda into neuron

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.
by ted
Wed Aug 12, 2020 10:43 am
Forum: MSWin
Topic: DLL load failed in Windows10
Replies: 4
Views: 265

Re: DLL load failed in Windows10

Instead of

import neuron
import hoc

try this:
from neuron import h

What happens?
by ted
Tue Aug 11, 2020 1:35 pm
Forum: NEURON + Python
Topic: Multiple stimulation of POINT_PROCESS per run
Replies: 3
Views: 248

Re: Multiple stimulation of POINT_PROCESS per run

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...
by ted
Mon Aug 03, 2020 11:32 pm
Forum: NEURON + Python
Topic: Ephaptic coupling of Axons
Replies: 1
Views: 193

Re: Ephaptic coupling of Axons

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