Search found 5591 matches

by ted
Thu Oct 10, 2019 11:14 am
Forum: NEURON + Python
Topic: Different v_init for different neurons in a network
Replies: 1
Views: 54

Re: Different v_init for different neurons in a network

No Python- or hoc-specific magic is involved. In pseudocode

Code: Select all

for each section {
  for each segment {
    set v to whatever initial value you want
  }
}
call finitialize() with no argument
Add whatever elaborations or refinements you like to do this on a cell-specific basis.
by ted
Wed Oct 09, 2019 10:29 am
Forum: Anatomically detailed models
Topic: 3D rotation in Cell Builder
Replies: 3
Views: 73

Re: 3D rotation in Cell Builder

1. From the CellBuilder export a hoc file that contains the statements that create the axon terminal. 2. Organize the "model specification" part of your code like this: code that specifies the geometry and topology of everything but the axon terminal a load_file() statement that reads the hoc file c...
by ted
Mon Oct 07, 2019 9:35 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 7555

Re: mixed model of artificial and conduction-based cells

asb wrote:Would you be happy to have a look at the model first to ensure it passes the litmus test?
If you want to suggest that a published model be included in ModelDB, then by all means, suggest it to the curator of ModelDB. That would be Tom Morse.
by ted
Mon Oct 07, 2019 11:58 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding delay to a graded synapse model
Replies: 2
Views: 53

Re: Adding delay to a graded synapse model

Forget about NetCon. A NetCon is just a threshold detector that places an event in a queue when a monitored variable crosses a threshold in a positive-going direction. Period. You're stuck with FIFO. Be prepared to explain to a reviewer what plausible physical mechanism would account for a fixed tim...
by ted
Sat Oct 05, 2019 11:49 am
Forum: Anatomically detailed models
Topic: 3D rotation in Cell Builder
Replies: 3
Views: 73

Re: 3D rotation in Cell Builder

First question: are all of these sections supposed to belong to a single cell, or is the axon terminal stuff supposed to be presynaptic and the ball and stick postsynaptic?
by ted
Tue Oct 01, 2019 12:49 pm
Forum: Getting started
Topic: monitor the attenuation of the peak value of the action potential with distance from the ion channel
Replies: 9
Views: 114

Re: monitor the attenuation of the peak value of the action potential with distance from the ion channel

If your primary interest is in spike propagation along an axon, why include a soma in your model? Physiologists who study spike propagation along sciatic nerve or squid axon almost never pay any attention to the soma, and typically work on isolated axon without a soma. If your interest is in how spi...
by ted
Tue Oct 01, 2019 10:15 am
Forum: NEURON Announcements
Topic: testing
Replies: 0
Views: 13

testing

Testing creation of a new topic
by ted
Sun Sep 29, 2019 1:34 pm
Forum: Getting started
Topic: monitor the attenuation of the peak value of the action potential with distance from the ion channel
Replies: 9
Views: 114

Re: monitor the attenuation of the peak value of the action potential with distance from the ion channel

That's much clearer, thanks. At a minimum, you need a model axon, and something to stimulate the axon. You should also have a graph that shows membrane potential along the length of the axon for at least the following reasons: 1. To verify that the stimulus is big enough to trigger a spike but not s...
by ted
Sat Sep 28, 2019 9:48 pm
Forum: Getting started
Topic: monitor the attenuation of the peak value of the action potential with distance from the ion channel
Replies: 9
Views: 114

Re: monitor the attenuation of the peak value of the action potential with distance from the ion channel

It sounds like you're starting a modeling project and need to work closely with a collaborator on it for two reasons. First, to define exactly what you are thinking about. A big problem is that this sentence doesn't make sense: "How can I apply a stimulus at a specific ion channel (Has to be ion cha...
by ted
Sat Sep 28, 2019 9:23 pm
Forum: ModelDB and other online sources of models
Topic: Model 3808 can't use Create Your Own\Single Cell
Replies: 1
Views: 54

Re: Model 3808 can't use Create Your Own\Single Cell

It's 22 year old legacy code. What's surprising is that any of it works at all.
by ted
Sat Sep 28, 2019 9:18 pm
Forum: ModelDB and other online sources of models
Topic: Model 135839 error issue
Replies: 1
Views: 37

Re: Model 135839 error issue

Everything works fine for me under Win 10, using the latest standard distribution installer for NEURON, i.e. version 7.7.2 7.7 (2b7985ba) 2019-06-20.
by ted
Sat Sep 28, 2019 8:53 pm
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 8
Views: 194

Re: MOD Files Compile But Fail To Load

Here is the response when running neurondemo: That's all that happened? No GUI tools appeared on screen? Clicking on the "Release" radio button did what? After clicking on "Release", clicking on the Init & Run button did what? With regard to your own source code, where are you putting it before you...
by ted
Fri Sep 27, 2019 11:23 am
Forum: NEURON + Python
Topic: Use NEURON's native GUI tools with Python!
Replies: 2
Views: 10456

Re: Use NEURON's native GUI tools with Python!

For some time now, all you have to do is specify a name when you use Python to create a section, and you do it like this: namestring = h.Section(name = ' namestring ') This creates a new section that has the Python name namestring and the hoc name _pysec. namestring . The hoc name can be used in an...
by ted
Fri Sep 27, 2019 10:55 am
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 8
Views: 194

Re: MOD Files Compile But Fail To Load

Some questions.
First, did this machine ever have a previous version of NEURON installed, and if so, did mechanisms load properly then?
Second, what happens when you execute the command
neurondemo
from the command line?
by ted
Thu Sep 26, 2019 6:38 pm
Forum: Getting started
Topic: reuse modelDB:84589
Replies: 2
Views: 156

Re: reuse modelDB:84589

Tom Morse, curator of ModelDB, has revised this model entry so that it works under MSWin and is easier to launch (including enabling "auto-launch" to work). He has also revised the README.html file accordingly. Many thanks, Tom!