Search found 5592 matches

by ted
Tue Jul 23, 2019 10:25 am
Forum: Employment and educational opportunities
Topic: workshops/courses
Replies: 2
Views: 722

Re: workshops/courses

Thank you for your interest. On Friday, Oct. 17, 2019 there will be a 1 day course on NEURON at the Society for Neuroscience Meeting in Chicago. The course description page and registration form are at https://neuron.yale.edu/neuron/static/courses/chi2019/chi2019.html Planning for a 2020 NEURON Summ...
by ted
Mon Jul 22, 2019 12:56 pm
Forum: Getting started
Topic: Find threshold with APCount
Replies: 4
Views: 579

Re: Find threshold with APCount

APCount doesn't find spike threshold. It monitors membrane potential at a particular location in a model cell, and returns the number of times that membrane potential at that location crossed a threshold in a positive-going direction. apc = h.APCount(section(x)) Here, section(x) should be written on...
by ted
Mon Jul 22, 2019 12:29 pm
Forum: Other questions
Topic: model setup: random events
Replies: 6
Views: 700

Re: model setup: random events

First a comment: the code examples are loaded with "magic numbers"--unnamed numerical constants, that is, constants whose values are embedded explicitly in the program. See this article in Wikipedia https://en.wikipedia.org/wiki/Magic_number_%28programming%29 Now for the source of the problem you en...
by ted
Thu Jul 18, 2019 10:31 am
Forum: Other questions
Topic: model setup: random events
Replies: 6
Views: 700

Re: Creating NetCon with null source in NEURON+Python

The possibilities are either 1. there is a mismatch between what is in your computer and what is in your head, so that there is some additional difference between the computational implementations of your variation 1 and 2 models or 2. you have run into a bug in NEURON Did you happen to implement yo...
by ted
Wed Jul 17, 2019 10:16 am
Forum: Specific models
Topic: e_pas in Poirazi2003 CA1 pyr cell model
Replies: 1
Views: 359

Re: e_pas in Poirazi2003 CA1 pyr cell model

e_pas for every compartment set to -112.55mV in the model!!! . . . I know this was done by the current-balance.hoc file to initialize the model to v_init, but this seems unphysiological. It was done to force the resting potential of the model to be v_init everywhere. The basic idea is expressed in ...
by ted
Mon Jul 15, 2019 8:27 pm
Forum: NEURON Announcements
Topic: NEURON course at the 2019 Society for Neuroscience Meeting
Replies: 0
Views: 376

NEURON course at the 2019 Society for Neuroscience Meeting

What: Using NEURON to Model Cells and Networks When: Friday, Oct. 18 from 9 AM to 5 PM Where: Downtown Chicago location to be announced Satellite event to the 2019 Society for Neuroscience Meeting This course provides a practical introduction to building and using models of neurons and networks wit...
by ted
Mon Jul 15, 2019 3:30 pm
Forum: Anatomically detailed models
Topic: Morphology import error
Replies: 4
Views: 622

Re: Morphology import error

It's a bad file. Look at the error messages that NEURON prints to the interpreter window. oc>warning ./morphology.swc: more than one tree: root at line 35 root at line 36 root at line 76 root at line 120 root at line 164 root at line 208 root at line 258 etc. for more than 20 lines. Open the file wi...
by ted
Mon Jul 15, 2019 12:16 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: How does a section recognize a mechanism's current?
Replies: 2
Views: 522

Re: How does a section recognize a mechanism's current?

I am quite new to NEURON. I am trying to implement a custom mechanism (mod file) that outputs a synaptic current. Are you quite sure that is necessary? There isn't something that already exists which, except for parameter values, would do exactly what you want? If there isn't, then have you tried l...
by ted
Fri Jul 12, 2019 10:05 am
Forum: NEURON + Python
Topic: Using FInitializeHandler to set initial voltages for a subset of cells
Replies: 2
Views: 486

Re: Using FInitializeHandler to set initial voltages for a subset of cells

First figure out how to initialize just one cell to -61 mV.
by ted
Thu Jul 11, 2019 10:07 am
Forum: Anatomically detailed models
Topic: Morphology import error
Replies: 4
Views: 622

Re: Morphology import error

Can you send me ted dot carnevale at yale dot edu the morphology file?
by ted
Thu Jul 11, 2019 10:06 am
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 24483

Re: Neurolucida to NEURON best practices?

Can you send me ted dot carnevale at yale dot edu a file that demonstrates the problem you encountered?
by ted
Sun Jul 07, 2019 10:42 am
Forum: The GUI
Topic: Shape plot section diameter too thin
Replies: 1
Views: 616

Re: Shape plot section diameter too thin

See the documentation of the Shape class--in particular, that class's len_scale() method.
by ted
Wed Jul 03, 2019 2:41 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Extending Single-Compartment to Multi-Compartment model
Replies: 4
Views: 692

Re: Extending Single-Compartment to Multi-Compartment model

We are curious about the contributions of the various mechanisms. Namely, what do the Ra and cm mechanisms do, and do you know why the book might have these mechanisms in all of the compartments? Ra and cm are not mechanisms. They are attributes of sections. A section is used to represent the prope...
by ted
Wed Jul 03, 2019 2:24 pm
Forum: Anatomically detailed models
Topic: Morphology import error
Replies: 4
Views: 622

Re: Morphology import error

If two or more intact cell morphologies are present, Import3d will just launch multiple CellBuilders (one for each cell morphology), and will not generate an error message. You got an error message, so most likely you have a morphology file in which at least one neurite is not connected to its paren...
by ted
Thu Jun 27, 2019 2:10 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Extending Single-Compartment to Multi-Compartment model
Replies: 4
Views: 692

Re: Extending Single-Compartment to Multi-Compartment model

Your model is your model. What you include in it, and what you omit, is up to you to decide. Such decisions should be based on the purpose that motivated implementation of the model in the first place. When a modeling project reaches a point at which the original model has been studied and conclusio...