Search found 5705 matches

by ted
Fri Apr 03, 2020 1:37 pm
Forum: NEURON + Python
Topic: inserting synaptic mechanisms from mod file
Replies: 1
Views: 68

Re: inserting synaptic mechanisms from mod file

First, a comment about the example code in your post: many of the statements in it are deprecated or useless or serve no useful purpose at the point at which they are executed. A strong suggestion: if you want a quick, up-to-date, and reasonably complete introduction to using Python to build NEURON ...
by ted
Fri Apr 03, 2020 10:49 am
Forum: Other questions
Topic: apply extracellular electric field and current
Replies: 3
Views: 113

Re: apply extracellular electric field and current

I used "record" as follows but still I can't calculate intracellular potential... //record membrane voltage objref dvm dvm = new Vector() dvm.record(&axon.v(.5)) //record extracellular voltage objref dvex dvex = new Vector() dvex.record(&axon.vext[1](.5))[/quote]You'll also want to record time, so ...
by ted
Sat Mar 28, 2020 11:05 am
Forum: Modeling networks
Topic: Minimal parallel ring network
Replies: 2
Views: 65

Re: Minimal parallel ring network

Thank you for posting your question, and for finding the problem and posting the solution so others who read this thread can learn. Bugs are common in non-trivial software projects. They can be minimized and often prevented by testing at every stage of development. In the context of implementing a c...
by ted
Fri Mar 27, 2020 10:49 am
Forum: Getting started
Topic: Question about tutorial
Replies: 9
Views: 4106

Re: Question about tutorial

You'll have to contact that tutorial's authors.

If you are starting a new modeling project with NEURON, it would be best for you to use Python to create the model specification etc.. Please see the link Scripting NEURON with Python on the Documentation page https://neuron.yale.edu/neuron/docs
by ted
Tue Mar 24, 2020 5:06 pm
Forum: Other questions
Topic: Importing stimulus waveforms
Replies: 3
Views: 55

Re: Importing stimulus waveforms

NEURON's defaut integrator is implicit Euler, which has first order accuracy. This means that a driven variable, be it a stimulus amplitude or a time-varying parameter, is effectively a staircase waveform--changes abruptly at each time step boundary, and remains constant until the next time step bou...
by ted
Tue Mar 24, 2020 12:35 pm
Forum: Other questions
Topic: Importing stimulus waveforms
Replies: 3
Views: 55

Re: Importing stimulus waveforms

if, for example, I use a TMS waveform recorded at 1 µs steps and a NEURON simulation time step dt of 5 µs for either of the two following cases, I get different results How different is "different"? Major qualitative difference, or just a noticeable quantitative difference while overall time course...
by ted
Mon Mar 16, 2020 11:36 am
Forum: Other questions
Topic: Action Potential propagation
Replies: 3
Views: 79

Re: Action Potential propagation

See the documentation of extracellular in the Programmer's Reference. The vext values are all referred to ground, which is assumed to have a potential of 0 mV. The hoc name for the potential at a point just outside the cell membrane of the currently accessed section is vext[0](x) where x is the norm...
by ted
Sun Mar 15, 2020 10:51 am
Forum: OS X
Topic: NRNGUI not working from command line after switch to zsh
Replies: 6
Views: 152

Re: NRNGUI not working from command line after switch to zsh

.bash_profile (and sometimes .bashrc) is often used as a place to add things to the PATH on login. Read those to find out where and how NEURON and InterViews were being added to the PATH under bash. Read the documentation of zsh to figure out what you have to do now.
by ted
Fri Mar 13, 2020 11:54 am
Forum: Other questions
Topic: apply extracellular electric field and current
Replies: 3
Views: 113

Re: apply extracellular electric field and current

Is it better to use Python If you're already familiar with Python, use Python. If you're already familiar with hoc and don't know much about Python, this would be a good time to switch to Python, especially if you will be doing much programming. If you don't know much (or any) Python or hoc, this i...
by ted
Mon Mar 09, 2020 11:49 am
Forum: NEURON + Python
Topic: NetStim and NetCon
Replies: 3
Views: 169

Re: NetStim and NetCon

In NetCon can we pass array elements (time of spike) as a source variable No, but you would have discovered this fact by reading the Programmer's Reference documentation of the NetCon class. Presumably you have some precalculated spike times that you would like to use. Download and expand the gzipp...
by ted
Tue Mar 03, 2020 11:46 am
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 241

Re: Incorporating a firing model to induce different stages of sleep

My own two bits: Regarding your first question, don't worry about it. The comment is a comment, not a warning. Adaptive integration is generally not useful in either serial or parallel simulations of networks, so you won't be using the CVODE integrator. And NEURON won't use IDA unless (1) its analys...
by ted
Mon Mar 02, 2020 11:31 am
Forum: Suggestions and Feedback
Topic: Mailing list for all topics?
Replies: 1
Views: 160

Re: Mailing list for all topics?

It's not clear that a mailing list would have any advantage over the Forum's topic threads. And anyone who wants to review the latest activity on the Forum can easily click on
Quick links / Active topics
by ted
Mon Mar 02, 2020 11:16 am
Forum: Modeling networks
Topic: Conflict Between SubsetDomainIterator and NetWork Builder
Replies: 3
Views: 89

Re: Conflict Between SubsetDomainIterator and NetWork Builder

The error message SubsetDomainIterator is not a template in /tmp/nrnLyc69M near line 12111 primary_apical_list_x = new SubsetDomainIterator(primary_apical_list, 0, 0, 0) suggested that the code that defines the SubsetDomainIterator class was not being executed. The SubsetDomainIterator class is a he...
by ted
Fri Feb 28, 2020 5:32 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 241

Re: Incorporating a firing model to induce different stages of sleep

Thanks for posting an excellent question.