Search found 5728 matches

by ted
Sun Mar 15, 2020 10:51 am
Forum: OS X
Topic: NRNGUI not working from command line after switch to zsh
Replies: 10
Views: 907

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: 526

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: 474

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: 684

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: 608

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: 330

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: 684

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

Thanks for posting an excellent question.
by ted
Fri Feb 28, 2020 11:15 am
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 684

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

ODEs can be implemented in mod files. A POINT_PROCESS can be used to add a bag of equations to NEURON. State variables are automatically RANGE variables, visible to hoc and Python. ASSIGNED variables need to be specified as RANGE or GLOBAL to be visible to hoc and Python; RANGE is the more flexible ...
by ted
Thu Feb 27, 2020 11:03 am
Forum: Modeling networks
Topic: Conflict Between SubsetDomainIterator and NetWork Builder
Replies: 3
Views: 330

Re: Conflict Between SubsetDomainIterator and NetWork Builder

Zip up the files needed to reproduce the error and email them to ted dot carnevale at yale dot edu and I'll let you know what I find out. What version of NEURON are you running (what is the first line that the interpreter prints out when NEURON starts), and what version of Mac OS (or whatever the co...
by ted
Wed Feb 26, 2020 11:16 am
Forum: The GUI
Topic: Issues with Saving and Retrieving
Replies: 9
Views: 6694

Re: Issues with Saving and Retrieving

Session files contain code that recreates GUI objects, such as graphs and panels. Loading a session file will recreate the GUI objects that were saved to it. Loading a session file will not launch a simulation. To launch a simulation you must execute a command such as run() or continuerun() (h.run()...
by ted
Tue Feb 25, 2020 10:36 pm
Forum: The GUI
Topic: Issues with Saving and Retrieving
Replies: 9
Views: 6694

Re: Issues with Saving and Retrieving

What happens if you launch a simulation?
by ted
Mon Feb 17, 2020 10:08 pm
Forum: UNIX/Linux
Topic: How do I collect data for plots without IV
Replies: 4
Views: 433

Re: How do I collect data for plots without IV

Indeed there is. It's the paper cited under the heading Parallel communication in NEURON in the 4th "ball and stick" tutorial-- Hines M.L. and Carnevale N.T. Translating network models to parallel hardware in NEURON, Journal of Neuroscience Methods 169 (2008) 425–455 The citation in the tutorial has...
by ted
Mon Feb 17, 2020 11:05 am
Forum: UNIX/Linux
Topic: How do I collect data for plots without IV
Replies: 4
Views: 433

Re: How do I collect data for plots without IV

"How do I collect data . . . " Use the Vector class's record() method. Documented in the Programmer's Reference. As I will be running NEURON on a supercomputer . . . Make friends with your local tech support people. Work through the "Scripting NEURON with Python" tutorial (see link on the Documenta...