Search found 5301 matches

by ted
Thu Sep 20, 2018 12:06 pm
Forum: Getting started
Topic: Single node with McIntyre equations fires without stimulus
Replies: 5
Views: 50

Re: Single node with McIntyre equations fires without stimulus

As far as I can tell from their paper, Mercadel et al. claim to have done essentially the same, i.e. to use just the modified HH equations and not the myelinated part of the McIntyre et al. model They represent internodes with resistors, which amounts to assuming that the effect of myelination is t...
by ted
Wed Sep 19, 2018 11:50 am
Forum: Getting started
Topic: Single node with McIntyre equations fires without stimulus
Replies: 5
Views: 50

Re: Single node with McIntyre equations fires without stimulus

In the field of computational neuroscience, there is often a significant difference between the published narrative description of a model and the actual model that the authors used to generate their published results. That's one of the reasons why ModelDB exists. You say your implementation of a mo...
by ted
Tue Sep 18, 2018 4:30 pm
Forum: NEURON + Python
Topic: undefined symbol: nrnmpi_myid
Replies: 3
Views: 26

Re: undefined symbol: nrnmpi_myid

Aha. Uninstall your current version of NEURON, and install the latest version for your particular operating system, which plays much more nicely with Python and shouldn't generate the error message you were getting. You will have to delete any old x86_64 directories and their contents, and recompile...
by ted
Tue Sep 18, 2018 2:12 pm
Forum: NEURON + Python
Topic: undefined symbol: nrnmpi_myid
Replies: 3
Views: 26

Re: undefined symbol: nrnmpi_myid

Open a terminal and execute the command neurondemo Do you see a message in the terminal that looks something like loading membrane mechanisms from /home/ted/bin/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so Additional mechanisms from files cabpump.mod cachan1.mod . . . and do you also see a ...
by ted
Tue Sep 18, 2018 2:06 pm
Forum: Anatomically detailed models
Topic: GUID keyword error when importing .asc
Replies: 3
Views: 74

Re: GUID keyword error when importing .asc

Every once in a while, a question comes up that has an easy answer. Not often enough.
by ted
Tue Sep 18, 2018 2:04 pm
Forum: Getting started
Topic: Single node with McIntyre equations fires without stimulus
Replies: 5
Views: 50

Re: Single node with McIntyre equations fires without stimulus

First, you need to be sure that your model's parameters and initialization are identical to those used by McIntyre et al.. Easiest way to check your model is to initialize your model, then use NEURON's Model View tool to examine parameter values. Easiest way to check the model used by McIntyre et al...
by ted
Tue Sep 18, 2018 1:46 pm
Forum: MSWin
Topic: downloading neuron on windows
Replies: 1
Views: 43

Re: downloading neuron on windows

Uninstall NEURON (use the uninstaller that comes with NEURON).
Make sure that your Python works.
Then reinstall NEURON and see if everything works properly.
by ted
Fri Sep 14, 2018 12:21 pm
Forum: Anatomically detailed models
Topic: How to calculate calcium concentration in multi-compartment model
Replies: 2
Views: 94

Re: How to calculate calcium concentration in multi-compartment model

A convenient and very powerful way to evaluate a model cell is to make an instance of it, then check it with the Model View tool. load_file("nrngui.hoc") load_file("GC.hoc") objref gc gc = new GranuleCell() Then with the GUI NEURON Main Menu / Tools / RunControl and click on the RunControl panel's I...
by ted
Fri Sep 14, 2018 11:55 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 23
Views: 153

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Apropos of mpicc etc.--
under CentOS 7.x (and probably Red Hat 7.x as well), mpicc ends up in /usr/lib64/mpich-3.2/bin. I had to add this to PATH myself.
by ted
Wed Sep 12, 2018 4:34 pm
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 23
Views: 153

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

First question: what neuron source code did you use? Did you get
https://neuron.yale.edu/ftp/neuron/vers ... 6.2.tar.gz
or did you get the latest development code from the github repository?

Second question: whichever one you got, did you get it after August 15?
by ted
Wed Sep 12, 2018 4:22 pm
Forum: MSWin
Topic: No display environment available
Replies: 1
Views: 69

Re: No display environment available

If you're using a MacBook Air, why are you posting to NEURON installation and configuration / MSWin which focusses on problems specific to use of NEURON under Microsoft Windows? This is what comes up when I load this. When you load what? What is .nrn_as2sh supposed to be? I don't see anything called...
by ted
Thu Sep 06, 2018 10:21 am
Forum: Anatomically detailed models
Topic: How to calculate calcium concentration in multi-compartment model
Replies: 2
Views: 94

Re: How to calculate calcium concentration in multi-compartment model

My question is how NEURON calculate calcium concentration used for calcium dependent channel? NEURON does what the model implementers tell it to do. You'll have to figure that out. This is a network model with several different cell classes, so the task is complicated. Here are some hints that migh...
by ted
Tue Sep 04, 2018 2:27 pm
Forum: Anatomically detailed models
Topic: GUID keyword error when importing .asc
Replies: 3
Views: 74

Re: GUID keyword error when importing .asc

Make a copy of the file. Edit the copy, deleting each line that contains a
(GUID "")
statement. Then try importing the copy.
by ted
Tue Sep 04, 2018 9:34 am
Forum: NEURON + Python
Topic: Error in bash.exe
Replies: 1
Views: 86

Re: Error in bash.exe

What is the first line that NEURON prints to the terminal when it starts? What operating system are you using?