Search found 95 matches

by neuromau
Tue Feb 18, 2014 10:45 pm
Forum: Getting started
Topic: Load a file within a template & use variables from template
Replies: 4
Views: 2665

Load a file within a template & use variables from template

Hello, I have a template that defines some variables within it. Within the template, I want to load a hoc file that references those variables (about 160 lines long). How can I do this? Here is a very simple example of what I want to do: 1. Load in the template definition in this file called testcla...
by neuromau
Thu Dec 19, 2013 6:32 pm
Forum: NEURON Announcements
Topic: NEURON bibliography
Replies: 1
Views: 10019

NEURON bibliography

Will there be an updated NEURON bibliography soon? I noticed this one is from January, 2012: http://www.neuron.yale.edu/neuron/stati ... ednrn.html
by neuromau
Fri Nov 22, 2013 3:05 pm
Forum: MSWin
Topic: Cygwin version used to compile NEURON?
Replies: 12
Views: 11811

Re: Cygwin version used to compile NEURON?

Michael, thanks for your quick help with this! I appreciate your work as always. It's such a relief to have a working NEURON again!
by neuromau
Thu Nov 21, 2013 11:43 pm
Forum: MSWin
Topic: Cygwin version used to compile NEURON?
Replies: 12
Views: 11811

Re: Cygwin version used to compile NEURON?

I ran into trouble using mknrndll with the new version. If I just compile a c++ program separately from NEURON in my stand-alone Cygwin installation using g++, it works fine. However, if I try to use mknrndll (either in the mintty bash or the separate mknrndll tool), I get this error: bash-4.1$ mknr...
by neuromau
Thu Nov 21, 2013 5:50 pm
Forum: MSWin
Topic: Cygwin version used to compile NEURON?
Replies: 12
Views: 11811

Re: Cygwin version used to compile NEURON?

Great, I installed this new version and it fixed the problem. Thank you!
by neuromau
Wed Nov 20, 2013 7:49 pm
Forum: MSWin
Topic: Cygwin version used to compile NEURON?
Replies: 12
Views: 11811

Cygwin version used to compile NEURON?

Hello, there is an issue with older versions of Cygwin and Windows 8.1. They have fixed it in their latest Cygwin version. I received the error after updating my computer to Windows 8.1, until I updated my Cygwin as well. Now I no longer receive the error except when I open NEURON using Cygwin. I do...
by neuromau
Tue Nov 05, 2013 7:45 pm
Forum: Specific models
Topic: Ion channel bugs in Santhakumar/Morgan dentate gyrus model
Replies: 0
Views: 12669

Ion channel bugs in Santhakumar/Morgan dentate gyrus model

Hello, we have come across a few bugs in the ion channels of the Santhakumar/Morgan model on on ModelDB ( http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=124513 ). We are addressing these in a future model version. As the cell models used in this model were fit to experimental data and thei...
by neuromau
Tue Nov 05, 2013 7:16 pm
Forum: Specific models
Topic: Running the Santhakumar/Morgan model
Replies: 1
Views: 10310

Re: Running the Santhakumar/Morgan model

Hi pascal, I just now noticed this post, sorry. The ModelDB version is meant to be run from the GUI. If you start NEURON, then load the 50knet.hoc file from within the NEURON GUI, this error will not occur. Let me know if you want a version of this code that runs independently from the GUI.
by neuromau
Tue Oct 08, 2013 11:54 am
Forum: MSWin
Topic: Necessary environment for custom NEURON compilation
Replies: 6
Views: 8997

Re: Necessary environment for custom NEURON compilation

Okay, thanks, I appreciate it! Also, if there's anything you want me to try on my machine, let me know. I don't mind editing files and trying the compile again, if you have some ideas of what edits might work.
by neuromau
Tue Oct 08, 2013 5:47 am
Forum: MSWin
Topic: Necessary environment for custom NEURON compilation
Replies: 6
Views: 8997

Re: Necessary environment for custom NEURON compilation

Correct, I was using the standard 7.3 code. I had assumed my environment was missing something and didn't think to try a newer version, sorry. I now pulled in the latest code from Mercurial and ran build.sh on version (19:44d6ec5724f4), and I'm not sure if the warnings it gave can be ignored, so I t...
by neuromau
Mon Oct 07, 2013 2:05 pm
Forum: MSWin
Topic: Necessary environment for custom NEURON compilation
Replies: 6
Views: 8997

Necessary environment for custom NEURON compilation

Hello, I'm following the directions for compiling the standard NEURON 7.3 dist on my Windows 8 64-bit machine using 64-bit Cygwin (http://neuron.yale.edu/neuron/download/compile_mswin). I get errors during make. Not sure if I am missing some Cygwin packages; here are some relevant ones I have instal...
by neuromau
Mon Oct 07, 2013 1:39 pm
Forum: MSWin
Topic: Incomplete directory tree within NEURON
Replies: 4
Views: 6703

Re: Incomplete directory tree within NEURON

So somehow an actual "cygdrive" folder got created in my C: drive, and it partially replicated the directory tree under my C: drive. The NEURON GUI would only look into that cygdrive folder, and couldn't look higher than its level. But it is fixed now. There was a newer version of Cygwin available. ...
by neuromau
Thu Oct 03, 2013 7:32 pm
Forum: MSWin
Topic: Incomplete directory tree within NEURON
Replies: 4
Views: 6703

Re: Incomplete directory tree within NEURON

I used nrn-7.3.i686-pc-cygwin-setup However, I've just realized that this problem is definitely broader than NEURON. Within MATLAB, path completion only works if I use the Windows path form (C:\...). If I use the Cygwin form of /cygdrive/c/..., then only one model subdirectory is available (the same...
by neuromau
Wed Oct 02, 2013 8:55 pm
Forum: MSWin
Topic: Incomplete directory tree within NEURON
Replies: 4
Views: 6703

Incomplete directory tree within NEURON

Hello, this may be a Cygwin issue and not a NEURON issue; I'm not sure. I'm on a 64-bit Windows 8 Machine using the NEURON 7.3 GUI. I have a main folder where I keep all my NEURON models; each model is in its own subdirectory. Lately when I open the NEURON 7.3 GUI and use the commands under the File...
by neuromau
Sat Sep 07, 2013 3:38 pm
Forum: MSWin
Topic: NEURON installation was fine, now somewhat broken [resolved]
Replies: 1
Views: 6239

Re: NEURON installation was fine, now somewhat broken

Also, I saw this in ivocmain.cpp: #if defined(CYGWIN) sprintf(nrn_props, "%s/%s", neuron_home, "lib/nrn.def"); #else sprintf(nrn_props, "%s\\%s", neuron_home, "lib\\nrn.def"); #endif So I tried removing my CYGWIN environmental variable and now the NEURON installation works again for numbers 2, 3, an...