Search found 43 matches

by tom_morse
Wed Dec 12, 2012 12:37 pm
Forum: General questions and discussions about computational neuroscience
Topic: Can I draw picture in compartment format in NEURON?
Replies: 2
Views: 13016

Re: Can I draw picture in compartment format in NEURON?

I am not sure what you mean by compartment format? If you mean just to display the cell in NEURON, first, import the cell in to NEURON by starting NEURON and using NEURON Main Menu - > Tools -> Miscellaneous -> Import3D Import3d_GUI[0] - choose a file (click checkbox) -> browse and select a swc file...
by tom_morse
Mon Aug 20, 2012 1:13 pm
Forum: Specific models
Topic: Questions about Traub’s model
Replies: 4
Views: 13285

Re: Questions about Traub’s model

Is -66.5425 close enough? I notice that the TCR model soma settles down to that if run for 10 seconds (10000ms). If this is adequate one could examine all the activation and inactivation variables and voltages in each compartment and initialize the model to them to start with a steady state. Note th...
by tom_morse
Sun Aug 19, 2012 11:22 pm
Forum: Specific models
Topic: Questions about Traub’s model
Replies: 4
Views: 13285

Re: Questions about Traub’s model

Regarding your first question on balancing the conductances: Traub set the max conductance values to reproduce electropysiology experiments as seen in the 2005 paper's appendix and previous papers. It is expected that there are ranges of values of max conductances that could also reproduce the exper...
by tom_morse
Mon Jul 30, 2012 5:10 pm
Forum: Specific models
Topic: Conduction along demyelinated axon
Replies: 2
Views: 15006

Re: Conduction along demyelinated axon

Are you looking for models for a particular disease, or neurons in a stage in development?

Here is a list of models in ModelDB that are relevant to Multiple Sclerosis (currently just 2):

http://senselab.med.yale.edu/ModelDB/Mo ... p?id=52406
by tom_morse
Tue Jun 26, 2012 2:35 pm
Forum: Specific models
Topic: Error: kCGErrorInvalidConnection
Replies: 4
Views: 14806

Re: Error: kCGErrorInvalidConnection

Hi Tyler, You are very welcome. I do not know yet why the TABLE macros were causing trouble. When I googled the Mac error message, for what it's worth, a reply to a request for help at an apple web site stated they were harmless: http://lists.apple.com/archives/carbon-dev/2011/Aug/msg00020.html -Tom
by tom_morse
Tue Jun 26, 2012 1:53 pm
Forum: Specific models
Topic: Error: kCGErrorInvalidConnection
Replies: 4
Views: 14806

Re: Error: kCGErrorInvalidConnection

Hi, I noticed that one problem is that the variables tau_m,tau_n,tau_h in HH.mod become nan (Not A Number) signifying that something bad has happened in the first time step. I found that if the table macro commands are commented out (with the colon character): : INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms...
by tom_morse
Fri Aug 05, 2011 3:01 pm
Forum: Specific models
Topic: NEURON implementation of Vogels & Abbott model
Replies: 4
Views: 14239

Re: NEURON implementation of Vogels & Abbott model

Ted's time constants update has been uploaded to ModelDB:

http://senselab.med.yale.edu/ModelDB/sh ... odel=83319
by tom_morse
Tue Apr 05, 2011 2:42 pm
Forum: Specific models
Topic: From ModelDB: Hu_etal_AIS_Nav1p6_and_1p2_2009
Replies: 5
Views: 13638

Re: From ModelDB: Hu_etal_AIS_Nav1p6_and_1p2_2009

I had to shorten the archive folder (directory) name in ModelDB to compile the mod files with mknrndll. Please start over by 1) download the updated archive from ModelDB from here: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=123897 2) extract the archive 3) run mknrndll, for example fro...
by tom_morse
Mon Apr 04, 2011 2:08 pm
Forum: Specific models
Topic: From ModelDB: Hu_etal_AIS_Nav1p6_and_1p2_2009
Replies: 5
Views: 13638

Re: From ModelDB: Hu_etal_AIS_Nav1p6_and_1p2_2009

Under Internet Explorer you should be able to auto-launch by clicking on the auto-launch button on the show model page (above link). For other browsers after you click the auto-launch button for the first time you will need to select to open the nrnzip file with an application that you then browse t...
by tom_morse
Tue Mar 29, 2011 5:18 pm
Forum: Specific models
Topic: From ModelDB: Hu_etal_AIS_Nav1p6_and_1p2_2009
Replies: 5
Views: 13638

Re: From ModelDB: Hu_etal_AIS_Nav1p6_and_1p2_2009

I assume you are trying to run this model:
http://senselab.med.yale.edu/ModelDB/Sh ... del=123897

I have found that it succesfully auto-launches on a windows xp machine with NEURON 7.1.

Can you get it to auto-launch in a browser? Which version of NEURON and operating system are you using?
by tom_morse
Fri Jun 04, 2010 11:48 am
Forum: Specific models
Topic: Difficulties running 84589
Replies: 4
Views: 13913

please try new version in ModelDB Re: Difficulties running 8

Colin Hales, Thanks for bringing this to our attention. We try to test models in modeldb to verify they run. In some cases (commercial applications or special platforms required) the models are not verified. This one apparently slipped through the cracks as I was able to reproduce the errors you fou...
by tom_morse
Wed Aug 12, 2009 9:31 am
Forum: UNIX/Linux
Topic: installing neuron by sources on fedora core 7
Replies: 3
Views: 3917

Re: installing neuron by sources on fedora core 11

I found the following yum command assisted NEURON and Interviews installation from sources on Fedora Core 11 FC11 yum install libXt-devel libext-devel readline-devel gcc-c++ libXext-devel Before I installed the above packages when I ran ./configure --prefix=`pwd` for iv-17 there was an error meassag...
by tom_morse
Wed Mar 11, 2009 11:18 am
Forum: ModelDB and other online sources of models
Topic: Problem with ModelDB availability
Replies: 5
Views: 16394

Re: Problem with ModelDB availability

Christoph, The building containing the modeldb server (senselab.med.yale.edu) had an emergency power outage that lasted from late yesterday afternoon to this morning E.S.T. (= GMT-5) and the server is currently back. Please email me, tom.morse@yale.edu, if you notice a problem with the server availa...
by tom_morse
Fri May 16, 2008 10:54 am
Forum: Getting started
Topic: NetCon.event doesn't respect NetCon.active
Replies: 6
Views: 3460

accept certificate permanently

We will update our certificate soon to be un-expired but still not (externally) certified. You can get around the extra certificate dialog boxes when visiting the forum by accepting the certificate **permanently** rather than choosing to **temporarily** accept the certificate. Once you have selected...
by tom_morse
Tue Sep 11, 2007 6:21 pm
Forum: Specific models
Topic: Quadroni Model scopmath library error
Replies: 1
Views: 12894

This problem was resolved by a suggestion by Michael Hines to add a dummy current to the calcium concentration mechanisms (called ifake in ca_soma.mod, ca_dist.mod, and ca_prox.mod in the updated ModelDB archive) which would then cause the solver calculation of the breakpoint to be at the same simul...