Search found 43 matches

by tom_morse
Tue Sep 04, 2007 11:23 am
Forum: UNIX/Linux
Topic: installing neuron by sources on fedora core 7
Replies: 3
Views: 3917

installing neuron by sources on fedora core 7

When installing neuron by sources on FC7 the following packages need to be installed so that header files for x11, readline, and the Xext libraries are available for the build: yum install libXt-devel libXext-devel readline-devel (End of of what is needed) The below error messages are included here ...
by tom_morse
Tue Sep 04, 2007 8:10 am
Forum: UNIX/Linux
Topic: installing neuron rpm on fedora core 7
Replies: 0
Views: 3356

installing neuron rpm on fedora core 7

I received the following error during compiling mod files on fedora core 7 with the NEURON -- Release 6.0.1 (1780) 2007-06-12 nrnivmodl: ... gcc -shared .libs/leak.o .libs/oldtsyn.o .libs/shunt.o .libs/thold.o .libs/mod_func.o -Wl,--rpath -Wl,/usr/local/nrn/i686/lib -Wl,--rpath -Wl,/usr/local/nrn/i6...
by tom_morse
Tue Aug 28, 2007 10:31 am
Forum: Adding new mechanisms and functions to NEURON
Topic: mod files with assert in verbatim failed under mswin
Replies: 0
Views: 2666

mod files with assert in verbatim failed under mswin

We received a request for help from a modeler who cound not get a NEURON simulation with mod files with assert statements such as this nmda.mod to work under mswin : COMMENT ----------------------------------------------------------------------------- Simple synaptic mechanism derived for first orde...
by tom_morse
Wed Aug 02, 2006 3:01 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: sodium pump .mod mechanism
Replies: 3
Views: 4849

In an attempt to bring more joy to ModelDB word searches I have added a hint link http://senselab.med.yale.edu/senselab/ModelDB/perlfect_hint.html on the ModelDB home page http://senselab.med.yale.edu/senselab/ModelDB/ on how to use the supplied perlfect engine driven search. Using the "+" character...
by tom_morse
Wed Jul 26, 2006 12:28 pm
Forum: OS X
Topic: opening anything from the modelDB
Replies: 2
Views: 4199

how to run neuron on the mac

Double check that you have compiled the mod files ( I see you said you did but maybe you are starting over now): 1) After the archive is unziped drag and drop the newly created folder onto the mknrndll icon. 2) Then drag and drop the mosinit.hoc from the folder onto the nrngui icon. (There might be ...
by tom_morse
Wed Jul 26, 2006 10:59 am
Forum: The GUI
Topic: Calculation in Matlab - Visualisation in Neuron
Replies: 4
Views: 7192

code sample

The following code sample displays a shape-shape plot by playing vectors into the voltage of the sections. It is better to voltage clamp the sections but this will probably work for you. The shp.ses file was created by saving the shape shape plot as a session file and is included after the long dash...
by tom_morse
Tue Jul 25, 2006 6:36 pm
Forum: The GUI
Topic: Calculation in Matlab - Visualisation in Neuron
Replies: 4
Views: 7192

try this for setting the voltage

Let's say you just had two compartments a soma and a dend
Then your program could say

soma.v(0.5)=10
dend.v(0.5)= -20

You might want to write matlab code that writes hoc code similar to above.
So you probably get the idea of what to do with your matlab values. If not please ask more.
by tom_morse
Thu Jan 12, 2006 1:35 pm
Forum: ModelDB and other online sources of models
Topic: models on the web
Replies: 2
Views: 19997

online database of neuronal, heart cell, and other models

Here is another neuronal (and mostly heart) modeling site:
http://nsr.bioeng.washington.edu/PLN/Me ... portal_url
by tom_morse
Mon Nov 07, 2005 4:07 pm
Forum: Other questions
Topic: translate postscript to jpeg, png, or other format with gimp
Replies: 0
Views: 3236

translate postscript to jpeg, png, or other format with gimp

Tip: There is a free graphics program called "gimp" that is available for the unix, windows, or mac OS X platforms at the web site http://www.gimp.org/

Gimp can translate graphic images from postscript (format of graphics output from NEURON) to jpg, png, tif, and many other formats.
by tom_morse
Thu Sep 15, 2005 6:36 pm
Forum: UNIX/Linux
Topic: installing neuron and interviews from sources: Fedora Core 4
Replies: 0
Views: 3873

installing neuron and interviews from sources: Fedora Core 4

We found that the workstation installation of RedHat Fedora Core 4 came without the X11 (X11R6) header files that normally come with a unix OS and that are required for building interviews (without these files running ./configure quits after an error message ... checking for X... no configure: error...
by tom_morse
Fri May 27, 2005 6:03 pm
Forum: Specific models
Topic: Cerebellar Purkinje cell
Replies: 1
Views: 16107

five (5) Cerebellar purkinje cell models in ModelDB

I wanted to explain how to use ModelDB to find Cerebellar purkinje cell's. Start from the ModelDB home page and then click on 'Find models of a particular Neuron type'. Then click on Cerebellar purkinje cell. You will be lead to the below link which has links to (currently 5) Cerebellar purkinje cel...
by tom_morse
Fri May 27, 2005 5:55 pm
Forum: ModelDB and other online sources of models
Topic: models on the web
Replies: 2
Views: 19997

links to computational neuroscience models and methods

Here are 10 URL's to models and methods from diverse fields in computational neuroscience: C-C++: 1) Rat phrenic motor neuron (Amini et al 2004) Files available.. http://www.ece.rice.edu/~jwc/PMN/ Genesis: 2) Emergent properties of networks of biological signaling pathways (Bhalla, Iyengar 1999) htt...
by tom_morse
Thu May 19, 2005 7:22 pm
Forum: ModelDB and other online sources of models
Topic: models on the web
Replies: 2
Views: 19997

models on the web

ModelDB and Visiome Platform are two databases of neuronal and network models: http://senselab.med.yale.edu/senselab/modeldb http://www.visiome.org Descriptions from their respective home pages: ModelDB provides an accessible location for storing and efficiently retrieving computational neuron model...