Search found 65 matches

by wwlytton
Fri Jul 03, 2009 11:21 am
Forum: Modeling networks
Topic: Measurements of Synchrony?
Replies: 4
Views: 3468

Re: Measurements of Synchrony?

Paul Tiesinga has a large number of sync measures and other ways of interpreting population spike patterns eg mean ISI for neuron n is tauN, CV is (stdev of tauNi)/<tauN> associate a particular interval statistic with the midpoint of the ISI The interspike interval of the combined set of network spi...
by wwlytton
Fri Feb 13, 2009 7:58 am
Forum: Reaction-diffusion in NEURON
Topic: Introduction and request for suggestions
Replies: 5
Views: 9919

Introduction and request for suggestions

We are planning to augment NEURON to implement biochemical reaction-diffusion (RD) as well as facilitated cytoplasmic transport in NEURON. This would involve complementing the present integration of the one-dimensional cable equation with a meshed integration of diffusing reactants in multiple 3D (c...
by wwlytton
Wed Aug 06, 2008 12:48 pm
Forum: Modeling networks
Topic: viewing a network topologically
Replies: 2
Views: 1921

Re: viewing a network topologically

you can use Hinton plots -- vec.hinton() -- to make x,y animations where each square is a single cell or a single compartment you can also use shapeplot after distributing the cells appropriately in the following image http://it.neurosim.downstate.edu/~billl/03jul19CA3cells.gif I threw down some cel...
by wwlytton
Wed Jun 18, 2008 1:17 pm
Forum: UNIX/Linux
Topic: version banner fails to update after reinstall
Replies: 0
Views: 1467

version banner fails to update after reinstall

(this problem may only apply if using separate source and build directories) after I updated with subversion, the version banner was not correct, still reflecting version from the prior installation 1. first check whether the version file is in fact old cat $SOURCE_DIR/src/nrnoc/nrnversion.h 2. if s...
by wwlytton
Mon Mar 24, 2008 11:04 pm
Forum: UNIX/Linux
Topic: Compilation of iv-17 on SGI IRIX64 6.5 fails
Replies: 3
Views: 5743

compiling NEURON under IRIX (IRIX64 6.5 10060437 IP30)

I did not run into any problem compiling iv-17 (the gcc was already 3.3) but did run into minor problems with compiling NEURON 1. I was unable to compile from source presumably due to antique autoconf etc under IRIX Solution: downloaded the prepared alpha version (http://www.neuron.yale.edu/ftp/neur...
by wwlytton
Tue Dec 18, 2007 11:22 am
Forum: Adding new mechanisms and functions to NEURON
Topic: WARNING x,y,z overlap in ARTCELLs with VERBATIM blocks
Replies: 0
Views: 1740

WARNING x,y,z overlap in ARTCELLs with VERBATIM blocks

When building a network it is natural to assign locations to an ARTIFICIAL CELLs using RANGE x,y,z be aware that this translates in the .c header to eg #define x _p[32] #define y _p[33] #define z _p[34] if you now use x, y or z in a VERBATIM block, there will be precompilation translation of those v...
by wwlytton
Mon Aug 27, 2007 4:07 pm
Forum: Specific models
Topic: Izhikevich Model
Replies: 9
Views: 15449

new Izhikevich model

The Izhikevich model has been replaced with a new improved version for NEURON. The new .mod file uses the WATCH statement so as to avoid the need to have an external NetCon looking for threshold passage A gsyn parameter has been added to allow activation from NetCons This makes it easy to include th...
by wwlytton
Thu Aug 16, 2007 2:51 pm
Forum: Specific models
Topic: Izhikevich Model
Replies: 9
Views: 15449

replacement

I have not been using the Izh. model and just posted it as a service. Paolo, please let us know what you want -- if you would like me to fix my implementation I would be happy to do so; if you would like to use Ron's implementation it sounds like he would be happy to provide it either way, I would s...
by wwlytton
Wed Aug 15, 2007 12:16 pm
Forum: Specific models
Topic: Izhikevich Model
Replies: 9
Views: 15449

model fix

did one of you want to fix this model or would you like me to fix it? sounds like the easiest thing would be to specify a specific flag in the implementation so as not to interfere with netcons unfortunately I do not have matlab so cannot compare to Izhekevich current model; I believe that Mike and ...
by wwlytton
Fri Dec 15, 2006 11:33 am
Forum: Other questions
Topic: random number generation
Replies: 0
Views: 2693

random number generation

Has anyone tested the randomizers available in NEURON for adequacy? I would like to use a randomizer to select a number in a seeded series by an index. Does anyone know how to do that with any of those available or with some other randomizer? I tested them for speed and was surprised at the discrepe...
by wwlytton
Thu Jun 29, 2006 7:42 pm
Forum: NEURON hacks
Topic: drawing on top of a figure
Replies: 0
Views: 9228

drawing on top of a figure

// $Id: drline.hoc,v 1.6 2006/06/29 23:36:22 billl Exp $ // click and drag left button to draw lines on top of a figure interactively // select graph to draw on with setdrl(Graph[]) // set color with clr, line width with lne // select 'Draw curve' for continuous drawing // select 'Arrow' to place a...
by wwlytton
Fri Apr 21, 2006 9:03 am
Forum: Adding new mechanisms and functions to NEURON
Topic: C++ code via NMODL with C wrappers?
Replies: 4
Views: 4816

C++ in mod

You cannot include C++ in mod files. However there are C++ packages in Neuron: vectors and lists that have wrappers compiled and therefore can be used. eg extern void vector_resize(); extern int vector_instance_px(); One could use these examples to include an additional file in the initial build and...
by wwlytton
Fri Oct 28, 2005 7:13 pm
Forum: Other questions
Topic: general: NEURON & CONDOR
Replies: 2
Views: 4029

We used Condor with Neuron 10 years ago but I don't remember anything much about the details of this.

It is possible to do a static compilation -- there is an --enable-static flag for configure

Bill
by wwlytton
Fri Oct 28, 2005 11:08 am
Forum: Modeling networks
Topic: Code for Lists of Synaptic Connections
Replies: 2
Views: 4840

network organziation

I go in the other direction -- I put the network together in a database and then use this to view and manipulate connectivity -- then I load the db into neuron alternatively I do have some code that reads out of cvode.netconlist to produce the database however you mentioned that you are having some ...
by wwlytton
Thu Oct 20, 2005 11:56 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How to specify include files in VERBATIM/ENDVERBATIM blocks
Replies: 1
Views: 3811

#include

You can include 'C' in VERBATIM blocks but not 'C++'

the VERBATIM block can also have CPP #INCLUDE statements

there is also an NMODL INCLUDE command which lets you use prewritten NMODL code as well