Search found 64 matches

by wwlytton
Fri Feb 13, 2009 7:58 am
Forum: Reaction-diffusion in NEURON
Topic: Introduction and request for suggestions
Replies: 5
Views: 8282

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: 1512

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: 1194

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: 5217

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: 1463

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: 13571

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: 13571

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: 13571

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: 2392

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: 8463

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: 4043

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: 3613

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: 4366

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: 3467

#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
by wwlytton
Fri Sep 23, 2005 12:40 pm
Forum: Modeling networks
Topic: how to use SaveState()?
Replies: 18
Views: 17877

SaveState is supposed to save the NetCon queue as well: (from NEURON ref manual) "The outstanding event delivery times are absolute. When restored, all outstanding events will be cleared and the retored event times and NetCon info will take their place. Note that it is not in general possible to cha...