Search found 66 matches
- Sat Sep 05, 2009 7:47 am
- Forum: General questions and discussions about computational neuroscience
- Topic: Another Synchrony Measure
- Replies: 1
- Views: 8167
Re: Another Synchrony Measure
the first thing to do is to get the binning done using either obj = vdest.hist(vsrc, low, size, width) OR newvect = vsrc.histogram(low, high, width) in order to do this you will need to pick up t vectors on a per-cell basis (as you said) you can do this by using indvwhere() vdest.indvwhere(vsource,&...
- Fri Jul 03, 2009 11:21 am
- Forum: Modeling networks
- Topic: Measurements of Synchrony?
- Replies: 4
- Views: 4665
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...
- Fri Feb 13, 2009 7:58 am
- Forum: Reaction-diffusion in NEURON
- Topic: Introduction and request for suggestions
- Replies: 5
- Views: 19045
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...
- Wed Aug 06, 2008 12:48 pm
- Forum: Modeling networks
- Topic: viewing a network topologically
- Replies: 2
- Views: 3292
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...
- Wed Jun 18, 2008 1:17 pm
- Forum: UNIX/Linux
- Topic: version banner fails to update after reinstall
- Replies: 0
- Views: 2263
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...
- Mon Mar 24, 2008 11:04 pm
- Forum: UNIX/Linux
- Topic: Compilation of iv-17 on SGI IRIX64 6.5 fails
- Replies: 3
- Views: 7118
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...
- 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: 2412
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...
- Mon Aug 27, 2007 4:07 pm
- Forum: Specific models
- Topic: Izhikevich Model
- Replies: 9
- Views: 40439
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...
- Thu Aug 16, 2007 2:51 pm
- Forum: Specific models
- Topic: Izhikevich Model
- Replies: 9
- Views: 40439
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...
- Wed Aug 15, 2007 12:16 pm
- Forum: Specific models
- Topic: Izhikevich Model
- Replies: 9
- Views: 40439
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 ...
- Fri Dec 15, 2006 11:33 am
- Forum: Other questions
- Topic: random number generation
- Replies: 0
- Views: 3287
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...
- Thu Jun 29, 2006 7:42 pm
- Forum: NEURON hacks
- Topic: drawing on top of a figure
- Replies: 0
- Views: 13437
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...
- 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: 5707
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...
- Fri Oct 28, 2005 7:13 pm
- Forum: Other questions
- Topic: general: NEURON & CONDOR
- Replies: 2
- Views: 4625
- Fri Oct 28, 2005 11:08 am
- Forum: Modeling networks
- Topic: Code for Lists of Synaptic Connections
- Replies: 2
- Views: 6071
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 ...