Search found 65 matches

by wwlytton
Mon May 30, 2011 9:45 am
Forum: UNIX/Linux
Topic: Neuron on Ubuntu Natty 11.04
Replies: 2
Views: 2082

Re: Neuron on Ubuntu Natty 11.04 --- readline problem

An unrelated problem with install on Natty: slow processing of input lines due to some kind of readline incompatibility. This manifested in an xterm by extremely slow cut and paste of commands into neuron with either the hoc or python prompt (slow line parsing) The solution was to use the NEURON nat...
by wwlytton
Sun Feb 20, 2011 7:33 am
Forum: NEURON + Python
Topic: TERMCAP/TERMINFO problems
Replies: 0
Views: 1928

TERMCAP/TERMINFO problems

A runtime error can arise due to conflicts between different terminal definitions provided by different versions of ncurses compiled in for NEURON vs Python. This will manifest as a series of "conflict" measures: eg Name collision between dumb dumb .... Name collision between att615-w att615-w att61...
by wwlytton
Fri Feb 18, 2011 6:59 pm
Forum: NEURON + Python
Topic: Raster plots in Python
Replies: 5
Views: 7601

Unable to get pylab.savefig() to work with nrniv -python

savefig for a pylab.scatter() or line plot works from native python but does not seem to work from the python interpreter when using 'nrniv -python' import pylab pylab.scatter([5,3,4],[1,7,8]) pylab.savefig("ff.png") # generates 'libpng error: zlib error' under nrniv pylab.savefig("ff.svg") # works ...
by wwlytton
Fri Feb 04, 2011 7:27 pm
Forum: NEURON + Python
Topic: Compling Problem
Replies: 21
Views: 16636

Re: Compling Problem

> .....python setup.py install ...... ok, this is the problem; this is the step I was trying to side-step; sorry I should have made that clear but had mistakenly been thinking that this was an optional rather than an obligatory step this step requires writing to python system directories rather than...
by wwlytton
Tue Feb 01, 2011 5:46 pm
Forum: NEURON + Python
Topic: Compling Problem
Replies: 21
Views: 16636

python import neuron problem

I still seem to be having this problem (or a very similar one?) 2 years on?? >>> import sys >>> sys.path.append('/usr/site/nrniv/nrn/share/lib/python') >>> import neuron Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/site/nrniv/nrn/share/lib/python/neuron/__init__....
by wwlytton
Fri Dec 24, 2010 9:57 am
Forum: NEURON + Python
Topic: multiple interpreters/multiple levels of py/N nesting
Replies: 0
Views: 2202

multiple interpreters/multiple levels of py/N nesting

A question and a problem. Q: What are the various advantages/disadvantages of choosing one of these many available routes to running NEURON with python?: 1. nrniv using nrnpython(); 2. nrniv -python; 3. python with import; 4. ipython with import (to get pylab); 5. sage with import Obviously a major ...
by wwlytton
Sat Dec 11, 2010 11:36 am
Forum: NEURON + Python
Topic: interactive pylab graphics
Replies: 1
Views: 1610

interactive pylab graphics

matplotlib offers interactive graphics through setting of variables in ~/.matplotlib/matplotlibrc backend : TkAgg interactive : True (see matplotlib.sourceforge.net/users/shell.html) This works from a regular python shell but does not seem to work from the python shell spawned by 'nrniv -python' pyt...
by wwlytton
Wed Apr 14, 2010 9:34 pm
Forum: Specific models
Topic: Izhikevich Model: Connecting Two Cells
Replies: 12
Views: 19967

Re: Izhikevich Model: Connecting Two Cells

take a look at my intf.mod in various models in modeldb
this uses 4 different synapse types for a single net_receive() block
by wwlytton
Wed Apr 14, 2010 3:25 pm
Forum: Specific models
Topic: Izhikevich Model: Connecting Two Cells
Replies: 12
Views: 19967

Re: Izhikevich Model: Connecting Two Cells

in the mod file the weight is handled by summation
so the sign of the weight determines whether the input is excitatory or inhibitory

} else { : synaptic activation
gsyn = gsyn+w
}

I may be missing the point of this thread -- what code are you trying to run that does not run?
by wwlytton
Sat Apr 10, 2010 6:03 pm
Forum: Specific models
Topic: Izhikevich Model: Connecting Two Cells
Replies: 12
Views: 19967

Re: Izhikevich Model: Connecting Two Cells

I don't offhand see why there would be any problem with convergence? What difficulty did you run into?
by wwlytton
Wed Mar 24, 2010 12:28 am
Forum: Employment and educational opportunities
Topic: postdoc and programmer jobs
Replies: 1
Views: 7511

postdoc and programmer jobs

Real people needed for research in virtual laboratory. We are recruiting programmers and postdocs for development of in silico brain (thalamus-cortex) for interfacing within a real sensorimotor task being performed online with ongoing cortical and thalamic recording. Project offers an unusual opport...
by wwlytton
Tue Feb 16, 2010 9:19 am
Forum: Specific models
Topic: Izhikevich Model: Connecting Two Cells
Replies: 12
Views: 19967

Re: Izhikevich Model: Connecting Two Cells

In the specific case of izh.mod the threshold monitoring is internal to the "cell" and the NetCon does no monitoring the thresholding is done here: WATCH (vv>thresh) 2 so the threshold is a RANGE variable that can be set different for each cell -- the default value is thresh=30 any post-connected Ne...
by wwlytton
Fri Feb 12, 2010 8:07 pm
Forum: Specific models
Topic: Izhikevich Model: Connecting Two Cells
Replies: 12
Views: 19967

Re: Izhikevich Model: Connecting Two Cells

reposting code as <code> // $Id: myizh.hoc,v 1.4 2010/01/26 19:20:38 billl Exp $ // load_file("izh.hoc") load_file("stdgui.hoc") nrnmainmenu() objref g[10] tstop=500 //* setup the cell create acell access acell objref izh,stim,nc,fih[2] cvode_local(1) acell izh=new IZH(0.5) //* parameters for differ...
by wwlytton
Fri Feb 12, 2010 5:05 pm
Forum: Specific models
Topic: Izhikevich Model: Connecting Two Cells
Replies: 12
Views: 19967

Re: Izhikevich Model: Connecting Two Cells

It's often easier to work within the context of a cell template. This is the way that the CellBuilder and NetworkBuilder sets things up so particularly helpful if you want to end up connecting this cell to some other cell type (eg a compartment cell or an event-driven ArtCell) Anyway, that's how I'v...
by wwlytton
Sat Sep 05, 2009 7:47 am
Forum: General questions and discussions about computational neuroscience
Topic: Another Synchrony Measure
Replies: 1
Views: 6716

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,"...