Search found 86 matches

by Bill Connelly
Fri Jan 11, 2013 1:22 am
Forum: Getting started
Topic: Xopen / load_file not working
Replies: 4
Views: 3319

Re: Xopen / load_file not working

Yes, you're absolutely right Ted. I've been moving the model around onto various different computers to try and improve speed and I'm dealing with just this issue. I can report that by re-associating the files with neuron.exe the problem goes away. Strange that drag and dropping doesn't do the same ...
by Bill Connelly
Tue Jan 08, 2013 9:39 pm
Forum: Optimization
Topic: The simulated data is not displaying in the multiple run fit
Replies: 1
Views: 6278

Re: The simulated data is not displaying in the multiple run

Okay, I see what is happening, the generator window doesn't update every time, only every 3 or 4... and as this simulation is running so painfully slowly on my laptop, I never gave it enough time.
by Bill Connelly
Sat Jan 05, 2013 11:53 pm
Forum: Optimization
Topic: The simulated data is not displaying in the multiple run fit
Replies: 1
Views: 6278

The simulated data is not displaying in the multiple run fit

Hi, I've been running through the multiple run fitter tutorial. http://www.neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html I thought I had it mostly figured out. However, now I am trying to use some real data. I load it all in just as described in the tutorial, however, when I press th...
by Bill Connelly
Sat Jan 05, 2013 6:58 pm
Forum: Getting started
Topic: Xopen / load_file not working
Replies: 4
Views: 3319

Re: Xopen / load_file not working

I might also add that when I right click on the mosinit.hoc file, and tell it to run with neuron.exe if I perform getcwd() I get... oc>getcwd() /cygdrive/c/Windows/system32/ On the other hand, if I drag and drop the mosinit.hoc onto the neurongui shortcut, I get oc>getcwd() /cygdrive/c/ I assume thi...
by Bill Connelly
Fri Jan 04, 2013 11:21 pm
Forum: Getting started
Topic: Xopen / load_file not working
Replies: 4
Views: 3319

Xopen / load_file not working

So I went to create a new model. I already had nrn7.1 but I thought I should install the new version. I did not delete the old one. Installation appeared to go fine. On the desktop I made the folder I was going to work in "TC1" and within that folder I put a folder "cells" which was going to contain...
by Bill Connelly
Wed Apr 14, 2010 5:45 am
Forum: General questions and discussions about computational neuroscience
Topic: Calcium "Clamping"
Replies: 0
Views: 9062

Calcium "Clamping"

Nature. 2010 Jan 14;463(7278):232-6. Long-term potentiation depends on release of D-serine from astrocytes. I'm trying to understand something from a recent paper and I knew this would be the place to ask. In that paper they state However, exogenous Ca2+ buffers, although they suppress rapid Ca2+ tr...
by Bill Connelly
Sun Nov 22, 2009 5:03 pm
Forum: Getting started
Topic: Error in Neuron Book Example?
Replies: 2
Views: 1636

Re: Error in Neuron Book Example?

Just in case you still can't find the problem (because I think we've all been there), compare what you have

Code: Select all

g.size(0.5, -80, 40)
to what the book has, very closely.

Hint: . and , are different things.
by Bill Connelly
Mon Nov 02, 2009 9:42 pm
Forum: General questions and discussions about computational neuroscience
Topic: Detailed Modeling of Synapses
Replies: 8
Views: 11809

Re: Detailed Modeling of Synapses

Just to throw my 2 cents in, in the one model I have tried to get published, I 'neglected' diffusional models of the synapse, simply because they added (essentially) nothing, and would have added a huge amount of computational complexity. The IPSCs I have recorded from my cells could nearly be perfe...
by Bill Connelly
Wed Oct 07, 2009 10:04 pm
Forum: General questions and discussions about computational neuroscience
Topic: Reciprocity?
Replies: 10
Views: 12400

Reciprocity?

Am I right in thinking that a section of dendrite between points A and B is reciprocal if injection a X pA of current at location A creates Y mV of deflection at location B AND injection of X pas of current at location B creates Y mV of deflection at location A? And if the connection between a dendr...
by Bill Connelly
Mon Oct 05, 2009 4:00 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: normrand() doesn't make normally distributed numbers
Replies: 2
Views: 1807

Re: normrand() doesn't make normally distributed numbers

...However normrand outside of a verbatim block does work, and the arguments do what I would expect.
by Bill Connelly
Mon Oct 05, 2009 7:14 am
Forum: Adding new mechanisms and functions to NEURON
Topic: normrand() doesn't make normally distributed numbers
Replies: 2
Views: 1807

normrand() doesn't make normally distributed numbers

Now I presume I'm doing something wrong here, but normrand() doesn't pull out numbers from a normal distribution. It looks more like a Lorentizian Distribution (see image) Also, the arguements (that I assumed were mean, stddev or mean, coefvar) doesn't seem to do a thing. I always get the same distr...
by Bill Connelly
Mon Oct 05, 2009 5:15 am
Forum: Adding new mechanisms and functions to NEURON
Topic: For loops in NMODL
Replies: 1
Views: 1473

For loops in NMODL

Do for loops exist in NMODL? Or do I have to break into a VERBATIM block? If so, is there any other conditional loop in NMODL? Are VERBATIM blocks always un-threadsafe?
by Bill Connelly
Sun Oct 04, 2009 4:55 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Hybrid Clamp
Replies: 1
Views: 2576

Hybrid Clamp

A voltage clamp that activates after the action potential. It seems to run very slowly. Is this simply due to the watch statement? I've never dealt with a breakpoint statement that isn't a ODE in some form. Is how I've done this fine? Finally, why does this behave strangely when gain is between 0.00...
by Bill Connelly
Sat Oct 03, 2009 7:47 am
Forum: Getting started
Topic: Making a netcon know what triggered it
Replies: 9
Views: 3198

Re: Making a netcon know what triggered it

So I had to include a delay from when the membrane potential hits zero to when the sodium conductance is shut off, because otherwise the the AP is stunted, and the AHP takes on a very different shape. (I tried just setting the threshold higher, but it didn't seem to work very well). I just wanted to...
by Bill Connelly
Fri Oct 02, 2009 11:12 pm
Forum: Getting started
Topic: Making a netcon know what triggered it
Replies: 9
Views: 3198

Re: Making a netcon know what triggered it

So this flag variable, is it automatically available inside any NET_RECEIVE block? And it just represents the second argument passed by a net_send function? Is there a full reference manual of NMODL somewhere?