Search found 219 matches

by Raj
Fri Oct 20, 2017 12:07 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 28926

Re: pump kinetic scheme

Dear Menica,

I am not an active Neuron user anymore. So unfortunately I cannot help.

I hope somebody else can help out.

Kind regards,
Raj
by Raj
Fri May 11, 2012 12:25 pm
Forum: Optimization
Topic: Saving Files in Multiple Run
Replies: 5
Views: 6818

Re: Saving Files in Multiple Run

Yes, it is in the hoc/mrc directory.
At the time I invested quite some time to get it documented and to provide working examples. Exposure at SimToolDB makes it more likely this effort pays off. It would be very welcome if it became available there.
by Raj
Fri May 11, 2012 12:03 pm
Forum: Optimization
Topic: Saving Files in Multiple Run
Replies: 5
Views: 6818

Re: Saving Files in Multiple Run

I wrote code specially for this purpose it is available with documentation and example code at
http://senselab.med.yale.edu/modeldb/Sh ... del=114359
by Raj
Thu Sep 15, 2011 10:11 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Can I force an assigned variable to be an integer in NMODL
Replies: 1
Views: 1438

Can I force an assigned variable to be an integer in NMODL

I wrote the NMODL file below, which defines an artificial cell which counts spikes/events of all the NetCons connected to it and fires when it reaches a predefined value. The firing of this cell is used to halt the simulation and subsequently save the results to file. It would be neat if the assigne...
by Raj
Thu Sep 15, 2011 8:01 am
Forum: Other questions
Topic: vector.record()
Replies: 3
Views: 1713

Re: vector.record()

This ModelDB http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=115357 entry with accession number 115357 contains code for printing the function M over time, and also for a special combination of E and I. That being said I like to point out that all "currents" in the IntFire4 (excitatory and ...
by Raj
Mon Jun 27, 2011 5:52 am
Forum: The GUI
Topic: 2 fitness generators in multirun fitter
Replies: 11
Views: 9612

Re: 2 fitness generators in multirun fitter

Both the error e1(dist,gbarHBegin,gbarHEnd,Steep, ...) between your simulation and electrophysiological data and the "distance" squared e2(dist,gbarHBegin,gbarHEnd,Steep, ...) from your parameters to those satisfying the algebraic relation are functions of your parameters . Nothing will stop you fro...
by Raj
Mon Jun 27, 2011 4:21 am
Forum: The GUI
Topic: 2 fitness generators in multirun fitter
Replies: 11
Views: 9612

Re: 2 fitness generators in multirun fitter

Dear Keivan, I assume you want the value of 6 to emerge from your fitting procedure. From my limited experience with optimization procedures I would think that you would have to combine the two fitness functions into a single fitness function. In this case you would probably have an error function a...
by Raj
Mon Jan 25, 2010 5:43 am
Forum: Getting started
Topic: Simple Question Output File
Replies: 2
Views: 1324

Re: Simple Question Output File

You might want to look at Konstantin Miller's post: https://www.neuron.yale.edu/phpBB2/viewtopic.php?f=8&t=134&p=290&hilit=Konstantin#p290 This solution works very well with matlab, but it should be possible to port it to other environments. I would like to hear it if someone has a python implementa...
by Raj
Wed May 27, 2009 8:08 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Rate modulated netstim
Replies: 1
Views: 1322

Rate modulated netstim

I want to create a netstim like mechanism but with a time modulated rate. The easiest ways coming to my mind to implement this are to play a vector into a parameter of the mechanism or alternatively to play the vector into an auxilary variable and then making this variable available to the mechanism...
by Raj
Thu Mar 19, 2009 4:58 am
Forum: UNIX/Linux
Topic: Loading hoc library from other location
Replies: 4
Views: 1914

Re: Loading hoc library from other location

Aha, yes that works. I admit that I also was confused by other copies lingering around in the tree. Which might be a particularity of my copy, but I found and had opened in my editor copies from $N\share\lib\hoc\netbild not $N\share\nrn\lib\hoc\netbild . Of course that was the one thing I was not ch...
by Raj
Wed Mar 18, 2009 1:08 pm
Forum: UNIX/Linux
Topic: Loading hoc library from other location
Replies: 4
Views: 1914

Re: Loading hoc library from other location

I have included in nrnenv: a definition of neuronhome dir N followed by export PATH="$N/share/lib/hoc:$N/share/lib/hoc/celbild:$N/share/lib/hoc/chanbild:$N/share/lib/hoc/import3d:$N/share/lib/hoc/lincir:$N/share/lib/hoc/mulfit:$N/share/lib/hoc/mview:$N/share/lib/hoc/netbild:$PATH" and the correct pa...
by Raj
Wed Mar 18, 2009 12:03 pm
Forum: UNIX/Linux
Topic: Loading hoc library from other location
Replies: 4
Views: 1914

Loading hoc library from other location

I have two versions of NEURON installed. One by our system administrator on the network and the latest standard distribution locally. It turns out that when running the latest standard distribution I am not loading hoc from that distribution but hoc from the other earlier installed distribution. So ...
by Raj
Tue Mar 17, 2009 6:36 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Alpha Synapse
Replies: 4
Views: 4481

Re: Alpha Synapse

I think it would be wise to test the current in voltage clamp, so that you know what your actual electrochemical potential is. Especially when the synapse is inserted in a tiny compartment the induced depolarization will change the (v-e) term rapidly. Note: The value of 0.68 is very specific for tau...
by Raj
Fri Aug 01, 2008 5:58 am
Forum: Modeling networks
Topic: NetCon.weight [i]
Replies: 5
Views: 2233

Re: NetCon.weight [i]

Fundamental to modeling. I think it is save to leave the adjective computational out. I remember that one of my former colleagues had to check all his formula's because some of them used results from papers using another convention for the direction of the magnetic field. In my own work I at some po...
by Raj
Thu Jul 31, 2008 7:19 pm
Forum: Modeling networks
Topic: NetCon.weight [i]
Replies: 5
Views: 2233

Re: NetCon.weight [i]

Printing the NetCon.syns was illuminating. Some of my NetCons contained other targets than expected. I supppose this is a blessing in disguise because it clearly showed the difference between what I thought my code was doing and what it actually did.

Thanks!