www.neuron.yale.edu

We included plotting code on ModelDB when writing about the IntFire4 mechanism: https://senselab.med.yale.edu/ModelDB/s ... del=115357

Admittedly it is old code, so I am not sure it will run with the latest version of Neuron.

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

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.

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

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...

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 (excit...

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 st...

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...

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 pytho...

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...

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...

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 ...

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 ...

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...

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...