Search found 89 matches

by pascal
Mon Jul 09, 2012 10:22 pm
Forum: Parallel NEURON
Topic: Writing data periodically throughout a simulation
Replies: 1
Views: 1827

Re: Writing data periodically throughout a simulation

I figured out the answer to question 2: I must declare the name of the file object with the command 'localobj forast'.
by pascal
Mon Jul 09, 2012 10:16 pm
Forum: Parallel NEURON
Topic: Writing data periodically throughout a simulation
Replies: 1
Views: 1827

Writing data periodically throughout a simulation

I recently wrote a block of code that outputs raster data periodically throughout a simulation, rather than all at once at the end: fo = new File() { fo.wopen("data/spikes.dat") } t_curr = 0 while (t_curr <= Tstop){ print "Time = ",t_curr if(t_curr + t_seg <= Tstop) { { pr.pnm.pcontinue(t_curr+t_seg...
by pascal
Tue Jun 19, 2012 4:43 pm
Forum: Other questions
Topic: Trying to use VecStim
Replies: 7
Views: 3584

Re: Trying to use VecStim

Thanks for the work-around. That works perfectly.
by pascal
Sat Jun 16, 2012 3:05 pm
Forum: Other questions
Topic: Trying to use VecStim
Replies: 7
Views: 3584

Re: Trying to use VecStim

Thanks for the explanation on NetStim. That makes sense. Also, I was able to induce a "crash" with some very simple code. First, I wrote the file test.hoc: objref vec vec = Vector(4) vec.x[1]=1 The code should generate an error, since the second line should be "vec = new Vector(4)". When I load test...
by pascal
Thu Jun 14, 2012 10:50 pm
Forum: Modeling networks
Topic: Simulating intermittent barrage of network activity
Replies: 9
Views: 5878

Re: Simulating intermittent barrage of network activity

Thanks so much, Ted. This toy model is officially working. I used a VecStim artificial cell to stimulate a NetStim artificial cell, which in turn stimulates a biophysical neuron. Here is the code for the network setup: begintemplate Cell_Cell public is_art public init, topol, basic_shape, subsets, g...
by pascal
Thu Jun 14, 2012 7:57 pm
Forum: Other questions
Topic: Trying to use VecStim
Replies: 7
Views: 3584

Re: Trying to use VecStim

Thanks, Ted, that seemed to work. I guess I just didn't think to compile the mod file, since when I use netstim.mod I don't need to compile it. Also, there are many other times when I receive an error and the program crashes without allowing me to read the error message--is there any way to prevent ...
by pascal
Thu Jun 14, 2012 5:36 pm
Forum: Other questions
Topic: Trying to use VecStim
Replies: 7
Views: 3584

Trying to use VecStim

I started learning how to implement VecStim by checking out the vecevent* files in nrn\examples\nrniv\netcon. I found that when I simply typed load_file("vecevent.ses"), it caused NEURON to crash almost instantly, so that I didn't even have time to read the error that was generated. I am running NEU...
by pascal
Wed Jun 13, 2012 8:47 pm
Forum: Modeling networks
Topic: Simulating intermittent barrage of network activity
Replies: 9
Views: 5878

Re: Simulating intermittent barrage of network activity

Sorry I'm slow with this...I'm confused because I thought you advised me to drive the NetStim with events. Also, I don't understand why it's not a good idea to stuff a bunch of events into the event queue--isn't that what NetStim typically does before a simulation starts? I thought netstim.start, ne...
by pascal
Tue Jun 12, 2012 4:32 pm
Forum: Modeling networks
Topic: Simulating intermittent barrage of network activity
Replies: 9
Views: 5878

Re: Simulating intermittent barrage of network activity

Thanks, Ted, that is really helpful. Following your advice, I was able to induce two separate barrages of input from NetStim using the following code: proc run(){ local i stdinit() //solve(tstop) //added the following 2 lines continuerun(3000) for(i=3001;i<4000;i=i+5){ nclist.object(0).event(i) } co...
by pascal
Sat Jun 09, 2012 2:09 pm
Forum: Modeling networks
Topic: Simulating intermittent barrage of network activity
Replies: 9
Views: 5878

Simulating intermittent barrage of network activity

I have inherited some code in which a network of 100 neurons receives a barrage of external stimulation at randomly-selected intervals (this is meant to simulate epileptic activity). The problem is that the code currently stores the time of every single externally-supplied synaptic event in a vector...
by pascal
Fri Jun 08, 2012 11:35 am
Forum: Getting started
Topic: NEURON BOOK Chapter 11 (rig.hoc)
Replies: 4
Views: 2605

Re: NEURON BOOK Chapter 11 (rig.hoc)

That makes sense. Thanks!
by pascal
Fri Jun 08, 2012 11:01 am
Forum: Getting started
Topic: NEURON BOOK Chapter 11 (rig.hoc)
Replies: 4
Views: 2605

Re: NEURON BOOK Chapter 11 (rig.hoc)

I am also working through chapter 11, but when I type load_file("runctl.ses") , I receive the error message nrniv: Couldn't find: runctl.ses in rig.hoc near line 1 load_file("runctl.ses") (I made sure to use a lower-case "L" and not a "1.") Where is this file supposed to be found? A search of the en...
by pascal
Tue Jun 05, 2012 1:16 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modifying standard Hodgkin-Huxley dynamics
Replies: 3
Views: 5078

Re: Modifying standard Hodgkin-Huxley dynamics

Thanks for the help, Ted. It definitely works now that I uncommented the q10 assignment. How do I investigate the voltage dependence of htau and ntau? I tried to record their values throughout the simulation, but that did not work, and I also I couldn't simply print them out using the 'print' comman...
by pascal
Mon Jun 04, 2012 4:39 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modifying standard Hodgkin-Huxley dynamics
Replies: 3
Views: 5078

Modifying standard Hodgkin-Huxley dynamics

I am new to NEURON, and I decided to learn how to modify mechanisms by trying to replicate the Wang-Buzsaki neuron (from the 1996 paper "Gamma Oscillation by Synaptic Inhibition in a Hippocampal Interneuronal Network Model"). The model is very simple, using a single compartment with Hodgkin-Huxley-l...