Search found 31 matches

by tsa
Thu Jun 26, 2008 11:45 am
Forum: Getting started
Topic: Multiple simulations: spawning a new graph on each run
Replies: 6
Views: 2607

Re: Multiple simulations: spawning a new graph on each run

I realized I omitted the vital line: graphlist[0].append(graph5). With its inclusion I now have a new graph created upon each trial and each new graph plots the voltage trace. However, each graph respawns the previous voltage trace as each new trial is automatically run. Is there a way to essentiall...
by tsa
Wed Jun 25, 2008 3:03 pm
Forum: Getting started
Topic: Multiple simulations: spawning a new graph on each run
Replies: 6
Views: 2607

Re: Multiple simulations: spawning a new graph on each run

The axis are scaled correctly and using "view = plot" does not reveal anything new. On a separate graph I can visualize the voltage traces as the simulations run, though each voltage trace is overwritten at the beginning of a new simulation. However, no traces appear on the graph's created by the my...
by tsa
Wed Jun 25, 2008 2:22 pm
Forum: Getting started
Topic: Multiple simulations: spawning a new graph on each run
Replies: 6
Views: 2607

Re: Multiple simulations: spawning a new graph on each run

Thanks Ted, however now I am returned multiple graph windows as the simulations complete but no voltage trace is plotted on any of the graphs.
My code for myrun is as follows:

proc myrun() {
graph5 = new Graph()
graph5.addvar("Cell[0].soma.v(0.5)", 3,1,0.8,0.9,2)
glist.append(graph5)
run()
}
by tsa
Wed Jun 25, 2008 10:53 am
Forum: Getting started
Topic: Multiple simulations: spawning a new graph on each run
Replies: 6
Views: 2607

Multiple simulations: spawning a new graph on each run

Hello, I am also trying to automate multiple simulations. I am examining a single bursting cell and varying a maximal conductance with each automated simulation. Though I have the automated process to vary the conductance and repeatedly run the simulation down correctly I have not figured out how to...
by tsa
Tue Aug 14, 2007 12:57 pm
Forum: Getting started
Topic: Plotting long periods of data
Replies: 8
Views: 4656

Hello, I have checked through my code and implemented your more efficient spike time capture method successfully. However, I still get the same bad_alloc error when, and only when, I include code for creating cumulative spike histograms in long simulations. I am able to run both long simulations whi...
by tsa
Thu Aug 09, 2007 1:41 pm
Forum: Getting started
Topic: Plotting long periods of data
Replies: 8
Views: 4656

Additionally, I have tried the error checking and when I run -dll with the path to special and init.hoc I am first told, in regards to the path to special, " invalid ELF header" and then the program runs until it errors attempting to insert a mod file which had already been complied and states "deta...
by tsa
Thu Aug 09, 2007 1:21 pm
Forum: Getting started
Topic: Plotting long periods of data
Replies: 8
Views: 4656

Here is my code for creating raster and cumulative histogram plots: objref netcon, vec, spikes, nil, graster objref vecs1[100], gg1, yy1 proc preprasterplot1() { spikes = new List() for i=0, hgcells.count()-1 { vecs1[i] = new Vector(0) vec = new Vector () hgcells.object(i).soma netcon = new NetCon(&...
by tsa
Wed Aug 08, 2007 2:58 pm
Forum: Getting started
Topic: Plotting long periods of data
Replies: 8
Views: 4656

Plotting long periods of data

Hello, I'm having trouble outputting long strings of data from NEURON. I have been using the simulator to create raster plotz and cumulative histogram plots of cell populations and then using Vector: Save to File to selecting the histogram trace to output. This works well as long as my simulation tr...
by tsa
Fri Jul 06, 2007 9:06 am
Forum: Other questions
Topic: Initializing seed with the system time
Replies: 7
Views: 6842

You were right Raj, I was putting my variable for strSeed in quotes within sscanf cause the errors. Thanks for your input
by tsa
Thu Jul 05, 2007 12:21 pm
Forum: Other questions
Topic: Initializing seed with the system time
Replies: 7
Views: 6842

What is the file type of "intSeed". I'm getting errors that it is not a double pointer but if i declare intSeed as a double NEURON gets stuck in a segmentation violation error loop. Thanks,
by tsa
Tue Jul 03, 2007 2:32 pm
Forum: Other questions
Topic: Initializing seed with the system time
Replies: 7
Views: 6842

I have been trying to use sscanf for this same task to convert the system date/time string to a number for seeding but I've been unsuccessful due to my ignorance of the formats used for sscanf. Every format I've tried listed in the programmers references returns an error of incorrect argument type. ...
by tsa
Thu Jun 14, 2007 12:09 pm
Forum: The GUI
Topic: Cumulative Frequency Spike Plot
Replies: 1
Views: 4023

Cumulative Frequency Spike Plot

Hello, I'm attempting to create code for a cumulative frequency spike plot for a population of 25 neurons similar to that which is included in the spikeplot feature of Network Builder. I've had success writing hoc to create raster plots for networks not created with the GUI but I'm having little luc...
by tsa
Thu May 31, 2007 11:45 am
Forum: Modeling networks
Topic: Threshold of SpikePlot
Replies: 1
Views: 2866

Threshold of SpikePlot

Hello, In modeling a network of cells with Network Builder I've noticed spikes are only recorded in SpikePlot when they have crossed a threshold of about +10 mV. Is there a way to change this threshold for SpikePlot? Additionally is there a way to change this threshold for individual cells/ cell typ...
by tsa
Thu May 24, 2007 11:32 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding an intracellular calcium concentration
Replies: 12
Views: 10401

The paper is: Purvis, L. Butera, R. Ionic Current Model of a Hypoglossal Motoneuron. J Neurophysiol 93. 723-733, 2005.

Their calcium accumulation mechanism is similar to that I originally posted on in this thread.
by tsa
Thu May 24, 2007 11:15 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding an intracellular calcium concentration
Replies: 12
Views: 10401

Thanks Ted. I now see noticeable fluctuation in Isk with a 1 ms /1 nA current pulse. However the magnitude of the peak is much lower 0.04 mA compared to 1 mA in the paper I'm working from. The calcium current also peak at a lower magnitude than expected (~ -1mA compared to -2.5 mA) I believe this is...