Search found 50 matches

by vladimirov
Sun Sep 18, 2011 2:19 pm
Forum: Modeling networks
Topic: Rasterogramm of two overlapping rings
Replies: 5
Views: 2882

Re: Rasterogramm of two overlapping rings

Ted, thank you so much for detailed response and the tips.
What are symbolic constants and how can I use them in this context? Is it like "a", "b", "c"? Can you give a small example or a link where I can find it?
Thanks!
by vladimirov
Thu Sep 15, 2011 3:34 pm
Forum: Modeling networks
Topic: Rasterogramm of two overlapping rings
Replies: 5
Views: 2882

Rasterogramm of two overlapping rings

Hi, I am simulating two cell rings (loops) which share some cells with each other. When I use the NetCon.record(), I find that the shared cells ids are missing for the first ring. The code is like this: proc spikerecord1() {local i localobj nc, nil tvec1 = new Vector() idvec1 = new Vector() for i=0,...
by vladimirov
Wed Aug 31, 2011 2:48 pm
Forum: Modeling networks
Topic: Hyperpolarizing current to every soma in a network - how?
Replies: 3
Views: 2642

Re: Hyperpolarizing current to every soma in a network - how

Wow, thank you very much, Ted. I think this solves my problem. Your mod file works fine. Here is how I use it: cell.soma insert bias area_soma=PI*cell.soma.diam*cell.soma.L*1e-8 // [mcm->cm2] AMP=0.1*1e-6 //[nA->mA], note that hyperpolarizing current is + (opposite to electrode current sign) cell.so...
by vladimirov
Wed Aug 31, 2011 12:08 pm
Forum: NEURON hacks
Topic: Syntax Highlighting for GNU Linux and MS Windows
Replies: 11
Views: 34622

Re: Syntax Highlighting for Notepad++

finally, I made syntax highlighting for notepad++ (for windows usres). I think it is better than the kate one. instructions: 1) install notepad++ 2) use a texteditor to replace content of the file userDefineLang.xml with provided one (see below). windows xp: "C:\Documents and Settings\<your user na...
by vladimirov
Wed Aug 31, 2011 10:53 am
Forum: Modeling networks
Topic: Hyperpolarizing current to every soma in a network - how?
Replies: 3
Views: 2642

Hyperpolarizing current to every soma in a network - how?

Hi, I wonder if there is an elegant way to apply a small hyperpolarizing current to all neurons (somas) of a large network. If I have a network of >10,000 neurons, it looks pretty weird to simulate as many IClamps each stuck into a soma and having the same current. Is there any way to simulate it in...
by vladimirov
Thu Aug 18, 2011 1:03 pm
Forum: Other questions
Topic: How to plot power spectrum
Replies: 1
Views: 1715

How to plot power spectrum

Hi, I am trying to analyse spectrum of a signal (power vs freq.), and I find that fft() and FFT() functions need some post-processing to do this. There is a function spctrm(), but its not clear from instructions how to use it. Are there any libraries for advanced signal analysis? Ideally, a procedur...
by vladimirov
Wed Aug 17, 2011 5:49 pm
Forum: Modeling networks
Topic: Plot a graph of sum of neuron potentials in network?
Replies: 7
Views: 2845

Re: Plot a graph of sum of neuron potentials in network?

Ok, got it. Now I will use List(), too. Thanks a lot!
by vladimirov
Wed Aug 17, 2011 11:33 am
Forum: MSWin
Topic: Is Neuron under Win slower than under Linux?
Replies: 4
Views: 6740

Re: Is Neuron under Win slower than under Linux?

Thank you, I did not know this option. I follow you advice and use the NetCon record() to visualize network activity _after_ simulation is done.
by vladimirov
Wed Aug 17, 2011 10:52 am
Forum: Modeling networks
Topic: Plot a graph of sum of neuron potentials in network?
Replies: 7
Views: 2845

Re: Plot a graph of sum of neuron potentials in network?

In you code examples, you store cells in List(). Why is it better than simply in an array like

Code: Select all

objref cells[100]
Any advantages?
by vladimirov
Wed Aug 17, 2011 2:00 am
Forum: MSWin
Topic: Is Neuron under Win slower than under Linux?
Replies: 4
Views: 6740

Re: Is Neuron under Win slower than under Linux?

Ok, then I keep on Win XP for now, and reduce the amount of graphical output during my simulations. Thank you!
by vladimirov
Tue Aug 16, 2011 4:17 pm
Forum: MSWin
Topic: Is Neuron under Win slower than under Linux?
Replies: 4
Views: 6740

Is Neuron under Win slower than under Linux?

Hi,
Does it make sense to run Neuron models under Linux rather than Windows to increase speed? As written in "Neuron Book", Windows is "a second-class OS" - does it also mean Neuron in Windows runs slower? What about batch mode? I use Win XP.
by vladimirov
Tue Aug 16, 2011 1:01 pm
Forum: Modeling networks
Topic: Plot a graph of sum of neuron potentials in network?
Replies: 7
Views: 2845

Re: Plot a graph of sum of neuron potentials in network?

At present stage (testing mode) its Ok. But now I see why the NetCon mechanism is superior for large networks. Thanks a lot!
by vladimirov
Mon Aug 15, 2011 11:51 am
Forum: Modeling networks
Topic: Plot a graph of sum of neuron potentials in network?
Replies: 7
Views: 2845

Re: Plot a graph of sum of neuron potentials in network?

Thank you. I actually followed examples in your book and added a procedure update_plot() to the step() proc step(){local i if(using_cvode_){ advance() } else for i=1,nstep_steprun{ advance() } update_plot() } proc update_plot(){ sum_spiking=0 v_thresh=-40 for i=1,ncells{ if(cell[i].soma.v>=v_thresh)...
by vladimirov
Mon Aug 15, 2011 6:03 am
Forum: Modeling networks
Topic: Plot a graph of sum of neuron potentials in network?
Replies: 7
Views: 2845

Plot a graph of sum of neuron potentials in network?

Hi, I constructed a network and now try to plot its state during the simulation: e.g. how many neurons are spiking as a function of time. So, basically I have ncells=100 objectvar cell[ncells+1] ... (cell definition and connecting) For instance, I need to plot how many somas (cell .soma.v) have volt...
by vladimirov
Fri Jul 15, 2011 2:03 pm
Forum: Anatomically detailed models
Topic: Detailed pyramids based on Traub 2005 model?
Replies: 1
Views: 1256

Detailed pyramids based on Traub 2005 model?

Hello, I am new to NEURON and wonder if there are anatomically detailed models of pyramidal neurons with axons. My starting point is the model of tufted pyramidal neuron from (Traub et al, 2005. A single column thalamocortical network model), for which I have the NEURON code from the ModelDB. So, I ...