Search found 70 matches

by menica
Tue Mar 12, 2019 9:59 am
Forum: Adding new mechanisms and functions to NEURON
Topic: adding noise to input
Replies: 1
Views: 159

Re: adding noise to input

I would like to create an input signal like this: i(t) = [is(t)+in(t)]+ I would like to positive part of the sum of is(t)=A*sin(2PI(t-del)f/0.0001)+ i0 and in(t) which is the noise part, solution of: tau*noise' = -noise+sigma*sqrt(2*tau)eta(t) where eta is a gaussian distribution I wrote this code, ...
by menica
Fri Mar 08, 2019 8:43 am
Forum: Adding new mechanisms and functions to NEURON
Topic: adding noise to input
Replies: 1
Views: 159

adding noise to input

Hi, I would like to modify the IClampnoise (https://www.neuron.yale.edu/phpBB/viewtopic.php?f=16&t=2055&p=17467# ) in order to tune the frequency of the input signal. I would like to have something similar to the current generated by a sinusoidal function as i= constantAmp*cos(2*pi*(t-del)*freq*(0.0...
by menica
Tue Feb 26, 2019 9:18 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding white nose to current injection
Replies: 10
Views: 6771

Re: Adding white nose to current injection

Hi, I would like to modify the IClampnoise in order to tune the frequency of the input signal I would like to have something similar to the current generated by a sinusoidal function as i= constantAmp*cos(2*pi*(t-del)*freq*(0.001)) where I can tune freq. How can I change the amp=f0+0.5(f1-f0)(tanh((...
by menica
Thu Jul 19, 2018 10:29 am
Forum: Getting started
Topic: compare vectors pairwise
Replies: 1
Views: 593

compare vectors pairwise

Hi, I would like to calculate the area overlapping between two currents curves y1 and y2. First,I need to select the points of the intersection which are given by all the points of y2(y2<y1) and then y1(y1<y2). I tryed this: Psec1 = y1.indwhere("<=", y2) Psec2 = y2.indwhere("<=", y1) areaint = dt*Ps...
by menica
Wed Mar 28, 2018 7:10 am
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 2209

Re: parallelize nested loop

Dear Ted,
thanks for your reply.
I tested the code with a printing command at different points of the code.
the only thing I can conclude is that maybe the submit command has a maximum number of arguments that can accept as input.
by menica
Mon Mar 26, 2018 10:55 am
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 2209

Re: parallelize nested loop

Hi, I changed the code, I used the initbatpar.hoc file example and now it is working, but I realized that I can sweep until 14 parameters only, when I add the 15 one it returns the following error: 0 unpack size=320 upkpos=70 type[0]=1 datatype=0 type[1]=1 count=1 Assertion failed: file bbsmpipack.c...
by menica
Fri Mar 23, 2018 11:36 am
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 2209

Re: parallelize nested loop

I discover a small error, I should have used the " " in the pc.submit(" "). But I am still not sure if my first step to the parallelization is correct. Any help in understanding this? Here the simple code I tested: load_file("nrngui.hoc") objref pc pc = new ParallelContext(2) print "number of hosts:...
by menica
Wed Mar 21, 2018 12:16 pm
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 2209

Re: parallelize nested loop

I simplified the problem in order to learn how to parallelize step by step. I manage to run in parallel but I am struggling now in retrieving the desired output from each simulation. I created, in this case, one folder with 4 files. At the moment I am using only 2. I would like to have as output: in...
by menica
Fri Mar 16, 2018 1:21 pm
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 2209

Re: parallelize nested loop

thanks
by menica
Wed Mar 14, 2018 12:57 pm
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 2209

parallelize nested loop

Hi, I am trying to parallelize my code. The parallelization formalism is new to me. I am performing a parameter sweep on 17 parameters. For each parameter, I settled in a vector the 3 values I wanted to sweep. Here is the nested looping code I was using: proc batrun() { local i, j ,k,l,m,n, p, q, r,...
by menica
Thu Feb 22, 2018 10:33 am
Forum: Getting started
Topic: Peak duration
Replies: 3
Views: 1018

Re: Peak duration

Hi, I implemented the code in hoc: // to record spike times objref vvec, tvec, inac tvec = new Vector() tvec.record(&t) // record time vvec = new Vector() vvec.record(&soma.v(0.5)) objref ncc,spvecc,nilc soma ncc = new NetCon(&v(0.5), nilc) ncc.threshold = -20 spvecc = new Vector() ncc.record(spvecc...
by menica
Wed Feb 21, 2018 6:39 am
Forum: Getting started
Topic: Peak duration
Replies: 3
Views: 1018

Re: Peak duration

dear Ted, thanks for your reply, I tried to implement this in hoc //Determine the baseline t2= tstop j2 = tvec.indwhere(">=", t2-1) V0baseline = vvec.mean(j2-stim[0].del, j2) //find the max and the corresponding index vmax = vvecE.max(j0start, j2) vmax_index = vvecE.max_ind(j0start, j2) //Calculate ...
by menica
Fri Feb 16, 2018 11:03 am
Forum: Getting started
Topic: Peak duration
Replies: 3
Views: 1018

Peak duration

Hi, I would like to modify this code in order to save the vmax_mhw(0.5), vhalf_mhw(0.5), hw_mhw(0.5) in vectors because I would like to consider the case of multiple spikes in one simulation. COMMENT Measures peak depol and calculates spike half width from the times at which v crosses a (depolarized...
by menica
Fri Dec 15, 2017 10:00 am
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 15
Views: 7203

Re: na_ion mechanism not inserted in section axon

Dear Hines, thanks. This means that it is not possible to have access to the icl produced by the point process in mA/cm2 in the nmodl code. Maybe I should convert it in the hoc code in the post-processing. If I save the syn.icl current in a vector, then I can multiply each value by conversion factor...