Search found 71 matches

Thu May 23, 2019 10:53 am
Forum: Hot tips
Topic: conversion units
Replies: 5
Views: 1293

conversion units

Hi, if I want to convert the current density INA [mA/cm2] in nA I should divide the current in mA/cm2 by the factor (area*(0.01)): INA/(area*(0.01)) if I want to convert the quantity X [mM/ms] in nA I should multiply by the FARADAY constant expressed in C/mol, by 10(numenbr of electrons in the Na+ )...
Tue Mar 12, 2019 9:59 am
Forum: Adding new mechanisms and functions to NEURON
Topic: adding noise to input
Replies: 1
Views: 520

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, ...
Fri Mar 08, 2019 8:43 am
Forum: Adding new mechanisms and functions to NEURON
Topic: adding noise to input
Replies: 1
Views: 520

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...
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: 8975

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((...
Thu Jul 19, 2018 10:29 am
Forum: Getting started
Topic: compare vectors pairwise
Replies: 1
Views: 957

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...
Wed Mar 28, 2018 7:10 am
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 3011

Re: parallelize nested loop

Dear Ted,
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.
Mon Mar 26, 2018 10:55 am
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 3011

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=1 datatype=0 type=1 count=1 Assertion failed: file bbsmpipack.c...
Fri Mar 23, 2018 11:36 am
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 3011

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:...
Wed Mar 21, 2018 12:16 pm
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 3011

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...
Fri Mar 16, 2018 1:21 pm
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 3011

Re: parallelize nested loop

thanks
Wed Mar 14, 2018 12:57 pm
Forum: Parallel NEURON
Topic: parallelize nested loop
Replies: 7
Views: 3011

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,...
Thu Feb 22, 2018 10:33 am
Forum: Getting started
Topic: Peak duration
Replies: 3
Views: 1597

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...
Wed Feb 21, 2018 6:39 am
Forum: Getting started
Topic: Peak duration
Replies: 3
Views: 1597

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.del, j2) //find the max and the corresponding index vmax = vvecE.max(j0start, j2) vmax_index = vvecE.max_ind(j0start, j2) //Calculate ...
Fri Feb 16, 2018 11:03 am
Forum: Getting started
Topic: Peak duration
Replies: 3
Views: 1597

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...
Tue Dec 19, 2017 9:59 am
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 15
Views: 8568

Thanks!!! :)