Search found 71 matches

by menica
Wed Sep 20, 2017 1:15 pm
Forum: Optimization
Topic: MRF to explore parameter space
Replies: 3
Views: 14592

Re: MRF to explore parameter space

Hi I am having some problems when I am trying to use more parameters. I want to run a simulation for every combination (in a range from 0 to 0.5) of the sodium and potassium conductances, for different values of the amplitude of the stimulating current. I can do it only changing two parameters, the ...
by menica
Thu Aug 17, 2017 2:38 pm
Forum: NEURON + Python
Topic: problems with import mod mechanism with python
Replies: 13
Views: 18597

Re: problems with import mod mechanism with python

Hi ,
I have Windows 7.

the dll file is indeed not loaded correctly:

NEURON -- VERSION 7.5 master (deea6c8) 2017-07-09
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2016
See http://neuron.yale.edu/neuron/credits

hello
oc>nrn_load_dll("nrnmech.dll")
0
oc>
by menica
Thu Aug 17, 2017 12:30 pm
Forum: NEURON + Python
Topic: problems with import mod mechanism with python
Replies: 13
Views: 18597

Re: problems with import mod mechanism with python

Hi , yest the dll file is created, and when i run hello.hoc with neuron, this is what is printed : NEURON -- VERSION 7.5 master (deea6c8) 2017-07-09 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2016 See http://neuron.yale.edu/neuron/credits hello oc> but I have still problem when I run .p...
by menica
Wed Aug 09, 2017 10:23 am
Forum: NEURON + Python
Topic: problems with import mod mechanism with python
Replies: 13
Views: 18597

Re: problems with import mod mechanism with python

Hi, I installed the new NEURON version and the "hello" is correctly printed. But I have still the same problem in inserting the mechanisms and in compiling them properly. When I use neuron with Python (downloaded with anaconda), it is able to import the gui, but I have still the same problem when I ...
by menica
Sun Aug 06, 2017 6:31 pm
Forum: NEURON + Python
Topic: problems with import mod mechanism with python
Replies: 13
Views: 18597

Re: problems with import mod mechanism with python

I tried to launch a hoc file directly from neuron with a compartment where I inserted the mechanism present in the same directory where the dll file is. On the terminal is printed: NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015 See h...
by menica
Fri Aug 04, 2017 1:41 pm
Forum: NEURON + Python
Topic: problems with import mod mechanism with python
Replies: 13
Views: 18597

Re: problems with import mod mechanism with python

I think it is not created correctly even if when I run the mknrndll it returns :
nrnmech.dll was built successfully
I tried to use the same mechanisms calling them in neuron and indeed they are not compiled well.
The path I am using is correct
by menica
Fri Aug 04, 2017 11:09 am
Forum: NEURON + Python
Topic: problems with import mod mechanism with python
Replies: 13
Views: 18597

Re: problems with import mod mechanism with python

Hi, I am typing in python
neuron.load_mechanisms('path_of_the_folder_where_mod_files_are')
and it returns as error:NEURON mechanisms not found in...
by menica
Wed Aug 02, 2017 7:34 am
Forum: NEURON + Python
Topic: problems with import mod mechanism with python
Replies: 13
Views: 18597

problems with import mod mechanism with python

Hi
I installed NEURON+python.
Now, when I compile the folder with the mod mechanisms using mknrndll, the nrnmech.dll file is created but the folder x86_64 is not created.
I think this is the reason why I cannot anymore import cell templete in hoc file from python.
Any suggestion?
Best,
Menica
by menica
Fri Jun 02, 2017 6:22 am
Forum: Modeling networks
Topic: Kuramoto model on a network with realistic cells
Replies: 0
Views: 12921

Kuramoto model on a network with realistic cells

Dear all, my goal is to construct a network of biophysical (simple) cells and connect them using the kuramoto equation in order to observe phase synchronization of neural oscillations : https://en.wikipedia.org/wiki/Kuramoto_model dtheta_{i}/dt=omega _{i}+(K/N)*sum _{j=1...N}*sin(theta _{j}-theta _{...
by menica
Mon May 08, 2017 6:10 am
Forum: Other questions
Topic: pump mechanism
Replies: 1
Views: 4930

Re: pump mechanism

Hi, I tried to step back and consider a single compartment where I inserted a Na leak current, pump Na, and Na accumulation mechanisms: Na leak: NEURON { SUFFIX ionleak USEION na READ ena,nai WRITE ina RANGE gna, ina } UNITS { (mV) = (millivolt) (mA) = (milliamp) (S) = (siemens) F = (faraday) (coulo...
by menica
Tue Apr 25, 2017 2:30 pm
Forum: Other questions
Topic: pump mechanism
Replies: 1
Views: 4930

pump mechanism

Hi, generally, in the Hodgkin-Huxley style model, the Na/K ion-pump is not explicitly modeled, instead, it is assumed that the passive conductance restores the resting membrane potential. I want to model the explicit effect that the Na/K pump has on the Na and K concentrations and then on membrane p...
by menica
Wed Apr 05, 2017 5:45 am
Forum: Other questions
Topic: wrong initialization or wrong mechanisms?
Replies: 9
Views: 5940

Re: wrong initialization or wrong mechanisms?

Thanks!
but in the Canavier model the pump is still electrogenic with the 3:2 stoichiometric ratio?
by menica
Tue Apr 04, 2017 12:22 pm
Forum: Other questions
Topic: wrong initialization or wrong mechanisms?
Replies: 9
Views: 5940

Re: wrong initialization or wrong mechanisms?

Dear Ted, could you please indicate me some examples (mod files) where the effect of the Na/K pump has been approximated with simple first order differential equations? I realized that a complex model at the moment is not what I want. I guess that when you said that in order to use an electrogenic p...
by menica
Thu Feb 09, 2017 1:09 pm
Forum: Parallel NEURON
Topic: bulletin board parallelization
Replies: 1
Views: 5442

bulletin board parallelization

Hi, I want to convert a code which performs simulations in series changing each run a parameter in a parallel simulation. I am using the ParallelContext to perform a bulletin board parallelization. Here the serial code: //after the Model set up and simulation parameters //stimulus set up: numeromax_...
by menica
Wed Oct 26, 2016 7:58 am
Forum: Optimization
Topic: Exploring parameter space
Replies: 5
Views: 7527

Re: Exploring parameter space

dear Ted, I tried with the same code (without the newgraph) to change the time between spikes (t_interp) at each run: proc batrun() { local i, gsaved gsaved = t_interp for i = 1,$1 { t_interp = i*$2 num_estim=(tstop-stim[0].del)/t_interp //re-calculate the number of stimuli accordin to the new t_int...