Search found 75 matches

by pascal
Thu Dec 05, 2019 1:03 am
Forum: Other questions
Topic: Computing LFP with use_fast_imem and extra_scatter_gather
Replies: 1
Views: 44

Re: Computing LFP with use_fast_imem and extra_scatter_gather

Never mind, I figured out the problem...I only printed out the LFP trace to three decimal places, and apparently the signal was so small that it required greater precision to see the fluctuations. Everything is working as it should.
by pascal
Wed Dec 04, 2019 2:51 pm
Forum: Other questions
Topic: Computing LFP with use_fast_imem and extra_scatter_gather
Replies: 1
Views: 44

Computing LFP with use_fast_imem and extra_scatter_gather

I have successfully implemented computation of the LFP in a previous network model using cvode.use_fast_imem and cvode.extra_scatter_gather (see https://www.neuron.yale.edu/phpbb/viewtopic.php?f=8&t=3656&p=15713&hilit=use_fast_imem+1#p15713 ) I am trying to use this same approach in a new network mo...
by pascal
Fri Oct 11, 2019 7:34 pm
Forum: Parallel NEURON
Topic: MPI simulation hangs
Replies: 1
Views: 746

Re: MPI simulation hangs

Upon further investigation, this appears to be an installation problem. I ran the exact same code on a different computer, and it had no issues running in parallel, completing the simulation perfectly (and giving identical results to a serial simulation). Both computers were running Windows 10, and ...
by pascal
Fri Oct 11, 2019 6:09 pm
Forum: Parallel NEURON
Topic: MPI simulation hangs
Replies: 1
Views: 746

MPI simulation hangs

I have a network simulation that runs just fine in serial, and it used to also work in parallel until I re-organized the code a bit (placing different classes in different files, and wrapping the code to actually run the simulation in its own function). The simulation periodically dumps data to file...
by pascal
Fri Jul 12, 2019 12:23 pm
Forum: NEURON + Python
Topic: Using FInitializeHandler to set initial voltages for a subset of cells
Replies: 2
Views: 640

Re: Using FInitializeHandler to set initial voltages for a subset of cells

Oh silly me, I need to use

pc.gid2cell(re_gid).soma.v=-61

Thanks Ted!
by pascal
Thu Jul 11, 2019 7:24 pm
Forum: NEURON + Python
Topic: Using FInitializeHandler to set initial voltages for a subset of cells
Replies: 2
Views: 640

Using FInitializeHandler to set initial voltages for a subset of cells

I am running a simulation in which I want all cells to be initialized to -68 mV, except for a subset of cells (RE cells), which I want to start at -61 mV. I've tried this code (where 'pc' is a ParallelContext object): def set_RE_voltages(): for re_gid in net.re_gidList: pc.gid2cell(re_gid).v=-61 if(...
by pascal
Thu May 30, 2019 6:09 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ion_style() to treat eca as a fixed parameter and cai as a dynamical variable
Replies: 2
Views: 648

Re: Using ion_style() to treat eca as a fixed parameter and cai as a dynamical variable

Okay, here’s what I put together: from __future__ import division from neuron import h, gui import matplotlib.pyplot as plt import numpy as np soma=h.Section(name='soma') #create object 'soma,' and make object variable 'name' equal to 'soma' soma.diam = soma.L = np.sqrt(100/np.pi) soma.cm = 1.0 soma...
by pascal
Wed May 29, 2019 7:21 pm
Forum: Specific models
Topic: Destexhe kinetic scheme for I_h
Replies: 2
Views: 764

Re: Destexhe kinetic scheme for I_h

Ah, that all makes perfect sense! Thanks!
by pascal
Wed May 29, 2019 5:55 pm
Forum: Specific models
Topic: Destexhe kinetic scheme for I_h
Replies: 2
Views: 764

Destexhe kinetic scheme for I_h

I am trying to use the thalamocortical cell from the paper "Ionic mechanisms underlying synchronized oscillations and propagating waves in a model of ferret thalamic slices" (1996). The model code can be found here: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3343#tabs-2 I have run ...
by pascal
Wed May 29, 2019 2:32 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ion_style() to treat eca as a fixed parameter and cai as a dynamical variable
Replies: 2
Views: 648

Using ion_style() to treat eca as a fixed parameter and cai as a dynamical variable

I am porting Bazhenov's 2002 thalamocortical model of sleep-wake transitions ( https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=28189#tabs-1 ) to NEURON. The model has a calcium current, as well as a calcium-dependent K+ current. As far as I can tell (I am trying to get the authors to re...
by pascal
Mon May 20, 2019 1:08 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 8
Views: 3861

Re: Where to find squid.hoc associated with hh.mod

Right, I get that the squid.hoc file I found was wrong, but I'm talking about the following hh.mod file (which I got from the NEURON 7.4 source code): TITLE hh.mod squid sodium, potassium, and leak channels COMMENT This is the original Hodgkin-Huxley treatment for the set of sodium, potassium, and l...
by pascal
Thu May 09, 2019 1:49 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 8
Views: 3861

Re: Where to find squid.hoc associated with hh.mod

Okay, I think I am getting a handle on ionic mechanisms in mod files. Those two links were very helpful. I still have a few questions: 1) When writing mod files for custom ionic currents, is there ever a situation where I would not want to include "THREADSAFE" within the NEURON block? 2) I noticed t...
by pascal
Wed Oct 10, 2018 11:04 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 8
Views: 3861

Re: Where to find squid.hoc associated with hh.mod

Thanks for the resources, Ted. I'll read through them and get back to you if I have any more questions.
by pascal
Tue Oct 09, 2018 5:43 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 8
Views: 3861

Re: Where to find squid.hoc associated with hh.mod

Okay, I believe I found it here: https://github.com/neurodroid/neurodroid/blob/master/nrn/squid.hoc Here is the code: /* Squid giant axon ap */ load_file("stdrun.hoc") /* Print v at every time step */ proc advance() { fadvance() print "ND ", v } create axon access axon insert hh gnabar_hh = gna gkba...