Search found 106 matches
- Thu Feb 27, 2020 7:33 pm
- Forum: Modeling networks
- Topic: Incorporating a firing model to induce different stages of sleep
- Replies: 14
- Views: 17737
Incorporating a firing model to induce different stages of sleep
I am developing a thalamocortical network model of sleep. Currently, various cortical ionic conductances (e.g. potassium currents) are altered by a "hand of God" that sets them to different values to induce different stages of sleep. I would like to develop the model so that the ionic cond...
- Thu Dec 05, 2019 1:03 am
- Forum: Other questions
- Topic: Computing LFP with use_fast_imem and extra_scatter_gather
- Replies: 1
- Views: 2558
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.
- Wed Dec 04, 2019 2:51 pm
- Forum: Other questions
- Topic: Computing LFP with use_fast_imem and extra_scatter_gather
- Replies: 1
- Views: 2558
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 ne...
- Fri Oct 11, 2019 7:34 pm
- Forum: Parallel NEURON
- Topic: MPI simulation hangs
- Replies: 1
- Views: 7595
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 ...
- Fri Oct 11, 2019 6:09 pm
- Forum: Parallel NEURON
- Topic: MPI simulation hangs
- Replies: 1
- Views: 7595
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...
- 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: 1929
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!
pc.gid2cell(re_gid).soma.v=-61
Thanks Ted!
- 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: 1929
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(...
- 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: 3110
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...
- Wed May 29, 2019 7:21 pm
- Forum: Specific models
- Topic: Destexhe kinetic scheme for I_h
- Replies: 2
- Views: 14639
Re: Destexhe kinetic scheme for I_h
Ah, that all makes perfect sense! Thanks!
- Wed May 29, 2019 5:55 pm
- Forum: Specific models
- Topic: Destexhe kinetic scheme for I_h
- Replies: 2
- Views: 14639
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...
- 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: 3110
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...
- Fri May 24, 2019 12:47 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Where to find squid.hoc associated with hh.mod
- Replies: 8
- Views: 9110
Re: Where to find squid.hoc associated with hh.mod
Thanks, Ted, that's very helpful.
- 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: 9110
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...
- 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: 9110
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...
- 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: 9110
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.