Search found 71 matches

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: 255

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!
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: 255

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: 291

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: 387

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: 387

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 ...
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: 291

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: 3233

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

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: 3233

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: 3233

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...
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: 3233

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.
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: 3233

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...
Tue Oct 09, 2018 12:13 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 8
Views: 3233

Where to find squid.hoc associated with hh.mod

I am learning to write my own MOD files, and I'm starting with hh.mod as a learning tool. The comment section in hh.mod says to see squid.hoc as an example of the hh mechanism's implementation...but I cannot find squid.hoc anywhere. It's not in my installation of NEURON, and I can't find it anywhere...
Thu Oct 04, 2018 11:02 pm
Forum: Specific models
Topic: Weird "trap" function in Bazhenov 2002 model
Replies: 4
Views: 1811

Re: Weird "trap" function in Bazhenov 2002 model

Fair enough, thanks. I just wanted a sanity check to make sure I wasn't missing something.
Thu Oct 04, 2018 10:42 am
Forum: Specific models
Topic: Weird "trap" function in Bazhenov 2002 model
Replies: 4
Views: 1811

Re: Weird "trap" function in Bazhenov 2002 model

Good question. I should have mentioned in my original post that yes, I have checked the source code you referenced (written in C++), and it incorporates this exact trap function. It's so bizarre that it makes the function discontinuous. I'll try emailing the authors one more time...
Wed Oct 03, 2018 11:27 am
Forum: Specific models
Topic: Weird "trap" function in Bazhenov 2002 model
Replies: 4
Views: 1811

Weird "trap" function in Bazhenov 2002 model

I am trying to code the Bazhenov 2002 sleep model in NEURON (ModelDB link: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=28189 ), and I have run across a very strange "trap" function for the fast sodium current in the cortical pyramidal cells. The details of this current are found in ...