Search found 89 matches

by pascal
Tue Jun 23, 2020 1:43 pm
Forum: Other questions
Topic: vector.play memory efficiency
Replies: 4
Views: 159

Re: vector.play memory efficiency

Here is the mod file Ted recommended for implementing vector.play in a memory-efficient way: COMMENT VecSyn, a "synaptic mechanism" whose conductance is driven by Vector.play. Actual synaptic conductance is gs. gs is the product of a scale factor k and gnorm, where gnorm is in microsiemens and its v...
by pascal
Wed Jun 17, 2020 6:57 pm
Forum: Other questions
Topic: vector.play memory efficiency
Replies: 4
Views: 159

Re: vector.play memory efficiency

The first option: a sampled time course of synaptic conductance.
by pascal
Wed Jun 17, 2020 2:04 pm
Forum: Other questions
Topic: vector.play memory efficiency
Replies: 4
Views: 159

vector.play memory efficiency

I have a simulation where I need to play hundreds of vectors into synaptic conductances. These vectors are all just scaled versions of one another. Here is an outline of the code: signal=np.loadtxt(#some txt file that defines trace for synapses gmax) syn_gmax_vec=h.Vector(signal) syn_veclist = [] fo...
by pascal
Wed Apr 08, 2020 3:18 pm
Forum: Modeling networks
Topic: Local Field Potentials
Replies: 4
Views: 6153

Re: Local Field Potentials

Also, here is a previous thread with code for a minimal working model to calculate the LFP:
viewtopic.php?f=8&t=3656&p=15713#p15713
by pascal
Sun Apr 05, 2020 2:00 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 961

Re: Incorporating a firing model to induce different stages of sleep

Okay, now I'm attempting to incorporate my firing rate model within a toy parallel network model. I started with the parallel ring network outlined here: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=12&t=4270 I then added a dummy section (for the firing rate model) to the 0th host. In general, ...
by pascal
Fri Mar 27, 2020 10:41 pm
Forum: Modeling networks
Topic: Minimal parallel ring network
Replies: 2
Views: 442

Re: Minimal parallel ring network

Never mind, I found my stupid mistake: I forgot to connect the dendrite to the soma. I was tempted to take this post down to save the embarrassment, but I figured I'd leave it up for posterity (since I couldn't find the code for this Python parallelized ring network anywhere online). Here's the work...
by pascal
Fri Mar 27, 2020 6:14 pm
Forum: Modeling networks
Topic: Minimal parallel ring network
Replies: 2
Views: 442

Minimal parallel ring network

I'm trying to implement the code for a minimal parallel ring network, from the 2019 NEURON Course (I could not find the code anywhere online, so I adapted it from the course book). When I run the program (in serial, for now), for some reason the code to stimulate the 0th cell has no effect. When I p...
by pascal
Sun Mar 15, 2020 7:03 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 961

Re: Incorporating a firing model to induce different stages of sleep

Perfect, thanks Robert. I see that your solution is exactly what I used before in the LinearMechanism implementation, but I thought it worked then only because I was passing a vector as the argument (i.e., I didn't realize that was the general way to dereference a pointer). Thanks again, and here's ...
by pascal
Wed Mar 11, 2020 4:27 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 961

Re: Incorporating a firing model to induce different stages of sleep

I decided to try to implement the program I last posted using mod files, rather than LinearMechanism. I almost have it, except for an issue with the callback function similar to what I encountered a few posts ago. When I define the runtime_callback (to be used by extra_scatter_gather), I want to sen...
by pascal
Wed Mar 04, 2020 12:53 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 961

Re: Incorporating a firing model to induce different stages of sleep

Ah, got it. The solution is to pass the vector 'y' to gnabar_callback, then access the 0th element within the function itself. The way I was doing it before, I was essentially just passing a constant value to gnabar_callback. Here's the updated code: from neuron import h from neuron.units import ms ...
by pascal
Tue Mar 03, 2020 1:32 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 961

Re: Incorporating a firing model to induce different stages of sleep

Okay, thanks for the replies. I understand better what's going on with LinearMechanism now. I took the toy model from a few replies ago, and I'm trying to tweak it by adding an HH soma and having a dialogue between it and the firing rate model. I added a callback to LinearMechanism that gives the FR...
by pascal
Mon Mar 02, 2020 12:50 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 961

Re: Incorporating a firing model to induce different stages of sleep

The LinearMechanism class looks very appealing, but I want to make sure I thoroughly understand it. A few questions: 1. I noticed in the documentation for LinearMechanism, there is the following warning: "Does not work with the CVODE integrator but does work with the differential-algebraic solver ID...
by pascal
Fri Feb 28, 2020 4:04 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 961

Re: Incorporating a firing model to induce different stages of sleep

Thank you both very much! That will certainly get me started.
by pascal
Thu Feb 27, 2020 7:33 pm
Forum: Modeling networks
Topic: Incorporating a firing model to induce different stages of sleep
Replies: 14
Views: 961

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 conductances a...
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: 562

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.