Search found 34 matches

by bschneiders
Thu Jun 07, 2018 6:02 pm
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 3188

Re: Different species parameters for different regions

Ok, I actually had to table that question (I have a workaround for a conference next week) but will definitely readdress it after to figure out if its my code or a more general neuron issue. However, I have yet another related follow up question. Given that my spines are quite small, I have seen som...
by bschneiders
Mon Jun 04, 2018 10:41 am
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 3188

Re: Different species parameters for different regions

A quick update: I tried splitting the Multi-Compartment Reaction into two separate ones so that I could use custom dynamics: ERin = rxd.MultiCompartmentReaction(ca[cyt]>ca[er],Jer_in,membrane=cyt_er_membrane,custom_dynamics=True) ERout = rxd.MultiCompartmentReaction(ca[cyt]<ca[er],Jer_out,membrane=c...
by bschneiders
Sat Jun 02, 2018 12:07 pm
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 3188

Re: Different species parameters for different regions

I have a follow up question to this. I am trying to initialize different calcium concentrations in different RxD regions (i.e. "cyt" and "er" as opposed to different neuron sections). I am following Neymotin et. al to do so ("Neuronal dendrite calcium wave model", 2015) as follows: cyt = rxd.Region(...
by bschneiders
Thu Apr 12, 2018 12:46 pm
Forum: Reaction-diffusion in NEURON
Topic: Radial diffusion using RxD?
Replies: 2
Views: 1813

Re: Radial diffusion using RxD?

Yes, nested shells would be awesome! I can get away with a single outer shell for now, as concentrations in that shell are what I'm most interested in, but nested shells would definitely be of interest and very useful. Thanks!
by bschneiders
Tue Apr 10, 2018 12:33 pm
Forum: Reaction-diffusion in NEURON
Topic: Radial diffusion using RxD?
Replies: 2
Views: 1813

Radial diffusion using RxD?

Is it possible to use the built-in RxD shells to support radial diffusion? I have only seen an RxD shell used as a membrane, and was wondering if they can also be used as segments of a section (i.e. multiple shells of a soma) as well.
Thanks!
by bschneiders
Thu Feb 15, 2018 7:03 pm
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 3188

Re: Different species parameters for different regions

On a completely unrelated note (and I'm only posting this because Rob told me to post about it to keep the issue relevant...), are you closer to making RxD such that you don't have to restart Python every time you change an RxD-related parameter? That would be awesome!
by bschneiders
Thu Feb 15, 2018 1:18 pm
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 3188

Different species parameters for different regions

What is the simplest way to allow a species to have different initial concentrations in different regions? Do I need to make two different "sub-species"? For example, I am working with a buffer "buf" that has a higher buffering capacity in the dendrites than in spines. I want to try having either a ...
by bschneiders
Fri Jan 26, 2018 2:17 pm
Forum: NEURON + Python
Topic: xpanel between python and hoc
Replies: 3
Views: 1986

Re: xpanel between python and hoc

Great - I just sent a toy model. Thank you!

Meanwhile I will look into your suggestions. One of the reasons I've been using python is to use the RxD module, but I'll look into making the morphology in hoc instead, and just using python for the RxD related parts.
by bschneiders
Wed Jan 24, 2018 12:34 pm
Forum: NEURON + Python
Topic: xpanel between python and hoc
Replies: 3
Views: 1986

xpanel between python and hoc

I made an xpanel for my model so that I can demo it for my collaborators. I found the translation between Python and hoc not so smooth though so I wanted to see if I was missing something. It seemed like all I would need to do is use "h.xvalue" to update constants, and then have my own initializatio...
by bschneiders
Mon Sep 25, 2017 1:53 pm
Forum: Other questions
Topic: Recording *current through a channel (mechanism)
Replies: 4
Views: 9173

Re: Recording *current through a channel (mechanism)

For anyone with similar questions - the issue was that I wasn't specifying the location along the section (as you would when referencing, say, the voltage). The following code does the job:

Code: Select all

icacar = neuron.h.Vector()
icacar.record(spinehead(.5)._ref_i_car)
by bschneiders
Sun Sep 17, 2017 6:23 pm
Forum: Other questions
Topic: Recording *current through a channel (mechanism)
Replies: 4
Views: 9173

Re: Recording *current through a channel (mechanism)

I have a follow up question. I can access the current at a given time now without a problem with: ica_car = spinehead.i_car However, I am still having trouble with the recording part. I suspect this is because the variable I reference is already specific to a section? But I am not sure. I am trying ...
by bschneiders
Thu Sep 14, 2017 5:00 pm
Forum: Other questions
Topic: Recording *current through a channel (mechanism)
Replies: 4
Views: 9173

Re: Recording *current through a channel (mechanism)

Ted, thank you for your quick reply. I did mean current (from which I'm ultimately calculating concentration, hence my slip up).

This is very helpful - I will try the (safer) second method you mentioned. And thanks for the reference at the end as well.
by bschneiders
Thu Sep 14, 2017 11:41 am
Forum: Other questions
Topic: Recording *current through a channel (mechanism)
Replies: 4
Views: 9173

Recording *current through a channel (mechanism)

Is there a way to record the charge* of an ion that flows through a channel defined as a mechanism? I am trying to record the calcium current that enters a spinehead through a calcium channel. I am doing the same for an NMDA channel, which is simple enough since it is a point process: ica_nmda = neu...
by bschneiders
Wed Apr 19, 2017 12:25 pm
Forum: Reaction-diffusion in NEURON
Topic: Absolute tolerance scale in RxD
Replies: 1
Views: 8738

Absolute tolerance scale in RxD

I have been getting numerical errors when simulating my model in RxD, and I think they are due to scaling within CVode. I've seen how to use the absolute tolerance scale multiplier for species specified in MOD files ( https://www.neuron.yale.edu/neuron/static/new_doc/simctrl/cvode.html#CVode.atolsca...