Search found 25 matches

by bschneiders
Fri Mar 01, 2019 9:48 am
Forum: Reaction-diffusion in NEURON
Topic: USEION in mod files for RxD species I created
Replies: 3
Views: 192

USEION in mod files for RxD species I created

Hi, I am trying to keep track of the maximum value of several concentrations using mod files (so that I don't have to record in a bunch of locations). This worked really well for calcium, but the same syntax doesn't work for species that I created with RxD. Here is what worked for calcium: NEURON { ...
by bschneiders
Fri Jan 18, 2019 3:08 pm
Forum: Reaction-diffusion in NEURON
Topic: updating Species and Rates inputs
Replies: 2
Views: 280

Re: updating Species and Rates inputs

Thank you, I will try that!
by bschneiders
Wed Jan 16, 2019 2:41 pm
Forum: Reaction-diffusion in NEURON
Topic: updating Species and Rates inputs
Replies: 2
Views: 280

updating Species and Rates inputs

Hi, I have a question about updating rxd.Species inputs. Up until now, I simply restart python when I need to update initial concentrations, etc. However, I'm now running scripts to rapidly run through parameter values, and it would be very convenient not to exit Python between runs. First of all, l...
by bschneiders
Tue Nov 27, 2018 12:48 pm
Forum: OS X
Topic: Segmentation fault with alpha version of 7.6
Replies: 0
Views: 550

Segmentation fault with alpha version of 7.6

Hi, I am wondering if I can get help with a segmentation fault when I run the new Neuron 7.6. I updated to Mojave, and therefore downloaded the alpha version of Neuron 7.6. I got past the issues from the installation forum page and have it running, but my model only works sometimes . I often get a s...
by bschneiders
Thu Nov 15, 2018 5:42 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 35
Views: 8113

Re: Installation problem Neuron

I ended up getting mine to work. I did the following: -added the same 3 flags mentioned by aaronmil to my bash_profile -deleted Neuron again and built it from source code -used the configure option --with-readline=no -did the following step after "make after_install" to make sure python and neuron c...
by bschneiders
Wed Nov 14, 2018 9:45 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 35
Views: 8113

Re: Installation problem Neuron

Hi all, I'm getting a similar issue. I updated to Mojave, and got the "ImportError: No module named hoc27" error when I tried to run Neuron again. Per this forum topic, I uninstalled anaconda, deleted Neuron 7.5, and then reinstalled anaconda 2.7 and downloaded Neuron 7.6. I updated Xcode, autoconf,...
by bschneiders
Thu Jun 07, 2018 6:02 pm
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 1860

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: 1860

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: 1860

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: 1055

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: 1055

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: 1860

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: 1860

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: 1154

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.