Search found 29 matches

by bschneiders
Mon Apr 29, 2019 4:53 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 1474

Re: Installing Neuron on macOS Mojave

By the way, thanks to help from Robert McDougal, I do have the packaged version of 7.6 working! For anyone else who was having issues with that on a Mac, it has been updated and it fixed what was causing my seg faults.
by bschneiders
Mon Apr 29, 2019 3:53 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 1474

Re: Installing Neuron on macOS Mojave

Hmm. My xcode command line tools are Apple LLVM version 10.0.1, but my Mojave is 10.14.4, so maybe that needs to be updated. I'll see if that does it. Thanks!
by bschneiders
Tue Apr 23, 2019 3:15 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 1474

Re: Installing Neuron on macOS Mojave

Thank you. With that, I get past the make error. Then, in the make install, I first was getting this error: clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command 'g++' failed with exit status 1 I didn't see this error on the Neuron forum, but on other forums ...
by bschneiders
Mon Apr 22, 2019 12:22 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 1474

Installing Neuron on macOS Mojave

Hi, I updated to Mojave a couple months ago (unfortunately) and have not been able to get my model to run on Neuron since then. I've been using a Linux machine in the meantime, but I decided to give it a shot again on my own machine this past week - it'd be convenient to run it on my own laptop. Las...
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: 704

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: 657

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: 657

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: 937

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: 36
Views: 12548

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: 36
Views: 12548

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: 2633

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: 2633

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: 2633

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: 1512

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: 1512

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!