Search found 19 matches

by RobinDS
Sun Nov 24, 2019 8:41 am
Forum: Getting started
Topic: How to reconstruct the 3D points of a morphology imported by Import3D
Replies: 7
Views: 446

Re: How to reconstruct the 3D points of a morphology imported by Import3D

ted wrote:
Fri Nov 22, 2019 9:10 pm
Please rephrase the question. I don't quite know what you're asking.
Is a child section's 0 end xyz always the same as its parent's 1 end xyz?
by RobinDS
Sat Nov 23, 2019 7:12 pm
Forum: Other questions
Topic: Could neuron be installed on Windows/MacOS through the command line?
Replies: 2
Views: 207

Could neuron be installed on Windows/MacOS through the command line?

Is there a possibility to install NEURON in a Windows/MacOS environment that doesn't have a GUI? Specifically Travis CI.
by RobinDS
Sat Nov 23, 2019 3:43 am
Forum: SimAgent
Topic: NeuroVM
Replies: 4
Views: 1322

Re: NeuroVM

Looks good! Thanks for this
by RobinDS
Fri Nov 22, 2019 4:31 pm
Forum: Other tools
Topic: Introducing Glia & Astrocyte: A NEURON package manager
Replies: 1
Views: 197

Re: Introducing Glia & Astrocyte: A NEURON package manager

Roadmap:

[X] Setting name conflict preferences using `glia select` and `glia.select`
[ ] Local mod file management
[ ] A hosted Glia package index
by RobinDS
Fri Nov 22, 2019 4:01 pm
Forum: Getting started
Topic: How to reconstruct the 3D points of a morphology imported by Import3D
Replies: 7
Views: 446

Re: How to reconstruct the 3D points of a morphology imported by Import3D

Ok, so I can safely assume that Neuron always connects sections end-to-end? What exactly does that x value represent then?
by RobinDS
Fri Nov 22, 2019 3:37 pm
Forum: NEURON + Python
Topic: Is it possible to run nrnivmodl from python?
Replies: 4
Views: 341

Re: Is it possible to run nrnivmodl from python?

Any specific reasons why nrnivmodl would not work after running the standard Windows installer?
by RobinDS
Fri Nov 22, 2019 2:44 pm
Forum: SimAgent
Topic: NeuroVM
Replies: 4
Views: 1322

Re: NeuroVM

Will there be anyone maintaining this with new versions?
by RobinDS
Fri Nov 22, 2019 1:54 pm
Forum: Other tools
Topic: Introducing Glia & Astrocyte: A NEURON package manager
Replies: 1
Views: 197

Introducing Glia & Astrocyte: A NEURON package manager

Hi! I'd like to proudly present the very first version of Glia: a package manager for NEURON. Glia Get it with: pip install nrn-glia It allows you to install package with either pip install <package-name> or glia install <package-name> and will automatically discover and compile the mod files within...
by RobinDS
Fri Nov 22, 2019 10:32 am
Forum: NEURON + Python
Topic: Is it possible to run nrnivmodl from python?
Replies: 4
Views: 341

Re: Is it possible to run nrnivmodl from python?

Sorry for the stream of consciousness. If anyone is interested in having Python compile their mod files. Here's how I did it for windows: nrn_path = os.getenv('NEURONHOME') os.chdir(neuron_mod_path) cyg_path = nrn_path.replace(":\\","\\").replace("\\","/") process = subprocess.Popen([ os.path.join(n...
by RobinDS
Fri Nov 22, 2019 10:06 am
Forum: NEURON + Python
Topic: Is it possible to run nrnivmodl from python?
Replies: 4
Views: 341

Re: Is it possible to run nrnivmodl from python?

These have been my shell attempts just to get a proof of concept going on my computer (hence the hardcoded directories) Using nrniv.exe process = subprocess.Popen(["C:\\nrn\\bin\\nrniv.exe", "-nopython", "c:/nrn/lib/hoc/mknrndll.hoc", neuron_mod_path], stdin=subprocess.PIPE, stdout=subprocess.PIPE, ...
by RobinDS
Fri Nov 22, 2019 9:38 am
Forum: NEURON + Python
Topic: Is it possible to run nrnivmodl from python?
Replies: 4
Views: 341

Is it possible to run nrnivmodl from python?

I'm making a package manager for NEURON called Glia, have a look here https://pypi.org/project/nrn-glia/. I'd like a platform independent way of compiling a set of folders, similar to how `nrnivmodl folder1 folder2 folder3` would work. Can I somehow import this from the neuron package and run in the...
by RobinDS
Thu Nov 21, 2019 11:30 am
Forum: NEURON hacks
Topic: NMODL file in different folder
Replies: 9
Views: 2315

Re: NMODL file in different folder

These are software deployment basics, but thanks for the heads up. libnrnmech.so inside of the hidden .libs folder does the trick
by RobinDS
Wed Nov 20, 2019 7:02 pm
Forum: Getting started
Topic: How to reconstruct the 3D points of a morphology imported by Import3D
Replies: 7
Views: 446

Re: How to reconstruct the 3D points of a morphology imported by Import3D

Sorry, by referring to the NEURON concepts and more general abstract concepts with the same words I've created a semantic mess. But the question is moot, I've solved the issue. One small question: If a section.parentseg().x = 0.5 and parent_section.n3d = 21, does that mean that section is connected ...
by RobinDS
Wed Nov 20, 2019 3:35 pm
Forum: NEURON hacks
Topic: NMODL file in different folder
Replies: 9
Views: 2315

Re: NMODL file in different folder

On Linux it generates a folder x86_64 and a file called a.out. How would I go about loading that?

The documentation mentions that nrn_load_dll works for Linux, but I don't see a dll file?
by RobinDS
Wed Nov 20, 2019 3:30 pm
Forum: UNIX/Linux
Topic: nrnivmodl missing -lX11
Replies: 1
Views: 219

Re: nrnivmodl missing -lX11

In my case it was because ld was unable to locate the libX11. If you run into a similar problem here's how to resolve it: [*] Check if you have the library or its dev variant installed, for -lX11, libX11 version 6, libx11-6 should be installed [*] Check ld in verbose mode ( ld -lX11 --verbose ) to s...