Search found 219 matches

by ramcdougal
Mon Mar 01, 2021 3:20 pm
Forum: Reaction-diffusion in NEURON
Topic: Running pde solver more than once
Replies: 6
Views: 10905

Re: Running pde solver more than once

When you change f_rate and b_rate , NEURON interprets that as changing the model, triggering a recompilation. If instead you used an rxd.Parameter , that just changes a parameter value, requiring no change to the model. See the bottom of this example which covers both changing initial conditions and...
by ramcdougal
Mon Mar 01, 2021 2:15 pm
Forum: NEURON + Python
Topic: Update to __init__.py?
Replies: 1
Views: 18

Re: Update to __init__.py?

As this is running on your own machine, consider updating your version of NEURON. The current release is 7.8.2.

You can get it from the NEURON website or directly from GitHub at https://github.com/neuronsimulator/nrn/ ... /tag/7.8.2
by ramcdougal
Thu Feb 25, 2021 7:49 pm
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 5
Views: 43

Re: Loading a morphology as a hoc file

If you want to create a CellBuilder from a HOC morphology, you can load the HOC morphology, then open a CellBuilder, click the Management tab, then Import - top level. Confirm by clicking "go ahead and import" and then you can work with it in the CellBuilder.
by ramcdougal
Thu Feb 25, 2021 9:06 am
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 5
Views: 43

Re: Loading a morphology as a hoc file

Can you expand your comment? What do you get and how is it different from what you expected?

If there's a HOC file morphology, you can load it from the GUI or from e.g. `h.load_file("my_morphology.hoc")`
by ramcdougal
Wed Dec 30, 2020 5:24 pm
Forum: NEURON + Python
Topic: Record and fadvance instead of run
Replies: 2
Views: 216

Re: Record and fadvance instead of run

Vectors must be initialized after calling record before advancing . Your other code works with h.run() because a run is basically an h.finitialize(h.v_init) combined with an h.continuerun(h.tstop) . The solution is to declare your timeVector before the h.finitialize call, i.e. something like: timeV...
by ramcdougal
Mon Jul 20, 2020 1:34 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 716

Re: color or color_list procedures in PlotShape

Hmmm... looks like that example depends on a change introduced about a month ago... so it's available in the "pip install" version for mac/linux or the windows nightly build . (Don't try to pip install on Windows, that will give a VERY old version of NEURON.) Sorry about that. So I guess t...
by ramcdougal
Tue Jul 07, 2020 4:48 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 716

Re: color or color_list procedures in PlotShape

Unfortunately the .plot for both matplotlib and plotly (available in 8.0 development version) does not currently support the .color or .color_list values and instead always color based on the value of some variable (v, by default). (Note that you can use .mark as in the documentation to highlight sp...
by ramcdougal
Mon Jul 06, 2020 9:28 am
Forum: NEURON Announcements
Topic: How to cite NEURON
Replies: 2
Views: 27073

Re: How to cite NEURON

Thanks for pointing this out.

The old link works now too.
by ramcdougal
Mon Jun 29, 2020 12:38 pm
Forum: NEURON + Python
Topic: Error recording channel current by passing string to Vector.record
Replies: 3
Views: 601

Re: Error recording channel current by passing string to Vector.record

Python provides a standard way of using a string to grab a property, namely the getattr function. e.g. if you have a section called soma and you wanted to get a pointer to a specific variable var from the 0.5 location, you could do ptr = getattr(soma(0.5).hh, f'_ref_{var}') Similarly, a second getat...
by ramcdougal
Mon Jun 29, 2020 10:32 am
Forum: Reaction-diffusion in NEURON
Topic: rxd.plugins interface in Neuron 7.7
Replies: 2
Views: 517

Re: rxd.plugins interface in Neuron 7.7

There was a significant revamp of the internals from 7.4 to 7.7 with the intent of speeding up calculations but it likely broke anything that depended on overriding internal functions. What kind of connections do you need? callbacks at each time step? reading and writing concentrations? do you need ...
by ramcdougal
Sun Jun 07, 2020 5:46 pm
Forum: UNIX/Linux
Topic: .mod files compilation issues
Replies: 4
Views: 3467

Re: .mod files compilation issues

Why did you compile NEURON from source?

Do you get this problem if you use the version from

Code: Select all

pip install neuron
How are you compiling the mod files? The x86_64 should appear in whatever folder you run nrnivmodl from.
by ramcdougal
Sun Jun 07, 2020 5:41 pm
Forum: MSWin
Topic: Windows 10, Permission Denied
Replies: 1
Views: 2180

Re: Windows 10, Permission Denied

You can't drop onto the main menu window directly, but I believe in Windows you can drop onto the icon . Three other options: (1) Select File - load hoc, change the filter from *.hoc to *.nrm, and then load your model that way. (2) type (using the correct filename): load_file("filename.nrm"...
by ramcdougal
Mon Jun 01, 2020 1:44 pm
Forum: OS X
Topic: Syntax Warning
Replies: 1
Views: 1061

Re: Syntax Warning

This is harmless. You can ignore it. Even though you're not using Python explicitly, NEURON will connect to Python to have it available (and Python is needed to enable certain functions). What happened was there was something in the NEURON internals that did not raise a Python warning until a change...
by ramcdougal
Mon Jun 01, 2020 1:35 pm
Forum: Other questions
Topic: loop structure
Replies: 3
Views: 871

Re: loop structure

You are creating a single file because your file creation is happening once, outside of the for loop. If you look at the Python example, you'll see I'm creating a new file every time with a different filename based on the trial number (trial0.csv, trial1.csv, trial2.csv, ...) You can generate filena...
by ramcdougal
Sat May 23, 2020 12:22 pm
Forum: Other questions
Topic: loop structure
Replies: 3
Views: 871

Re: loop structure

Python, HOC, and most programming languages use a for loop to run the same code a fixed number of times. e.g. in Python, we'd write for trial in range(100): # do stuff here and in HOC, we might write: for (trial = 0; trial < 100; trial += 1) { // do stuff here } NEURON provides the h.Random (or just...