Search found 267 matches

by ramcdougal
Tue Feb 20, 2024 3:33 pm
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 9956

Re: can't open DISPLAY

I'm not saying you should do this, but just to double-check, do NEURON's graphics work when NEURON is launched from an xterminal?
by ramcdougal
Tue Feb 20, 2024 12:23 pm
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 9956

Re: can't open DISPLAY

Do any other X11 applications work?

e.g. what happens if you run "xeyes" from the terminal?
by ramcdougal
Fri Oct 27, 2023 11:11 am
Forum: Employment and educational opportunities
Topic: Postdoctoral position in computational neuroscience methods (NEURON simulator)
Replies: 0
Views: 237814

Postdoctoral position in computational neuroscience methods (NEURON simulator)

The McDougal lab at Yale University seeks one or two highly motivated Postdoctoral Associates to advance the frontiers of neuroscience simulation. In addition to papers, etc, this work will be shared with the community in the form of enhancements to the NEURON simulator. Related lab projects include...
by ramcdougal
Sun Oct 01, 2023 2:01 pm
Forum: NEURON + Python
Topic: Different total area from python and hoc cell class
Replies: 5
Views: 20030

Re: Different total area from python and hoc cell class

tl;dr: a difference of this magnitude is expected and should not meaningfully change your results. The Python version is ever so slightly more accurate. There is a subtle difference in the implementation between HOC and Python that can create these tiny differences (here less than 0.001 µm^2): In HO...
by ramcdougal
Sun Sep 03, 2023 4:36 pm
Forum: Anatomically detailed models
Topic: Voltage gradient and color scale in anatomically detailed model in Python
Replies: 1
Views: 21701

Re: Voltage gradient and color scale in anatomically detailed model in Python

The trick here is that calling ps.plot(plotly) returns a go.Figure. And then anything you can do with regular plotly graphs, you can do with that... I don't particularly like the below solution, but one way is to create a hidden 2D graph that has a colorbar: A full, working example is at: https://co...
by ramcdougal
Sun Sep 03, 2023 3:48 pm
Forum: Reaction-diffusion in NEURON
Topic: Setting ion specifications in rxd leads to region overlap error
Replies: 2
Views: 23977

Re: Setting ion specifications in rxd leads to region overlap error

Perhaps there was a Python session where code was ran and then those lines were reran in the same session?

If you run as a script or just restart your session everything should just work.

For parameter sweeps, the model doesn't need to be redefined each time, only the parameter needs to be changed.
by ramcdougal
Tue Aug 22, 2023 6:44 pm
Forum: MSWin
Topic: MSWin11 + Anaconda, Neuron 8.2.2
Replies: 6
Views: 26381

Re: MSWin11 + Anaconda, Neuron 8.2.2

For what it's worth, I always use a regular windows terminal (cmd) and not bash on Windows.

Bash is historically more of a linux/mac thing.
by ramcdougal
Mon Aug 07, 2023 5:28 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL code no longer works in version 8.2
Replies: 7
Views: 25364

Re: NMODL code no longer works in version 8.2

I think the main issue you're running into here is that NEURON is trying to be too helpful. You're getting a bunch of "conflicting types" errors because some things are now available directly to NMODL without needing a VERBATIM declaration. What happens if you simply remove the three exter...
by ramcdougal
Fri Jul 28, 2023 10:43 am
Forum: NEURON + Python
Topic: Play a Unique Vector to Each Model Segment
Replies: 1
Views: 20412

Re: Play a Unique Vector to Each Model Segment

Whenever recording a variable or playing into a variable, you must use a pointer ; that is, play into seg.playtest._ref_xx not into .xx . To store different values of xx at different locations, you must declare xx as a RANGE. (If you use GLOBAL, it is the same at all locations.) (POINTERs do not loc...
by ramcdougal
Thu Jun 29, 2023 3:02 pm
Forum: NEURON + Python
Topic: Gap junction network not seeming to conduct
Replies: 3
Views: 21936

Re: Gap junction network not seeming to conduct

Note that vgap in your mod file is supposed to be the voltage of the OTHER half of the gap junction... but here, all the fromCenters are on cones[0] and the other side is also set to be cones[0], so your vgap and v are the same, hence no current flow. Likewise for toCenter. That is, change it to: ga...
by ramcdougal
Thu Jun 29, 2023 11:05 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NameError: Name Not Defined for Distributed Mechanism
Replies: 3
Views: 18078

Re: NameError: Name Not Defined for Distributed Mechanism

@AMaxion's approach works, but for the record, the original was also correct except that it was missing a leading h. . That is, you can do any of the following: h.mathews_KLVA.insert(axon) axon.insert(h.mathews_KLVA) axon.insert('mathews_KLVA') Personally, I like the first one because you can insert...
by ramcdougal
Thu Jun 29, 2023 10:54 am
Forum: NEURON + Python
Topic: h.continuerun() behavior different when cvode is active
Replies: 2
Views: 20945

Re: h.continuerun() behavior different when cvode is active

Anytime you change something in a CVode simulation after initialization, you must run: h.CVode().re_init() to let CVode know. This is true for both time and state variables. from neuron import h h.load_file("stdrun.hoc") soma = h.Section("soma") t = h.Vector().record(h._ref_t) h....
by ramcdougal
Thu Jun 29, 2023 10:39 am
Forum: NEURON + Python
Topic: Unable to access current attribute.
Replies: 1
Views: 20372

Re: Unable to access current attribute.

Double check that the na12 mechanism was inserted in that section. (You can test with e.g. h.cell.soma[0].psection() ) Assuming it has been inserted, then you should be able to access it via either h.cell.soma[0](0.5).na12.ina_ina or h.cell.soma[0]soma(0.5).ina_ina_na12 . I prefer the first way beca...
by ramcdougal
Thu Jun 01, 2023 10:13 pm
Forum: NEURON + Python
Topic: ModelView and ModuleNotFoundError: No module named 'numpy'
Replies: 7
Views: 25114

Re: ModelView and ModuleNotFoundError: No module named 'numpy'

A follow up question: how did you install NEURON? From the paths, it looks like you ran in macOS. Doing a "pip install neuron" is supposed to handle all the dependencies, including numpy. (This works for linux and macOS, but unfortunately we don't support pip on Windows.) I believe the und...
by ramcdougal
Thu Jun 01, 2023 9:59 pm
Forum: Parallel NEURON
Topic: Thread-safe non-voltage POINTER variables
Replies: 4
Views: 20319

Re: Thread-safe non-voltage POINTER variables

I'm not sure if I understand enough of what's happening to be able to say if NEURON's rxd mechanism would be useful... ... but you may want to check out the MOD file in Figure 13 of doi:10.3389/fninf.2022.847108 and the surrounding discussion. There we have a synapse that receives event-driven input...