Search found 267 matches
- Tue Feb 20, 2024 3:33 pm
- Forum: OS X
- Topic: can't open DISPLAY
- Replies: 14
- Views: 2136
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?
- Tue Feb 20, 2024 12:23 pm
- Forum: OS X
- Topic: can't open DISPLAY
- Replies: 14
- Views: 2136
Re: can't open DISPLAY
Do any other X11 applications work?
e.g. what happens if you run "xeyes" from the terminal?
e.g. what happens if you run "xeyes" from the terminal?
- Fri Oct 27, 2023 11:11 am
- Forum: Employment and educational opportunities
- Topic: Postdoctoral position in computational neuroscience methods (NEURON simulator)
- Replies: 0
- Views: 200332
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...
- Sun Oct 01, 2023 2:01 pm
- Forum: NEURON + Python
- Topic: Different total area from python and hoc cell class
- Replies: 5
- Views: 13172
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...
- 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: 15171
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...
- 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: 17465
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.
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.
- Tue Aug 22, 2023 6:44 pm
- Forum: MSWin
- Topic: MSWin11 + Anaconda, Neuron 8.2.2
- Replies: 6
- Views: 19425
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.
Bash is historically more of a linux/mac thing.
- 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: 18284
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...
- Fri Jul 28, 2023 10:43 am
- Forum: NEURON + Python
- Topic: Play a Unique Vector to Each Model Segment
- Replies: 1
- Views: 13662
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...
- Thu Jun 29, 2023 3:02 pm
- Forum: NEURON + Python
- Topic: Gap junction network not seeming to conduct
- Replies: 3
- Views: 15091
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...
- 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: 14103
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...
- Thu Jun 29, 2023 10:54 am
- Forum: NEURON + Python
- Topic: h.continuerun() behavior different when cvode is active
- Replies: 2
- Views: 14296
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....
- Thu Jun 29, 2023 10:39 am
- Forum: NEURON + Python
- Topic: Unable to access current attribute.
- Replies: 1
- Views: 13572
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...
- Thu Jun 01, 2023 10:13 pm
- Forum: NEURON + Python
- Topic: ModelView and ModuleNotFoundError: No module named 'numpy'
- Replies: 7
- Views: 17883
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...
- Thu Jun 01, 2023 9:59 pm
- Forum: Parallel NEURON
- Topic: Thread-safe non-voltage POINTER variables
- Replies: 4
- Views: 16486
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...