www.neuron.yale.edu

@urid's advice is good. The development version (on linux: pip install neuron-nightly) provides types (and thus allows type annotation) for the different types of NEURON objects; e.g.: >>> import neuron >>> neuron.__version__ '9.0a-336-g8e3de3305+' >>> from neuron import h, hoc >>> vec = h.Vector() ...

I think your hypothesis is correct: apply_async does a task in parallel with whatever happens after that, which in your case is to reset the recording vectors. as_numpy is a O(1) method because all it does is create a new data structure referring to the same memory locations as the Vector. Effective...

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?

Do any other X11 applications work?

e.g. what happens if you run "xeyes" from the terminal?

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...

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...

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...

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.

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.

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...

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...

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...

@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...

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....

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...