www.neuron.yale.edu

Sorry for the long lapse, but things have been unusually busy here for the past few weeks. A 1981 reference is pretty ancient; experimental methods have improved considerably since then. However, it's a good starting point. See if you can find a publication that cited it, reports relevant experiment...

Thanks. As you so concisely stated in that issue

numpy should not be required for users only using HOC with no reaction-diffusion.

But the record for 2nd simulation, i.e. variables"soma_v_2" and "t_2" return nothing. I didn't tell you to do this # record for 2nd simulation soma_v_2 = h.Vector().record(my_cell.soma(0.5)._ref_v) t_2 = h.Vector().record(h._ref_t) did I? Omit those two statements, and at the en...

Easy. Launch the first simulation. After that stops, make whatever parameter changes you like. Then execute if (cvode.active()) { cvode.re_init() } else { fcurrent() } or, if you prefer to use Python, execute the equivalent Python statements, which should be something like if (h.cvode.active()==TRUE...

See
Using events to implement parameter changes during a run
in the Hot tips area of the Forum.

Yes, that example is written in hoc, but it's very simple, and by referring to NEURON's Python documentation at nrn.readthedocs.io I'm sure you'll be able to figure out what to do.

Actually no apologies are necessary. You ran into an instance of something that should never happen: a booby trap dependency, and worse, it looks like a gratuitous dependency (one that shouldn't exist in the first place because it is unnecessary). IMO all valid dependencies should either resolve aut...

What is there about Izap that would interfere with a simulation "proceeding synchronously"?
What is there about BSB that prevents it from using a point process that works perfectly well with NEURON?

You could: * take a course in computational neuroscience. Try to get one that focuses on modeling real neurons, not mathematicians' or physicists' neurons * read a book. Most neuroscience textbooks are written by people who are experts in anatomy, or behavior, or molecular biology, or maybe genomics...

Currently, I am using the version 3.last of the Brain Scaffold Builder That's interesting in itself. Where can people learn more about the Brain Scaffold Builder? I would like to implement a sinusoidal current clamp You have come to the right place. Get https://www.neuron.yale.edu/ftp/ted/neuron/iz...

So this bug bit you too, Bill! It was just recently discovered, and the cause and fix are yet to be determined. Meanwhile, we're fortunate that other Python libraries, e.g. plotly, do work properly with NEURON.

Here is the file you wanted
https://www.neuron.yale.edu/ftp/ted/neuron/spdemo.zip

Are the action potentials modeled using mutlicompartmental modeling in NEURON all or none? That depends entirely on the equations that are being solved. It is possible to use NMODL and/or a state machine) to implement a model that approximates all or none spiking as closely as is possible with fini...

Hmm, would be good to resolve this soon, in case it reveals a bug that needs to be fixed--especially since we're going to be doing a NEURON course next month. Can you point me to the model in question if it exists in ModelDB, or alternatively zip up all the necessary hoc, py, mod, and ses files and ...

Perhaps my previous reply was too cryptic. The problem with the equivalent circuit in your Mon Apr 24, 2023 7:48 pm post is that ignores the fact that the paths between the internal node of dend 0 (i.e. 0.5) and the proximal internal nodes of dends 1 and 2 overlap. Where does this overlap occur? In ...

Easily done with mechanisms specified in NMODL. Doubtless the rxd approach is more elegant and expressive.