Search found 6173 matches

by ted
Fri Jun 02, 2023 12:21 am
Forum: NEURON + Python
Topic: ModelView and ModuleNotFoundError: No module named 'numpy'
Replies: 7
Views: 96

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

Thanks. As you so concisely stated in that issue
numpy should not be required for users only using HOC with no reaction-diffusion.
by ted
Thu May 25, 2023 9:51 am
Forum: NEURON + Python
Topic: How to cut the simulation in-between into two runs?
Replies: 6
Views: 93

Re: How to cut the simulation in-between into two runs?

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...
by ted
Tue May 23, 2023 10:53 am
Forum: NEURON + Python
Topic: How to cut the simulation in-between into two runs?
Replies: 6
Views: 93

Re: How to cut the simulation in-between into two runs?

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...
by ted
Mon May 22, 2023 2:59 pm
Forum: NEURON + Python
Topic: How to cut the simulation in-between into two runs?
Replies: 6
Views: 93

Re: How to cut the simulation in-between into two runs?

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.
by ted
Thu May 18, 2023 10:56 am
Forum: NEURON + Python
Topic: ModelView and ModuleNotFoundError: No module named 'numpy'
Replies: 7
Views: 96

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

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...
by ted
Wed May 17, 2023 1:27 pm
Forum: Other questions
Topic: Sinusoid current implementation
Replies: 3
Views: 84

Re: Sinusoid current implementation

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?
by ted
Wed May 17, 2023 1:22 pm
Forum: Getting started
Topic: How to Interpret Simulation Results
Replies: 1
Views: 57

Re: How to Interpret Simulation Results

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...
by ted
Tue May 16, 2023 6:42 pm
Forum: Other questions
Topic: Sinusoid current implementation
Replies: 3
Views: 84

Re: Sinusoid current implementation

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...
by ted
Tue May 16, 2023 11:44 am
Forum: NEURON + Python
Topic: Plotshape question
Replies: 2
Views: 61

Re: Plotshape question

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.
by ted
Sun May 14, 2023 11:42 am
Forum: Anatomically detailed models
Topic: All or none action potentials?
Replies: 1
Views: 82

Re: All or none action potentials?

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...
by ted
Wed May 03, 2023 12:31 pm
Forum: MSWin
Topic: NEURON crashes in Windows 11
Replies: 4
Views: 144

Re: NEURON crashes in Windows 11

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 ...
by ted
Wed May 03, 2023 12:20 pm
Forum: Anatomically detailed models
Topic: Compartments vs Segments vs Sections
Replies: 8
Views: 129

Re: Compartments vs Segments vs Sections

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 ...
by ted
Tue May 02, 2023 11:08 pm
Forum: Reaction-diffusion in NEURON
Topic: Recording individual fluxes on a species that includes multiple mechanisms
Replies: 4
Views: 97

Re: Recording individual fluxes on a species that includes multiple mechanisms

Easily done with mechanisms specified in NMODL. Doubtless the rxd approach is more elegant and expressive.
by ted
Fri Apr 28, 2023 1:25 pm
Forum: The GUI
Topic: Problem plotting PlotShape
Replies: 15
Views: 1697

Re: Problem plotting PlotShape

I can't say anything about colab. You might try NEURON 8.2.1 or 8.2.0.