Search found 6317 matches

by ted
Fri Mar 15, 2024 11:32 am
Forum: NEURON Announcements
Topic: 2024 NEURON Summer Course description
Replies: 0
Views: 8903

2024 NEURON Summer Course description

Location and dates The 2024 NEURON Summer Course will be held at Brown University in Providence, RI from Sunday, June 16, through Friday, June 21, 2024. Application and registration Space is limited, and applications will be considered in the order received. The deadline for application and payment...
by ted
Fri Mar 15, 2024 11:31 am
Forum: NEURON Announcements
Topic: The 2024 NEURON Summer Course
Replies: 0
Views: 6236

The 2024 NEURON Summer Course

The 2024 NEURON Summer Course Location: Brown University, Providence, RI Dates: Sunday, June 16, through Friday, June 21, 2024 Faculty: Ted Carnevale, Robert McDougal, and guest speakers TBA Application deadline: Monday, June 3, 2024 This intensive multi-day course is designed for those who are pla...
by ted
Sat Mar 02, 2024 12:43 pm
Forum: NEURON + Python
Topic: Diameter of a Squid Giant Axon Model
Replies: 6
Views: 9316

Re: Diameter of a Squid Giant Axon Model

Here's a strategy for empirical estimation of the "phenomenological membrane time constant" of an underdamped neuron. It is an experimentalist's equivalent of "linearizing" a set of equations in the vicinity of an operating point. The idea is to analyze the cell's response to sma...
by ted
Thu Feb 29, 2024 1:21 am
Forum: NEURON + Python
Topic: Diameter of a Squid Giant Axon Model
Replies: 6
Views: 9316

Re: Diameter of a Squid Giant Axon Model

Great questions. They should be part of the qualifying exams for anyone studying membrane biophysics or the dynamics of biological neurons. How many would pass such an exam? That's a different question. Phenomenological inductance in excitable membranes is a rather old observation. You'll want to re...
by ted
Tue Feb 27, 2024 11:21 am
Forum: NEURON + Python
Topic: Diameter of a Squid Giant Axon Model
Replies: 6
Views: 9316

Re: Diameter of a Squid Giant Axon Model

That's not a trivial question at all, even though the answer may seem obvious in retrospect. The "HH patch model" is a model of a patch of squid axon membrane. The L and diam values make the patch have an area of 100 um2. Why 100 um2? Because for this area of membrane, if some ion X has a ...
by ted
Wed Feb 21, 2024 1:18 pm
Forum: ModelDB and other online sources of models
Topic: couldn't run model from modelDB
Replies: 1
Views: 8997

Re: couldn't run model from modelDB

Many model entries, like this one, include a readme file that contains hints for usage. Delete the nrnmech.dll or .x86_64 directory that was generated when you ran nrnivmodl, and then see if the model authors' instructions are helpful.
by ted
Tue Feb 20, 2024 6:28 pm
Forum: NEURON + Python
Topic: Saving fixed timestep data using cvode variable timestep integration
Replies: 2
Views: 6897

Re: Saving fixed timestep data using cvode variable timestep integration

Thank you for an interesting post. This is what I'd do: keep using cvode and allow my data to not be recorded at regular intervals and then after the simulation resample my data This is best because it works, produces "correct" results, and saves your time. NEURON's Vector class has an int...
by ted
Mon Feb 12, 2024 11:22 am
Forum: NetPyNE
Topic: Usage of simConfig.recordDipolesHNN
Replies: 2
Views: 8467

Re: Usage of simConfig.recordDipolesHNN

Referred to Salvador Dura
by ted
Wed Feb 07, 2024 4:34 pm
Forum: Other questions
Topic: Zero sum of currents
Replies: 5
Views: 6070

Re: Zero sum of currents

More good questions! Thanks for the pointer to the simulation that was giving you problems. I'll take a look at it. it is hard to collect all types of currents just by reading their names True. But there are two ways to get a net membrane current variable that is the sum of all membrane currents (io...
by ted
Tue Feb 06, 2024 5:22 pm
Forum: Other questions
Topic: Zero sum of currents
Replies: 5
Views: 6070

Re: Zero sum of currents

Download https://www.neuron.yale.edu/ftp/ted/neuron/conscharge.zip, unzip it, read the contents of init.hoc, and then execute nrngui init.hoc and follow the instructions in init.hoc's header. This program confirms conservation of charge regardless of whether a point current source (synapse, IClamp, ...
by ted
Tue Feb 06, 2024 2:02 pm
Forum: Other questions
Topic: Zero sum of currents
Replies: 5
Views: 6070

Re: Zero sum of currents

First let me thank you for using NEURON in your work, and also for asking an excellent question. We tried to collect all the membrane currents . . . [but] the momentary sum of the currents was not zero This statement raises several interesting issues about conservation of charge and current. To star...
by ted
Tue Jan 30, 2024 12:25 pm
Forum: Other questions
Topic: Out of range error (when applying high-voltage pulses)
Replies: 9
Views: 10501

Re: Out of range error (when applying high-voltage pulses)

you say that my code does not implement extracellular stimulation Not true. Here's what I actually wrote: The code you sent does not implement extracellular stimulation, and the code example in your post on the Forum doesn't disclose much The first part of that is The code you sent does not impleme...
by ted
Sun Jan 28, 2024 11:32 am
Forum: The GUI
Topic: Somas not being positioned properly
Replies: 7
Views: 9826

Re: Somas not being positioned properly

You're quite welcome. Thank you for using NEURON in your research!
by ted
Fri Jan 26, 2024 5:01 pm
Forum: Other questions
Topic: Out of range error (when applying high-voltage pulses)
Replies: 9
Views: 10501

Re: Out of range error (when applying high-voltage pulses)

Similar to McIntyre et al., I applied a voltage to each compartment (segment) to represent extracellular stimulation. But the source code provided by McIntyre et al. (available at modeldb.science/3810) doesn't apply "a voltage to each compartment." Instead, it uses _intracelluar_ stimulat...
by ted
Fri Jan 26, 2024 12:03 pm
Forum: The GUI
Topic: Somas not being positioned properly
Replies: 7
Views: 9826

Re: Somas not being positioned properly

Interesting. There has been a lot of development since those versions; is there a reason you can't use NEURON 8.2.2? Marginally related thoughts: IMO _set_position is more code than necessary to do the job. For any cell instance, it should be sufficient to pt3dchange just the 3d points that belong t...