Search found 6301 matches
- Fri Mar 15, 2024 11:31 am
- Forum: NEURON Announcements
- Topic: The 2024 NEURON Summer Course
- Replies: 0
- Views: 940
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...
- Sat Mar 02, 2024 12:43 pm
- Forum: NEURON + Python
- Topic: Diameter of a Squid Giant Axon Model
- Replies: 5
- Views: 1050
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...
- Thu Feb 29, 2024 1:21 am
- Forum: NEURON + Python
- Topic: Diameter of a Squid Giant Axon Model
- Replies: 5
- Views: 1050
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...
- Tue Feb 27, 2024 11:21 am
- Forum: NEURON + Python
- Topic: Diameter of a Squid Giant Axon Model
- Replies: 5
- Views: 1050
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 ...
- 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: 1076
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.
- Tue Feb 20, 2024 6:28 pm
- Forum: NEURON + Python
- Topic: Saving fixed timestep data using cvode variable timestep integration
- Replies: 2
- Views: 815
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...
- Mon Feb 12, 2024 11:22 am
- Forum: NetPyNE
- Topic: Usage of simConfig.recordDipolesHNN
- Replies: 2
- Views: 873
Re: Usage of simConfig.recordDipolesHNN
Referred to Salvador Dura
- Wed Feb 07, 2024 4:34 pm
- Forum: Other questions
- Topic: Zero sum of currents
- Replies: 5
- Views: 977
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...
- Tue Feb 06, 2024 5:22 pm
- Forum: Other questions
- Topic: Zero sum of currents
- Replies: 5
- Views: 977
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, ...
- Tue Feb 06, 2024 2:02 pm
- Forum: Other questions
- Topic: Zero sum of currents
- Replies: 5
- Views: 977
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...
- Tue Jan 30, 2024 12:25 pm
- Forum: Other questions
- Topic: Out of range error (when applying high-voltage pulses)
- Replies: 9
- Views: 5343
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...
- Sun Jan 28, 2024 11:32 am
- Forum: The GUI
- Topic: Somas not being positioned properly
- Replies: 7
- Views: 3995
Re: Somas not being positioned properly
You're quite welcome. Thank you for using NEURON in your research!
- Fri Jan 26, 2024 5:01 pm
- Forum: Other questions
- Topic: Out of range error (when applying high-voltage pulses)
- Replies: 9
- Views: 5343
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...
- Fri Jan 26, 2024 12:03 pm
- Forum: The GUI
- Topic: Somas not being positioned properly
- Replies: 7
- Views: 3995
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...
- Fri Jan 26, 2024 12:47 am
- Forum: The GUI
- Topic: Somas not being positioned properly
- Replies: 7
- Views: 3995
Re: Somas not being positioned properly
I have to state that this mapping is as intended, and of little functional importance. Yes, it is of no functional imporance to the computer, but it will be a potential source of confusion to those who may read or reuse your code in the future. It's never a good idea to deliberately embed confusing...