Search found 6290 matches
- Fri Mar 22, 2024 1:04 am
- Forum: Other questions
- Topic: Results Don't Converge with Decreasing Time Step
- Replies: 3
- Views: 138
Re: Results Don't Converge with Decreasing Time Step
I thought it may have more to do with NEURON than any specific code chunk NEURON is a "permissive environment" in the sense that there are lots of ways to write code that runs without error messages but actually does something other than what its author thought it was doing. In that sense...
- Thu Mar 21, 2024 11:46 am
- Forum: OS X
- Topic: loading a model into neutron
- Replies: 1
- Views: 134
Re: loading a model into neutron
An error message of the form
foo is not a MECHANISM
generally means that you need to compile the mod file that defines foo. Time to read mod files: what they are, and how to use them in the Hot tips area of the NEURON Forum (viewtopic.php?t=3263)
foo is not a MECHANISM
generally means that you need to compile the mod file that defines foo. Time to read mod files: what they are, and how to use them in the Hot tips area of the NEURON Forum (viewtopic.php?t=3263)
- Tue Mar 19, 2024 2:21 am
- Forum: Other questions
- Topic: Results Don't Converge with Decreasing Time Step
- Replies: 3
- Views: 138
Re: Results Don't Converge with Decreasing Time Step
Alas, Carnac the Magnificent has shuffled off his mortal coil, leaving behind those who can only scry bugs in software that they hold in hand, or at least run on their own machines to reproduce whatever it is. So if you zip up just enough code to reproduce what you describe, I'll see what I can disc...
- Fri Mar 15, 2024 11:32 am
- Forum: NEURON Announcements
- Topic: 2024 NEURON Summer Course description
- Replies: 0
- Views: 153
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...
- Fri Mar 15, 2024 11:31 am
- Forum: NEURON Announcements
- Topic: The 2024 NEURON Summer Course
- Replies: 0
- Views: 306
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: 520
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: 520
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: 520
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: 394
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: 284
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: 459
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: 643
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: 643
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: 643
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: 4724
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...