Search found 6297 matches

by ted
Tue Apr 09, 2024 1:27 am
Forum: NEURON + Python
Topic: NetStim causes SaveState crash
Replies: 4
Views: 109

Re: NetStim causes SaveState crash

Sure, everything can be done entirely by writing code--hoc or Python or some combination of both--but NEURON's InterViews-based GUI provides many powerful tools for getting a lot done with little or no programming effort. And these tools give you immediate access to key parameters. Very useful for i...
by ted
Mon Apr 08, 2024 1:32 pm
Forum: Hot tips
Topic: Extracellular stimulation and recording
Replies: 9
Views: 101887

Re: Extracellular stimulation and recording

I'm sure that some modelers have implemented python code based on the hoc example, but I don't know of any sources that are available online. Maybe it's time for there to be an "official" example (well, one from a "trusted source" or at least a source that is willing to support i...
by ted
Mon Apr 08, 2024 12:34 pm
Forum: NEURON + Python
Topic: NetStim causes SaveState crash
Replies: 4
Views: 109

Re: NetStim causes SaveState crash

I don't think you have to do SaveState. I just uploaded

Code: Select all

https://www.neuron.yale.edu/ftp/ted/neuron/segmentedrun.zip
which contains hoc and python examples that include event-driven synaptic transmission. Try either one by executing
nrngui demo.hoc
or
python -i demo.py
by ted
Thu Apr 04, 2024 8:15 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: "xtra is not a mechanism"
Replies: 7
Views: 75

Re: "xtra is not a mechanism"

The problem isn't your files. NEURON and Windows have changed a lot since 2021. Uninstall NEURON, then download and install the latest version from nrn.readthedocs.io. Then delete the nrnmech.dll file, run nrnivmodl, and see what works.
by ted
Thu Apr 04, 2024 11:00 am
Forum: Adding new mechanisms and functions to NEURON
Topic: "xtra is not a mechanism"
Replies: 7
Views: 75

Re: "xtra is not a mechanism"

(I split these posts from the thread that they were part of, because these have nothing to do with extracellular stimulation and everything to do with adding new mechanisms to NEURON) In the directory where you ran nrnivmodl execute this command nrngui NEURON will print several lines of messages to ...
by ted
Wed Apr 03, 2024 2:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: "xtra is not a mechanism"
Replies: 7
Views: 75

Re: Extracellular stimulation and recording

An error message of the form foo is not a mechanism means that your hoc or python file uses a mechanism called foo, but either 1. you haven't compiled the mod file that defines the properties of foo or 2. if you did compile it, the results of compilation were written in some directory where NEURON d...
by ted
Tue Apr 02, 2024 11:52 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: "xtra is not a mechanism"
Replies: 7
Views: 75

Re: Extracellular stimulation and recording

Hi, firoozeh. Open a terminal and cd into the directory that contains the py, hoc, ses, and mod files. At the system prompt execute nrngui stimsphere.hoc Did that work? What did NEURON print to the terminal? Exit NEURON and try python -i stimsphere.py (or maybe you have to execute python3 -i stimsph...
by ted
Fri Mar 22, 2024 1:04 am
Forum: Other questions
Topic: Results Don't Converge with Decreasing Time Step
Replies: 3
Views: 141

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...
by ted
Thu Mar 21, 2024 11:46 am
Forum: OS X
Topic: loading a model into neutron
Replies: 1
Views: 155

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)
by ted
Tue Mar 19, 2024 2:21 am
Forum: Other questions
Topic: Results Don't Converge with Decreasing Time Step
Replies: 3
Views: 141

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...
by ted
Fri Mar 15, 2024 11:32 am
Forum: NEURON Announcements
Topic: 2024 NEURON Summer Course description
Replies: 0
Views: 183

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: 382

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: 5
Views: 529

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: 5
Views: 529

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: 5
Views: 529

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 ...