Search found 6393 matches

by ted
Wed Feb 19, 2025 2:42 pm
Forum: Other questions
Topic: Factors Influencing NEURON Simulation Run Time Beyond Total Compartment Count?
Replies: 1
Views: 16180

Re: Factors Influencing NEURON Simulation Run Time Beyond Total Compartment Count?

Runtime depends on model complexity. A crude but effective measure of complexity is the total number of ODEs. For every segment there is one ODE for the cable equation, plus one ODE for each state variable of every mechanism associated with that segment that requires numerical integration. This incl...
by ted
Wed Feb 19, 2025 2:15 pm
Forum: Other questions
Topic: error
Replies: 1
Views: 15125

Re: error

About this Forum: If you need to paste code, be sure to surround it with the proper markup (that's what the < / > formatting button is for). Otherwise things like leftsquarebracket i rightsquarebracket will be treated as formatting instructions (interpreted as "italic"). Here's how to fix ...
by ted
Mon Feb 17, 2025 10:11 am
Forum: Modeling networks
Topic: Adding extracellular stimulus to network of neurons
Replies: 9
Views: 53990

Re: Adding extracellular stimulus to network of neurons

I asked because DBS protocols use biphasic, charge-balanced waveforms. Vector play works for arbitrary waveforms. If the conductive medium is nondispersive ("purely resistive"), then the time course of extracelluar potential vx(x,y,z) will be of the form A(x,y,z)*f(t) where f is a function...
by ted
Fri Feb 14, 2025 12:00 am
Forum: Modeling networks
Topic: Adding extracellular stimulus to network of neurons
Replies: 9
Views: 53990

Re: Adding extracellular stimulus to network of neurons

Haven't been much help yet--you've done all the work so far. Implementing stimulation will be easy if you only need a single rectangular pulse--the IClamp class will do for that. But what if your stimulus current should have a more complex time course, e.g. two or more monophasic rectangular pulses,...
by ted
Thu Feb 06, 2025 12:58 pm
Forum: NEURON + Python
Topic: kernel dying in unusual circumstances
Replies: 1
Views: 19663

Re: kernel dying in unusual circumstances

To provide specific advice, I will have to know what you're trying to do. All that is clear from the example code is that 1. it assumes that soma2 and dend2 have the same nseg value. This is unlikely to be true. 2. it assumes that this nseg value changes on every pass through the "for seg in se...
by ted
Wed Feb 05, 2025 5:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Boltzmann and elementary charge values
Replies: 6
Views: 52778

Re: Boltzmann and elementary charge values

To give specific advice, I'll have to reproduce the error for myself. Can you email the mod file in question to ted dot carnevale at yale dot edu?
by ted
Mon Feb 03, 2025 12:02 pm
Forum: NEURON + Python
Topic: list the mechanisms loaded from the nrnmech.dll.file
Replies: 3
Views: 22438

Re: list the mechanisms loaded from the nrnmech.dll.file

I have 100's of ion channel mechanisms and i would like to be able to choose which ones I insert in my model This isn't hard. In your model setup code use conditional statements code whose execution is controlled e.g. by command line switches or statements in a text file. That way you'll have a tex...
by ted
Sat Feb 01, 2025 12:33 pm
Forum: Modeling networks
Topic: Adding extracellular stimulus to network of neurons
Replies: 9
Views: 53990

Re: Adding extracellular stimulus to network of neurons

Given a point neuron, extracellular stimulation can be represented by a current source attached to the model cell, but the question then is: how to determine the amplitude and time course of that current? Amplitude is clearly a function of assumed location of the model cell in the conductive medium,...
by ted
Sat Feb 01, 2025 12:06 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Boltzmann and elementary charge values
Replies: 6
Views: 52778

Re: Boltzmann and elementary charge values

Regardless of the programming language, it is generally not a good idea to embed magic numbers (numerical constants) in code. Instead, it is best to use a variable whose value will not be changed during a simulation. In NMODL you could define a symbolic constant by declaring its name and assigning a...
by ted
Fri Jan 31, 2025 3:02 pm
Forum: NEURON + Python
Topic: list the mechanisms loaded from the nrnmech.dll.file
Replies: 3
Views: 22438

Re: list the mechanisms loaded from the nrnmech.dll.file

It's not a good idea to do that, unless you enjoy setting booby traps for yourself and anyone who tries to reuse your code. Specification of the mechanisms used by a model should be made by hoc or Python statements.
by ted
Fri Jan 31, 2025 2:58 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Boltzmann and elementary charge values
Replies: 6
Views: 52778

Re: Boltzmann and elementary charge values

Are you asking about a statement in a hoc or Python file, or in a mod file?
by ted
Thu Jan 30, 2025 12:41 pm
Forum: Suggestions and Feedback
Topic: Example projects and guidance?
Replies: 1
Views: 38134

Re: Example projects and guidance?

General comments: NEURON is a great tool, but should the project's emphasis be on the tool or on some scientific question? Examples of the former would focus on topics related to applied math (e.g. efficient methods for solving large sets of differential equations) or computer science (dealing with ...
by ted
Wed Jan 29, 2025 12:34 pm
Forum: Modeling networks
Topic: Adding extracellular stimulus to network of neurons
Replies: 9
Views: 53990

Re: Adding extracellular stimulus to network of neurons

The difference between what you expected to happen, and what actually happened, has nothing to do with software, let alone software bugs. You have rediscovered a consequence of Maxwell's equations and Gauss's law. Suggested reading in this Forum: https://www.neuron.yale.edu/phpBB/viewtopic.php?p=107...
by ted
Wed Jan 22, 2025 2:58 pm
Forum: OS X
Topic: NEURON 8.2 install / OS X 15.2 Sequoia / Python 3.12.7 Anaconda installation difficulties
Replies: 3
Views: 46292

Re: NEURON 8.2 install / OS X 15.2 Sequoia / Python 3.12.7 Anaconda installation difficulties

Hmm, old links at the old web site. Time to migrate any useful content from www.neuron.yale.edu to someplace else, and then shut down the old site (which is way too heavy on style and customization, and a big pain to maintain). Always go to nrn.readthedocs.io for the most recent standard distributio...
by ted
Mon Jan 06, 2025 7:57 pm
Forum: NEURON Announcements
Topic: 2025 NEURON Spring Course description
Replies: 0
Views: 45538

2025 NEURON Spring Course description

Location and dates The 2025 NEURON Spring Course will be held at Arizona State University in Tempe, AZ from Sunday, March 9, through Friday, March 14, 2025. Application and registration Space is limited, and applications will be considered in the order received. The deadline for application and pay...