Search found 6393 matches
- 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...
- 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 ...
- 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...
- 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,...
- 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...
- 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?
- 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...
- 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,...
- 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...
- 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.
- 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?
- 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 ...
- 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...
- 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...
- 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...