www.neuron.yale.edu

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 ...

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...

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...

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...

The 2025 NEURON Spring Course Location: Arizona State University, Tempe, AZ Dates: Sunday, March 9, through Friday, March 14, 2025 Faculty: Ted Carnevale, Robert McDougal, and guest speakers TBA Application deadline: Friday, February 28, 2025 The NEURON Spring Course is identical to the NEURON Summ...

Well, you're on the right track, but this can be done without explicit, formal use of callbacks. And the resulting code could be easily understood by all, even those who are new to Python. Some of the following discussion is for the benefit of others who may read this thread but have less experience...

Here is the primary consideration: reusing code that is known to have serious problems is inadvisable for many reasons. It wastes the time and effort of whoever reuses it, because it jeopardizes publication of results, not to mention support of current or future work. And it's not good for computati...

Well, maybe not so quickly, allowing for intrusions like a grant application. Here at last are properly written implementations of AMPAergic and NMDAergic synaptic transmission https://www.neuron.yale.edu/ftp/ted/neuron/ampanmda.zip along with demonstration programs that illustrate usage via hoc and...

Assuming that the time course of seg's extracellular potential is specified by the vector pair gvec and stim_t_vec, then the correct syntax for Vector.play is gvec.play(seg._ref_e_extracellular, stim_t_vec) This should force seg.e_extracellular to follow the time course specified by the vector pair ...

< revised from initial post > The chief problem with the models of NMDAergic and AMPAergic synaptic transmission used and published by Basak and Narayanan (2018) is they are implemented as point processes but their parameters and variables have units that are appropriate not for point processes but ...

Before digging into implementational details, it is a good idea to verify that what we know, or think we know, makes sense. This is especially important when it comes to mathematical formulas and units. A synapse generates a current that is specified in "absolute units" (e.g. nA in NEURON)...

I modified the two synaptic NMODL files by declaring USEION na WRITE inas USEION k WRITE iks In a USEION statement, the variable name declared in the USEION clause dictates the form of the names declared in the READ and WRITE clauses. Also, NEURON only "knows" about na, k, and ca, so any ...

There may be some ways to reduce complexity, but I'll have to ask some questions. Here's a big suggestion (I don't know why Lavzin et al. didn't do this): The mod files for several mechanisms generate nonspecific currents. Presumably you want to attribute those currents to corresponding ion fluxes, ...

Interesting questions. I was wondering if it makes any sense in some cases (such as mine) to model a multicompartment soma. Depends on the temporal and spatial scales that are relevant to the phenomena you are studying. For structures roughly the size of somas in vertebrates, there is no need to use...

when I run the cell more than once in the same kernel, I get an error That's strange. What do you mean "run more than once in the same kernel"? just call h.run() again, and then execute the "plot results" code? That should work if you did it in plain python, without using Jupyte...