www.neuron.yale.edu

the cell I create is composed of h.SectionList() and not a neuron cell() object First, a bit of terminological clarity. NEURON has no such thing as a "neuron cell() object". It's up to the user to decide what types of cells are to be represented in a network model, then for each of those ...

Wrapping up the example from my post of Thu Aug 22, 2024--during the stimulus, the membrane potentials for compartments A and C approach 0.5 mV and -0.5 mV, respectively. Immediately after the end of the stimulus, the membrane potentials reverse polarity and then decay toward 0 as time advances. The...

The limitations are such as . . . only if the electrotonic length is small enough to neglect longitudinal currents Not so. The mathematical derivation and discussion that are presented in justification of the activating function approach make the tacit assumption that the axon / nerve fiber / neuri...

if anybody reads this post, I suggest the following for discussion about this topic and other interesting ones: 10.1016/j.jphysparis.2011.10.003 An excellent suggestion. For those who don't immediately recognize the DOI, the citation is Joucla S, Yvert B. Modeling extracellular electrical neural st...

Why? Because you don't understand the limitations of the "activating function" approach. Frank Rattay was quite explicit about those limitations in at least one of his many articles, but he didn't reiterate them in all. Your task, if you are willing to accept it, is to track down those lim...

Yes, that's the imprecision of fixed precision floating point arithmetic. Then I remember that few parameters of any biological system are known to more than two significant figures and shudder after looking at the documentation again I ran the following test and see that I can just supply a time h....

Great, glad to help! Please remember to let us know when you publish something that reports work done with NEURON.

Time to (re-)read the documentation of the Vector class's record() method at nrn.readthedocs.io. I bet it has been a long time since you last read it. It's hard to retain all that stuff after a single reading, especially the parts that don't pertain to the problem at hand (which is usually simple da...

I haven't seen this CA1_PC_cAC_sig[0].soma[?] yet, but my guess would have been that it meant that "soma" is an "indexed" name, i.e., that when the "soma" thing was initially created, it was done with a statement of the form create soma[1] so that more than one section ...

Thanks for posting that! For others who may read this thread, executing nrniv -h at the system prompt prints a list of options that may be specified when launching NEURON from a terminal. These options can also be passed to NEURON's python module through the NEURON_MODULE_OPTIONS environment variabl...

For embarrassingly parallel problems like this I have always used NEURON's bulletin-board style parallelization with MPI, so I can't give you any advice about python multiprocessing. That said, here's a suggestion that could reduce data storage requirements a bit: record the state variables that hav...

To quote my previous post If nrnivmodl is run under Windows and encounters an NMODL file that relies on things that are not available in Windows, like SIGHUP, it will generate an error message and quit. Models that require such mechanisms are incompatible with Windows. Do you know if there's a trivi...

Tried nrnivmodl with NEURON 8.2.2 under Win 10, and had the same problem. The killer error appears to be 'SIGHUP" undeclared Apparently Windows doesn't have SIGHUP or anything equivalent to it--see http://stackoverflow.com/questions/3614020/ddg#3614203 If nrnivmodl is run under Windows and enco...

Just did a fresh install of latest version of Anaconda Python and NEURON under Win 10--specifically NEURON 8.2.6+ HEAD dated 2024-07-24. neurondemo works fine, which confirms that at least some mod files can be compiled. But trying to compile the mod files from modeldb.science/195615 produces the sa...

Under Linux nrnivmodl succeeds with 8.0a, 8.2.3, and 8.2.4 HEAD. I'll try with Windows.