www.neuron.yale.edu

Here's an implementation that does almost everything via procedures, and contains some (not so) latent hints. Imports and definitions first from neuron import h, gui ### Model and simulation parameters # KISS when developing/debugging # this means small nets, short run times, few spikes # make symbo...

Actually, h.verbose could be an interesting feature.

Just out of curiosity: what performance boost are you getting?

Try inserting
coreneuron.verbose = 0
after
coreneuron.enable = True

You might glean some other useful stuff from
https://github.com/neuronsimulator/nrn/ ... _direct.py

I am assuming I should proceed with that first part of your reply?

Please do.

I forgot to mention that the NetCon that monitors the postsynaptic potential should have the same threshold as is specified in the NMODL's WATCH statement. For STDPE2, that would be the value of the RANGE variable thresh. For a synaptic mechanism S that can handle multiple input streams, the cleanes...

Interesting problem. Just in case you ran into a NEURON bug: what version of NEURON is running on your Mac, and what version is the cluster using?

Yow, instead of quoting your message and replying to it, in a hurry I made the mistake of editing your message. At least I captured your questions so we can continue the discussion.

The easy way to discover tpost is to attach a NetCon to the segment that has the instance of the STDPE2 class, and use that NetCon's record() method to capture local postsynaptic "spike times" to a Vector. What's not so clear to me is how you are capturing the tpre values. Are you recordin...

I've noticed the installer from https://www.neuron.yale.edu/neuron/download is version 8.2.0, and it kept giving one of my students a "no module named hoc" error. They eventually used the installer found on nrn.readthedocs.io and it is version 8.2.3 and this works fine. Just thought I sho...

The first step is for you to disclose the code of the mod file that you are actually using (either include it in your next post, or better yet provide a URL to where you found it). Statements like
"the STDP mod file created by so and so"
mean almost nothing because text files are fungible.

Algorithmic details aside, there is one hard fact that should be kept in mind: most parameters of biological systems are known to only very limited precision. For a multitude of reasons, the precision of measurements of neuronal morphology obtained with light microscopy is at best about 0.2 um, but ...

First, a question. What version of NEURON are you using?

Next, a suggestion. Use as simple a workflow as possible, that is, import the morphometric data, but _don't_ discretize the model cell, and don't add or alter any biophysical properties. What results do you get?

Downloaded a zip file from NeuroMorpho that was supposed to contain a couple of "log files" and two morphology files: one that NeuroMorpho calls "Original" and another called "Standardized". Expanding the zip file revealed two morphology files, one called 2M3.asc (in Ne...

From the printout generated by topology() that you provided, it looks like 1. there is only one root section 2. the root section is called soma 3. there is one axon and six dendritic trees and 4. the proximal ends of the axon and all dendritic trees are attached to the 1 end of the soma In the morni...

Neuromorphic renderings of the electrotonic transformation might be pretty and seemingly intuitive, but many users find logA vs. X plots to be far more informative.