www.neuron.yale.edu

NEURON's GUI tools provide a "no code" way to not only create cell classes from morphometric data files but also to verify the integrity and appropriateness of such data. The workflow involves using the Import3d and CellBuilder tools. Online documentation is available, but it would take ve...

The general workflow for developing network models starts by defining the cell classes that will be used. One useful way to organize network model code is to factor the code into several files. For example, for each cell class there would be a file that defines the anatomical and biophysical propert...

Final comments: have you verified that your morphology files are suitable for computational modeling with NEURON? Are there orphaned branches, bottlenecks or other oddities affecting neurite diameters (e.g. minimum diameter larger than 1 um, "favorite numbers")? Is there evidence of z axis...

More code than I like to paste as a single lump in one of these threads. Example of Python code that creates a cell class with morphology read from an SWC file. This was developed by Robert McDougal as one possible answer to one of the in-class hands-on exercises. It uses matplotlib to display simul...

Nice clean code. Looks like somebody has experience with C or Matlab. General suggestions when developing network models: First define and test each cell class all by itself. Then try creating and connecting just two cells. Cell classes are important for several reasons. First is avoiding collisions...

You might find a solution to your problem by reading about specification of geometry with Python https://nrn.readthedocs.io/en/latest/python/modelspec/programmatic/topology/ geometry.html#geometry-geometry or hoc https://nrn.readthedocs.io/en/latest/hoc/modelspec/programmatic/topology/geometry.html#...

I will assume that you are using the code in https://www.neuron.yale.edu/ftp/ted/neuron/extracellular_stim_and_rec.zip . The amplitude and time course of the extracellular stimulus is calculated by the procedure stim_waveform() in the file stim.hoc. The functionality of that procedure is very limite...

Hello NEURON community: This post talks about the underlying equation of AlphaSynapse. https://www.sas.upenn.edu/LabManuals/BBB251/NIA/NEUROLAB/HELP/alphasyn.htm I am wondering if the "v", postsynaptic voltage, is constant (and set as resting voltage) or should change during current injec...

I seem to have misplaced my scrying stone, and without that it is difficult to diagnose the unseen. Perhaps you could share what you mean by "add the 3D location" e.g. by providing code examples of what you did that worked, and what you did that didn't work.

Good Python suggestion, urid. Here are some NEURON-specific comments: First, just to make sure that everyone who reads this thread knows what we're writing about-- 1. NMODL's global variables. An NMODL-specified mechanism's PARAMETERs are global by default (have the same value in all segments in whi...

You're quite welcome, Shaina. Glad to help!

I've never seen this msg signify a discontinuity. It's usually caused by NMODL code with rate constants that involve exponential functions. Typically the exp is in a denominator where limiting the value returned by exp(x) to exp(700) will do no harm. Nothing will blow up numerically, and your simula...

Hi, Shaina. Sorry about the delay, but I've been traveling a bit after the course we did at ASU week before last. Open a terminal and cd into the the folder that holds your code. If there is a file called nrnmech.dll, delete it. Or if you see a folder called x86_64, delete that and all its contents....

The ODE for each segment is of the form transmembrane capacitive current + transmembrane ionic current = sum of all currents arriving in the segment from adjacent segments + sum of all currents that enter the segment from all point processes that generate currents Notice that current in these equati...

The primary utility of multisplit is to achieve load balance in network simulations, and that is useful only when the network contains a very few model cells that are very large. Otherwise the performance boost will not be worth the programmer's effort required to restructure your model. Few single ...