www.neuron.yale.edu

if I use the exact same code with a built-in mechanism like ExpSyn (in place of the custom mechamisms), the events are added at the expected times and sections Sounds like you're launching stock NEURON, rather than the nrnivmodl-created executable executable that contains the compiled mechanisms. W...

For any real neuronal morphology the soma electrically extremely compact--it is essentially isopotential for all frequencies at which the cable equation is relevant. You can run a simple test to prove this to yourself. Create a model cell in which the soma's morphology is specified using the pt3d s...

https://github.com/chlubba/PyPNS presents instructions for installation and configuration, including install & config of NEURON 7.6.7. Those instructions don't work?

Why the factor 2? Good-you're thinking for yourself. NEURON's spatial discretization uses the central difference approximation to the second spatial derivative of membrane potential. Consequently numerical integration of the discretized cable equation generates solutions at locations that correspon...

When running simulations of a model that is not spontaneously active, i.e. has a stable resting potential, it is generally a good idea to initialize the model to its steady state, and delay the onset of perturbations such as stimuli (current clamps, synaptic activations etc.) until t (h.t to all you...

You're welcome. A few things I forgot to say-- To see the effects of changing synaptic weight at the times specified in tvec require that h.tstop be set to at least 80 ms (100 would be fine). When running simulations of a model that is not spontaneously active, i.e. has a stable resting potential, i...

Interesting problem. You're very close to getting it right. No need to disclose your model cell; it's easy enough to make an isolated soma and use that for interactive software development. from neuron import h, gui # the built-in GUI is very convenient for development and debugging soma = h.Section...

If you're already familiar with Python, why not stick with Python? from neuron import h, gui # or, if you prefer, # from neuron import h # h.load_file('stdgui.hoc') . . . next execute your python code that reads the swc file . . . # then execute the legacy hoc file that does whatever useful stuff yo...

According to Wang et al That's quite a paper. Lots of experiments, lots of results. I think it would be best to have a simulation with rapid onset and washout Drug effects are often represented as simple parameter changes, without regard to the actual time course of application or washout. The mode...

OK, finally I see what you're trying to do. I was fixated on the details of transmitter release itself, thinking that you were concerned with intracellular diffusion of calcium, and went off on a tangent without carefully reading your post from Saturday. My mistake--please put all that aside. The qu...

PDEs are fine as mathematical descriptions of diffusion in a spatially continuous system, but they're not suitable for numerical simulations. You can't just stick a PDE into NMODL. Instead, you must first design a diffusional geometry: a set of "well stirred compartments" whose shapes and ...

The equation I would like to implement is D(\partial^2c)/(\partial x^2)=(cVmax)/(c+Km) Are you sure? coh.mod doesn't contain any variables named c, x, Vmax, or Km. It does have variables called C and km, but C is already completely controlled by other assignment statements, and presumably neither C...

I think this reply might be useful to both of you. is there some documentation or an example of how to implement multithreaded simulation without the NEURON GUI? No. I am aware of one published article that implemented multithreaded simulation without mapping NEURON's "parallel computing" ...

A message from Melvin Selim at Neuromatch: Neuromatch Academy (NMA) is offering two courses this year from July 11th to July 29th 2022 which will run in parallel online. Applications for students and teaching assistants are now open until April 20th, 2022. NMA-Computational Neuroscience Flagship cou...

"As proof of concept" first create a non-parallelized implementation of your model cell, and work with that a bit to make sure that (1) parameter values are correct, and (2) simulation results are what you expected to observe. soma.cm = 9e-3 # membrane capacitance uF/cm2 Experimental evide...