Search found 6013 matches

by ted
Tue May 24, 2022 12:14 pm
Forum: NEURON + Python
Topic: Mechanisms ignored when attempting to initialize events
Replies: 1
Views: 67

Re: Mechanisms ignored when attempting to initialize events

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...
by ted
Thu May 19, 2022 9:47 am
Forum: General questions and discussions about computational neuroscience
Topic: Numerical Integration in Computational Neuroscience
Replies: 3
Views: 50

Re: Numerical Integration in Computational Neuroscience

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...
by ted
Thu May 19, 2022 9:36 am
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 133

Re: NEURON 7.6.7 - Permission denied. Python not available.

https://github.com/chlubba/PyPNS presents instructions for installation and configuration, including install & config of NEURON 7.6.7. Those instructions don't work?
by ted
Wed May 18, 2022 11:29 am
Forum: General questions and discussions about computational neuroscience
Topic: Numerical Integration in Computational Neuroscience
Replies: 3
Views: 50

Re: Numerical Integration in Computational Neuroscience

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...
by ted
Thu May 12, 2022 1:54 pm
Forum: Hot tips
Topic: Defer perturbations until after the start of a simulation
Replies: 0
Views: 54

Defer perturbations until after the start of a simulation

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...
by ted
Thu May 12, 2022 1:51 pm
Forum: Modeling networks
Topic: Vector play issue
Replies: 3
Views: 129

Re: Vector play issue

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...
by ted
Tue May 10, 2022 4:09 pm
Forum: Modeling networks
Topic: Vector play issue
Replies: 3
Views: 129

Re: Vector play issue

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...
by ted
Mon Apr 25, 2022 11:46 am
Forum: NEURON + Python
Topic: Uploading .swc file through .hoc
Replies: 3
Views: 152

Re: Uploading .swc file through .hoc

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...
by ted
Thu Apr 21, 2022 2:48 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Help with adding equation to mechanism
Replies: 7
Views: 348

Re: Help with adding equation to mechanism

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...
by ted
Tue Apr 12, 2022 12:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Help with adding equation to mechanism
Replies: 7
Views: 348

Re: Help with adding equation to mechanism

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...
by ted
Sun Apr 10, 2022 11:51 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Help with adding equation to mechanism
Replies: 7
Views: 348

Re: Help with adding equation to mechanism

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 ...
by ted
Thu Apr 07, 2022 12:34 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Help with adding equation to mechanism
Replies: 7
Views: 348

Re: Help with adding equation to mechanism

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...
by ted
Thu Apr 07, 2022 12:21 pm
Forum: Parallel NEURON
Topic: Parallelizing sections within a single cell in python without using GUI
Replies: 3
Views: 221

Re: Parallelizing sections within a single cell in python without using GUI

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" ...
by ted
Tue Apr 05, 2022 1:34 pm
Forum: NEURON Announcements
Topic: Neuromatch Academy
Replies: 0
Views: 415

Neuromatch Academy

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...
by ted
Tue Mar 29, 2022 1:06 pm
Forum: Parallel NEURON
Topic: Parallelizing sections within a single cell in python without using GUI
Replies: 3
Views: 221

Re: Parallelizing sections within a single cell in python without using GUI

"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...