Search found 6009 matches

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: 49

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: 119

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: 119

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: 146

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: 318

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: 318

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: 318

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: 318

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: 217

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: 393

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: 217

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...
by ted
Fri Mar 25, 2022 12:07 pm
Forum: NetPyNE
Topic: After updating to MacOS 12.3 Monterey
Replies: 5
Views: 168

Re: After updating to MacOS 12.3 Monterey

I'm unable to recompile my mod files as there's no NEURON folder in the Applications, and hence no compiler that I can see at least..
Try opening a terminal, cd to the folder that contains your mod files, then at the system prompt execute the command
nrnivmodl

Did that work?
by ted
Wed Mar 23, 2022 3:34 pm
Forum: NEURON Announcements
Topic: EBRAINS Brain Simulation School 2022
Replies: 0
Views: 122

EBRAINS Brain Simulation School 2022

Attend the EBRAINS Brain Simulation School 2022 to learn about the many, powerful computational neuroscience tools available in the EBRAINS Infrastructure. This course will be held May 30 through June 3 in Palermo, Italy. To learn more or apply, see https://www.humanbrainproject.eu/en/education/BRAI...
by ted
Tue Mar 22, 2022 12:02 pm
Forum: NEURON + Python
Topic: Problem plotting PlotShape
Replies: 7
Views: 640

Re: Problem plotting PlotShape

Same problem Which problem? The first code example from neuron import h from matplotlib import pyplot main = h.Section(name='main') dend = h.Section(name='dend') dend.connect(main) ps = h.PlotShape(False) ps.plot(pyplot) pyplot.show() works for me, although ps.plot(pyplot) does generate this warnin...
by ted
Thu Feb 17, 2022 12:33 am
Forum: Reaction-diffusion in NEURON
Topic: Assignments in time and time-dependent functions
Replies: 2
Views: 175

Re: Assignments in time and time-dependent functions

If you're interested in simulating anything more than "single shot synaptic activations" of the kind illustrated in figs 1-3 and 7 of V. et al., you'll probably want to use NMODL to implement an event-driven synaptic mechanism that can respond to a series of two or more presynaptic spikes.