Search found 5591 matches

by ted
Wed Aug 21, 2019 9:35 am
Forum: Modeling networks
Topic: "turn off" Netstim in the middle of simulation
Replies: 4
Views: 431

Re: "turn off" Netstim in the middle of simulation

I can use NetCon.active(0) to turn the NetStim events off at&after detected time point. Alternatively, by setting NetCon.weight=0 works similarly. You should probably run a test to make sure that whatever you're doing is working properly. Executing netcon.weight[0] = 0 at some time t should prevent...
by ted
Tue Aug 20, 2019 10:17 am
Forum: Getting started
Topic: multiple pulse current clamp point process
Replies: 2
Views: 305

Re: multiple pulse current clamp point process

Good question. See I just want a current clamp that will deliver a sequence of current pulses at regular intervals. in the FAQ list https://neuron.yale.edu/neuron/faq/general-questions This is also mentioned in the Hot tips area of the forum under How to make IClamp deliver multiple pulses or a wave...
by ted
Mon Aug 19, 2019 2:12 pm
Forum: Modeling networks
Topic: "turn off" Netstim in the middle of simulation
Replies: 4
Views: 431

Re: "turn off" Netstim in the middle of simulation

Not flag. weight. weight is an attribute of a NetCon. Quoting directly from the documentation of NetStim: If, in the on=1 state, the stimulator receives a negative weight event, the stimulator will change to the off state. But to do that, you'd have to create a special NetCon, with negative weight, ...
by ted
Mon Aug 19, 2019 10:10 am
Forum: Modeling networks
Topic: "turn off" Netstim in the middle of simulation
Replies: 4
Views: 431

Re: "turn off" Netstim in the middle of simulation

I already implemented real-time detection part Good. That's the hard part. When the condition "time to turn off the NetStim" happens, use a NetCon's event() method to send an event with weight < 0 to the NetStim that you want to turn off. Read the Programmer's Reference documentation of the NetStim...
by ted
Thu Aug 15, 2019 3:41 pm
Forum: NEURON + Python
Topic: Convert Python to Hoc
Replies: 4
Views: 445

Re: Convert Python to Hoc

It should be possible to use NEURON's Import3d tool to convert the swc file to a hoc file. Adding an axon and assigning biophysical properties will be easy. Easier yet would be to have the Import3d tool export to a CellBuilder, then use the CellBuilder to set up Subsets, spatial discretization, and ...
by ted
Thu Aug 15, 2019 9:54 am
Forum: NEURON + Python
Topic: Convert Python to Hoc
Replies: 4
Views: 445

Re: Convert Python to Hoc

It will be interesting to know if the translated version of the model produces results identical to the original, and if not, what fixes are necessary to resolve the problem.
by ted
Thu Aug 08, 2019 10:59 am
Forum: Anatomically detailed models
Topic: How does 'Z. F. Mainen and T. J. Sejnowski (1996)' model work?
Replies: 2
Views: 467

Re: How does 'Z. F. Mainen and T. J. Sejnowski (1996)' model work?

trying to modify morphology of detailed models Read about 3d specification of model geometry. In fact, read everything on this page https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/topology/geometry.html or the corresponding page for hoc https://www.neuron.yale.edu/neuron/sta...
by ted
Thu Aug 08, 2019 10:23 am
Forum: OS X
Topic: code is incompatible with this neuron version
Replies: 1
Views: 326

Re: code is incompatible with this neuron version

Answered on the FAQ ("frequently asked questions") page of the NEURON Forum https://neuron.yale.edu/neuron/faq/general-questions -- see I installed a new version of NEURON, and now I see error messages . . . While you're there, you might find it useful to look at some of the other questions and answ...
by ted
Tue Aug 06, 2019 9:35 am
Forum: NEURON + Python
Topic: DLL load failed & No module named hoc error
Replies: 2
Views: 379

Re: DLL load failed & No module named hoc error

Code: Select all

import neuron
Good guess, but do this instead:

Code: Select all

from neuron import h
If you plan on using NEURON's GUI tools, do this

Code: Select all

from neuron import h,gui
If you intend to take advantage of its standard run time library

Code: Select all

from neuron import h
h.load_file("stdgui.hoc")
by ted
Wed Jul 31, 2019 10:48 pm
Forum: Specific models
Topic: How to add Na+ inactivation to Courtemanche et al Am J Physiol 1998 275:H301
Replies: 1
Views: 444

Re: How to add Na+ inactivation to Courtemanche et al Am J Physiol 1998 275:H301

The link you provide is not to the file that implements the Na-Ca exchange mechanism--instead, it produces a list of ModelDB models "that contain the Current : Na/Ca exchanger". None of them happens to be by Courtemanche et al., which is very strange indeed, since the very paper by Courtemanche et a...
by ted
Wed Jul 31, 2019 10:29 pm
Forum: Parallel NEURON
Topic: Periodically saving results during simulation
Replies: 1
Views: 341

Re: Periodically saving results during simulation

See
Dealing with simulations that generate a lot of data
https://neuron.yale.edu/neuron/docs/dea ... e-lot-data
The example is in hoc, but it's easy to implement the same approach with Python.
by ted
Thu Jul 25, 2019 3:44 pm
Forum: Other questions
Topic: model setup: random events
Replies: 6
Views: 662

Re: model setup: random events

I seem to be still getting minor variations in voltage in some cases. Looks like I'll have to be able to reproduce this in order to figure out what's going on. Can you zip up the necessary code and email it to ted dot carnevale at yale dot edu? and also include instructions for how to reproduce wha...
by ted
Tue Jul 23, 2019 11:34 am
Forum: Modeling networks
Topic: SaveState.restore() causes various error
Replies: 1
Views: 364

Re: SaveState.restore() causes various error

Did you ever use SaveState before, to do anything? Build a toy model and try it out with that toy model. When you get that right, try something more complicated.
by ted
Tue Jul 23, 2019 11:32 am
Forum: Getting started
Topic: Find threshold with APCount
Replies: 4
Views: 549

Re: Find threshold with APCount

Important facts 1. The NEURON simulator can be used to execute programs written in hoc, or Python, or programs that contain hoc and Python statements. 2. Because of fact 1, there are two versions of NEURON's online Programmers' Reference. One focuses on how to use NEURON with Python, and the other ...
by ted
Tue Jul 23, 2019 10:25 am
Forum: Employment and educational opportunities
Topic: workshops/courses
Replies: 2
Views: 688

Re: workshops/courses

Thank you for your interest. On Friday, Oct. 17, 2019 there will be a 1 day course on NEURON at the Society for Neuroscience Meeting in Chicago. The course description page and registration form are at https://neuron.yale.edu/neuron/static/courses/chi2019/chi2019.html Planning for a 2020 NEURON Summ...