Search found 5542 matches

by ted
Thu Aug 15, 2019 3:41 pm
Forum: NEURON + Python
Topic: Convert Python to Hoc
Replies: 4
Views: 77

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: 77

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: 89

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: 88

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: 95

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: 133

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: 82

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: 257

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: 159

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: 214

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: 226

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...
by ted
Mon Jul 22, 2019 12:56 pm
Forum: Getting started
Topic: Find threshold with APCount
Replies: 4
Views: 214

Re: Find threshold with APCount

APCount doesn't find spike threshold. It monitors membrane potential at a particular location in a model cell, and returns the number of times that membrane potential at that location crossed a threshold in a positive-going direction. apc = h.APCount(section(x)) Here, section(x) should be written on...
by ted
Mon Jul 22, 2019 12:29 pm
Forum: Other questions
Topic: model setup: random events
Replies: 6
Views: 257

Re: model setup: random events

First a comment: the code examples are loaded with "magic numbers"--unnamed numerical constants, that is, constants whose values are embedded explicitly in the program. See this article in Wikipedia https://en.wikipedia.org/wiki/Magic_number_%28programming%29 Now for the source of the problem you en...
by ted
Thu Jul 18, 2019 10:31 am
Forum: Other questions
Topic: model setup: random events
Replies: 6
Views: 257

Re: Creating NetCon with null source in NEURON+Python

The possibilities are either 1. there is a mismatch between what is in your computer and what is in your head, so that there is some additional difference between the computational implementations of your variation 1 and 2 models or 2. you have run into a bug in NEURON Did you happen to implement yo...
by ted
Wed Jul 17, 2019 10:16 am
Forum: Specific models
Topic: e_pas in Poirazi2003 CA1 pyr cell model
Replies: 1
Views: 145

Re: e_pas in Poirazi2003 CA1 pyr cell model

e_pas for every compartment set to -112.55mV in the model!!! . . . I know this was done by the current-balance.hoc file to initialize the model to v_init, but this seems unphysiological. It was done to force the resting potential of the model to be v_init everywhere. The basic idea is expressed in ...