Search found 6358 matches
- Fri Jul 15, 2005 5:30 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: psth and calculating firing rates
- Replies: 2
- Views: 8605
Re: psth and calculating firing rates
Michael Hines, or probably Bill Lytton, can tell you where the source code for the Vector class's methods is located. In order to take advantage of psth, you will first have to bin your spike times. You can do binning as postprocessing i.e. after the end of a simulation run, so its implementation ca...
- Fri Jul 15, 2005 4:57 pm
- Forum: Anatomically detailed models
- Topic: failure to "update" diam
- Replies: 1
- Views: 4700
Computation of effective L and diam is deferred
NEURON keeps 3D data in internal data structures that respond immediately in response to the various pt3d . . . statements. However, determining effective diameters, areas etc. requires actual computation, so for the sake of efficiency is deferred until a func or proc is called that really needs suc...
- Thu Jul 14, 2005 1:01 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Using a variable value from a mechanism
- Replies: 2
- Views: 5077
Use POINTER. For specific examples of the use of POINTER, see the gap junction and continuous transmitter release models in chapter 10 of The NEURON Book http://www.neuron.yale.edu/ftp/ted/book/revisions/chap10indexedref.pdf I see that the documentation of PARAMETER has been slightly mangled in the ...
- Wed Jul 13, 2005 11:00 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Error message "Is not a template" when using .mod
- Replies: 1
- Views: 6239
Re: Error message "Is not a template" when using .
nmodl files which compiled fine to make .o files .o files are only intermediate results and can be discarded. What counts is the file called nrnmech.dll (under MSWin and OS X); under UNIX or Linux, the important stuff tucked away in a subdirectory so you don't see it. Either way, when you start NEU...
- Wed Jul 13, 2005 10:26 am
- Forum: Other questions
- Topic: errno=22?
- Replies: 1
- Views: 4150
Not much, but you already knew that. It's a runtime error, so at least it points you to the vicinity of the statement that caused the problem. To get any more specific, I'd have to see the code that caused it. Best would be a minimal collection of code that reproduces the problem. If it fits in abou...
- Mon Jul 11, 2005 7:03 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Old .mod files with CVODE and NetStim
- Replies: 4
- Views: 6652
- Mon Jul 11, 2005 11:11 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Old .mod files with CVODE and NetStim
- Replies: 4
- Views: 6652
Re: Old .mod files with CVODE and NetStim
In addition to whatever problems may affect the code you're wrestling with, there are some possible sources of confusion here. Let's dispel them first. 1. In NetStim comments, it says that a CVODE object must exist in order for NetStim to work This might be true, but I don't see such a statement in ...
- Fri Jul 08, 2005 10:51 am
- Forum: Other questions
- Topic: load_template vs xopen
- Replies: 1
- Views: 4216
I will assume that you have already looked these up in the Programmer's Reference. If not, by all means do so. Since you're using MSWin, it's on your PC; click on Documentation in the NEURON program group, then look in the alphabetical listing. Now my own comments. About the only place you'll encoun...
- Thu Jul 07, 2005 12:14 pm
- Forum: General questions and discussions about computational neuroscience
- Topic: Compartmentally?
- Replies: 0
- Views: 6357
Re: Compartmentally?
Not a silly question, really. First let's eliminate the notion of "biological compartmentalization" from the discussion. "Biological compartmentalization" is an inescapable fact: biological processes occur in restricted spatial and temporal scales, which are set by physical and/o...
- Thu Jul 07, 2005 11:12 am
- Forum: Modeling networks
- Topic: How to set specific initial voltage for different neurons
- Replies: 1
- Views: 6189
This is a special instance of a custom initialization. A good introduction to initialization in NEURON is presented in chapter 8 of the NEURON book, which you can pick up from http://www.neuron.yale.edu/ftp/ted/book/revisions/ The general strategy for custom initializations is to use a custom proc i...
- Fri Jun 24, 2005 8:00 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: cai cut in half
- Replies: 2
- Views: 5992
Re: cai was 5e-5
By "NMODL article" I presume you mean the expanded version of the article Hines, M.L. and Carnevale, N.T. Expanding NEURON's repertoire of mechanisms with NMODL. Neural Computation 12:995-1007, 2000. There are several different ways to initialize ionic concentrations, and the "correct...
- Fri Jun 24, 2005 7:46 pm
- Forum: Getting started
- Topic: How to move neuron in space without changing its dimensions
- Replies: 5
- Views: 7721
How to specify the apparent location of a model cell
The root* section controls the apparent location of a model cell in a Shape plot. The easiest way to control the apparent location of a model cell is to create a small dummy section that is used as the root. Then you won't have to tinker with any of the pt3dadd statements for any of the sections you...
- Fri Jun 24, 2005 1:18 pm
- Forum: Other questions
- Topic: how to export an array
- Replies: 1
- Views: 3232
- Thu Jun 23, 2005 12:09 pm
- Forum: Other questions
- Topic: Vector manipulation and play
- Replies: 4
- Views: 5815
Is there anyway to somehow check/see whether a line of code is getting implemented at every timestep or not? Embed print statements. Best to try new ideas in the small, i.e. on a toy problem with minimal complexity. Is there any info available anywhere with advice on the onject-orientated nature of...
- Wed Jun 22, 2005 12:56 pm
- Forum: Other questions
- Topic: how to clamp the whole segment?
- Replies: 1
- Views: 3333