Search found 5785 matches

by ted
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: 4856

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...
by ted
Wed Jul 13, 2005 10:26 am
Forum: Other questions
Topic: errno=22?
Replies: 1
Views: 3603

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...
by ted
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: 5437

You're right, there it is. I need to start reading things to the very end. In my own programming, I always use the standard run system and so have never run afoul of this "bug." Much legacy hoc code, including some that is in ModelDB, has been written by people who prefer to use their own code for e...
by ted
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: 5437

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 ...
by ted
Fri Jul 08, 2005 10:51 am
Forum: Other questions
Topic: load_template vs xopen
Replies: 1
Views: 3683

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...
by ted
Thu Jul 07, 2005 12:14 pm
Forum: General questions and discussions about computational neuroscience
Topic: Compartmentally?
Replies: 0
Views: 5442

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/or physiological barr...
by ted
Thu Jul 07, 2005 11:12 am
Forum: Modeling networks
Topic: How to set specific initial voltage for different neurons
Replies: 1
Views: 4893

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...
by ted
Fri Jun 24, 2005 8:00 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: cai cut in half
Replies: 2
Views: 4670

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" one depends o...
by ted
Fri Jun 24, 2005 7:46 pm
Forum: Getting started
Topic: How to move neuron in space without changing its dimensions
Replies: 5
Views: 6325

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...
by ted
Fri Jun 24, 2005 1:18 pm
Forum: Other questions
Topic: how to export an array
Replies: 1
Views: 2803

If by "array" you mean "Vector" then use the Vector class's printf method. Documentation of the Vector and File classes is on your PC already if you are using MSWin. Otherwise, see http://www.neuron.yale.edu/neuron/static/docs/help/neuron/general/classes/vector/vect.html#printf and http://www.neuron...
by ted
Thu Jun 23, 2005 12:09 pm
Forum: Other questions
Topic: Vector manipulation and play
Replies: 4
Views: 4886

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...
by ted
Wed Jun 22, 2005 12:56 pm
Forum: Other questions
Topic: how to clamp the whole segment?
Replies: 1
Views: 2805

Set nseg = 1. This has the same effect as if you stuck a silver wire down
the length of the section.
by ted
Wed Jun 22, 2005 12:48 pm
Forum: Other questions
Topic: path length calculation
Replies: 1
Views: 2987

Re: path length calculation

i'd like to print out the distance from each section (from the point on at which it is connected to its parent) to the soma. This proc showdist() { local offset distance(0, 0.5) forall { printf("\n") print secname() for (x) { print x, " ", x*L, " ", distance(x) } } } will print the distance from ev...
by ted
Wed Jun 22, 2005 12:32 pm
Forum: Modeling networks
Topic: repetitive firing neuron
Replies: 1
Views: 4066

"Best" depends on the details of what you want to use it for. It turned out that your own application would be satisfied by an artificial spiking cell (integrate and fire neuron). IntFire2, which is built into NEURON, does what you want, although it is somewhat limited in that inhibitory and excitat...
by ted
Tue Jun 21, 2005 1:06 am
Forum: Other questions
Topic: Vector manipulation and play
Replies: 4
Views: 4886

Re: Vector manipulation and play

Ok, what I want to do is record some variables (voltages) during a run and during the same run play an algebraic expression (product of two recorded voltages) of these recorded variables back into another variable (synaptic weights), but I can't work out how to do this---any ideas??????? Lots. 1. T...