Search found 5725 matches

by ted
Tue Aug 23, 2005 11:45 am
Forum: Modeling networks
Topic: parallel simulations of networks
Replies: 6
Views: 8750

Go to "Publications about NEURON"
http://www.neuron.yale.edu/neuron/bib/nrnpubs.html
and get
Lytton, W. and Hines, M. Independent variable timestep integration of
individual neurons for network simulations. Neural Computation, in press.
Preprint available as NC2913.pdf
by ted
Tue Aug 23, 2005 7:27 am
Forum: Adding new mechanisms and functions to NEURON
Topic: CVode corrector convergence
Replies: 8
Views: 20149

Well, sometimes bizarre things do happen, typically as a consequence of something that was overlooked, which is why I asked. NMODL has many traps, even for the wary. To diagnose the problem, it will be necessary for me to be able to reproduce it. It would be most helpful if you could cobble up as si...
by ted
Mon Aug 22, 2005 7:50 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: CVode corrector convergence
Replies: 8
Views: 20149

Re: CVode corrector convergence

All of a sudden I started getting errors when trying to run my model
Meaning you started with code that worked fine, made no changes to anything,
and poof! error messages started to appear?
by ted
Sat Aug 20, 2005 5:51 pm
Forum: Anatomically detailed models
Topic: Reducing complex models to equivalent cables
Replies: 9
Views: 10717

Re: Code for converting to a single equivalent cable

I have been trying to modify the attshape.hoc file I hope you were working on a duplicate copy of attshape.hoc, in some directory other than where attshape.hoc is located. It's not a good idea to do anything to the installed files or directories themselves; too easy to break stuff or--much worse--i...
by ted
Tue Aug 16, 2005 1:37 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: two questions about channel builder
Replies: 3
Views: 4646

I learn something new every day. NEURON Main Menu / Build / Channel Builder / Import KSChan does indeed offer a list of "uncontrolled" KSChans (i.e. KSChans that are not already managed by a ChannelBuilder GUI tool. But I wonder if there are any side-effects to be concerned about. To find out, I sav...
by ted
Tue Aug 16, 2005 11:25 am
Forum: MSWin
Topic: Possible solution for: oc> Cannot allocate memory
Replies: 3
Views: 5542

Thanks. I haven't seen that error msg yet, but if it occurs I now know
what to do.
by ted
Tue Aug 16, 2005 11:24 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Stability of steady state approximation
Replies: 3
Views: 5718

Re: Stability of steady state approximation

[quote=]I'm wondering whether the steady state approximation is introducing excessive stiffness (in the form of a time constant equal to 0) into the dynamics, leading to instability of the steady state approximation?[/quote] Probably. Using your toy model "as is," reducing dt to 0.005 ms or changing...
by ted
Tue Aug 16, 2005 10:23 am
Forum: Adding new mechanisms and functions to NEURON
Topic: two questions about channel builder
Replies: 3
Views: 4646

Re: two questions about channel builder

These are good questions. - I create a channel and everything works fine with it: I can insert it into my compartment and it behaves as expected. But then, if I close the CB window, how can I edit the channel model again? If I call the CB, another session is started as if I'm creating a new channel....
by ted
Tue Aug 09, 2005 5:51 pm
Forum: Other questions
Topic: how to read from, and record data into binary files?
Replies: 7
Views: 10056

Excellent, Konstantin! Score a big point for portability of binary files.
by ted
Sat Aug 06, 2005 2:02 pm
Forum: Other questions
Topic: continue simulation until numSpikes = n
Replies: 2
Views: 3718

Using the event delivery system to terminate a simulation

It should be much more efficient to do what you want with NEURON's event delivery system. In its simplest form, the NetCon class's record() method can capture spike times to a Vector for your later use, e.g. objref nc, nil nc = new NetCon( source , nil) objref stv stv = new Vector() nc.record(stv) I...
by ted
Sat Aug 06, 2005 11:15 am
Forum: Anatomically detailed models
Topic: Reducing complex models to equivalent cables
Replies: 9
Views: 10717

It's done all the time, but there's no gold standard for how to do it; as you have noted, there are lots of approaches to desiging reduced compartmental models, e.g. Bush, P.C. and Sejnowski, T.J. Reduced compartmental models of neocortical pyramidal cells. Journal of Neuroscience Methods 46:159-166...
by ted
Tue Aug 02, 2005 9:11 pm
Forum: Getting started
Topic: Variable step size per default?
Replies: 1
Views: 3903

Very good question, Konstantin. NEURON's default integration method is implicit ("backward") Euler, which has the distinct advantage that when dt is much larger than the largest time constant in a passive system, the states of that system reach their "infinite time" values in a single integration st...
by ted
Tue Aug 02, 2005 9:03 pm
Forum: Getting started
Topic: Passing an objref array by reference to a function
Replies: 3
Views: 4728

I've always found arrays to be limiting, because no matter how many objects I think I need today, sure enough, tomorrow I need a different number. Lists are a far more flexible way to deal with multiple objects, even objects of different classes (although this simple example sticks with objects of t...
by ted
Tue Aug 02, 2005 8:45 pm
Forum: Other questions
Topic: how to read from, and record data into binary files?
Replies: 7
Views: 10056

The most powerful and flexible way to deal with file i/o is to use the File class's metods, which are described here http://www.neuron.yale.edu/neuron/static/docs/help/neuron/general/classes/file.html#File Using binary formats risks generating future problems for oneself because of cross-application...
by ted
Tue Aug 02, 2005 8:32 pm
Forum: Other questions
Topic: periodic stimulation?
Replies: 1
Views: 4254

Whatever works. But the most flexible approach is to use a mechanism that takes advantage of NEURON's event delivery system. Here's the NMODL code for Ipulse1 and Ipulse2, which can deliver one or more pulses at regular intervals. Both use self-events to govern switching the current on and off. Alth...