Search found 86 matches

by Bill Connelly
Thu Oct 24, 2013 4:17 am
Forum: Getting started
Topic: vector.play massively slowing down simulation
Replies: 2
Views: 1827

Re: vector.play massively slowing down simulation

Thanks Ted, Well that certainly stopped the slowdown over repeated running... However, the first run is still 1,000,000 times slower than it should be, due to the play (or something associated with it). For the moment I'm going to try to make a mod file, rather than running play into an iclamp. But ...
by Bill Connelly
Wed Oct 23, 2013 9:53 am
Forum: Getting started
Topic: vector.play massively slowing down simulation
Replies: 2
Views: 1827

vector.play massively slowing down simulation

So I have a multicompartment model, that usually only takes a few milliseconds to run a 3000 ms simulations. I'm trying to play in arbitrary currents. However, as soon as I include the vector.play() function, the simulation slows down by about a factor of 1,000,000. The analysis code is listed below...
by Bill Connelly
Wed Oct 23, 2013 7:37 am
Forum: Getting started
Topic: vector.play doesn't work when executed inside of proc
Replies: 2
Views: 2104

vector.play doesn't work when executed inside of proc

I was starting to write this function to allow me to play in arbitrary waveforms via IClamp (starting with simple EPSCs, with a mind to build up to chirp/zap functions). The code works when I enter it directly into the nrn window, but when I try to execute it as a function, it doesn't work (no error...
by Bill Connelly
Tue Mar 05, 2013 11:05 am
Forum: Other questions
Topic: I wish...
Replies: 1
Views: 1029

I wish...

I wish it was easier to "hot swap" dlls. Sometimes one has quit a complex experimental rig set up, and you wish you could change something in a MOD file, and the only way is to quit out and start again. I know one should do ones best to make the hoc load all that up, but sometimes it isn't practical...
by Bill Connelly
Wed Feb 27, 2013 6:16 am
Forum: Anatomically detailed models
Topic: Why am I getting a section stack overflow?
Replies: 4
Views: 7024

Re: Why am I getting a section stack overflow?

Oh, I always forget that in neuron the for() loop can do that. Quite a clever little trick. Thanks for your help!
by Bill Connelly
Wed Feb 27, 2013 6:08 am
Forum: Adding new mechanisms and functions to NEURON
Topic: convergence failed repeatedly: err=-7.
Replies: 2
Views: 2035

Re: convergence failed repeatedly: err=-7.

Oh, well that is an obvious mistake. I can report that after fixing that (Setting phi before the call to rates() ), the error has gone away. I'll still send it along to you, just in case you're curious.
by Bill Connelly
Sat Feb 23, 2013 3:24 am
Forum: Anatomically detailed models
Topic: Why am I getting a section stack overflow?
Replies: 4
Views: 7024

Re: Why am I getting a section stack overflow?

Hi Ted, Just in case you haven't been told it recently, you are such a benefit to the neuroscience community. I can think of few others who do so much to help so many in science. Secondly, yes, I know that while statement is super clumsy, but I couldn't for the life of me figure out a way to step do...
by Bill Connelly
Fri Feb 22, 2013 10:45 am
Forum: Adding new mechanisms and functions to NEURON
Topic: convergence failed repeatedly: err=-7.
Replies: 2
Views: 2035

convergence failed repeatedly: err=-7.

Very strange error I was using a model of a t-type calcium channel, but wanted to add temperature sensitivity into it. It looks like this COMMENT This T-type calcium current was originally reported in Wang XJ et al 1991 This file supplies a version of this current identical to Quadroni and Knopfel 1...
by Bill Connelly
Thu Feb 21, 2013 2:34 pm
Forum: Anatomically detailed models
Topic: Why am I getting a section stack overflow?
Replies: 4
Views: 7024

Why am I getting a section stack overflow?

This function crashes out at the same point, everytime, halfway through the nested for functions. I'm sure I've run simulations that have called run() more times than this, so I'm not sure what the problem is. The function doesn't seem truly recursive (which I've read is a common cause for stack ove...
by Bill Connelly
Tue Feb 19, 2013 9:46 am
Forum: Adding new mechanisms and functions to NEURON
Topic: _ion_cai ???
Replies: 2
Views: 2016

_ion_cai ???

So I'm aware that in a VERBATIM block, _ion_X is used to access the concentration of ion X from neuron (right?). However, I've seen quite a few models that have partway through the code VERBATIM cai = _ion_cai; ENDVERBATIM With no other verbatim blocks around. Am I right in thinking that this is unn...
by Bill Connelly
Mon Feb 04, 2013 5:01 pm
Forum: Anatomically detailed models
Topic: Square like soma: pt3dadd and diam_shape()
Replies: 5
Views: 3244

Re: Square like soma: pt3dadd and diam_shape()

Yes, I wondered about that... Okay, so a more general question, how does NEURON take the x,y,z,diam and decide which axis to throw the diam out in? i.e. it's easy to think about when, like in this example, only the z axis is changing, so you get a straight line, with a series of truncated cones... O...
by Bill Connelly
Mon Feb 04, 2013 11:21 am
Forum: Anatomically detailed models
Topic: Square like soma: pt3dadd and diam_shape()
Replies: 5
Views: 3244

Re: Square like soma: pt3dadd and diam_shape()

I believe I'm having a very similar problem. I'm trying to borrow the geometry of Bill Lyton's model here When I bring up a shape plot, it appears as if there is no soma, however, if I rotate the model, I can see the soma is there. i.e. it appears to be 2d. I checked that the soma appears to have th...
by Bill Connelly
Mon Feb 04, 2013 4:55 am
Forum: General questions and discussions about computational neuroscience
Topic: Different maths for dealing with the gating particle???
Replies: 3
Views: 15479

Re: Different maths for dealing with the gating particle???

Very interesting...

So then is there any computation reason why someone would essentially insert a few more lines of code that convert alpha and beta into tau and inf, and then essentially convert it back later on? I assume it is for some conceptual reason?
by Bill Connelly
Fri Feb 01, 2013 12:53 pm
Forum: General questions and discussions about computational neuroscience
Topic: Different maths for dealing with the gating particle???
Replies: 3
Views: 15479

Different maths for dealing with the gating particle???

I "understand" the concept that if we have the reaction A <--> B With the forward rate Kf and the backwards rate Kb, then we can say dA/dt = -Kf . A + Kb . B From that, I understand, when it comes to HH kinetics, we could say, in the DERIVATIVE block n' = alpha(v)*(1-n) - beta(v)*n However, I very r...
by Bill Connelly
Sat Jan 12, 2013 4:29 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Adrunge ?
Replies: 1
Views: 1591

Adrunge ?

Notice: adrunge is not thread safe So I've been able to figure out that I am using a Runge-Kutta algorithm but I don't specify it. Is there a way to get around this so I can make the mechanism threadsafe TITLE Hippocampal HH channels : : Fast Na+ and K+ currents responsible for action potentials : I...