Search found 85 matches

by Bill Connelly
Thu Mar 10, 2016 3:53 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Noise MOD creating strange voltage discontinuities
Replies: 3
Views: 5686

Re: Noise MOD creating strange voltage discontinuities

Okay, that makes a lot of sense. I thought it was going to be something vaguely along those lines. And thank you, that fixes the problem. But can I ask, WHY does it fix the problem? i.e. if BREAKPOINT is called twice? I would have thought by packing the RNG off to another function, and then calling ...
by Bill Connelly
Mon Mar 07, 2016 8:39 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Noise MOD creating strange voltage discontinuities
Replies: 3
Views: 5686

Noise MOD creating strange voltage discontinuities

So I have been using a mod file for creating membrane noise based on a very simple Ornstein–Uhlenbeck process of current. However, the other day, I noted that if I increase the current then the membrane potential behaves very very strangely. Here is an image of the noise behaving normally in a simpl...
by Bill Connelly
Sat Mar 05, 2016 7:30 pm
Forum: Other questions
Topic: Accessing the 2008 course documents online
Replies: 1
Views: 741

Accessing the 2008 course documents online

I am trying to find some notes on the linear circuit builder and I remembered that the 2008 course documents had a section on doing that. So I tried to access them here: https://www.neuron.yale.edu/neuron/static/courses/2008/course/handson.html or here https://www.neuron.yale.edu/neuron/static/cours...
by Bill Connelly
Sat Mar 05, 2016 5:25 pm
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 9603

Re: Neuron as a Python Module Redux

You're a legend. I thought I had that bit all sorted out because the NEURONHOME and PYTHONPATH were all set already. But yes, still needed to add something to path. Excellent, thank you very much, I am in your debt.
by Bill Connelly
Fri Mar 04, 2016 11:37 pm
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 9603

Neuron as a Python Module Redux

So it's getting around to 4 years since the last thread on this was started, so I feel another one is in order. I've read through the other threads but the advice does not really make sense to me, or does it work when it does. Specifics: I'm running Windows 8.1 on a 64 bit machine, I'm running 64 Bi...
by Bill Connelly
Tue Oct 28, 2014 10:50 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling mEPSC single channel noise in neurons
Replies: 2
Views: 1289

Re: Modeling mEPSC single channel noise in neurons

I answered Steve's question elsewhere, but I thought I'd paste in the same answer I gave there, in this forum, just incase anyone stumbles across it. I will hope that I'm not too terribly wrong. Obviously this is possible. Like everything in NEURON, you can make it as simple, or as complex as you wo...
by Bill Connelly
Tue Mar 25, 2014 5:22 pm
Forum: Anatomically detailed models
Topic: Correctly calculating total current over section
Replies: 3
Views: 5973

Re: Correctly calculating total current over section

Okay, excellent.. just wanted to check that as some of the numbers didn't quite seem right.

I have to interpolate before summation, because I'm using variable time step, and hence one runs time points are not at the same as another... or is there some fancy function I'm unaware of to deal with that?
by Bill Connelly
Tue Mar 25, 2014 4:13 pm
Forum: Anatomically detailed models
Topic: Correctly calculating total current over section
Replies: 3
Views: 5973

Correctly calculating total current over section

So each segment reports current as mA/cm2 . It is tempting to vector.record them... then sum them all up with vector.add() into a new vector, and then divide that by the total section area. However, that is not correct (not even thinking about units at that point) because each segment could have a d...
by Bill Connelly
Fri Jan 31, 2014 2:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: "normrand is not thread safe"
Replies: 3
Views: 1923

Re: "normrand is not thread safe"

Just a very simple Random Current generator NEURON { POINT_PROCESS Inoise RANGE tau, amp RANGE new_seed NONSPECIFIC_CURRENT i } PARAMETER { dt //ANOTHER QUESTION, DO I NEED THIS HERE????? tau = 50 (ms) amp = 0.001 (nA) } ASSIGNED { i } INITIAL { i = 0 } BREAKPOINT { i = i - (dt*i)/tau + dt*amp*normr...
by Bill Connelly
Fri Jan 31, 2014 11:44 am
Forum: Adding new mechanisms and functions to NEURON
Topic: "normrand is not thread safe"
Replies: 3
Views: 1923

"normrand is not thread safe"

A) I'm being told normrand is not thread safe. Is there anything I can do to make it so? Are any of the other random variables threadsafe? B) What is the logic behind this? In my head you could things could be threadsafe so long as you were essentially running completely independent equations of dif...
by Bill Connelly
Thu Jan 09, 2014 11:29 am
Forum: MSWin
Topic: HOC not being associated to nrn, and I can't get it to work
Replies: 2
Views: 4811

Re: HOC not being associated to nrn, and I can't get it to w

I might add that if I install 7.2, that 7.2 works fine.
by Bill Connelly
Thu Jan 09, 2014 11:06 am
Forum: MSWin
Topic: HOC not being associated to nrn, and I can't get it to work
Replies: 2
Views: 4811

HOC not being associated to nrn, and I can't get it to work

So I've running the 32 bit version of nrn 7.3 on a brand new Windows 7 PC. (I tried the 64 bit version first, but it was giving me errors even when I tried to run makenrndll) Neuron itself appears to be working fine. If I run nrngui, change the working directory, and load the right .HOC file, everyt...
by Bill Connelly
Wed Nov 13, 2013 11:15 am
Forum: The GUI
Topic: Problem with Print & File Window Manager
Replies: 1
Views: 4343

Problem with Print & File Window Manager

So I wanted to use the Print: Ascii feature of the Print & File Window Manager. The simulation is quite long. 12 seconds. Problems occurs when it starts to save passed 10 seconds. As can be seen from the datafile it saves 9999.9 -69.1285 -67.7425 9999.92 -69.1285 -67.7565 9999.94 -69.1286 -67.7706 9...
by Bill Connelly
Thu Oct 24, 2013 11:36 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Why do I need to mention the variable in RANGE?
Replies: 1
Views: 975

Why do I need to mention the variable in RANGE?

So I was trying to implement a current based synapse. Simple right? I started with this code NEURON { POINT_PROCESS isyn RANGE del, amp, tau1, tau2, i ELECTRODE_CURRENT i } UNITS { (nA) = (nanoamp) (mV) = (millivolt) } PARAMETER { del=0 (ms) tau1=.5 (ms) <1e-3,1e6> tau2=1 (ms) <1e-3,1e6> amp=0 (nA) ...
by Bill Connelly
Thu Oct 24, 2013 4:17 am
Forum: Getting started
Topic: vector.play massively slowing down simulation
Replies: 2
Views: 1250

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 ...