Search found 27 matches

by ylzang
Wed Jan 06, 2016 1:45 am
Forum: Reaction-diffusion in NEURON
Topic: calcium diffusion in different shells
Replies: 8
Views: 7869

Re: calcium diffusion in different shells

Thanks for the reply. Yes, I am collaborating with other experimentalist and I will contact him to get more details. Thanks again.
by ylzang
Mon Jan 04, 2016 2:35 am
Forum: Reaction-diffusion in NEURON
Topic: calcium diffusion in different shells
Replies: 8
Views: 7869

Re: calcium diffusion in different shells

I hope to compare the model computed calcium transients including the amplitude, rise and decay dynamics with experimental observations. I think experimentally measured calcium-bounded dye signal should represent the average concentration.Sure, but the average of what? 1. Is all of the dye in the c...
by ylzang
Thu Dec 31, 2015 8:55 pm
Forum: Reaction-diffusion in NEURON
Topic: calcium diffusion in different shells
Replies: 8
Views: 7869

Re: calcium diffusion in different shells

Thanks for ramcdougal and Ted's explanation. I hope to compare the model computed calcium transients including the amplitude, rise and decay dynamics with experimental observations. I think experimentally measured calcium-bounded dye signal should represent the average concentration. Is this correct...
by ylzang
Wed Dec 30, 2015 9:22 pm
Forum: Reaction-diffusion in NEURON
Topic: calcium diffusion in different shells
Replies: 8
Views: 7869

calcium diffusion in different shells

In the Neuron Book, there is a cdp model used as Example 9.8 in Chapter 9. I have a question about this model. In this model, the calcium concentration in the outermost shell is regarded as the model output Cai. I think this value is much higher than the average calcium concentration. In some recent...
by ylzang
Sun Oct 18, 2015 9:14 pm
Forum: Getting started
Topic: run control
Replies: 4
Views: 5956

Re: run control

ted wrote:

Code: Select all

oc>x = 0
oc>for i=1,2500 x+=0.2
oc>x
	500 
oc>x-500
	-1.9838353e-11
oc>x = 0
oc>for i=1,35000 x+=0.02
oc>x-700
	-3.4663117e-10
Got it now?
got it.
by ylzang
Sat Oct 17, 2015 10:07 pm
Forum: Getting started
Topic: run control
Replies: 4
Views: 5956

Re: run control

Sounds like finite precision arithmetic and roundoff error. At a minimum read this: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=8&t=1686&p=12613 just the roundoff error? the default value of float_epsilon is 1e-11. Do you mean I cannot control the last recorded data point to be at 700 ms? I u...
by ylzang
Sat Oct 17, 2015 9:54 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Histogram method for a vector
Replies: 4
Views: 6628

Re: Histogram method for a vector

ted wrote:Make your own replacement. Test this to make sure it works properly.

Code: Select all

// $o1 vector whose elements are to be binned
// $2 binwidth
// $3 left edge of first bin
obfunc binvec() { localobj tobj
  tobj = $o1.c
  tobj.sub($3)
  tobj.div($2)
  return tobj.apply("int")
}
Thanks, this is really great.
by ylzang
Fri Oct 16, 2015 3:48 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Histogram method for a vector
Replies: 4
Views: 6628

Re: Histogram method for a vector

Suggest reading the Programmers' Reference documentation of the Vector class's hist and histogram methods https://www.neuron.yale.edu/neuron/static/new_doc/programming/math/vector.html and then trying them on a toy problem to determine whether one of them produces suitable results in a short enough...
by ylzang
Fri Oct 16, 2015 3:38 am
Forum: Getting started
Topic: run control
Replies: 4
Views: 5956

run control

dt = 0.2 tstop = 500 while (t<tstop) { fadvance()} dt = 0.02 tstop = 700 while (t<tstop) { fadvance() count+=1 For the first period, when t< 500 ms, it was calculated at t = 0.2,0.4..., and finally 500. For the second period, in my simulation, it was calculated at 500.02, 500.04,... and finally 700...
by ylzang
Thu Oct 01, 2015 1:51 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Histogram method for a vector
Replies: 4
Views: 6628

Histogram method for a vector

I am wondering whether Vector.histogram can return the bin number of each data in the edge? Just like the function in Matlab, [bincounts,ind] = histc(data,bin ranges) I know it is easy to get this value by iterations, but it will cause a terrible time consumption in my simulation. It will be used in...
by ylzang
Thu Jun 25, 2015 3:15 am
Forum: Reaction-diffusion in NEURON
Topic: The dimension problem of the difusion
Replies: 3
Views: 6773

Re: The dimension problem of the difusion

Thanks Ted. I am considering the problem of real calcium diffusion. For example, as you know the BK current will sense calcium to be activated. With recent experiments, BK current only sense the P type calcium current near it. In this case, do you think the following will make sense? Separate the cy...
by ylzang
Thu Jun 11, 2015 8:39 pm
Forum: Reaction-diffusion in NEURON
Topic: The dimension problem of the difusion
Replies: 3
Views: 6773

The dimension problem of the difusion

Hello, I have a simple problem, but I am not sure about the answer. If I used both the radial and longitudinal diffusion in my calcium buffering model. Then this diffusion is 2D, right?