## Search found 27 matches

- 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.

- 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...

- 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...

- 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...

- Sun Oct 18, 2015 9:14 pm
- Forum: Getting started
- Topic: run control
- Replies:
**4** - Views:
**5956**

### Re: run control

got it.ted wrote:Got it now?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`

- 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...

- 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

Thanks, this is really great.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") }`

- 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...

- 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...

- 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...

- 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...

- 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?