Search found 220 matches

by Raj
Tue Oct 17, 2006 4:40 pm
Forum: Getting started
Topic: access to section!
Replies: 6
Views: 4541

Just define a function, example:

Code: Select all

func myfunc(){
  return diam
}
and call it:

Code: Select all

forsec dendriticSections {
  print myfunc()
}
by Raj
Tue Oct 17, 2006 3:22 am
Forum: Getting started
Topic: access to section!
Replies: 6
Views: 4541

forall { print secname() } gives you all section names. Alternatively you can use the topology function: http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/topology.html#topology The output of this function also gives you how they are connected and you can read of the information you ...
by Raj
Mon Oct 16, 2006 5:21 am
Forum: Other questions
Topic: prntout of plots
Replies: 2
Views: 4102

You can use <ctrl><Print> to get the whole screen on your clipboard then you can use <ctrl> v to paste it into powerpoint.

You can use <alt><Print> to get the active window on your clipboard then you can use <ctrl> v to paste it into powerpoint.
by Raj
Mon Oct 16, 2006 5:12 am
Forum: Getting started
Topic: what is drive_channel in ATPase Ca-pump
Replies: 2
Views: 3540

As far as I can see the drive_channel is part o fthe description of a calcium channel. This mechanism includes both a channnel and a pump.
by Raj
Mon Oct 16, 2006 5:09 am
Forum: Getting started
Topic: access to section!
Replies: 6
Views: 4541

by Raj
Sun Oct 15, 2006 2:45 pm
Forum: Anatomically detailed models
Topic: coupling compartment
Replies: 2
Views: 4245

The trick Mainen Sejnowski use is in ModelDB in the code for their 1996 paper. If you connect section A to the middle of a section B then axial resistance of section B does not contribute to the coupling between the sections A and B, and you can use this to control the coupling. The trick however on...
by Raj
Wed Oct 11, 2006 7:56 am
Forum: Other questions
Topic: A code that works on the interpreter but not in a hoc file!
Replies: 1
Views: 2845

Your hoc-code in the original file seems to be within parentheses and probably even in a function. If so you have to make sure that rvm exist before, you can then later reallocate it at a larger/ not predefined size. Sp probably adding: objref rvm outside of a block or function will solve your probl...
by Raj
Wed Oct 11, 2006 6:07 am
Forum: Modeling networks
Topic: ph info
Replies: 1
Views: 3183

Very few conductances modeled in NEURON depend on pH. Most of them depend on membrane potential only and many others depend on internal ion concentrations of calcium, potassium and sodium. Because the dependence on pH is conceptually not different from depending on other ion concentrations you shoul...
by Raj
Sun Oct 01, 2006 5:35 pm
Forum: Getting started
Topic: vector save every run()
Replies: 5
Views: 6407

Best option is to save to binary format and pick that up in matlab, see this topic: https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=134&highlight=konstantin+miller Alternatively I think a simple load command might suffice in your case: load filename should give you the content of the file filenam...
by Raj
Sun Oct 01, 2006 3:46 pm
Forum: Getting started
Topic: vector save every run()
Replies: 5
Views: 6407

Did you put objref data,fok outside of the functions aswell? By the way the data might actually get appended to the existing file.
by Raj
Sun Oct 01, 2006 8:50 am
Forum: Getting started
Topic: vector save every run()
Replies: 5
Views: 6407

You have overwritten the standard run command, if you do not include the original commands that are in that function you end running only your self written code. The original procedure is (nrn 5.8: stdrun.hoc) proc run() { running_ = 1 stdinit() continuerun(tstop) } Including this in your code gives...
by Raj
Mon Sep 11, 2006 8:34 am
Forum: Getting started
Topic: I/V clamp electrod
Replies: 19
Views: 14732

just, i don't know why do you devide by 100 1nA = 100*10pA So if your ica is given in units of 10pA/um2 and your area in um2 you have to divide the numerical value of the current you obtain by a hundred to get the current in nA. between SEVClamp.i and (1 or 2 or ? ) 1-soma[0].i_cap*24058.317/100 2-...
by Raj
Sun Sep 10, 2006 4:52 pm
Forum: Getting started
Topic: I/V clamp electrod
Replies: 19
Views: 14732

Dear Reza, Just changing the clamp voltage will already lead to a capacitive current, because the capacitance needs to be charged. I set every possible conductance I could find to zero. This is a debugging strategy eliminate as many sources of confusion as you can find and try to address its cause. ...
by Raj
Sun Sep 10, 2006 1:35 pm
Forum: Getting started
Topic: I/V clamp electrod
Replies: 19
Views: 14732

Dear Reza, I played around with the model you pointed out. There the difference between the clamp current and the capacitive current disappears if I go to smaller time steps 0.0025 ms in this case works. If I plot SEVClamp.i and soma[0].i_cap*24058.317/100 together in one plot there is a pronounced ...
by Raj
Sun Sep 10, 2006 7:18 am
Forum: Getting started
Topic: I/V clamp electrod
Replies: 19
Views: 14732

Which leaves us with a fundamental question about the internal workings of NEURON. As far as I know the membrane potential is indeed calculated directly from the currents so you are right the pump current in your mechanism doesnot contribute to the ica current and therefore not to the clamp current ...