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by gabrielleg
Wed Jun 04, 2008 2:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: simple internal calcium concentration
Replies: 8
Views: 12991

Thanks for your reply. My initialization is based on something I found in the NEURON book, section 8.4.2. Writing initialization routines in NEURON is still a mystery to me. I haven't been able to get a handle on the details of how they work. In particular, changing things like the size of dt and th...
by gabrielleg
Tue Jun 03, 2008 12:51 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: simple internal calcium concentration
Replies: 8
Views: 12991

Ok. So the trivial things aren't the problem here. F, tau, L, and C0 are all assigned in hoc code. 1. cai0 was also set in hoc code (actually it's set in a template code, but this is almost the same thing). I tried setting it explicitly in the mod code like you said and this did something strange. T...
by gabrielleg
Mon Jun 02, 2008 6:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: simple internal calcium concentration
Replies: 8
Views: 12991

simple internal calcium concentration

Hi, I've been trying to get my code for internal calcium concentration to work. It should be really simple, but for some reason, it's not working. Even though there is plenty of inward calcium current, cai won't budge from the C0 value (which is kind of like cai0, but not; it's the "background ...
by gabrielleg
Tue May 13, 2008 10:29 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Units specified by NEURON
Replies: 3
Views: 3179

Hey, thanks for clearing that up. I didn't want to have to go back and write in scale factors everywhere until I was sure I'd have to. Also, modlunit was helpful. I'm starting to accumulate many scale factors in my mod files. Out of curiosity, why does NEURON use mA/cm2 instead of nA/um2? Biological...
by gabrielleg
Mon May 12, 2008 4:49 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Does NEURON automatically update Equilibrium potential?
Replies: 1
Views: 3044

Does NEURON automatically update Equilibrium potential?

If I'm writing a mechanism for internal calcium accumulation that is similar to Example 9.6 for Extracellular Potassium Accumulation (in the NEURON Book), can I explicitly calculate a new equilibrium potential for calcium (eca) in that mechanism, or does NEURON update eca automatically without my ha...
by gabrielleg
Mon May 12, 2008 4:42 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Units specified by NEURON
Replies: 3
Views: 3179

Units specified by NEURON

If I've put calcium current in my ASSIGNED block with units of nA/cm2, does NEURON override my choice of units and calculate ica in terms of mA/cm2 anyway?

Code: Select all

ASSIGNED
  {
  ica (nA/cm2)
  eca (mV)
  F (mM/nA)
  C0 (mM)
  tauca (ms)
  L (um)
  diam (um)
  }
-g
by gabrielleg
Fri May 09, 2008 5:47 pm
Forum: Other questions
Topic: Creating my own section variables?
Replies: 3
Views: 2817

I found a way around my issue. I guess I didn't need a section variable. But out of curiosity, is it possible to create your own section variables?

g
by gabrielleg
Fri May 09, 2008 4:03 pm
Forum: Other questions
Topic: Creating my own section variables?
Replies: 3
Views: 2817

Creating my own section variables?

Hi, I'm trying to find out how to make my own section variable (or something like it). I would like to specify a different Cm for each section in order to get area out of it. I don't want to use L and diam to get area. I'm building a 2 compartment model of a cell and will eventually make a small net...

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