Ion channel modeling with whole cell and a genetic algorithm (Gurkiewicz and Korngreen 2007)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:97756
"... Here we show that a genetic search algorithm in combination with a gradient descent algorithm can be used to fit whole-cell voltage-clamp data to kinetic models with a high degree of accuracy. Previously, ion channel stimulation traces were analyzed one at a time, the results of these analyses being combined to produce a picture of channel kinetics. Here the entire set of traces from all stimulation protocols are analysed simultaneously. The algorithm was initially tested on simulated current traces produced by several Hodgkin-Huxley–like and Markov chain models of voltage-gated potassium and sodium channels. ... Finally, the algorithm was used for finding the kinetic parameters of several voltage-gated sodium and potassium channels models by matching its results to data recorded from layer 5 pyramidal neurons of the rat cortex in the nucleated outside-out patch configuration. The minimization scheme gives electrophysiologists a tool for reproducing and simulating voltage-gated ion channel kinetics at the cellular level."
Reference:
1 . Gurkiewicz M, Korngreen A (2007) A numerical approach to ion channel modelling using whole-cell voltage-clamp recordings and a genetic algorithm. PLoS Comput Biol 3:e169 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Channel/Receptor;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; NEURON (web link to model);
Model Concept(s): Ion Channel Kinetics; Methods; Markov-type model;
Implementer(s): Korngreen, Alon [alon.korngreen at gmail.com];
: Two state kinetic scheme for Potassium channel
: Contains four kinetic parameters and one max conductance parameter.
NEURON {
      SUFFIX KCHANNEL
      USEION k READ ek WRITE ik
      RANGE g, gbar,a12,a21,z12,z21
}
UNITS {
	(mA) = (milliamp)
	(mV) = (millivolt)
	(pS) = (picosiemens)
	(um) = (micron)
} 

PARAMETER {
      gbar = 0     (pS/um2)
      a12 = 0.01   (/ms)
      a21 = 0.02   (/ms)
      z12 = 0.01   (/mV)
      z21 = 0.02   (/mV)
}

ASSIGNED {
      v    (mV)
      ek   (mV)
      g    (pS/um2)
      ik   (mA/cm2)
      k12  (/ms)
      k21  (/ms)
}

STATE { c o }

BREAKPOINT {
      SOLVE states METHOD sparse
      g = gbar*o
      ik = (1e-4)*g*(v - ek)
}

INITIAL { SOLVE states STEADYSTATE sparse}

KINETIC states {   		
        rates(v)
	~c <-> o (k12,k21)
	CONSERVE c+o=1
}

PROCEDURE rates(v(millivolt)) {

      k12 = a12*exp(z12*v)
      k21 = a21*exp(-z21*v)
}