Calcium waves in neuroblastoma cells (Fink et al. 2000)

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Accession:125745
Uses a model of IP3-mediated release of Ca from endoplasmic reticulum (ER) to study how initiation and propagation of Ca waves are affected by cell geometry, spatial distributions of ER and IP3 generation, and diffusion of Ca and mobile buffer.
Reference:
1 . Fink CC, Slepchenko B, Moraru II, Watras J, Schaff JC, Loew LM (2000) An image-based model of calcium waves in differentiated neuroblastoma cells. Biophys J 79:163-83 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Unknown;
Cell Type(s): Neuroblastoma;
Channel(s): I_SERCA;
Gap Junctions:
Receptor(s): IP3;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Virtual Cell (web link to model);
Model Concept(s): Calcium dynamics; Calcium waves;
Implementer(s): Carnevale, Ted [Ted.Carnevale at Yale.edu]; Fink, Charles C [cfink at uwm.edu];
Search NeuronDB for information about:  IP3; I_SERCA;
// set up shape plots with 10 evenly-spaced values

NUMVALS = 10 // # levels in the color map

IP3MINVAL = 0.0025
IP3MAXVAL = 0.025

CAMINVAL = 1.2e-4
CAMAXVAL = 12e-4

// set up RGB vectors for specifying shape plot color maps

objref rvec, gvec, bvec

proc buildmapvecs() { local i
  rvec = new Vector(NUMVALS)
  gvec = new Vector(NUMVALS)
  bvec = new Vector(NUMVALS)
  for i = 0, NUMVALS-1 {
    rvec.x[i]=fscan()
    gvec.x[i]=fscan()
    bvec.x[i]=fscan()
//    print i, rvec.x[i], gvec.x[i], bvec.x[i]
  }
}

buildmapvecs()

// RGB values for thermal scale (yellow-white hottest, purple coolest

111     0       111
143	30	93
185     55      64
223     76      42
245     120     11
255     155     0
255     195     0
255     233     0
255     255     0
255     255     200

// use the RGB vectors to set up color map for shape plot passed as $o1

proc setmap() { local i
  $o1.colormap(rvec.size())
  for i = 0, rvec.size()-1 {
    $o1.colormap(i, rvec.x[i], gvec.x[i], bvec.x[i])
  }
}

// shape plot of ip3i

objref ip3sh
ip3sh = new PlotShape(0)
ip3sh.size(-10.209,151.019,-80.4855,80.4853)
ip3sh.view(-10.209, -80.4855, 161.228, 160.971, 265, 105, 200.64, 200.32)
fast_flush_list.append(ip3sh)

ip3sh.exec_menu("Shape Plot")
ip3sh.variable("ip3i")
ip3sh.exec_menu("Show Diam")

setmap(ip3sh)
ip3sh.scale(IP3MINVAL, IP3MAXVAL)

// shape plot of cai

objref cash
cash = new PlotShape(0)
cash.size(-10.209,151.019,-80.4855,80.4853)
cash.view(-10.209, -80.4855, 161.228, 160.971, 265, 369, 200.64, 200.32)
fast_flush_list.append(cash)

cash.exec_menu("Shape Plot")
cash.variable("cai")
cash.exec_menu("Show Diam")

setmap(cash)
cash.scale(CAMINVAL, CAMAXVAL)

stdinit() // so IP3 shape plot shows initial color

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