madsas/pyneuron
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Fohlmeister JF, Miller RF. Impulse encoding mechanisms of ganglion cells in the tiger salamander retina. J Neurophysiol 1997 Oct;78(4):1935-47 A reprint of this article can be obtained from http://jn.physiology.org/cgi/reprint/78/4/1935 This model is initially setup to produce figure 1 automatically. After viewing the currents, you may simulate figure 3a in the followng way. 1) close the 6 graph windows. 2) Destroy the SEClamp object by executing the statement objref VoltageClamp 3) Select the NEURONMainMenu/File/LoadSession menuitem and double click on the fig3a.ses file. 4) press the Init&Run button. The following parameter changes to the current working code supplied by Bob Miller's lab were made in collaboration with Michael Hines in order to semi-quantitatively reproduce figures 1 and 3a. 1) Table 1 indicates that gnabar_spike = .05 S/cm2. However the curves for the Na-current portion of Fig 1 use the default mod file value of gnabar_spike = .04 . 2) The initial Ca Rev. Potential of Fig 1 requires that the Table 1 value of celsius = 22 degC be used instead of NEURON's default value of 6.3. This statement was added to the current.hoc file. 3) To get the fig 1 behavior of slowly increasing calcium concentration with constant calcium current over 10 ms we modified current.hoc so that depth_cad = 3 (microns) taur_cad = 10 (ms) instead of the working code values of 2.5 and 1.5 respectively. 4) The working code used a spherical soma of 5um in diameter. This was changed to 25um as indicated in the paper and gives the results of fig 3 when a current of .02 nA is injected which is the amount specified in the paper. The largest discrepancy is that the amplitude of Ca-activated K-current is lower in this example model than is indicated in fig 1 of the paper. Questions about how to execute the model should be addressed to michael.hines@yale.edu. Questions about parameters should be addressed to J. F. Fohlmeister, Physiology Dept., 6-255 Millard Hall University of Minnesota 435 Delaware St. SE. Minneapolis, MN 55455 20120109 capump.mod updated from euler to derivimplicit: see for more: http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592 - TMM 20130826 Update from Ted Carnevale: capump.mod cleaned up to 1) reflect this mechanism is just a simple calcium accumulation mechanism that approximates pump action by a first order decay of cai and 2) since neither drive_pump nor kt were used for anything, every mention of them was deleted for clarity's sake.
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