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// genesis
// Customized userprefs.g to run the molluscan burster simulation with neurokit
echo Using local user preferences
/**********************************************************************
**
** 1 Including script files for prototype functions
**
**********************************************************************/
/* file for standard compartments */
include compartments
/* file for channels */
include ASTchan_tut
/**********************************************************************
**
** 2 Invoking functions to make prototypes in the /library element
**
**********************************************************************/
/* To ensure that all subsequent elements are made in the library */
ce /library
make_cylind_compartment /* makes "compartment" */
// override defaults of -60 mV and -63 mV to give typical Aplysia R15 values
EK = -0.068
EA =-0.068
make_Na_aplysia_ag // Na
make_K_trit_agt // K
make_KA_moll_cs // A
make_Ca_aplysia_ag // Ca
make_B_trit_st // B
make_Ca_conc // Ca_conc
make_Kc_aplysia_gt // K_C
// Eliminate K inactivation - it has little effect
setfield K Ypower 0
ce / /* return to the root element */
disable /library
/**********************************************************************
**
** 3 Setting preferences for user-variables.
**
**********************************************************************/
/* See defaults.g for default values of these */
str user_help = "README"
user_cell = "/mollusc"
user_pfile = "mollusc.p"
user_runtime = 40.0
//user_intmethod = 0
//user_dt = 0.0005 // 0.5 msec if method 0
user_intmethod = 11 // Hines Crank-Nicholson
user_dt = 0.002 // 2 msec if method 11
user_refresh = 5
user_inject = 0 // default injection current (nA)
// Set the scales for the graphs in the two cell windows
user_ymin1 = -0.1
user_ymax1 = 0.05
user_xmax1 = 40.0
user_xmax2 = 40.0
user_ymin2 = 0.0
user_ymax2 = 200e-6
user_yoffset2 = 0.0
user_numxouts = 2
user_field2 = "Ca"
user_path2 = "Ca_conc"
user_colmin2 = 0 // use appropriate color scale for Ca_conc values
user_colmax2 = 0.00015
include I_plots // "run paradigm" will plot currents, but slows execution
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