File contents

Routine Name:   setupalpha

Description:    Sets up A and B tables of voltage-dependent gates based on
                generic equations describing the form of the alpha and beta
                rate functions.

Usage:          setupalpha channel-element gate AA AB AC AD AF BA BB BC BD BF \
                   -size n -range min max

                channel-element   This must be a tabgate or a tabchannel i.e.
                                  a voltage-dependent gate or channel with
                                  tabulated activation functions.

                gate              The name of the gate (must be X, Y, or Z).

                AA-AF             Coefficients A to F of the alpha table 
                                  (see below).

                BA-BF             Coefficients A to F of the beta table 
                                  (see below).

                -size n           Number of divisions in the table 
                                  (default = 3000).

                -range min max    Range of the table (default: min = -0.100; 
                                  max = 0.050).

                
                This routine makes it easy to set up the A and B tables of 
                tabulated channels or gates (tabchannel or tabgate objects) 
                when the equations describing the rate constants alpha and 
                beta are of the form:

                y(x) = (A + B * x) / (C + exp((x + D) / F))

                Many standard channels have alpha and beta parameters that can
		be cast into this form.  In these cases to set up the tables
		we can simply call setupalpha with the parameter values as
		arguments to the function.  Since there are both alpha and
		beta variables, we use the coefficients AA-AF to refer to the
		alpha variable and BA-BF to refer to the beta variable.

		setupalpha calls the TABCREATE action of the tabchannel or
		tabgate to allocate tables with n divisions (n + 1 entries)
		representing x values from min to max.  It then evalutes the
		functions at these points to fill the tables.

                tabgates have tables for the alpha and beta rate variables, so
                these alpha and beta values are used to directly fill the
                tables.  The gates of a tabchannel each have an A table that
                holds alpha values, and a B table that contains alpha + beta.
                These tables are filled with A = alpha and B = alpha + beta.

                The tables are by default set up in "no interpolation" mode, 
                which means that the process of finding the correct table
                value is simply a lookup operation.  With 3000 divisions in 
                the table (i.e. the table size is 3001) the lookup usually
                provides sufficient accuracy.  If not, you can override this 
                behavior; see the tabchannel documentation.  The range of the
                activation variable is between -0.100 and 0.050 by default.
                This is adequate for most voltage-dependent channels, but 
                can be overridden using the -range option.

Example:        from Scripts/neurokit/prototypes/traub91chan.g:

                create  tabchannel      Kdr_hip_traub91
                        setfield        ^       \
                        Ek              {EK}    \                  //      V
                        Gbar            { 150 * SOMA_A }    \      //      S
                        Ik              0       \                  //      A
                        Gk              0       \                  //      S
                        Xpower  1       \
                        Ypower  0       \
                        Zpower  0
 
                setupalpha Kdr_hip_traub91 X               \
                           {16e3 * (0.0351 + EREST_ACT)}   \  // AA
                           -16e3                           \  // AB
                           -1.0                            \  // AC
                           {-1.0 * (0.0351 + EREST_ACT) }  \  // AD
                           -0.005                          \  // AF
                           250                             \  // BA
                           0.0                             \  // BB
                           0.0                             \  // BC 
                           {-1.0 * (0.02 + EREST_ACT)}     \  // BD
                           0.04                               // BF
                
                This command sets up the X gate (activation gate) of Traub's
                delayed-rectifier potassium channel (Kdr_hip_traub91).
                SOMA_A and EREST_ACT are constants defined in the script
                file.  Note that the C value for the A table (AC) is -1; this
                can cause problems in general but does not cause any problems
                here (see below).

Notes:		For tabgate elements, which represent only a single gate, the
		 "gate" argument is ignored, but it should still be given as
		X, Y, or Z.  The setuptau command is similar to setupalpha,
		but uses the state variables tau and minf instead.

          	If the alpha and beta rate constant of your channel cannot be
		described using the above equation, you must fill the tables
		with one of the other methods described in the tabchannel
		documentation, or The Book of GENESIS, Chapter 19 (2nd ed.).

                The rate equation described above has a removable singularity
                when C = -1 at the point x = -D (which is, unfortunately, a
                common case).  In this case the routine may generate
                inaccurate results due to roundoff errors.  We STRONGLY
                RECOMMEND that if you must use a C value of -1 you check the
                resulting activation curves by using Neurokit (in the "Edit
                Channel" mode) to see if they look reasonable.  If they do
                not then you will have to define the channel using a script
                function as mentioned above.  Such a function will result in
                a slower setup time for the channel but will be much more
                accurate.

See also:       tabchannel, tabgate, setuptau, tweakalpha, tweaktau, Tables