Tutorial scripts to teach how to develop models of second messengers
and calcium dynamics.

In order to run these scripts, you must first install "Chemesis", a library
of biochemical reaction objects for modeling calcium concentration.  To do
this, unpack chemesis2.0.tar.gz and install according to the instructions in
the included README file.  This will produce a new genesis executable
"chemesis" that incorporates the new Chemesis objects.  The latest version
of Chemesis may be obtained from
http://www.krasnow.gmu.edu/avrama/chemesis.html.

Tutorial05.g is a script that builds the three biochemical reactions on the
22-23 slides in the presentation Blackwell-Wambamm2005.ppt It uses parameters
in param.g, and graphs for illustration are created in graphs.g.  The same
reactions are also programmed for the XPPAUT simulator, in the file
mglu-ip3.ode.  This file has optional G_alpha and IP3 degradation.

cal*.g are a series of 4 scripts that build up calcium dynamics in a
step by step manner.  It implements the model shown on the last two
slides of the Blackwell-Wambamm2005 presentation, and uses most of the
chemesis2.0 objects explained.

cal1.g creates a single compartment with interaction between calcium and buffer

cal2.g creates a two compartment model: dendrite and soma.  The
calcium - buffer reaction is set up in each compartment in a function
called cabuf, which implements the pools and reaction introduced in
cal1.g.  The function simplies the code, so it doesn't have to be
repeated once for each compartment. One additional object/element is
required to allow for diffusion between compartments.

cal3.g creates the two compartment model of cal2.g, and then adds ip3
induced calcium release into the soma.  Within cal3.g, two of the
release elements are created, for illustrative purposes.  The
remaining elements are created in a function that is called.

cal4.g adds a SERCA pump to the model in cal3.g in order to more
quickly re-establish calcium equilibrium.

mglu-ip3-kkit.txt explains how to use Kinetikit to perform the same
calculations.