This directory contains 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 chemesis2.1.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.gmu.edu/departments/krasnow/CENlab/chemesis.html.

Tutorial05.g is a script that builds the three biochemical reactions shown
on slides 22-23 of the of the Blackwell WAM-BAMM 2005 presentation at
http://www.wam-bamm.org/WB05/Tutorials/advanced-tutorials/blackwell/index.html.
It uses parameters in param.g,and graphs for illustration are created in
graphs.g.  The same reactions are also programmed for xppaut, in the file
mglu-ip3.ode.  This file has optional G_alpha and IP3 degradation.

CALx.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 WAM-BAMM 2005 presentation, and uses most of the chemesis
objects that are described.

These examples are further described in Blackwell, 2005 (K. T. Blackwell,
Modeling Calcium Concentration and Biochemical Reactions, Brains, Minds and
Media, urn:nbn:de:0009-3-2245, available from http://www.brains-minds-media.org).

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, and mglu-ip3.ode is a similar script for use with XPPAUT.
