Copyright Upinder S. Bhalla 1997-2001
National Centre for Biological Sciences, 
Bangalore, India.
email: bhalla@ncbs.res.in

This is the 'examples' directory for the kinetics package. Everything in this
directory is copyrighted by Upinder S. Bhalla as shown above, and is released
under the terms of the GNU Public License. Please see the COPYRIGHT notice
in the directory above for more details.

Contents:

README		: this file
feedback.g	: Feedback model with bistability. Described in the tutorial
			document and in the corresponding chapter for the
			Book of Genesis.
psearch.g	: Program for running parameter exploration on feedback model
pkc.g		: Model of protein Kinase C regulation.
inhib_fb.g  	: Inhibitory feedback model, which also exhibits bistability.
                        It has only a couple of minor changes with respect to
                        the feedback.g model. This model also contains a table
                        set up to give step inputs for generating a conc-eff
                        curve. This table is not activated by default; you
                        will need to double-click the table icon and turn the
                        stimulus ON to get it to work.  The model has the very
                        neat property that it will happily go into the
                        metastable state when it is started up without any
                        changes. If one now alters the last digit of the conc
                        term on X or Y (or if you want to be really clean, on
                        X_prd or Y_prd), the symmetry is broken and the system
                        falls into one of the true bistable states. Try it
                        out.
			
iplot.xplot	: Resultant conc-eff curve for inhib_fb.g file.
transport.g	: Example of using the transporter element. Requires
			at least GENESIS 2.2. This simulates the translocation 
			of an enzyme product to the nucleus, which results
			in synthesis of a blocker, which is transported back
			to the cytoplasm to block the enzyme. You get a nice
			series of decaying oscillations.

end_prd_inhib.g	: Example of end-product inhibition from the tutorial in
			sections 2, 3 and 4.

group_epi.g	: Grouped version of end_prd_inhib model, from the tutorial
			in section 5.

y.data		: Example table I/O file with y point only on each line.
xy.data		: Example table I/O file with x y pairs on each line.

all117.g	: Example of monstrous research simulation from 
			Bhalla and Iyengar, Science 1999. It will need
			variable timesteps with small initial dt to run
			properly.

stoch_cycle.g	: Example of a stochastic simulation of a molecule which can
			exist in 4 states.
