0README

Sun Jul 24 22:19:07 MST 2005


Examples
|-- fd
|   |-- 0NOTE
|   |-- Makefile
|   |-- fd
|   `-- fd.c			source: application lsoda to driven oscillator
|-- run-1
|   |-- 0NOTE
|   |-- runHaldane		Haldane mechanism
|   |-- runMM			Michaelis-Menten mechanism
|   |-- runbi1			playing with a triangle of reactions
|   |-- runbi2				ditto
|   |-- runcht_amide		chymotrypsin, amide substrate
|   |-- runcht_ester		chymotrypsin, ester substrate
|   |-- runcht_ester1			ditto, different concn E, S
|   |-- runlacatmase		beta-lactamase
|   |-- runldh_0		ldh: 0 deg. 
|   |-- runldh_50		ldh: 50 deg.
|   |-- runldh_50_rev		ldh: 50 deg., reverse direction (from pyruvate)
|   |-- runlys			lysozyme with chitohexose
|   |-- runone_stepA		one intermediate reaction
|   `-- runtwo_step		two intermediates
|-- run-2
|   |-- 0NOTE
|   |-- S
|   |-- conc.list
|   |-- mk_set			run simul over set of concns, in conc.list
|   |-- one_step		temp. jump compared to mix - one intermediate
|   |-- prep_nologx		variant prep script
|   |-- run			basic react wrapper - MM mechanism
|   `-- two_stepa		temp. jump compared to mix - two intermediates
`-- run-3
    |-- 0NOTE
    |-- ldh-k			data for ldh reaction - ignore
    |-- mk-lys			simul lysozyme mech at set of concentrations
    |-- mk_conc_rate		simul Michaelis-Menten at set of concns
    |-- rate			react wrapper used for above MM simul
    `-- rate-lys			ditto for lysozyme


EXAMPLES
     Subdirectories under src/react/Examples have scripts that  apply  react
     to various mechanisms, mostly enzyme reactions.  These run under Mac OS
     X.  The examples are mostly tutorial to demonstrate  reaction  kinetics
     to  students.  The shell scripts generate the two input files for react 
     (.m and .p); the steps comprising a particular enzyme mechanism and the 
     rate constant associated  with each step  are taken from the literature.
     Generally  the simulation output,  after some prepping,  is piped into a 
     crude display program, ttygraph, which generates  a  labeled plot  in  a 
     24x80 xterm window.  Of course, nicer displays are produced with the use 
     of S or xgobi or the corresponding R programs.


John Rupley
 rupley@u.arizona.edu -or- jar@rupley.com
 30 Calle Belleza, Tucson AZ 85716 - (520) 325-4533; fax - (520) 325-4991
 Dept. Biochemistry & Molecular Biophysics, Univ. Arizona, Tucson AZ 85721
