0README

Wed Jul 27 14:34:47 MST 2005


Simplex-1991
|-- 0NOTE
|-- 0README
|   
|-- Makefile			compiles, builds, tests ldhfit and linefit
|   
|-- Doc				directory - documentation for simplex fit
|   |-- 0README
|   |
|   |-- Data_redn.txt			documentation, ascii files
|   |-- Input.txt
|   |-- Output.txt
|   |-- Simplex.txt
|   |
|   |-- simplex.1			man page - groff man macros
|   |-- simplex.1.ps				& more readable formats
|   |-- simplex.1.txt
|   `-- simplex.1.txt-nobs
|   
|-- Ldh				directory - sources, executable, tests:
|   |					    function for nonlinear least-sq fit
|   |					    of lactate dehydrogenase enzyme
|   |					    rate data
|   |-- 0NOTE
|   |-- 0README
|   |
|   |-- Makefile
|   |-- ldhfit				executable - function + simplex library
|   |-- ldhfit.c			C-code for function
|   |
|   |-- ldhfit.dat			ldh rate data, independent variables
|   |						2 reactant & 1 product concn,
|   |						parameter and control values 
|   |						= input for ldhfit
|   |-- ldhfit.out			output from ldhfit, under macosx
|   |-- ldhfit1991.test1991		above differently named
|   |
|   `-- tests				directory - tests of ldhfit program
|       |-- ldhfit.test1-4d30			1991 output, under sgi 4d30
|       |-- ldhfit.test1-mod-4d30		above, edited so can diff with 
|       |					    output of macosx compiledd 
|       |					    program (rearranged order
|       |					    of output - ldhfit.c code 
|       |					    changed btwn 1991 & now)
|       |-- ldhfit.test2-4d30			etc. etc.
|       |-- ldhfit.test2-mod-4d30
|       |-- ldhfit.testx-4d30
|       |-- ldhfit.testx-mod-4d30		as above, except fit without
|       |					    quadratic approximation
|       |					    (simplex only used in fit)
|       |-- test.data
|       |-- test.data-bounds
|	|
|       |-- test.out
|       |-- test.out-macosx			current results, under macosx
|       `-- test.outx-macosx			current results, no quad approx
|
|-- Lib				directory - sources simplex fit library
|   |-- 0NOTE
|   |-- 0README
|   |
|   |-- Makefile
|   |-- simpdefs.h
|   |-- simpdev.c
|   |-- simpfit.c
|   |-- simpinput.c
|   |-- simplib0.c
|   `-- simpmain.c
|
|-- Line			directory - sources, executable, tests:
|   |					    function for linear least-sq fit
|   |					    of test set of data to straight line
|   |					    compare with hand calcutions
|   |-- 0NOTE
|   |-- 0README
|   |
|   |-- Makefile
|   |-- linefit				executable - function + simplex library
|   |-- linefit.c			C-code source for function
|   |
|   |-- linefit.dat			data, parameters - input for linefit
|   |
|   |-- linefit.out			results of fit
|   |
|   `-- tests				directory - various tests of linefit
|       |-- linefit.test1-4d30
|       |-- linefit.test1-mod-4d30		1991 results, under 4d30,
|       |					    edited as above
|       |-- linefit.test2-4d30
|       |-- linefit.test2-mod-4d30
|       |-- linefit.test2003-octane
|	|
|       |-- test.data
|	|
|       |-- test.out
|       `-- test.out-macosx			current results, under macosx
|   
|-- biphasic				directory - explore model: two protein
|   |						    species, each irreversibly
|   |						    reacting to give product;
|   |						    related to lexA cleavage
|   |-- 0NOTE
|   |-- 0README
|   |-- 1-README.2exp
|   |
|   |-- Makefile
|   |-- biphasic				executable
|   |-- biphasic.c				C source for function
|   |
|   |-- bgall.test				script to run biphasic
|   |-- mk.data.awk
|   |-- mk.plot
|   |-- plotall.test				script to plot results
|   |-- prep					script to prep results for plot
|   |
|   |-- test.data.9x				data, control input for biphasic
|   |
|   |-- test.out.9-1991				1991 results of fit, under 4d30
|   |-- test.out.9x				current macosx results
|   |
|   |-- test.plot.9-1991			as above, plots
|   `-- test.plot.9x
|   
|-- lexa                        directory - analysis of measurements of the
|   |					    pH dependence of the rate of 
|   |					    autolysis (autocatalytic cleavage)
|   |					    of wild-type and mutant lexA 
|   |					    (data from John Little laboratory);
|   |-- 0NOTE
|   |-- 0README
|   |-- 1-README.fits
|   |-- 1-README1.erratum
|   |-- 1-README1.jlittl
|   |
|   |-- Makefile			
|   |-- lexfitB				executable, model B, lexa cleavage data 
|   |-- lexfitB.c			C code for above
|   |-- lexfitken			executable, model ken, lexa ....
|   |-- lexfitken.c			C code for above
|   |
|   |-- bgallB				script wrapper - lexfitB -> results file
|   |-- lex.prep
|   |-- longprep
|   |-- mk.special
|   |-- mk.theory
|   |-- plot.theory
|   |-- plotallB			script - plot data & calcd values
|   |-- prep
|   |-- rawdata.lexa
|   |-- runallB				script - combine bgallB and plotallB
|   |-- sd.awk
|   |-- theory.prep
|   |
|   |-- results.B			directtory - results from lexfitB
|   |   |-- lexa.data.1				data, cntrl values, param set 1
|   |   |-- lexa.data.1-1991
|   |   |-- lexa.data.2				same, param set 2
|   |   |-- lexa.data.2-1991
|   |   |-- lexa.data.3				etc
|   |   |-- lexa.data.3-1991
|   |   |
|   |   |-- lexa.out.1				fit results, parm set 1, macosx
|   |   |-- lexa.out.1-1991A			old fit results, under sgi 4d30
|   |   |-- lexa.out.2				etc.
|   |   |-- lexa.out.2-1991
|   |   |-- lexa.out.3
|   |   |-- lexa.out.3-1991
|   |   |
|   |   |-- lexa.plot.1				plot data & calcd - parm set 1
|   |   |-- lexa.plot.1-1991			etc
|   |   |-- lexa.plot.2
|   |   |-- lexa.plot.2-1991
|   |   |-- lexa.plot.3
|   |   |-- lexa.plot.3-1991
|   |   |
|   |   |-- lexa.plotth.1-1991			plot data & calcd curves - set 1
|   |   |-- lexa.plotth.2-1991
|   |   |-- lexa.plotth.3-1991
|   |   |
|   |   |-- bgallB -> ../bgallB
|   |   |-- lex.prep -> ../lex.prep
|   |   |-- lexfitB -> ../lexfitB
|   |   |-- longprep -> ../longprep
|   |   |-- mk.special -> ../mk.special
|   |   |-- mk.theory -> ../mk.theory
|   |   |-- plot.theory -> ../plot.theory
|   |   |-- plotallB -> ../plotallB
|   |   |-- prep -> ../prep
|   |   |-- runallB -> ../runallB
|   |   `-- theory.prep -> ../theory.prep
|   |
|   `-- results.B.corr			directory - more results lexA data fits
|       |-- kendata-1992			data, cntrl, params - lexfitken
|       |-- kendata.one-1992
|       |-- kendatax
|       |-- kendatax.one
|       |
|       |-- kenout-1992				4d30 results, fit with lexfitken
|       |-- kenout.one-1992			etc
|       |-- kenoutx				current macosx fit results
|       |-- kenoutx.one				etc
|       |
|       |-- lexa.data.1-1992			data, cntrl, params - lexfitB
|       |-- lexa.data.x
|       |
|       |-- lexa.out.1-1992			4d30 output
|       |-- lexa.out.x				current macosx results
|       |
|       |-- lexa.plot.1-1992			4d30 plots of data and calcd
|       |-- lexa.plot.x				macosx
|       |
|       |-- bgallB -> ../bgallB
|       |-- lex.prep -> ../lex.prep
|       |-- lexfitB -> ../lexfitB
|       |-- lexfitken -> ../lexfitken
|       |-- longprep -> ../longprep
|       |-- mk.special -> ../mk.special
|       |-- mk.theory -> ../mk.theory
|       |-- plot.theory -> ../plot.theory
|       |-- plotallB -> ../plotallB
|       |-- prep -> ../prep
|       |-- runallB -> ../runallB
|       `-- theory.prep -> ../theory.prep
|   
`-- mmfit			directory - three programs to fit enzyme rate
    |					    data to Michaelic-Menten equation
    |-- 0NOTE
    |-- 0README
    |-- data.sample
    |
    |-- Makefile
    |-- mmfit				executable	| nonlinear least-sq
    |-- mmfit.c				C source	| fit,
    |-- mmfit.dat			data,parameters	| uniform weights
    |-- mmfit.dat-1991					|
    |-- mmfit.out			results, macosx	|
    |-- mmfit.out-2003			results, 2003 sgi octane |
    |
    |-- recip_nowt			executable	| linear least-sq fit
    |-- recip_nowt.c			C source	| Lineweaver-Burke eqn
    |-- recip_nowt.out			results, macosx	| uniform weight
    |					use same data	| BAD!
    |					file as recipfit|
    |
    |-- recipfit			executable	| linear least-sq fit
    |-- recipfit.c			C source	| Lineweaver-Burke eqn
    |-- recipfit.dat			data,parameters	| 1/V^4 weights
    |-- recipfit.dat-1991				| GOOD! 
    `-- recipfit.out			results, macosx	| 



The Makefile in the directory "Simplex-1991" compiles, builds, and
tests two fitting programs, "ldhfit" and "linefit":

	cd Simplex-1994
	[make spotless]		#if you want to build from scratch
	make all		#to ensure linefit and ldhfit are built
	make testline
	make testldh
	make testldhx


All directories below Simplex-1991 that have code, compile and run
under Mac OS X.  The makefiles, found in the following directories, work,
i.e., compile the various programs or library and generally run tests:

	./Lib/Makefile
	./Ldh/Makefile
	./Line/Makefile
	./biphasic/Makefile
	./lexa/Makefile
	./mmfit/Makefile


Various directories have "0NOTE" and "0README" files: the latter likely to
have useful descriptions; the former, notes on porting, etc., of limited
interest except for myself.

For further information, in addition to the documentation files (in
"Simplex-1991/Doc"), please read the man page ("man simplex"), and
the paper by Nelder and Mead (1965) (see the pdf file
"../nelder-mead-paper.pdf").


There are three applications directories under Simplex-1991:

	mmfit
		three programs to fit enzyme rate data to the
		Michaelis-Menten equation (rate law):
			mmfit - built from mmfit.c
				nonlinear least squares
			recipfit - from recipfit.c
				linear least squares fit of
				Lineweaver-Burke eqn
				with correct weights (1/V^4)
			recip_nowt - recip_nowt.c
				linear least squares fit of
				Lineweaver-Burke eqn, but....
				with wrong weighting (equal weights)

	lexa
		analysis of measurements of the pH dependence of
		the rate of autolysis (autocatalytic cleavage) of
		wild-type and mutant lexA (data from John Little's
		laboratory);
			data fit by two models:
				lexfitB (lexfitB.c) 
				lexfitken (lexfitken.c)
			models have up to eight variable parameters

			scripts to display fit results with crude graphics 
			program (piped to ttygraph):
				prep
				plotallB
				plot.theory
				etc.

			results in directories:
				Simplex-1991/lexa/results.B
				Simplex-1991/lexa/results.B.corr

	biphasic
		play with triangle of irreversible reactions, wrt
		cleavage of lexA.


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