**** E-Predict v. 1.0 README, June 2005 ****


INTRODUCTION

	This version of E-Predict is an open-source implementation of
	the algorithm described in

	Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL.
	E-Predict: A Computational Strategy for Species Identification Based
	on Observed DNA Microarray Hybridization Patterns.
	Genome Biology, 2005.

	The algorithm is implemented as a web application intended for
	installation on	a web server to be run remotely via a web browser.
	The main program (epredict.pl) is a Perl CGI script, which requires
	Perl 5.0 or later to run. The implementation uses three C++
	executables (metrics, normidist, and vecnormViro) for number crunching
	tasks requiring speed.

	The software is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
	OR CONDITIONS OF ANY KIND (see license info below).


INCLUDED FILES

	LICENSE
	README

	cgi-bin/
		Csnips.pm
		epredict.pl
		csnips/
			metrics
			normdist
			vecnormViro

	data/
		Epred_paper_example1.vdar
		Epred_paper_example2.vdar
		Epred_paper_example3.vdar
		Epred_paper_example4.vdar
		other/
			2004-07-22.ematrix
			2004-07-22.ematrix.params
			MV_72worst_medRaw500_badYdens.uwts
			oligo_annotation

	src/
		makefile
		metrics.cpp
		normdist.cpp
		vecnormViro.cpp
		


SYSTEM REQUIREMENTS

	Running server such as Apache v. 1.3 or	later,
	Perl 5.0 or later with CGI.pm


INSTALLATION

	1. Uncompress E-Predict_v1.0.tar.gz

	2. Make the uncompressed E-Predict_v1.0 directory and subdirectories
		readable and executable by the server. An easy way to do this
		is to place the entire E-Predict_v1.0 directory in the
		cgi-bin directory already used by your server.

	3. Edit paths to the E-Predict and cgi-bin directories ($root and
		$cgi_bin variables) in epredict.pl

	4. Edit path to the csnips directory ($snips variable) in Csnips.pm

	5. This should do it on most UNIX/LINUX machines. To run the
		application, simply point your web browser to epredict.pl.
		For example, the URL might look like this --
	"http://www.yourserver.edu/cgi-bin/E-Predict_v1.0/cgi-bin/epredict.pl"

	6. Executables of the C++ components (metrics, normdist, and
		vecnormViro) are included and should work without recompiling
		on most UNIX/LINUX machines. If needed, these components
		can be recompiled using the makefile in the src/ subdirectory.
		The makefile will automatically move the executables into
		the E-Predict_v1.0/cgi-bin subdirectory. Note - a C++ compiler
		like G++ is required.


USAGE

	Run epredict.pl by pointing your web browser to the script's URL.
	A settings page will be displayed. Select a desired dataset from
	the four provided examples (described in Urisman et. al, 2005).
	Press 'Submit' to run the algorithm.


LICENSE

	E-Predict v. 1.0 is licensed under the Apache License, Version 2.0.
   	A copy of the license is included in this distribution or can be
	viewed at http://www.apache.org/licenses/LICENSE-2.0