Read Me

GeneX Server README -- Gene Expression Database Server

  <CVS versioning line removed, as we no longer use CVS>
  
  Authors:  Harry Mangalam, hjm@tacgi.com
            Jason Stewart, jason@openinformatics.com

LEGAL HOOP JUMPING
==================

Copyright (c) 2001 National Center for Genome Resources. 
Copyright (c) 2001-2002 Open Informatics
All rights reserved.  

This package is free software. It is distributed under the terms of
the Academic Free License (see LICENSE for details).

The authors of this software make no claims as to the performance or
reliability of this product. Use it at your own risk. If you find it
helpful, We're very happy for you, if not, don't hold us responsible.

Description
===========

The GeneX system is not a simple application; it consists of a number of 
parts:

- The data model (see the PDF file docs/GeneX-Schema.pdf)

- The Genex.pm Perl module that provides the capability to manipulate the
  database as well as utilities to read and write the MAGE-ML that is the
  common transport protocol between database(s) and client(s).

- The MicroArray Gene Expression-Markup language , an XML that both the
  utilities  and the Database can both read and write.

- The Mason-based Web GUI to the database and all the scripts required to
install the package, administer the system, load arrays and browse the
data.  The analytical parts of the systems are being implemented via
plug-ins to the OpenOffice spreadsheet program so that users can query and
retrieve data into a familiar spreadsheet application and use it's
built-in functions to help analyze and filter the data.

- it does NOT include but does depend on a number of Open Source packages,
including the Perl scripting language, the OpenOffice.org office suite for
interacting with the database, the PostgreSQL object relational database,
the apache web server and a variety of its components, especially mod_perl
and Mason.  The process by which to install all these bits is described in
the INSTALL doc.

All these parts have been combined as a decent, functioning (if minimal)
starting point, but we require your input to make them better.   If you don't
complain, we can't fix/improve it.  Since this is an Open Source Project, we're
also looking for others to contribute ideas and code, so please speak up!


How To Get The Latest Version
=============================

Use the following URL to get the current information about GeneX:

  http://genex.sourceforge.net/

To get the latest version of Genex, you have to check it out of the
subversion code repository.  Despite what may look like a weird syntax,
it's very simple and guarantees that you'll get (and can maintain) the
latest version of GeneX:

 svn co http://genex2:110/svn/trunk/genex-server

(in order to perform this command, you will of course need the subversion
client - on Debian, as root, do this:

apt-get install subversion



Software
--------

- Operating System: Unix-like, preferably Linux. We have successfully
  installed GeneX on Intel and PowerPC architectures, with RedHat 8.x and
  Debian Sid systems.  We develop on and recommend Debian UNSTABLE as a
  GeneX server platform.  YOu can use a commercial Debian-based system to
  install the base system and then upgrade to unstable (aka Sid) once it's
  functional.  I recommend the MEPIS or LibraNet Debian distros as
  starting points.

   It has also been successfully installed on Solaris, tho not recently. 
  
  Other flavors of Unix should work, but will require tweaking.

- Utility software: All recent, full Linux distros include (and
  GeneX depends on): 
  * gnu tar, 
  * gnu text & file utils (version >= 2 as gnu sort < version 2 
    doesn't sort exponents)
  * sendmail (or a sendmail replacement such as exim)
  * Perl >=5.8.0 
  * apache web server, version 1.3.x.  (NOT apache version 2)

- Other Packages: Some distros will include these apps which are
  also needed for full functionality.  If you cannot find them on your
  system already with 'which', 'whereis' or 'locate', you'll have to
  add them yourself via RPM or dpkg/apt-get. Most easily found at rpmfind.net
  or get the debs or tarballs from the URLs below.

  * Postgres (>=7.3) => http://www.postgresql.org
  * libexpat         => http://sourceforge.net/projects/expat/

  In order to produce the html versions of the DTD's you will also
  need a modified version of Earl Hood's excellent perlSGML utilities
  that we distribute from:
    http://genex.ncgr.org/genex/download/genex-server/perlSGML.2001Jan23.tar.gz
    (supplies the dtd2html utility to generate the docs for the DTDs)
    
    
!!These should be installed BEFORE trying to install the GeneX components!!    

    >>>>>> See the INSTALL file for Full details <<<<<<<


Feedback
========

We're grateful you're giving GeneX a spin, and we hope you enjoy the
trip. If you have any comments or questions, please let us know at:
   
   genex-dev@lists.sourceforge.net 

(we really mean that - Please let us know!)

<the genex development team>
  

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