README for EdgeExpressDB (eeDB) system

EdgeExpressDB is a system for working with "systems biology" data.
It is a federated database, webservice and AJAX client system
with easy instance creation, many pre-made loader scripts
and a standard set of webservices.  In addition the FANTOM4
EdgeExpressDB website code is provided to be used as is or
to give inspiration for new website creation.
In order to main inter-operability, the webservices should
not be altered, but new web-service engines can be made.
In addition the system provides some levels of 
data-processing capabilities through the EEDB::Tools.

This initial release is not as well documented as hoped, 
but the system is easy to install and use so I hope what
we do provide will be OK for "early adopters".
Future releases will include better documentation in
addition to new features and services.

Please also see our paper in GenomeBiology and please
reference it if you use the EdgeExpressDB system for your research.

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs,
expression dynamics and regulatory interactions.
Genome Biol. 2009 Apr 19;10(4):R39. 
Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de
Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR.
PMID: 19374773 [PubMed - as supplied by publisher]


Refer to the pod for full documentation and an example script, 
or to the following mirrors:

1/ http://search.cpan.org/perldoc?EEDB
2/ http://search.cpan.org/~jms

copyright (c) 2006-2009 Jessica Severin

CONTACT POINT
-------------

jessica.severin@gmail.com <Jessica Severin>
http://search.cpan.org/~jms

LICENSE
-------

* Software License Agreement (BSD License)
* EdgeExpressDB [eeDB] system
* copyright (c) 2006-2009 Jessica Severin
* All rights reserved.
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*     * Redistributions of source code must retain the above copyright
*       notice, this list of conditions and the following disclaimer.
*     * Redistributions in binary form must reproduce the above copyright
*       notice, this list of conditions and the following disclaimer in the
*       documentation and/or other materials provided with the distribution.
*     * Neither the name of Jessica Severin nor the
*       names of its contributors may be used to endorse or promote products
*       derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ''AS IS'' AND ANY
* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDERS BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


OVERVIEW
--------
MQdb.pm is a base toolkit for working with relational databases in the context
of a federation of object databases. It provides some base federation support
and a variation on other Object-relational-mapped template systems.

VERSION
-------
0.953 Monday May 18, 2009

DOCUMENTATION
-------------
The following documentation is available:
USER_INSTALL
and pod in perldoc format (type perldoc EEDB::... on command line)

INSTALLATION INSTRUCTIONS
-------------------------
please see the USER_INSTALL document since this system is more than
just perl modules.  There are scripts, schemas, and webservices
that also need to be installed.

the script install.sh and eedb_create_instance.pl will do most of the work


KNOWN BUGS & ISSUES
-------------------
none at this time.

COMMENTS/FEEDBACK
-----------------
Please email your feedback, comments, questions to the email address at the top
of this document. I will do my best to answer promptly. 

Jessica Severin <jessica.severin@gmail.com>

