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

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>