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BioPerl BioSQL ORM
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Bio/DB
model
scripts
sql
t
Changes
MANIFEST
Makefile.PL
README

README

# $Id$

This directory contains code from the bioperl-db CVS repository. 
===================================================================
There are currently 2 logical projects contained within here, a system
for sequence file storage in a relational (currently only mysql)
database and a system for storage of marker and map information within
a relational database (currently only mysql supported).


Information about Bio::DB Interface with a mysql Sequence database.
===================================================================

This project was started by Ewan Birney with major work by Elia Stupka
with continued support by the bioperl community.  It's purpose is a
standalone sequence database with little external dependancies and
tight integration with bioperl.  Support for more databases and
bindings in java and python by Biojava and Biopython projects are
welcomed.  All questions and comments should be directed to the
bioperl list <bioperl-l@bioperl.org> and more information can be found
about the related projects at http://bio.perl.org and
http://www.open-bio.org.

Currently the necessary modules for this project are in the Bio/DB
directory with the necessary sql in the sql/basicseqdb-ARCH (where
ARCH is db architecture supported - currently only mysql). 

Related scripts located in the scripts directory:

load_seqdatabase.pl     - example of how to load seqs in the
		          database
bioentry2flat.pl        - dump sequence data into rich sequence
		          format flatfile representation
caching_corba_server.pl - setup a corba sequence caching server
test_bioenv.pl          - test the bioenv of a running server
bioenv_server.pl        - setup a CORBA sequence server


Hard and Fast install instructions.

1) a mysql db server 

2) an account on the server

Running 'make test' should now work. To set the options for the test
suite, look into t/DBTestHarness.pm and make a file called
DBTestHarness.conf

3) Make a single SQL database. In general many biological 
   "databases" will go into a single SQL instance

4) do the following (substituting your db name where appropriate)

   % mysql -u someone sqldbname < sql/basicseqdb-mysql.sql

5) scripts/load_seqdatabase.pl should now work.

6) write down any problems, complaints and send them to bioperl ;)

Information about Bio::DB::Map modules and database interface
===================================================================

These modules are Copyright Jason Stajich 2001 and are licensed
according to the perl Artistic license (see
http://www.perl.com/pub/language/misc/Artistic.html).

This project was started by Jason Stajich as an attempt to build a
single normalized repository for marker and map data to facilitate map
integration and exploring comparative genomic questions.  All queries
should be addressed to Jason Stajich <jason@chg.mc.duke.edu> or the
bioperl list <bioperl-l@bioperl.org>.  More information about this and
related projects can be found at http://bio.perl.org and
http://www.open-bio.org.

Currently the necessary modules for this project are in the Bio/DB/Map
directory with the necessary sql in the sql/markerdb-ARCH (where
ARCH is db architecture supported - currently only mysql). 

This project is very much in development.  In the planning stages are
cgi scripts to interface with modules and allow researchers to
integrate different map locations with sequence data.  

Scripts for loading private genetic and marker maps are also to be
provided.

Related scripts located in the scripts directory:


download_marker_data.pl - automate downloading of marker information
			  for local testing and faster installation

load_marshfield_map.pl - load marshfield genetic map data from
			 published data and associated marker primers
			 from NCBI STS repository, either from local
			 data or directly from the primary source
			 (requires live internet connection).

load_whitehead_markers.pl - load whitehead STS markers and related RH
			    map information from 1997 publication,
			    either from local data or directly from
			    the primary source (requires live internet
			    connection).

load_genethon_data.pl - load genethon CA repeat markers and genetic
			map from 1995 Nature publication, either from
			local data or directly from the primary source
			(requires live internet connection).

load_genemap_data.pl - load genemap99 markers and map information from
		       NCBI repository of the March 1999 published
		       data, either from local data or directly from
		       the primary source (requires live internet connection).



Information about modules formerly contained within this CVS module
===================================================================
Bio::EnsemblLite - Deprecated
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