# $Id: README,v 1.9 2001/11/16 14:50:02 elia Exp $ This code currently works properly with the bioperl 0.7.x series of stable releases and should not be used with the "live" (main-trunk) code. 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 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' works fine. 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 or the bioperl list . 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