[BioSQL-l] Announcement: BioSQL v1.0.0 released

Hilmar Lapp hlapp at gmx.net
Thu Mar 6 00:03:26 EST 2008

BioSQL v1.0.0 Release

I am extremely pleased to announce the release of version 1.0.0
(code-named Tokyo, see below) of BioSQL. The release can be
downloaded at the following location, in the following formats:

http://biosql.org/DIST/biosql-1.0.0.zip (has Windows-style EOL)

MD5 signatures (http://biosql.org/DIST/SIGNATURES.md5):
MD5(biosql-1.0.0.tar.bz2)= 2b09a821b9d94bb1e94c3c79dc2f4cff
MD5(biosql-1.0.0.tar.gz)= e47982d979ddb98aae640b5ab55ce2c6
MD5(biosql-1.0.0.zip)= 06913c8639ca4fe7f9000b556d8a04ed

The core BioSQL schema is a generic, extensible relational model for
sequences, sequence features, their annotation, and ontology terms. It
is also designed as the interoperable persistence interface between
the Bio* projects.

This version of the schema has essentially been the same since
November 2004. Software that worked with schema versions downloaded
from CVS (or, as of lately, svn) after November 2004 should work with
all 1.0.x releases.

This release contains
  - the core BioSQL schema as DDL (Data Definition Language) for the
    following RDBMSs: MySQL, PostgreSQL, Oracle, HSQLDB, and Apache  
  - ancillary (but optional) schema files for PostgreSQL,
  - documentation and an ERD (Entity-Relationship Diagram), and
  - a Perl script that can pre-load (and update) a BioSQL instance with
    the NCBI taxonomy.

Installation instructions for MySQL and PostgreSQL are in the file
INSTALL, and the file doc/bj_and_bsql_oracle_howto.htm has
instructions for installing the Oracle version.

Additional information regarding BioSQL, including links to language
bindings, a roadmap to future releases and enhancements, and possible
local optimizations is available from the BioSQL website at

On behalf of the BioSQL developers,

       Hilmar Lapp


BioSQL in general and this releases in particular owes enormously to a
number of number of people and would not exist without their
contributions, the contributions of people on the biosql-l mailing
list, and the support of other developers and users from the Bio*

Ewan Birney created the first version of the schema and during the
2003 BioHackathon in Singapore tested and wrote much of the INSTALL
document. Elia Stupka and Chris Mungall made significant changes at
the 2002 BioHackathons in Tucson, AZ, and Cape Town, South
Africa. Aaron Mackey was instrumental in the changes made at the
Singapore BioHackathon, which set the path to the version (code-named
'post-Singapore') that eventually stabilized as v1.0. Matthew Pocock
and Thomas Down provided important input for the ontology model.

This release and the accompanying work on cleaning up, updating
documentation, and jump-starting a useful (wiki) website was
irreversibly set in motion at the BioHackathon 2008 in Tokyo, and
would not have happened without the active encouragement from
several participants, especially Heikki Lehvahslaiho, Mark Schreiber,
Richard Holland, and Raoul Bonnal. Finally, without the superb and
prompt help from Mauricio Herrera Cuadra and Jason Stajich with
various wiki and other admin issues that occasionally reared their
heads we wouldn't have made it to this point.

In recognition of the role the BioHackathon 2008 played in getting
this release out the door, and in keeping with an informal tradition
held up since the first BioHackathon, I am code-naming the 1.0.x
release series the Tokyo release series of BioSQL.

Thank you to everyone!


BioSQL is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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