Archive for the ‘OBDA / BioSQL’ Category
Sunday, May 2nd, 2010
I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors:
Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms
Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, ...
Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, BioRuby, Biopython, Blipkit, Community, Development, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | No Comments »
Sunday, March 21st, 2010
The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code. Our list of project ideas and mentors is linked from the O|B|F GSoC page.
Student applications must be submitted to Google by April 9, 2010, see the official GSoC 2010 FAQ. That is ...
Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, BioRuby, Biopython, Blipkit, Community, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | No Comments »
Tuesday, December 15th, 2009
We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months after the release of Biopython 1.52. This is our first release since migrating from CVS to git for source code control.
There have been some additions to our core objects - ...
Posted in Biopython, Code, Development, OBDA / BioSQL, OBF Projects | No Comments »
Wednesday, August 13th, 2008
This is a belated news entry announcing the second BioSQL v1.0 (code-named Tokyo) release, v1.0.1, which was made on August 2, 2008. It is available from the BioSQL downloads page.
This version of the schema should be fully backwards compatible with the v1.0.0 schema for nearly all software and queries. The ...
Posted in OBDA / BioSQL | Comments Off
Thursday, March 6th, 2008
After a long wait and several earlier attempts, version 1.0.0 (code-named Tokyo, see below) of BioSQL has finally been released. The release can be downloaded at http://biosql.org/DIST/ as .tar.gz, .tar.bz, and Zip (which also has Windows-style end-of-line characters) archives. The full release announcement can be found in the BioSQL mailing ...
Posted in OBDA / BioSQL | No Comments »
Sunday, September 21st, 2003
I posted the slides for the Bioperl-db/BioSQL talk I gave at BOSC03.
-hilmar
Posted in BOSC/ISMB, BioPerl, OBDA / BioSQL | Comments Off
Saturday, August 30th, 2003
Hi Everyone,
Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers.
Simply put -- Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from ...
Posted in BioDAS, BioJava, BioMOBY, BioPerl, Biopython, General, OBDA / BioSQL | Comments Off
Thursday, June 12th, 2003
Do you need to access sequences from multiple places? Would you like
to easily retrieve your own local sequences from indexed flat files,
all other sequences on species X from department wide raletional
database and the rest from global internet servers?
The Open Biological Database Access (OBDA) System was designed so that
one could use ...
Posted in BioJava, BioPerl, Biopython, OBDA / BioSQL | No Comments »
Friday, May 23rd, 2003
Hilmar writes:
I got the Oracle version of the biosql schema fully migrated, at least as far as I can tell from here. I'm going to commit the new version some time today. There will also be a sql*plus migration script from pre-Singapore to the current version that supposedly keeps your ...
Posted in OBDA / BioSQL | Comments Off
Friday, February 28th, 2003
Hilmar writes:
Here's the background.
The current code in the bioperl-db adaptors to biosql run the connection with AutoCommit off, which means the client determines the transaction. Load_seqdatabase.pl (the main script for loading databases into biosql) treats one sequence entry as one transaction. If any sql statement required for loading the sequence ...
Posted in BioPerl, OBDA / BioSQL | Comments Off