BioSQL and Bioperl-db inching towards…

[ May 23, 2003 ]

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 data intact (be sure to read the disclaimer though).

New biopython.org website

[ May 11, 2003 ]

The day you’ve been waiting for is finally here. That’s right, it’s time for a brand new biopython.org website! Woo. […]

new tab sequence format

[ April 17, 2003 ]

Heikki writes: Philip Lijnzaad has written a new sequence format module called ‘tab’. It is in CVS. Here is the […]

Windows PPM for bioperl-1.2.1 available

[ April 8, 2003 ]

Nigam Shah has created the necessary PPM/PPD distribution files for bioperl-1.2 .1 that will allow ActiveState perl users on Windows […]

MOBY-DIC-III pictures & meeting minutes…

[ April 8, 2003 ]

March 15-16, 2003 — About a dozen Moby developers gathered recently. Minutes from the meeting are online at http://www.biomoby.org/twiki/bin/view/TWiki/CarnegieTAIR and […]

Bioperl-1.2.1 released

[ March 31, 2003 ]

The release is available at http://www.bioperl.org/ftp/DIST/bioperl-1.2.1.tar.gz and is propagating around CPAN now.

prerelease bioperl-1.2.1 available for testing

[ March 30, 2003 ]

We need you! Please download and help test a potential 1.2.1 release candidate that is available at http://bioperl.org/ftp/birney/bioperl-1.2.1-rc2.tar.gz If all […]

Stanford releases GO::Termfinder modules

[ March 25, 2003 ]

GO::TermFinder will take a list of genes (any name that appears in an annotation file will do, though there are […]

Foundation views wrongly characterized in…

[ March 25, 2003 ]

In the March 2003 issue of Genome Technology, “Opposite Strand” contributor Gerald Barnett’s insightful article on “free choice for open […]

New mailing list Bioped-l

[ March 17, 2003 ]

A new mailing list has been created for discussion of software system for genotypes, pedigrees, and linkage data at http://www.open-bio.org/mailman/listinfo/bioped-l […]

Bioperl v1.2.1 RC1 available for…

[ March 16, 2003 ]

A release candidate for an eventual Bioperl 1.2.1 release is online at: http://bioperl.org/ftp/birney/bioperl-1.2.1-rc1.tar.gz We need people to install and test […]

NCICB reviews two LSID Resolution…

[ March 16, 2003 ]

Members of the caCORE team at the NCICB have been discussing if and how best to use LSIDs. Attached is […]

Technical Report on Semantic Standards

[ March 12, 2003 ]

Andrew Farmer writes: Here’s the current revision of my writeup on semantic standards; the only major difference between this and […]

Moby Messaging Layer Technical Report…

[ March 10, 2003 ]

MOBY PROJECT: TECHNICAL REPORT ON WEB MESSAGING LAYER Date: March 9, 2003 Author: Lincoln Stein Version: 1.0 This report concerns […]

Ontology overhaul: migration to 1.2…

[ March 10, 2003 ]

This is the last call for people to test drive and/or criticize the Bio::Ontology & Bio::OntologyIO re-design and implementation.

The interfaces and modules to look at comprise of Bio::Ontology::OntologyI, Bio::Ontology::TermI, and Bio::OntologyIO. If you care about implementations (as Aaron says most people do rather than bothering with interfaces), check out Bio::Ontology::Ontology, Bio::Ontology::Term, and Bio::OntologyIO.

Prototype of a new biopython.org…

[ March 8, 2003 ]

Brad has been working hard on trying to put together a new biopython.org page that incorporates the open-bio news server […]

Working on the Biopython Website

[ March 7, 2003 ]

Brad is working on an update of the Biopython website and is so obsessed with it that he is working […]

BioPerl List Summary – January…

[ March 4, 2003 ]

As I seem to be volunteering for more and more BioPerl documentation jobs recently, I thought I’d pool my resources […]