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.

Brad has been working hard on trying to put together a new biopython.org page that incorporates the open-bio news server and the look and feel of the upcoming open-bio page.

Brad is working on an update of the Biopython website and is so obsessed with it that he is working on it during his minimal lunch time in which he should be enjoying the nice friendly sunshine of a Georgia friday. This is really not exciting news, but I need some Biopython news to test the news gathering capabilities of the main Biopython page. More info once I actually get something accomplished.

As I seem to be volunteering for more and more BioPerl documentation jobs recently, I thought I’d pool my resources and recycle some of my tuits to write a list summary. Expect these to be sporadic and incomplete; my goal is to highlight important questions, changes, fixes, and proposals, not recapitulate all list traffic.

Nat Goodman gave a talk on his impressions with BioPerl at a recent OReilly Bioinformatics Technology Conference.

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.

Hilmar writes: Triggered by what happened during the hackathon in Singapore, the Bioperl Ontology object model needs to undergo a number of changes that I’m going to describe below, along with a proposal how to resolve the issues. I have largely implemented the proposal and barring major objections I’m ready to commit tonight or tomorrow morning.

Date: February 24, 2003 Author: Lincoln Stein Version: early This report concerns the messaging layer of the Moby project, that point at which semantic information is exchanged between the data consumer (i.e. the biologist) and the data provider (i.e. the model organism system administrator). There are a wide variety of possible messaging systems. Here are a number of prominent ones listed in rough chronological order.

Mark has updated his “Biojava in Anger” website to add three more tutorials.

Generic and gene-specific coordinate system mappers are ready for use. These modules can ease the pain of mapping sequence features from one sequence coordinate to other ones, e.g. from cds to genomic and chromosomal. See the announcement at http://bioperl.org/pipermail/bioperl-l/2003-February/011110.html Code and documentation updates were finished at the Singapore BioHackathon. The fixes will be part of the upcoming 1.2.1 bioperl release.

Ewan talks about how one becomes a bioperl developer and how those invitations to hackathons get sorted out… http://bioperl.org/pipermail/bioperl-l/2003-February/011226.html