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
[Excerpt] …Bioperl hackers who have been at Singapore have been discussing the next generation of sequence feature handling.
About 30 open source informatics developers are hacking away in Singapore now working on various efforts. The main website is at http://hackathon.open-bio.org and contains links to the Blog site and the picture gallery.
Urgent notice –> Primary CVS server has been relocated to pub.open-bio.org “dev.open-bio.org” – our primary developer server is down in Boston with a corrupt password file.
Mark reports: Just noticed a little snippit about biojava in the latest issue of the scientist http://www.the-scientist.com/yr2003/jan/labcon_030127.html (free registration required to view the article)
Jason reports: Bioperl 1.2 was mentioned in ‘The Scientist’ (free registration required to read this link) http://www.the-scientist.com/yr2003/jan/labcon_030113.html