Posts

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 fails unexpectedly, the whole transaction is rolled back, otherwise it is committed once the entry and all its annotation went in successfully. The emphasis rests on ‘unexpectedly’: INSERTs may fail due to unique key violations, which is caught and triggers a look-up of the affected entry by unique key. E.g. a dbxref may already exist; if so, it needs to be looked up in order to establish the association with the bioentry.

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. Even though some of these things significantly change the API, we (I, backed by the core people) propose to migrate these changes over to the ‘stable’ 1.2 branch, to be able to release bioperl-db (bridges to the biosql schema) in dependency on a stable bioperl branch.

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).

Mark has updated his “Biojava in Anger” website to add three more tutorials. One on OrderNDistributions another on WeightMatrices and one on Profile HMMs.

The website URL is http://bioconf.otago.ac.nz/biojava/

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

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. As any developer - and indeed user - who has used bioperl might have noticed, our sequence feature model is quite complex - this is because we have a number of drivers, in particular…

The full message was posted to the bioperl-l mailing list and can be read online at http://bioperl.org/pipermail/bioperl-l/2003-February/011225.html

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. Chris blames the Solaris audit subsystem for not liking root commands issued via SSH connections :)

We have moved the CVS repositories to a Linux box called “pub.open-bio.org”. Developer accounts have been created but with different passwords. Email the OBF Sysadmin team at root-l@open-bio.org to get your new password.

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)