Nat Goodman gave a talk on his impressions with BioPerl at a recent OReilly Bioinformatics Technology Conference.
The powerpoint slides can be downloaded here: http://conferences.oreillynet.com/presentations/bio2003/goodman_nat.ppt
All of the conference talks can be downloaded here (worth checking out): http://conferences.oreillynet.com/pub/w/21/presentations.html
From the session info:
Goodman
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.
[Read More]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.
[Read More]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).
[Read More]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
[Read More]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