Bioperl

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 goes well the official bioperl-1.2.1 will be released early next week.

GO::TermFinder will take a list of genes (any name that appears in an annotation file will do, though there are caveats for ambiguous names), an ontology file, and an annotation file, and determine the P_values for the observed frequency of annotation to those genes for each GO node. There are currently some differences between how the P-values are

The full announcement can be read here: http://bio.perl.org/pipermail/bioperl-l/2003-March/011707.html

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 this package on as many systems and architectures as possible.

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.

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.

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.

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