BioneQ, the Quebec Bioinformatics Network, is organizing the first North American BioJava Bootcamp from August 18th to 22nd. We have invited Matthew Pocock to come to Montreal to present the material that has been presented to the European Bootcamps for quite some time now. On the agenda (preliminary): -Sequence I/O and manipulations; -BLAST and FASTA parsing; -Using databases with BioJava; -Intro to Sequence GUI.
Heikki has converted some Bioperl workshop materials to a web slide show that is available here: http://www.ebi.ac.uk/~lehvasla/bioperl/
Thomas Down writes: After a long series of pre-releases (and many bug fixes), I’ve just finished building BioJava 1.30. Source, binaries, and javadocs can all be found at: http://www.biojava.org/download/ As with the pre-releases, separate binaries are available for java platform releases 1.3 and 1.4. The 1.4 releases include some extra features which depend on jdk1.4 extensions such as the java.nio package.
Rhett Sutphin provides a mini-primer and some example code that shows how to view Chromatogram files with java.
Do you need to access sequences from multiple places? Would you like to easily retrieve your own local sequences from indexed flat files, all other sequences on species X from department wide raletional database and the rest from global internet servers?
Mark writes: The tutorial site BioJava in Anger has been updated so the code examples reflect the new APIs in the upcomming BioJava 1.3 release.
Shawn Hoon announces the release of bioperl-run-1.2.0 which is an extention to the bioperl framework that contains modules that act as wrappers for common informatics applications.
Jonathan Epstein has a simple script and directions for browsing bioperl list traffic offline via a mobile device.
Tony writes: I have just checked in to the Bio::Das perl beta CVS repository (“Bio-Das2”) a collection of modules that creates a minimal DAS reference server from a single AGP file (or a directory of one or more files). There is also a sample server script in the “eg” directory.
Jason writes: I’ve added a parser for the ab initio gene predictor GlimmerM in Bio::Tools::Glimmer. Tests are added to t/Genpred.t now. It follows the Bio::Tools::AnalysisParser interface which support the next_prediction call and returns a Bio::Tools::Prediction::Gene object in the same way as Genscan. I also have some scripts for building the training set file so you can run Glimmer on other species.
Hilmar writes: I got the Oracle version of the biosql schema fully migrated, at least as far as I can tell from here. I’m going to commit the new version some time today. There will also be a sql*plus migration script from pre-Singapore to the current version that supposedly keeps your data intact (be sure to read the disclaimer though). This means we’re getting ready to release Biosql 1.0, possibly as early as next week.