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.
The day you’ve been waiting for is finally here. That’s right, it’s time for a brand new biopython.org website! Woo. Thanks to the hard work of Chris Dagdigian and your Biopython team, we’ve got our new website set up on a new up to date Linux server. Come check out all the excitement at biopython.org.
Heikki writes: Philip Lijnzaad has written a new sequence format module called ’tab’. It is in CVS.
Nigam Shah has created the necessary PPM/PPD distribution files for bioperl-1.2 .1 that will allow ActiveState perl users on Windows machines to easily install the bioperl suite and the most common bioperl external module dependencies. The PPD file is online at http://bioperl.org/ftp/DIST/Bioperl-1.2.1.ppd.
March 15-16, 2003 – About a dozen Moby developers gathered recently.