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.
The bootcamp will be at the Universite de Montreal and the registration fee is $250US. If you are interested, use the following link to register:
[Read More]Heikki has converted some Bioperl workshop materials to a web slide show that is available here:
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.
Highlights of this release include:
- Packed storage of sequence data in memory
- Better support for the OBDA database access standards
- Improvements to the parsers for output from tools like blast and fasta.
- Many enhancements to the FeatureFilter system.
[Read More]Rhett Sutphin provides a mini-primer and some example code that shows how to view Chromatogram files with java.
His full posting can be read here: http://pw600a.bioperl.org/pipermail/biojava-l/2003-June/003896.html
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?
The Open Biological Database Access (OBDA) System was designed so that one could use the same application code to access data from all three of the database types by simply changing a few lines in a “configuration file”. This makes application code more portable and easier to maintain.
[Read More]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. Take a peek at http://bioconf.otago.ac.nz/biojava
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.
The full release announcement can be read here: http://bioperl.org/pipermail/bioperl-l/2003-May/012308.html
Jonathan Epstein has a simple script and directions for browsing bioperl list traffic offline via a mobile device.
The full post can be read online at: http://bioperl.org/pipermail/bioperl-l/2003-May/012287.html
Tony writes: {{ double-space-with-newline }} 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.
Briefly, the server is started using something like:
cd ./eg
./agpserver --dsn ncbi31 --port 3000 --agpfile ./AGP/chr1.agp
It can then be used by a DAS client in the normal way. It is simple (no frills!) and capable of serving assembly information, entry_points, DSN info, features across a segment and features by ID. No other DAS commands are supported yet.
[Read More]