The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer’s Google Summer of Code. Our list of project ideas and mentors is linked from the O|B|F GSoC page.
Student applications must be submitted to Google by April 9, 2010, see the official GSoC 2010 FAQ. That is less than three weeks away!
[Read More]I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects:
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants Peter J. A. Cock ( Biopython), Christopher J. Fields ( BioPerl), Naohisa Goto ( BioRuby), Michael L. Heuer ( BioJava) and Peter M. Rice ( EMBOSS). Nucleic Acids Research, doi:10.1093/nar/gkp1137
This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.
[Read More]Hi Everyone,
Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers.
Simply put – Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from one ISP to a different Tier 1 internet backbone.
[Read More]The “Biojava in Anger: A Tutorial and Recipe Book for Those in a Hurry” posted online at http://www.biojava.org/docs/bj_in_anger/index.htm has been translated into French and Japanese
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]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
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/