Archive for the ‘BioJava’ Category
Sunday, May 2nd, 2010
I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors:
Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms
Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, ...
Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, BioRuby, Biopython, Blipkit, Community, Development, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | No Comments »
Sunday, March 21st, 2010
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 ...
Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, BioRuby, Biopython, Blipkit, Community, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | No Comments »
Thursday, December 17th, 2009
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 ...
Posted in BioJava, BioPerl, BioRuby, Biopython, Blogroll, Community, Development, Documentation, General, OBF, OBF Projects | No Comments »
Saturday, August 30th, 2003
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 ...
Posted in BioDAS, BioJava, BioMOBY, BioPerl, Biopython, General, OBDA / BioSQL | Comments Off
Sunday, July 27th, 2003
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
Posted in BioJava | Comments Off
Friday, June 27th, 2003
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 ...
Posted in BioJava | Comments Off
Wednesday, June 18th, 2003
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 ...
Posted in BioJava | Comments Off
Tuesday, June 17th, 2003
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
Posted in BioJava | Comments Off
Thursday, June 12th, 2003
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 ...
Posted in BioJava, BioPerl, Biopython, OBDA / BioSQL | No Comments »
Thursday, June 5th, 2003
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
Posted in BioJava | Comments Off