Heuer Bio Java Bosc2008
Transcript of Heuer Bio Java Bosc2008
Biojava Project Update
Bioinformatics Open Source Conference (BOSC) 2008Toronto, CA
18 Jul 2008
● Biojava home page– http://biojava.org
● Source code and related documentation:– Version 2.1 of the GNU Lesser General Public
License (LGPL)● Wiki documentation:
– Version 1.2 of the GNU Fee Documentation License
● Hosted by Open Bioinformatics Foundation (O|B|F)– http://open-bio.org
Project history
Project history
● Alphabets and Symbols● Basic Sequence
manipulation● Translation● Proteomics● Sequence I/O● Annotations● Locations and Features● BLAST and FASTA
● Counts and Distributions● Weight Matrices and
Dynamic Programming● User Interfaces● BioSQL and Sequence
Databases● Genetic Algorithms● Protein Structure● Ontologies● Phylogenomics
Major features
Latest version
● Latest version 1.6, released Apr 2008– Phylogenomics package improved and expanded
● 2007 Google Summer of Code (GSOC'07) student Boh-Yun Lee
– PDB file parser improved– Genetic algorithm package improved– Bug fixes and documentation improvements– Requires JDK 1.5 or later– Revision control migrated from CVS to Subversion
● In any software development project there is a natural tension between revolution and evolution.
● In a Free and Open Source project:– People work on their own time.– People work on what they want.– Some people are evolutionaries, others are
revolutionaries, and some are both at different times.
– Both approaches are important and need to be cultured.
● http://incubator.apache.org/learn/rules-for-revolutionaries.html
● The Second (or third) System problem
● "It's important to remember that when you start from scratch there is absolutely no reason to believe that you are going to do a better job than you did the first time."
– http://www.joelonsoftware.com/articles/fog0000000069.html
● But we're gonna try it (again) anyway
● Biojava home page– http://biojava.org
● Biojava BOF session T.B.A.