Monday, January 18, 2010

BioJava Hackathon - Day 1


I am going to blog every day about the BioJava Hackathon, so you can stay updated with what is happening here in Cambridge.

In the morning I gave this presentation around which we had several discussions about what are the most critical issues we want to solve. The issues are:

  • Installation problems. Getting the latest checkout of the new Maven based build system causes problems for some of us. Sorting our the installation procedure is a major topic of the afternoon. It works successfully with the latest Eclipse, the m2eclipse plugin and subclipse plugin. Some of the NetBeans based developers also reported no problems during installations.
  • Features. The Biojava features should become a first class citizen. This means it should be possible to instantiate them independently of sequence objects.
  • Simplify Sequences: Sequences should be Strings as far as possible. Only convert them to Sequence objects if required.
  • Some of the BioJava 3 docu is not up to date and can lead to misunderstandings. The latest BioJava 3 code is available in the trunk
  • Memory efficiency: Make sure that iterating over RichSequences is memory efficient. (Fix a memory leak there)
  • Bytecode: The Biojava - core module should not require the Bytecode module.
Andy Yates is tweeting about it at