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


  1. Andreas, please let me know how best I can help.

    I would like to see a checklist of tasks to do that every one could submit to and claim from. On the wiki?

    No one else has shown up in #biojava on irc at yet. :)

  2. Seems that none of the developers that are taking part are using IRC... We are all on Google Chat or Skype. If you want to take part via any of these, send me your details so I can add you...

  3. I've also added Biojava to, which would allow real-time commit notification via irc if we were to set up a svn post-commit script, or were to subscribe the ping email address to a svn commit notification mailing list, which as far as I know doesn't currently exist.

    As it is now, will poll every 15 minutes.

  4. I will update soon, the packages and classes for which I will write Cook Book Examples.

    Subrata Sinha