Tuesday, January 19, 2010

BioJava Hackathon - Day 2

Yesterday's contributor who added most lines of code is Michael Heuer, who is joining the hackathon from remote (i.e. somewhere in the US). He added the new FASTQ parser to BioJava. Well done Michael!

During the morning session we did a "Post Up", a silent and structured way of doing brainstorming. This was in order to come up with a new requirement how to do some state of the art pushing on the sequence modules. Scooter moderated a discussion where we focused on biologically meaningful representations of biological sequences. A Chemical Compound will be at the core of any sequence representation and we want to have different types of sequences like Chromosome sequence, Scaffold, DNA, RNA, Protein, and Sugars.

We started with test-driven development for the new sequence interfaces and then we will wrap the existing sequence code with the new interfaces. Here you can see us during the brainstorming session:

On the 3D structure side of things, we added a new 3D structure-gui module that is going to provide the Model View Control interface for the various open source viewers.


  1. If it hasn't been mentioned before, the Sequence Ontology (http://www.sequenceontology.org/) is a great resource for class names. It would be a shame if we used different definitions for classes than defined there.

  2. If your going to make the core representation a chemical compound then surely a sequence should be called a polymer?

  3. Yea, I like the idea of using names from the Sequence Ontology as class names. probably compound is not the best term...