[Biojava-l] Convince us to use BioJava (and come to the next bootcamp)

[Phillip Lord]

>>>>> "Tom" == Tom Hudson <hudsont@uncwil.edu> writes:

  Tom> A research group here at UNCW is starting a couple of
  Tom> bioinformatics projects in Java.  I said, "look here, there's
  Tom> this open-source group on the web that's created a huge amount
  Tom> of code already, let's use it!"

  Tom> The responses I've gotten have been on the order of "Eww, 600+
  Tom> classes. I can write my own parser faster than I can figure out
  Tom> what they're doing." and "We don't need data models anywhere
  Tom> near that complex."  So why should we use BioJava?  The
  Tom> "overview" on the web page hasn't convinced anybody here.

  Tom> (Caveats: right now we're a bunch of computer people and a
  Tom> bunch of biologists, with nobody really cross-trained; I
  Tom> understand that some day the biologists may start asking
  Tom> questions that require a nested-feature view of the world, but
  Tom> haven't convinced the other computer people to plan for that
  Tom> day yet, and the biologists can't think of any right now.)


Sit some of your more sane biologists down in a room, with some of
your more sane computer people. Work out what questions you want to
address computationally. Make sure the computer people bully the
biology people till they have straight answers about exactly what it
is they want to do. 

Then have the computer people work out what they will need to code to
do it. From that work out whether you need biojava or not. 

Personally I have found that once you start to pick a large library
apart then its easier to understand than you think its going to
be, so I would not let that be a metric. 

But knowing what you are going to do is vital.

Phil