[Biojava-l] BioJava3 Use Cases

[Richard Holland]

Hi guys,

I'd like to repeat an earlier request for use cases to guide the new
BioJava 3 development work. We have a wiki page for this but it hasn't
seen many updates:

http://biojava.org/wiki/BioJava_3_Use_Cases

Could anyone who has a task which BioJava cannot currently achieve, or
does not achieve correctly, please add that task to this wiki page, so
that we can try and implement it in the new code.

A template for a use case has been provided on that same wiki page
which you should follow when submitting your own suggestions.
Basically the rule is that saying something like 'I want microarray
support' isn't likely to get much of a response, but asking for a
specific function, e.g. 'I want to be able to parse MAGE files' or 'I
want to use XYZ technique to analyse my own chip designs', will get
you a lot further.

I'm setting a cut-off date for the initial list of use-cases at August
1st. Whatever's on the page at that point will be considered for
implementation in the first phase of development over the next 6
months, along with updates or transfers of functionality from the
existing code base where appropriate. Anything that gets added to the
list after that date will only get implemented in the second later
phase, date indeterminate as yet, unless whoever submits the use case
also chooses to submit their own code to solve it!

cheers,
Richard

--
Richard Holland
Bioinformatics Software Developer
Eagle Genomics
http://www.eaglegenomics.com/