At least Christian and I are going to ISMB/ECCB, and the preceeding BOSC
and 'codefest' - i.e. a bioinformatics hackathon. We should start
thinking of some tasks to address, and there's a common document for the
codefest (see attached main from Brad Chapman).
Some things I'd be interested in:
* Separating out a bio-core library. There is a bit of overlap
between the different libraries, I think there's a market for a
small common library with the most common, shared, data
definitions.
* benchmarking the bio library. I used to have a hacked quickcheck
for this, but it doesn't work after moving to QC2. A better
approach is to use criterion for this.
* Iteratee-based parsing and analysis. I really need to experiment
with iteratees and enumerators to get a better feel for how they
work in practice. This is likely to be more a learning
experience than resulting in useful code, but who knows?
* Cleaning up parser interfaces. Unless we decide to move
everything to iteratees, I'd like all file formats in bio
to follow the '{de,en}codeFoo,{read,write}Foo'(etc) pattern.
And of course, the perennial task of improving documentation and adding
test cases...
Also, broadening our horizons a little:
* Look into packaging of libraries and applications (rpms and debs),
especially 'flower' and 'flowsim', but perhaps others as well.
* Integrate applications with Galaxy or other platforms.
This is just some stuff I thought of, doubtlessly I've missed many
important and interesting things, so please suggest or vote for whatever
tasks you prefer to see worked on!
-k
--- Begin Message ---
Hello everyone;
Thanks so much for signing up for Codefest 2011. I'm thrilled to see
so many interested developers and am looking forward to a fun two
days of coding:
http://www.open-bio.org/wiki/Codefest_2011
This mailing list is setup to help facilitate introductions and
discussions leading up to our trip to Vienna. The work and content
of Codefest is completely dictated by you, the attendees, so we have
a month to decided on a plan of attack that will make it a productive
two days. I put together a shared public Google document we can use for
collecting discussions, and kicked things off with some suggestions
for work related to the CloudBioLinux project:
https://docs.google.com/document/d/1EFe9YszL5Lp5FjZjJLFhWepsto1jhC6oASWcG4Wlnds/edit?hl=en
Please feel welcome to mention other ideas on the list or in the
document, and also just say hello and introduce yourselves.
Looking forward to beautiful Vienna,
Brad
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If I haven't seen further, it is by standing in the footprints of giants
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