[Bioperl-l] Bioperl hackathon?

Ewan Birney birney@ebi.ac.uk
Fri, 3 Aug 2001 00:41:01 +0100 (BST)

On Thu, 2 Aug 2001, Jon Orwant wrote:

> Due to some particularly nice encounters at the Open Source
> convention, I've gotten fascinated by bioinformatics, and I'm trying
> to help out with our upcoming bioinformatics conference (Jan. 28 to
> Jan. 31 in Tucson).
> We've got Lincoln Stein and Ewan Birney as two of our five keynotes
> (the others being Gene Myers, Terry Gaasterland, and Jim Ostell),
> which naturally raises the question: Should there be a bioperl
> hackathon at the conference?  

That would be cool. 

I'm not sure how many of "us" will be there (me of course, other
people?). Our yearly shin-dig is beside ISMB each year, but it less
hacking and more talking so a hack-a-thon is not such a bad idea. I know
that other people have been talking about more exotic (south of the
equator) locations as well in the same sort of time frame, so we should be
careful to coordinate these things.

The sorts of things that could be considered are:

(a) making scripts which use bioperl (jason - do you want to speak
up?) and/or up'ing the whole documentation

(b) working with biojava/biopython on more interoperation/infrastructure

In many ways I am keen on (b) - I think we sort of need one/two days with
key bioperl/biojava/biopython people together working on the live code
bases on the same machine. I just don't know whether in the middle of a
conference we can pull this off as I suspect we will need some serious
concentration to make interoperation between the three projects and things
like bioperl-db (I should rename this to biosql...) really work. Hmmmm.

Conferences seem to have a lot of people/talking/beer drinking, but maybe
that's just me.

Anyway - as for other groups, from my perspective the other key groups are
biojava (matt pocock, thomas down and others) biopython (jeff chang,
andrew dalke, brad chapman), DAS (xml in bioinformatics
effectively) (robin dowell, lincoln stein, thomas down). Other people
which would be nice to get in would be EMBOSS crowd, more Ensembl
representation than just me (Arne Stabenau). 

All interesting grist to the mill, but I guess my worries are twofold:

(a) trying to do something serious in the middle of a conference seems
hard. I feel we need a more bootcamp thing of 3/4 dedicated days, just
the developers, not many learners...

this might be me being biased

(b) flight costs. Alot of people (myself included) blow our travel budget
on ISMB and for the Europeans, flying alot of people to Arizona is going
to cost... (then again it is Janurary...)

If (a) is not a worry (does the Perl conference really develop serious
code in the middle of it or does it just really be a high-bandwidth
discussion area?) and if some enlightened company/angel/whatever can help
out with (b) so we can get the right people there ... then ... let's do