[Bioperl-l] Bioperl hackathon?
Mon, 6 Aug 2001 14:48:40 -0700
At 12:41 AM +0100 8/3/01, Ewan Birney wrote:
>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.
Yes, I definitely second this one. There's a lot more infrastructure
that we can leverage off each other. Some examples:
- regression testing - No, not off all of it, but there's a portion
of regression tests that's sharable across code bases. In Biopython,
we've been collecting examples of database records and blast results
to test our parsers against. There's nothing about these records
that are project-specific, and we could get more efficient coverage
of things if the various projects shared them.
- checking on external data sources - Everytime a database format
changes, a server goes down, a server changes APIs, etc. breaks our
code. For a while, I've wanted a system that will monitor various
bioinformatics databases to detect changes and alert us when
- naming standards - There's been some intermittent traffic on the
mailing lists for ways to name databases and sequence accessions.
Andrew led a BoF at BOSC (I think) on it. This is *definitely*
something we don't want to do indepedently for each project. That
would result in a lot of headaches later on trying to map in-between
But for this to happen will require getting us all in the same room
hacking together. While the BoF's at ISMB are useful for getting
consensus, it doesn't seem to generate much usable code.
So, yes, I think it's vitally important to get a hackathon with
representatives from multiple groups.
That said, I'd like to echo other people's concerns that cost will be
an issue. It's an issue for me and likely for other people in
Biopython and other projects. A lot of us are doing this work on our
free time. Making time to attend a hackathon is tough enough (but
can probably be justified), but finding resources to fund it is