[emboss-dev] [Bioperl-l] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010

Peter biopython at maubp.freeserve.co.uk
Fri Jan 29 10:36:40 UTC 2010

Hi all,

This is a great topic but should be continue it on just the one mailing list?
Is there a suitable BOSC list, or how about the general Open Bio list?

On Thu, Jan 28, 2010 at 9:17 PM, Mark Wilkinson <markw at illuminae.com> wrote:
> Brad, this sounds exciting!
> One thing strikes me, though - by asking for the sub-projects to propose
> the "grand challenge" themselves the one thing you can guarantee is that
> the "grand challenge" is solvable (or more likely, already solved!)
> Other "grand challenge" kinds of meetings have an independent third party
> pose the problem that has to be solved, and then all groups work toward a
> solution and compare their results.  This would, IMO, be more revealing of
> the "state of the art" in each Open-Bio project, and point out where the
> weaknesses are that we should be focusing on...  Someone (for example,
> you!) could act as the moderator to ensure that the "grand challenge" was
> at least a reasonable one, within the scope of what an Open-Bio project
> *should* be able to solve...
> Just my CAD $0.02
> Mark

One possible problem with having Brad act as moderator is his ties to
Biopython (plus it would be a shame if we'd be one man down for trying
to solve the challenges - grin). Having a project representative "sign off"
on the challenge might work - or simply the whole of the BOSC committee
which is quite balanced. Alternatively some kind of panel of challenges does
seem a good way to reduce individual project bias (as suggest by Scooter),
but there will still need to be a judging committee.

I'm curious what kind of challenges the BOSC committee had in mind -
would something like taking a newly sequence bacteria and producing
an automated annotation as a GenBank, EMBL, or GFF  file be too
ambitious for example? There are already several major projects
to do this e.g. RAST http://rast.nmpdr.org/


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