[Bioperl-l] Bioperl hackathon?

[Jason Stajich]

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).
> 
Fun isn't it!

> 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?  
> 
> I'm not thinking of talks where someone preaches the magic of bioperl
> to the teeming masses -- we'll definitely have that.  What we were
> thinking of was supporting the bioperl developers somehow.  This could
> be as modest as a BoF session at night, or as grand as allocating a
> meeting room for a day or two and providing a wireless network for you
> to hack together.  If you'd be interested in that, send me mail.
> 
> Speaking for O'Reilly, we want to help you folks accomplish whatever
> bizarre freak experiments you're up to -- but unlike other technical
> areas, we don't have much in-house experience when it comes to
> biology.  So what can we do to help?
> 

Alot of what we need for advancing our project (bioperl) is not much
different than any other open-source project - time and people in the same
place to put the ideas together both on a whiteboard and on our laptops.  
The hack-a-thon would help get more code down and also coordinate our
efforts better than the emails and occasional conference calls.

A two-fold purpose would be for coordination with other bio{*} projects.
It is invaluable to have everyone in the same room, we probably
accomplished more in the 6hrs of BioCORBA meetings than we would have over
3 weeks on the email list I suspect.  While I LOVE perl, I think that the
only way for us to produce really usable tools is to pool our resources
and take a approximately the same approach from all the different
languages. Also helps the standards projects work properly too.

Some of the things I am focusing on are building scripts and ultimately 
applications on top of the API our our package.  This will (hopefully)
make the toolkit more usuable to more people so that not everyone has to
be a programmer to do simple bioinformatics (wish they could all be
programmers though...).  

Having a bunch of us in the same room would likely make it simple to
accomplish a great deal and keep a common flavor and standard throughout
the code (which is important for newbies).

> Also, if there are particular topics other than bioperl that you'd
> like to see at the conference, let me know and I'll forward them on to
> Lorrie LeJeune (lorrie@oreilly.com), our program chair (and
> bioinformatics editor, and artist behind the C. elegans drawing on the
> cover of our bioinformatics book).  There's a call for participation at
> http://conference.oreilly.com/biocon/cfp.html, although we'll probably
> extend the proposal deadline until the end of August.  
> 
Had a couple of ideas will at least throw them your way if I think they're
really reasonable fodder.

> Speaking of C. elegans, I've been trying to read up on bioinformatics,
> and I have to say that this worm you seem to like so much is really
> disappointing -- I hadn't realized until yesterday that it was just
> 1 mm long.  This is like learning that Tom Cruise is only 5'7".  
> 
We should send you some closeups of drosophila and see if you like Jeff
Goldbloom better.


> -- 
> Jon Orwant, Ph.D.                     orwant @ oreilly.com
> CTO, O'Reilly & Associates, Inc.    http://www.oreilly.com
> 90 Sherman St, Cambridge MA 02140      (617) 354-5800 x599
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/