[Bioperl-l] Offering to help

Bryan Bishop kanzure at gmail.com
Tue Mar 3 12:21:46 EST 2009


On Tue, Mar 3, 2009 at 11:14 AM, Chris Fields <cjfields at illinois.edu> wrote:
> For a Moose-based bioperl implementation I suggest a separate repo
> completely.  We're using svn currently on dev.open-bio.org, though I and a
> few others are also using git.  I'm neutral on the matter but it's possible
> the consensus may be to keep everything in the open-bio svn repo (not
> everyone has git or uses it).

Yes, I've been figuring that the protocols work should be done in a
separate repository for now anyway, I just haven't got around to
starting the code, although with XML::Simple it should be easier or
quicker to do than I'm making it out to be. Part of the issue is that
there needs to be some good thought put into what exactly the schema
should be or how exactly to represent the information, which I've
always had a little bit of anxiety over. It would be fantastic if I
could somehow come up with an easy format and a wizard creation tool
front-end for something like protocol-online.org, since all of those
protocols truly deserve to be in some sort of microformat, whether
CLP-ML or something based off of YAML. Maybe I'll post a thread soon
outlining what a discussion would have to go over to make sure there's
no shooting of self in the foot, to come up with that relatively
mature API or microformat, and see what others on the list have to say
about it? My background is more computer science than bioinformatics
and biology (even though I've been in biology labs longer (strange)),
so it would be great to get some support on that front.

- Bryan
http://heybryan.org/
1 512 203 0507



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