[Bioperl-l] Offering to help

Bryan Bishop kanzure at gmail.com
Tue Mar 3 09:56:36 EST 2009


On Tue, Mar 3, 2009 at 8:34 AM, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 3, 2009, at 7:55 AM, Bryan Bishop wrote:
>>> If there is anything else that you feel that I would be able to do, I'd
>>> be happy to. My current field is more involved with wet-lab work
>>> (antibody engineering), but I like programming a lot and I think this
>>> will be a great chance to keep learning while still contributing.
>>
>> I've been doing some work on XMLization of lab protocols. Would you be
>> interested in this? It's kind of a cross-section of managing an
>> experiment and doing some programming, meanwhile bioperl has
>> traditionally focused on access to bioinformatics datasets, which
>> sadly doesn't include protocols (yikes!).
>
> For an example of how to get involved with BioPerl search the mail archives
> for the recent Bio::DB::HIV work by Mark Jensen, now in BioPerl 1.6.

Neat. I'll have to look into that.

> We would happily support lab protocols if we have a standard to go by (i.e.
> schema to work with) and someone willing to code and maintain modules

Have you looked into CLP-ML? I wrote up a pcr.xml example the other
day, I think I linked to it in my second to last post (maybe). (I'm on
the run, sorry for not linking at the moment.)

> related to their use.  As for a place to fit in, we have the various
> Bio::Biblio modules; I could easily see protocols fitting into that
> namespace, though I have to admit I'm unfamiliar with the overall
> structure/purpose of Bio::Biblio.

What? Is that a BibTeX parser module?

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



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