pygr gets some summer love

(pygr is a neat bioinformatics framework in Python.)

After some commenters on my last post seemed happy to hear that pygr was the focus of some summer work, I realized I had only discussed the pygr summer work in a post to the biology-in-python list.

Whoops.

So, here's the scoop: not only is pygr the focus of Rachel McCreary's Google Summer of Code project, but Jenny Qian will be using pygr to build an ENSEMBL interface, also as part of the Google Summer of Code.

That's not all!

In addition to Rachel and Jenny (under the sterling mentorship of Chris Lee, Robert Kirkpatrick, Namshin Kim, and myself) I have two MSU students working with me over the summer, Alex Nolley and Marie Buckner. They'll both be working with pygr-related things, although like Jenny their efforts may end up being more on ways to use pygr than on pygr's code itself.

I also have a grad student or two that may drop in on pygr, if only to use it for something research-y.

So all in all, pygr will get a lot of love this summer. Hopefully we can polish the code and documentation and tutorials to the point where the learning curve is as minimal as it can get, and this fabulous package will become readily available to many others...

Why am I personally putting so much effort into pygr? Well, I've been using it more and more over the last few months, and (somewhat like scipy) it's transformed my work by turning annoyingly difficult data organization problems into trivial Python transformations. I can literally throw together a custom genome browser in a matter of hours -- I've implemented two or three already, for different projects -- and it has enabled several new research program. pygr seems to be one of those rare packages (kind of like Python itself) that is not only functional and effective but presents a unified and coherent intellectual interface. pygr is the only good middleware layer I've seen for sequence intertwingling in bioinformatics. It's not that mature yet, but it has serious promise, and I'm hoping to get in on the ground floor, so to speak :).

cheers,

--titus


Legacy Comments

Posted by Anthony on 2008-05-09 at 17:09.

Ok, I'll bite.  I'm a grad student doing bioinformatics, and have been
using Java for most of my programming... mainly because we have an API
for it for Ensembl.  (Between perl and Java, I'll take Java anyday.)
However, recently, I've been customizing and working around the API,
which I generally consider a bad thing.    In any case, so long as
there's an API for python, it might be worth switching - I've got
several 10's of kloc, so migrating now wouldn't be a bad thing.
What's the best way to get involved and/or started with pygr and the
future Ensembl API?

Posted by Titus Brown on 2008-05-10 at 13:38.

Hi Anthony, not sure what to say.  Right now I think pygr has a bit of
a learning curve, so if you're more focused on getting specific work
done I'd stick with what you have.  OTOH, if pygr fits your needs and
you want to give it a serious try, then you have a good opportunity to
learn about it during the summer when there will be LOTS of help
available.    The ENSEMBL API is planned but not yet underway.
Anyway, the place to look is the pygr-dev list, <a
href="http://groups.google.com/group/pygr-
dev?hl=en">http://groups.google.com/group/pygr-dev?hl=en</a>    Hope
to see you there!

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