[09:41] <rmg51> Morning
[11:04] <JonathanD> Morning.
[12:11] <teddy-dbear> Morning peoples, dogs, turkeys, hamsters and everything else
[14:37] <InHisName> morning all
[16:13] <ChinnoDog> afternoon
[18:06] <InHisName> It's also a good one, too, ChinnoDog
[18:42] <jthan> I miss when this was like the most active LoCo around.
[18:42] <jthan> jedijf: y u kill vibes?
[18:53] <jedijf> jthan: not me ...look up - mojo marauders abound
[18:54] <jthan> lolwut
[18:56] <jthan> waltman: Graph theory.
[18:56] <jthan> jedijf: what's that supposed to mean?
[18:56] <waltman> jthan: It's all about graph theory.
[18:56] <jthan> waltman: Have you ever done any work with genome assembly on the compsci side of things? lol
[18:57] <waltman> I have not, no.
[18:57] <jthan> daww.
[18:57] <jthan> Finding people that have done that is apparently not as easy as I'd hoped.
[18:57] <jthan> We only have one lab on campus here that does it pretty heavily.
[18:57] <jthan> I JUST WANNA TAKE SOMEONE TO COFFEE AND LEARN A LITTLE
[18:58] <waltman> oh, you want to learn?
[18:58] <jthan> I do.
[18:58] <jthan> I have a bunch of yeast genomes that don't match up to the references
[18:58] <jthan> I'm trying to take the 40% that doesn't match up and somehow get it to align/piece it together/find genes
[18:59] <jthan> There are a lot of programs that do this in part, and some are even open source, but they're only as good as what you give them..
[18:59] <waltman> Isn't that what BLAST does?
[18:59] <jthan> So I need to find a way to script finding some kind of patterns and getting some possibilities
[18:59] <jthan> Sort of.. BLAST is kind of rudimentary at this point
[19:00] <jthan> It only looks at local regions of DNA
[19:00] <jthan> whereas I'm working with a full genome
[19:00] <waltman> there are roughly a zillion things in the bioperl package, but I've never used any of them
[19:00] <jthan> and it looks specifically for a certain type of similarity.
[19:00] <jthan> yeah - I have been reading some of the docs on bioperl
[19:00] <jthan> A lot of people just rely on Python it seems
[19:00] <waltman> http://www.barnesandnoble.com/w/combinatorial-pattern-matching-algorithms-in-computational-biology-using-perl-and-r-gabriel-valiente/1101538438?cm_mmc=googlepla-_-textbook_instock_75up_pt99-_-q000000633-_-9781420069730&ean=9781420069730&isbn=9781420069730&kpid=9781420069730&r=1 ?
[19:01] <waltman> http://www.amazon.com/Algorithms-Strings-Trees-Sequences-Computational/dp/0521585198 was the book I was really looking for
[19:01] <jthan> Oh nifty.
[19:01] <waltman> jthan: there's undoubtedly something in scipy for that
[19:01] <jthan> You use that book before?
[19:02] <waltman> I checked it out of Drexel's library one, but didn't have a need for it. Seemed good though.
[19:02] <jthan> I'll have to see if we have it, and if not get it from somewhere else.
[19:02] <waltman> What university are you at?
[19:02] <jthan> CU Boulder
[19:02] <waltman> ah
[19:02] <jthan> Working now under Robin Dowell
[19:04] <waltman> The only person I know of at Drexel who does that is Gail Rosen. Might be more, I don't know. And there's a bigger group over at upenn.
[19:04] <waltman> I work with images, not sequences.
[19:04] <jthan> I know a few people in bioinformatics at Brown, but they're currently all on an overseas trip together doing some kind of research.
[19:06] <jthan> Mostly just trying to get a headstart before they actually hand me the genome data
[19:06] <jthan> Trying to find which programs/libraries people have had the best results with
[19:06] <jthan> Maybe write a few of my own scripts to play around with.
[19:07] <jthan> http://www.safaribooksonline.com/library/view/python-for-bioinformatics/9780763751869/
[19:07] <jthan> Interesting
[19:08] <waltman> Are you coming at this from the bio end or the computer science end?
[19:08] <jthan> Well... I'm more educated on the bio end, but I think initially I need to come at it more so from the computer science end.
[19:10] <waltman> CS folks tend to not know what a protein is.
[19:10] <jthan> :-p I've learned that the hard way.