=== patbarron is now known as monkeybot === monkeybot is now known as patbarron [09:41] Morning [11:04] Morning. [12:11] Morning peoples, dogs, turkeys, hamsters and everything else === Guest76815 is now known as InHisName [14:37] morning all [16:13] afternoon [18:06] It's also a good one, too, ChinnoDog [18:42] I miss when this was like the most active LoCo around. [18:42] jedijf: y u kill vibes? [18:53] jthan: not me ...look up - mojo marauders abound [18:54] lolwut [18:56] waltman: Graph theory. [18:56] jedijf: what's that supposed to mean? [18:56] jthan: It's all about graph theory. [18:56] waltman: Have you ever done any work with genome assembly on the compsci side of things? lol [18:57] I have not, no. [18:57] daww. [18:57] Finding people that have done that is apparently not as easy as I'd hoped. [18:57] We only have one lab on campus here that does it pretty heavily. [18:57] I JUST WANNA TAKE SOMEONE TO COFFEE AND LEARN A LITTLE [18:58] oh, you want to learn? [18:58] I do. [18:58] I have a bunch of yeast genomes that don't match up to the references [18:58] 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] 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] Isn't that what BLAST does? [18:59] So I need to find a way to script finding some kind of patterns and getting some possibilities [18:59] Sort of.. BLAST is kind of rudimentary at this point [19:00] It only looks at local regions of DNA [19:00] whereas I'm working with a full genome [19:00] there are roughly a zillion things in the bioperl package, but I've never used any of them [19:00] and it looks specifically for a certain type of similarity. [19:00] yeah - I have been reading some of the docs on bioperl [19:00] A lot of people just rely on Python it seems [19:00] 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] http://www.amazon.com/Algorithms-Strings-Trees-Sequences-Computational/dp/0521585198 was the book I was really looking for [19:01] Oh nifty. [19:01] jthan: there's undoubtedly something in scipy for that [19:01] You use that book before? [19:02] I checked it out of Drexel's library one, but didn't have a need for it. Seemed good though. [19:02] I'll have to see if we have it, and if not get it from somewhere else. [19:02] What university are you at? [19:02] CU Boulder [19:02] ah [19:02] Working now under Robin Dowell [19:04] 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] I work with images, not sequences. [19:04] 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] Mostly just trying to get a headstart before they actually hand me the genome data [19:06] Trying to find which programs/libraries people have had the best results with [19:06] Maybe write a few of my own scripts to play around with. [19:07] http://www.safaribooksonline.com/library/view/python-for-bioinformatics/9780763751869/ [19:07] Interesting [19:08] Are you coming at this from the bio end or the computer science end? [19:08] 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] CS folks tend to not know what a protein is. [19:10] :-p I've learned that the hard way.