/srv/irclogs.ubuntu.com/2014/09/16/#ubuntu-us-pa.txt

=== patbarron is now known as monkeybot
=== monkeybot is now known as patbarron
rmg51Morning09:41
JonathanDMorning.11:04
teddy-dbearMorning peoples, dogs, turkeys, hamsters and everything else12:11
=== Guest76815 is now known as InHisName
InHisNamemorning all14:37
ChinnoDogafternoon16:13
InHisNameIt's also a good one, too, ChinnoDog18:06
jthanI miss when this was like the most active LoCo around.18:42
jthanjedijf: y u kill vibes?18:42
jedijfjthan: not me ...look up - mojo marauders abound18:53
jthanlolwut18:54
jthanwaltman: Graph theory.18:56
jthanjedijf: what's that supposed to mean?18:56
waltmanjthan: It's all about graph theory.18:56
jthanwaltman: Have you ever done any work with genome assembly on the compsci side of things? lol18:56
waltmanI have not, no.18:57
jthandaww.18:57
jthanFinding people that have done that is apparently not as easy as I'd hoped.18:57
jthanWe only have one lab on campus here that does it pretty heavily.18:57
jthanI JUST WANNA TAKE SOMEONE TO COFFEE AND LEARN A LITTLE18:57
waltmanoh, you want to learn?18:58
jthanI do.18:58
jthanI have a bunch of yeast genomes that don't match up to the references18:58
jthanI'm trying to take the 40% that doesn't match up and somehow get it to align/piece it together/find genes18:58
jthanThere 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
waltmanIsn't that what BLAST does?18:59
jthanSo I need to find a way to script finding some kind of patterns and getting some possibilities18:59
jthanSort of.. BLAST is kind of rudimentary at this point18:59
jthanIt only looks at local regions of DNA19:00
jthanwhereas I'm working with a full genome19:00
waltmanthere are roughly a zillion things in the bioperl package, but I've never used any of them19:00
jthanand it looks specifically for a certain type of similarity.19:00
jthanyeah - I have been reading some of the docs on bioperl19:00
jthanA lot of people just rely on Python it seems19:00
waltmanhttp://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 ?19:00
waltmanhttp://www.amazon.com/Algorithms-Strings-Trees-Sequences-Computational/dp/0521585198 was the book I was really looking for19:01
jthanOh nifty.19:01
waltmanjthan: there's undoubtedly something in scipy for that19:01
jthanYou use that book before?19:01
waltmanI checked it out of Drexel's library one, but didn't have a need for it. Seemed good though.19:02
jthanI'll have to see if we have it, and if not get it from somewhere else.19:02
waltmanWhat university are you at?19:02
jthanCU Boulder19:02
waltmanah19:02
jthanWorking now under Robin Dowell19:02
waltmanThe 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
waltmanI work with images, not sequences.19:04
jthanI know a few people in bioinformatics at Brown, but they're currently all on an overseas trip together doing some kind of research.19:04
jthanMostly just trying to get a headstart before they actually hand me the genome data19:06
jthanTrying to find which programs/libraries people have had the best results with19:06
jthanMaybe write a few of my own scripts to play around with.19:06
jthanhttp://www.safaribooksonline.com/library/view/python-for-bioinformatics/9780763751869/19:07
jthanInteresting19:07
waltmanAre you coming at this from the bio end or the computer science end?19:08
jthanWell... 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.19:08
waltmanCS folks tend to not know what a protein is.19:10
jthan:-p I've learned that the hard way.19:10

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