| === patbarron is now known as monkeybot | ||
| === monkeybot is now known as patbarron | ||
| rmg51 | Morning | 09:41 |
|---|---|---|
| JonathanD | Morning. | 11:04 |
| teddy-dbear | Morning peoples, dogs, turkeys, hamsters and everything else | 12:11 |
| === Guest76815 is now known as InHisName | ||
| InHisName | morning all | 14:37 |
| ChinnoDog | afternoon | 16:13 |
| InHisName | It's also a good one, too, ChinnoDog | 18:06 |
| jthan | I miss when this was like the most active LoCo around. | 18:42 |
| jthan | jedijf: y u kill vibes? | 18:42 |
| jedijf | jthan: not me ...look up - mojo marauders abound | 18:53 |
| jthan | lolwut | 18:54 |
| 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 | 18:56 |
| 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 | 18:57 |
| 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 | 18:58 |
| 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 | 18:59 |
| 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 ? | 19:00 |
| 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? | 19:01 |
| 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 | 19:02 |
| 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. | 19:04 |
| 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. | 19:06 |
| jthan | http://www.safaribooksonline.com/library/view/python-for-bioinformatics/9780763751869/ | 19:07 |
| jthan | Interesting | 19:07 |
| 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. | 19:08 |
| waltman | CS folks tend to not know what a protein is. | 19:10 |
| jthan | :-p I've learned that the hard way. | 19:10 |
Generated by irclog2html.py 2.7 by Marius Gedminas - find it at mg.pov.lt!