Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-03-06

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All times shown according to UTC.

Time Nick Message
00:48 faceface deafferret: galaxy is OK
00:48 faceface once you learn how to wrap your package
00:48 * faceface wonders why packages are not unwrapped
00:48 faceface er
00:48 faceface oh yeah
00:49 faceface here is the problem for you to solve, you lucky monkies!
00:50 faceface given teh sequence 'forward-primer-x1-ssr-x2-reverse-primer' where only the sequence x1 and x2 are unknown (but known total length)... HHHHHHHH... how best to match 500 such patterns on 60,000 sequences of total length 700 mb.
00:50 * faceface gasps
00:50 faceface the forward and reverse primer are short, and should match exactly
00:51 faceface .... or maybe one or two mismatches...
00:51 faceface ssr is known but far from unique
00:52 faceface total length is known , x1 / x2 being the same size as forward and revers primer
00:52 * faceface waves teh magic wand...
00:52 faceface and the answer is... ?
00:52 faceface bowtie?
00:52 faceface meh
00:52 faceface night
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03:41 driveby_bot /home/svn-repositories/bioperl: r16912 (cjfields) : fix remoteblast parsing (almost complete refactor of retrieve_blast)
03:41 driveby_bot Diff: http://tinyurl.com/ykc3rcz
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12:50 headache joined #bioperl
12:50 headache hi
12:51 headache there is no biojava irc channel?
12:51 headache i wish to discuss of some java modules partecipating for GSoC 2010
13:44 deafferret headache: I don't know actually... sorry. we can talk about bioperl if you like  :)
13:44 deafferret I don't know any java
13:47 headache deafferret, i'm sorry but i know any perl
13:47 headache :D
13:48 headache deafferret, i've sent an email to mailing list yesterday but i've received no response
13:48 headache i'm talking here because there is no irc channel for biojava project
13:48 mmenegali joined #bioperl
13:49 headache mailing list sent to me only a messeage
13:49 headache -Unprocessed
13:49 headache my message
13:49 headache -Done
13:51 deafferret well, you're certainly welcome to hang out if you like
13:51 deafferret other people might know some java
13:51 deafferret I have to head out for the morning, I'm here most of the week
13:51 deafferret take care!  :)
13:53 headache deafferret, ok :)
13:54 headache i'm a student and i will graduate i 2010 maybe for september i know java and junit 4.x i've practiced TDD in spare time
13:55 headache but i have no knowledge neither  in bioninformatic field nor in open source development process
13:55 headache i hope this will not limit my partecipation/application
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16:39 mmenegali i'm thinking about applying to gsoc, with OBF as my mentor organization. i don't have any experience with bioinformatics, but i do have a lot of interest in biology (i've read "DNA", by james watson, and some of richard dawkins' book). my question is: on what should i focus studying this month so i can improve my chances of being selected?
16:40 mmenegali i've found two book called "Beginning Perl for Bioinformatics" and "Mastering Perl for Bioinformatics", by james tisdall. would those books help?
16:42 mmenegali *two books
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