Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-04-01

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All times shown according to UTC.

Time Nick Message
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10:47 Jun joined #bioperl
10:47 Jun hello
10:47 Jun Does anyone know anything about Google summer of code?
12:13 Jun Sorry, I am newbie here. Is anyone involved in the summer of code? I really need some help on that.
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15:26 perl_splut might want to try on the mailing list, Jun
15:37 deafferret ...@o..
15:48 Jun Thx. I just mailed my application to the mail list :D
15:54 deafferret hahah  http://www.thinkgeek.com/stuff/​41/monolith-action-figure.shtml
15:55 deafferret for the exploding of the monolith
15:56 rbuels "zero points of articulation!"
16:29 * pyrimidine points to http://www.bioperl.org/wiki/Google_Summ​er_of_Code#Major_BioPerl_reorganization
16:31 rbuels hehe
16:31 rbuels pyrimidine++
16:40 * pyrimidine out to lunch (in more ways than one)
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18:18 deafferret hahahaha.... I thought the project was to "blow up the monolith" ?
18:19 rbuels yeah .... but we've got to keep a positive tone i guess
18:19 deafferret uh
18:20 deafferret Project X.  "Don't do Project X!"
18:20 deafferret BioPerl is too blue. "Preserve the blueness!"
18:21 deafferret Save the monolith ... by ending its painful existence.
18:22 deafferret How about "It's full of *s!"
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18:44 driveby_bot /home/svn-repositories/bioperl: r16944 (lstein) : merged changes
18:44 driveby_bot Diff: http://tinyurl.com/y8ujvwe
18:45 rbuels great commit message.
18:45 rbuels :-p
18:48 deafferret rbuels: how dare you question the Stein?
18:48 * deafferret lashes rbuels 30 times
18:49 rbuels oh i'll certainly question the stein's version control practices.
18:49 rbuels lol
18:49 * rbuels fears not
18:50 deafferret rbuels: IF STEIN POOPS IN YOUR SHOES YOU WILL COUNT YOUR LUCKY STARS
18:51 deafferret it's so cute how code.open-bio.org is down again
18:51 deafferret is anyone paid to admin that thing?
18:53 deafferret uh... anyone know what this person is talking about?   https://rtg.ist.unomaha.edu/​/Ticket/Display.html?id=977 guest guest
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19:14 perl_splut no clue, but I don't work there, heheh
19:15 pyrimidine deafferret: I'm guessing they have a tons of seq reads generated from transposon insertions and want to know where they map to in the genome (I'm guessing tracking gene knowckouts)
19:15 pyrimidine *knockouts
19:16 pyrimidine so, I guess they haven't heard about this thing called BLAST
19:16 perl_splut probably not, which is why they are asking for help
19:17 perl_splut or they have and don't want to go through the reports manually
19:17 pyrimidine hmm, let's think, 1) BLAST reads against genome, 2) find closest gene to reads, 3) $$PROFIT$$
19:18 dnewkirk There's profit to be had in this field?
19:18 pyrimidine well, it is april 1
19:18 dnewkirk :)
19:19 deafferret lol
19:19 deafferret well, I know nothing about transposon data management
19:20 * deafferret installs *.gmod.org
19:20 rbuels yikes
19:21 dnewkirk Why use blast and not bowtie? Or am i misunderstanding what you mean by reads...
19:21 deafferret dnewkirk: https://rtg.ist.unomaha.edu/​/Ticket/Display.html?id=977 guest guest
19:21 pyrimidine nah, it should just be managing seq reads, then using a db to find the closest genes.
19:21 deafferret that paste was right before you joined the channel
19:21 rbuels actually, since you guys are all here, what are your favorite programs for aligning cdnas to genomes with the introns done nicely?
19:22 deafferret pyrimidine: but ALL the reads are on the SAME SERVER! They are all equally "close!"
19:22 deafferret rbuels: NERD!
19:22 pyrimidine dnewkirk: bowtie would also work, dep. on the number of seq reads and whether the genome of interest has already been indexed.  If it
19:22 * rbuels has only ever used genomethreader, but it seems so damn slow and memory-hungry
19:22 dnewkirk ahh, I understand now
19:22 perl_splut nope. some electrons are closer than others
19:22 pyrimidine *it's a small number it might be faster to just BLAST it
19:22 perl_splut gotta watch out for that PEP though
19:23 * deafferret assigns ticket 977 to dnewkirk
19:23 pyrimidine i don't worry much about memory (have 48G)
19:23 * pyrimidine is spoiled
19:24 perl_splut I don't worry about memory either. I just forget everything I'm told and go through life happy :)
19:24 rbuels pyrimidine: memory matters when i need to run it across the cluster
19:24 rbuels pyrimidine: cause each node only has 4g
19:24 pyrimidine rbuels: that does suck.
19:24 rbuels pyrimidine: what do you use? sim4?
19:25 rbuels i have a couple big proc and mem boxes, but those are always being hammered by assembly jobs
19:25 pyrimidine Until recently I didn't use anything (I worked with bacterial genomes).  Much easier!
19:25 rbuels lol
19:25 rbuels yes i suppose that would simplify things
19:25 rbuels dnewkirk: align cdnas with nice introns?
19:26 rbuels deafferret?
19:26 deafferret rbuels: yes?
19:26 rbuels dammit participate in my poll!
19:26 rbuels i swear, kids these days.
19:26 deafferret rbuels: http://jays.net/images/noidea.jpg
19:26 rbuels lol
19:27 deafferret you guys get all sciency and I can't help but grip by booze and firearms tighter
19:27 deafferret and dirtbikes
19:28 perl_splut what are things that have been made better by science, Alex
19:28 * pyrimidine sees UN black helicopters on the horizon...
19:29 deafferret bowtie ran awesome for us earlier this week on this 8GB RAM, 8 CPU box
19:30 pyrimidine rbuels: exonerate: http://www.ebi.ac.uk/~guy/exon​erate/beginner.html#est2genome
19:30 deafferret mouse mm9
19:30 rbuels yeah there's that ...
19:30 * pyrimidine can't vouch for it
19:32 dnewkirk I use exonerate actually
19:33 dnewkirk It's not a common task for me though
19:41 pyrimidine rbuels: http://seqanswers.com/forums/showthread.php?t=43
19:43 rbuels sigh.
19:44 rbuels too damn many tools.
19:44 rbuels and most of them suck, no doubt.
19:44 deafferret why would people use a forum format for that?
19:44 pyrimidine just pick the ones that work ;-)
19:44 rbuels pyrimidine: that's a good list to have around
19:44 rbuels pyrimidine: thanks
19:44 pyrimidine np
19:45 deafferret wow. 12 *pages* of comments
19:46 deafferret huh... "I think the problem is that the wiki is so bad for threaded conversations, we need a place to discuss the wiki..."
19:46 pyrimidine rbuels: here's the updated one (original thread was closed): http://seqanswers.com/wiki/Software
19:47 deafferret wow   http://seqanswers.com/wiki/Special:BrowseData
19:47 deafferret lol Is the software maintained?: Maybe (196) · No (1) · Yes (36)
19:47 * deafferret hugs him some bioinformatics
19:47 pyrimidine yep, saw that.
19:49 rbuels maybe
19:49 rbuels lol
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