Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-03-02

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All times shown according to UTC.

Time Nick Message
00:18 brunov joined #bioperl
01:13 dferret mmmmmmm
01:17 dferret /win 2
01:17 * dferret boos
01:25 rbuels hmmmm...
03:54 driveby_bot joined #bioperl
03:54 driveby_bot /home/svn-repositories/bioperl: r16878 (maj) : make overwrite behavior work
03:54 driveby_bot Diff: http://tinyurl.com/yjeyuza
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16:11 dferret ..o.@
16:11 rbuels heh
16:12 dferret the poopcam is no laughing matter
16:12 rbuels ahem.   sorry.
16:12 dferret my dissertation may not be important to YOU, but poopcams are the foundation of a whole new line of scientific inquiry. You'll see.
16:15 * rbuels nods sagely
16:17 rbuels Variable Trends in Fecal Composition of E. Maximus
16:19 dferret :)
16:19 dferret that was much more interesting than the certificate-expiration spec I was reading. thanks for the distraction
16:20 dferret yesterday: cutting edge sequencing. today: taking hotel certificates away from people
16:20 * dferret leads a blessed life
16:20 rbuels A New Paradigm for Nutrient Absorption in the Lower Intestine of L. cyclotis
16:20 dferret oh, and you were right - the t-shirt says "Length ^REALLY DOES^ Matter"
16:21 dferret not sure if my son can wear that to middle school or not  :)
16:21 rbuels lol, that is questionable.
16:22 rbuels in middle school, i got in trouble for less.
16:22 dferret but, but... 140 nucleotide bases is important sometimes!
16:22 dferret don't call my mom! I need paired-end reads!
16:22 rbuels hahahah
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18:32 rbuels pyrimidine: not a lot of gsoc ideas on there yet besides the reorganization
18:36 dferret that's enough for 30 students right there?  :)
18:37 pyrimidine have to give it a bit of time.  There are definitely a few areas that need improvement/simplification/annihilation :)
18:40 rbuels pyrimidine: should i submit a mentor organization app on behalf of OBF?
18:42 pyrimidine yes, but contact Jason re: what needs to be done (I think he's still prez)
18:42 * rbuels nods
18:43 rbuels emailed.
18:44 pyrimidine \o/
18:44 rbuels lol, i also bombarded the nescent call for mentoring ideas with about half a dozen wild-ass things just now
18:44 * rbuels is in a rare mood today
18:44 * rbuels grits his teeth
18:45 * pyrimidine now hoping to get bioperl6 working for the Rakudo* release next month...
18:45 * rbuels is probably manic
18:45 pyrimidine at least bits of it
18:45 rbuels oh cool
18:46 pyrimidine it's blowing up against rakudo master atm, waiting on some important bits to be implemented
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20:03 * pyrimidine thinks a simple AssemblyIO fixes for a 3-4 month project is not good enough
20:04 rbuels me neither
20:04 rbuels i'm waiting for some ideas from people that, like, know about biology and stuff
20:04 rbuels ;-)
20:05 pyrimidine now, a refactoring of Align, LocatableSeq, Assembly for consistency might be better
20:06 pyrimidine or maybe creation of lightweight sequence classes
20:06 pyrimidine or lazy parsers for common formats
20:06 pyrimidine see?  I came up with three right there!
20:06 * rbuels points at the wiki
20:07 * pyrimidine working on it...
20:29 pyrimidine okay, added those ideas.  I put the lazy/lightwieght classes together primarily b/c they should be interrelated.
20:31 pyrimidine rbuels: maybe a post to the open-bio list to get ideas from the other Bio* would be beneficial.
20:31 rbuels pyrimidine: where would the ideas go
20:31 rbuels pyrimidine: email thread?  wiki?
20:31 pyrimidine open-bio wiki?
20:32 * rbuels looks
20:32 pyrimidine http://www.open-bio.org/wiki/Main_Page
20:33 rbuels perhaps rename this page to remove year, and give it a yearly structure?
20:33 rbuels http://www.open-bio.org/wiki​/Google_Summer_of_Code_2009
20:35 pyrimidine That's a good start.  Hilmar set this up last year (note the New section on that page)
20:36 pyrimidine ...including a link to last year's proposal.
20:37 pyrimidine Is GMOD doing anything with GSoC?  That's another thought...
20:37 rbuels its a nice page
20:37 rbuels yeah, i just sent a broadside today with some suggestions for GMOD/nescent
20:37 rbuels lol
20:37 * rbuels forwards it to pyrimidine
20:49 pyrimidine good ideas; would be nice to get you some help on Bio::Schema::Chado
20:49 * rbuels nods vigorously
20:49 rbuels mst is fairly interested in helping the bio world
20:50 rbuels we were talking about schema composition issues and such.
20:50 rbuels he can probably help with finding students
20:50 pyrimidine the more help the better
20:51 deafferret wow. mst is... um... not gentle.
20:51 rbuels oh, he's got a heart o' gold
20:51 pyrimidine Jason had mentioned Hilmar has thought about setting up DBIx::Class-based middleware for BioSQL
20:52 pyrimidine deafferret: just 'cause he uses the F-word a lot doesn't mean he's mean, just blunt :-D
20:52 deafferret um, ok. I wouldn't vouch for mst helping students. good luck.
20:53 rbuels i would.  vouch.
20:53 * rbuels vouches
20:53 rbuels but it would be me, anyway
20:53 * pyrimidine wonders if having mst as mentor would be like 'House'
20:53 rbuels lol
20:53 deafferret he comes off as a total asshole. I love the guy, but I wouldn't intentionally subject anyone but the thickest skinned veterans towards him. $0.02.
20:54 deafferret patience: 0.
20:54 rbuels he's capable of toning it down
20:54 deafferret oh? I've never seen that.
20:54 rbuels heh
20:55 deafferret mst++ # http://clab.ist.unomaha.edu/​~jhannah/tmp/mst_jhannah.jpg
20:55 deafferret but students? eeek. /me shuts up now
20:56 rbuels ho ho ho
20:58 pyrimidine I think he has to be a bit, erm, forceful to get his point across.  suppose sometimes that can come across a little 'asshole-y'.
20:59 pyrimidine I do think, in a large majority of cases, he makes a good point (the recent 'Fuck perl 6' post comes to mind)
20:59 pyrimidine http://www.shadowcat.co.uk/bl​og/matt-s-trout/f_ck-perl-6/
21:05 deafferret I do not dispute that mst is brilliant, opinionated, and full of good ideas.
21:11 dnewkirk ahh perl 6
21:11 dnewkirk brings almost as much rumbling as the python vs. perl debate in our lab :)
21:11 pyrimidine why?
21:12 pyrimidine ii understand the python vs perl, but I always thought perl5 vs perl6 was a bit goofy
21:13 dnewkirk we sit staring at computer monitors for 8+ hours a day, so we have to have something to banter about. It's all in good fun anyway, nothing serious.
21:14 pyrimidine I've seen a few serious (and pretty nasty) ones.  those are alluded to in the mst article.
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21:16 dnewkirk yeah. most in our group use what works for them or switch when needed for a certain project. there are much larger fish to fry.
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23:44 * deafferret fries some more fish

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