Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-11-25

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All times shown according to UTC.

Time Nick Message
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02:31 Biome biome: Chris Fields master SHA1-1c82574
02:31 Biome IO role, but not working yet, just a stub with some carried over methods for the moment
02:31 Biome http://bit.ly/8v2c1B
02:31 Biome biome: Chris Fields master SHA1-1e11f64
02:32 Biome PrimarySeq test updates
02:32 Biome http://bit.ly/66u264
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02:33 deafferret ooo... that bit.ly paste is cool  :)
02:33 deafferret (the bot pasting those URLs, not that paste specifically)
02:34 * deafferret loves his some whitespace github diffs
02:34 deafferret him
02:34 deafferret loves him
02:34 deafferret loves him some
02:34 deafferret loves him some whitespace
02:34 deafferret loves him some whitespace github
02:34 deafferret loves him some whitespace github diffs
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20:30 kanzure joined #bioperl
20:30 kanzure hello
20:31 kanzure oh shit you're dan
20:31 kanzure hey dan :) how are you
20:31 kanzure er, wrong channel. was talking to faceface
20:31 rbuels well that was interesting
20:31 rbuels lol
20:31 kanzure heh :)
20:31 kanzure faceface and i go way back
20:32 rbuels faceface: oh shit!  you're dan???
20:32 rbuels ;-)
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21:13 driveby_bot /home/svn-repositories/bioperl: r16397 (fangly) : Implemented a more robust algorithm to calculate the effective assembly parameters in Bio::Assembly::ContigSpectrum
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21:14 driveby_bot /home/svn-repositories/bioperl: r16398 (fangly) : Fixed typos
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22:24 driveby_bot /home/svn-repositories/bioperl: r16399 (maj) : pre-alpha Bio::Assembly::IO class for bam/sam format
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22:26 driveby_bot /home/svn-repositories/bioperl: r16400 (maj) : keyword subst
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22:48 driveby_bot /home/svn-repositories/bioperl: r16401 (cjfields) : add n parameter (not tested) courtesy Nevo Band (not Neko Case)
23:00 faceface kanzure: :-)
23:01 faceface meet rbuels
23:01 rbuels lol
23:01 faceface hey rob
23:02 faceface kanzure: downloadable hardware eh?
23:02 faceface how does/will that work?
23:05 * rbuels downloads a 72-inch plasma tv
23:07 rbuels faceface: could you please make sure the axis hotel has good wireless
23:08 rbuels if you don't i'm going to revoke your bioperl license
23:09 faceface rbuels: axis?
23:10 rbuels that's where glenn said they were going to have sol2010
23:10 faceface when is that? (what rather)
23:10 faceface don't know it... but if its in dundee... you can get on the fibers :-)
23:11 rbuels it's in dundee
23:11 faceface cool
23:12 faceface now... not sure if they'll *have* fiber optic broad band...
23:12 faceface so you'll be coming?
23:12 rbuels he said they're going to rent out the whole hotel
23:12 faceface awesome
23:13 faceface I've been working on OPas
23:14 rbuels what's that
23:16 faceface oligo pooled arrays
23:16 faceface for SNP genotyping
23:16 faceface I hope the SNPs we picked will be any good!
23:17 faceface how do you share mapping data?
23:17 rbuels "mapping data" is a little vague
23:17 rbuels you mean alignments of things to things?
23:17 faceface I have a bunch of in-silico mapping results, and are getting info from several experemental sources
23:17 faceface yes it is vague
23:18 faceface yes
23:18 faceface alignments of things to thing and other things, some with positions (approximate) and links with scores
23:19 rbuels it really depends on who you're giving it to
23:19 faceface ;-)
23:19 faceface mappers
23:19 faceface ?
23:19 rbuels cause lots of places don't know how to use many file formats
23:19 rbuels .ace maybe?
23:19 rbuels readable by consed
23:19 rbuels or other things too
23:19 faceface peraPS
23:20 rbuels if you're giving people SNPs for them to squirt clear liquids and confirm them...
23:20 faceface just wondering if you had experience in coordinating mapping on tom proj
23:20 rbuels then they are going to want to visualize them
23:20 rbuels david francis asked me to call some SNPs a while ago
23:20 faceface right
23:20 faceface you squirted>
23:20 faceface ?
23:20 rbuels i gave him some gff3 and he said 'wtf do i do with this'
23:21 * rbuels is grossly oversimplifying
23:21 rbuels oversimplifying the actual interactions we had i mean
23:21 faceface power low here just in case I 'dissapear'
23:21 rbuels well plug the heck in
23:21 rbuels silly
23:21 faceface rbuels: I know you lie. He spelled WTF didn't he?
23:21 rbuels even with those huge british plugs
23:21 faceface hehe
23:21 faceface british plugs are beset
23:21 faceface beset
23:21 kanzure rbuels: i know you were joking w/ the plasma tv, but that's literally what we mean
23:21 faceface dang
23:22 kanzure it's like apt-get except for real this time
23:22 faceface hey kanzure
23:22 kanzure hello faceface
23:22 rbuels kanzure: download the data to make a thing, and have some kind of fabricator thingy to make it?
23:22 kanzure rbuels: yes and no
23:22 kanzure rbuels: many people don't have a fabricator-thingy
23:22 rbuels i've heard of that ... some kind of printer that squirts plastic
23:22 kanzure rbuels: so it spits out instructions for a human to do that
23:22 kanzure yes but that's lame IMHO
23:22 kanzure i mean it works for plastic stuff, but too many people are making everything out of plastic
23:23 kanzure some things are not meant to be made out of plastic :)
23:23 rbuels like chairs
23:23 kanzure haha
23:23 kanzure actually i think i had some plastic chairs when i was a kid growing up
23:23 kanzure out on the patios
23:23 rbuels well that explains a lot
23:23 rbuels this fabrication obsession
23:23 kanzure http://adl.serveftp.org/dokuwiki/skdb
23:23 rbuels it was the plastic chairs
23:23 kanzure it's all in python
23:24 kanzure there's also some planned hooks into biopython
23:24 kanzure so you can download lab equipment
23:24 rbuels /kick kanzure this is bioperl
23:24 rbuels lol
23:24 kanzure or automatically print out microfluidic circuits for lab experiments
23:24 kanzure oh crap
23:24 kanzure you're right
23:24 rbuels hahaha
23:24 kanzure i'm sorry. i'll shut up
23:24 * rbuels reaches for his jihad stick
23:24 kanzure :)
23:24 rbuels ;-)
23:24 kanzure but no, i do perl too
23:25 kanzure there's just no wrapper yet
23:25 rbuels so "downloadable hardware" is really "downloadable instructions for making things"
23:25 kanzure well, no
23:25 kanzure imagine your printer
23:25 kanzure it seems to print stuff out, yes?
23:25 kanzure it could draw something, say
23:25 kanzure but you could also have instructions to draw something
23:25 kanzure so
23:25 kanzure basically it's a two-pronged approach
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23:25 kanzure there's *both* downloadable instructions and downloadable hardware
23:25 kanzure the instructions are always available
23:25 kanzure but sometimes you have a CNC machine like a lathe or router or mill
23:26 kanzure in which case you can just generate gcode and have it make your thingy
23:26 rbuels ah
23:26 kanzure lots of small machine shops have something called a "shopbot". it's a 'cheap' (~$10k) CNC router
23:26 kanzure lots of labs have automatic pipetting machines. ok, not many of them :)
23:26 kanzure but you get the idea
23:27 kanzure i've been meaning to come up with some way of parsing biology/lab protocols
23:27 kanzure i have this large dataset of 50MB of protocols.. maybe a perlmonger can help me?
23:27 rbuels hmmm
23:27 faceface :-)
23:27 rbuels it's all a matter of how clean the data is
23:27 rbuels and i would bet dollars to donuts that this is.....
23:27 faceface kanzure: I'm sure you saw ross kings robotic lab papers?
23:27 rbuels horrible
23:28 kanzure faceface: no
23:28 rbuels limey translation:  pounds to scones
23:28 kanzure rbuels: all data is terrible
23:28 faceface lol
23:28 kanzure faceface: link?
23:28 rbuels quid to ... squid?
23:28 faceface it got blogged to buggery, but I cant find the paper...
23:28 faceface http://news.bbc.co.uk/1/hi/sci/tech/7979113.stm
23:29 kanzure oh this is just "The Robot Scientist"
23:29 kanzure yeah it's on sourceforge
23:29 faceface robotic lab / scientist
23:29 faceface what is on sf?
23:29 kanzure their code
23:29 kanzure http://expo.sf.net/
23:29 faceface cool, because that was glossed ofver in the paper
23:30 kanzure to be honest i'm not too impressed by them
23:30 faceface 'a computer is like a giant electronic brain...'
23:30 kanzure because they're using lots of proprietary hardware
23:30 kanzure it was specifically designed for their project
23:30 faceface they don't feel like making it open?
23:30 kanzure i think they bought it from a manufacturer
23:31 faceface I think it may take years before open hardware starts to catch on
23:31 kanzure if you watch the videos you'll see some logos
23:31 kanzure not at all
23:31 kanzure it's already catching on
23:31 kanzure but the real problem is that if it /does/ catch on even more,
23:31 faceface George church is pushing it, but I don't know any others... appart from you of course
23:31 kanzure oh please
23:31 kanzure what is george doing
23:31 faceface polonator
23:31 kanzure nope
23:31 kanzure link me to the schematics
23:31 rbuels i bet the killer app for open hardware would be pipettors
23:31 faceface that is the first examp... you know I never looked
23:32 kanzure faceface: they're not there
23:32 kanzure he's totally bullshitting
23:32 faceface sucks
23:32 faceface did you email him?
23:32 kanzure rbuels: it turns out that well plates have terrible tolerances
23:32 kanzure faceface: yes he doesn't reply to my emails
23:32 kanzure remember i'm just "some kid"
23:32 faceface kanzure: pretend to be a professor
23:33 kanzure rbuels: i think the pipette tips are plastic injection molded.
23:33 kanzure faceface: of what institution?
23:33 faceface the best you can fake
23:33 kanzure University de Hatakj, Bruzikki
23:34 faceface is there something like sf for hardware? I guess its CaD
23:34 kanzure faceface: when will you ever come back to #hplusroadmap?
23:34 faceface hehe
23:34 kanzure faceface: http://thingiverse.com/
23:34 kanzure also we're making a replacement for thingiverse
23:34 faceface I found it too interesting
23:34 kanzure http://adl.serveftp.org/skdb/web/web.py
23:34 faceface I could hapily spend all day in there
23:34 faceface $job needs me...
23:34 kanzure basically it's a website for open source hardware projects
23:35 kanzure with a git backend for all projects
23:35 kanzure also on-site CAD rendering
23:35 kanzure ack i'm so terrible. i keep linking to python source code :(
23:35 faceface lol, I'm sure rob was only joking
23:35 faceface besides,
23:35 faceface besides, #openbio seems dead
23:36 kanzure i have some perl in here i think: http://adl.serveftp.org/sk​db/import_tools/del_repo/ and http://adl.serveftp.org/dokuwiki/scripts
23:36 kanzure but none related to the bioperl libraries
23:36 faceface kanzure: += 0.5
23:37 kanzure hm?
23:37 faceface well... your not ++ because its not bioperl, but you get points for perl ;-)
23:37 kanzure do i get points for biopython?
23:38 * faceface spasms
23:38 faceface (only joking)
23:39 faceface 'the other bio'
23:39 faceface ;-)
23:39 faceface well... I've got to sleep.
23:39 kanzure alright. i need to get back to work.. have a few bugs in skdb that need fixing
23:39 kanzure night
23:39 faceface are you at at university these days?
23:39 faceface (just befor eI go)
23:39 kanzure err sort of :)
23:39 faceface well... sounds good :)
23:40 faceface night
23:40 rbuels yeah, i should roll out to the gym
23:41 * rbuels grunts in a very manly way
23:41 rbuels lol
23:41 kanzure that was a very manly grunt
23:41 kanzure even a wookie would concur
23:41 * rbuels flexes his strapissimus gigantii
23:41 rbuels unnggghhh
23:41 kanzure you can stop now
23:41 rbuels ok enough of this foolishness
23:41 rbuels jinx
23:41 rbuels out

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