--- Log opened Sat Nov 24 00:00:25 2012
--- Day changed Sat Nov 24 2012
00:00 < yashgaroth> well surely you could take the pathway out of neurons and then couple their downstream effect to whatever you'd like
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00:01 < nmz787> i think i saw one system in saccharomyces that was recajiggerable
00:01 < nmz787> or kluyveromyces
00:02 < nmz787> but last time i checked was ~2 years ago
00:02 < yashgaroth> oh I imagine you'd need to re-kerjigger it quite extensively, and I suppose I was assuming mammalian cells for some reason
00:03 < yashgaroth> and I assume by TLC you mean thin layer chromatography?
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00:25 < nmz787> yashgaroth: yes, thin layer chromatography
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00:31 < nmz787> GPCR reporters would be useful for pharma development, or some sort of directed evolution feedback...
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04:08 < abetusk> http://www.indiegogo.com/DrinkSavvy  .  Any ideas on how they do this?
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06:25 <@kanzure> merged.. https://github.com/kanzure/pokecrystal/pull/44
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08:15 < strangewarp> kanzure: I know you occasionally do weird pokemans hacking. You might find this impressive: http://www.youtube.com/watch?v=p5T81yHkHtI
08:17 <@kanzure> it isn't loading for me, but is this the speed run hack where by moving through the item menus after the intro you're able to beat the game?
08:17 <@kanzure> ah seems to be
08:18 < strangewarp> No
08:18 < strangewarp> It's a TAS hack where you can inject new code directly into the RAM
08:19 <@kanzure> the z80 is a fairly hilarious processor
08:19 <@kanzure> it just keeps going no matter what you throw at it
08:19 < strangewarp> indeed X)
08:20 < chris_99> TAS=?
08:20 < Mariu> oh
08:20 <@kanzure> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/
08:21 < Mariu> z80 Spectrum PCs ?
08:21 <@kanzure> gameboy
08:21 < Mariu> oh
08:21 < strangewarp> chris_99: Turn And Save, I think ..
08:21 < Mariu> :p
08:21 < chris_99> you can inject code on x86 too :)
08:22 < strangewarp> The impressive part is that all the code injection is done using the standard interface, while running Pokemon Yellow :p
08:22 < chris_99> yeah that's cool
08:22 <@kanzure> i haven't been able to get gdb to work with an emulator yet
08:23 < chris_99> hmm, does it attach?
08:24 < chris_99> i wrote this to hack around with the JVM via ptrace, https://github.com/anfractuosity/procmod
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08:32 <@kanzure> i don't want to attach to the emulator, i want to attach to the running instance
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12:07 < pasky> kanzure: i have been trying to make sense out of the 1000genomes data but without much luck...
12:09 <@kanzure> pasky: i would use something like http://bowtie-bio.sourceforge.net/crossbow/index.shtml if i was going to do alignment on that data
12:09 < pasky> I meant more like what dataset is what
12:11 <@kanzure> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README.ftp_structure
12:11 < pasky> there seems to have been multiple sequences of each subject, and overally I'm just confused; but I don't know that much about bioinformatics and maybe I want too much yet when expecting to just find a single data file per subject
12:12 <@kanzure> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README.alignment_data
12:12 <@kanzure> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README.sequence_data
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12:13 < pasky> I've been reading some of that, but not too carefully since I wanted to just get my hands on any human genome in less than 10 minutes ;)
12:13 < pasky> I'll reread it again
12:13 <@kanzure> most sequencers read tiny segments of dna at a time
12:13 <@kanzure> and then you use alignment software to throw it all together and find in which order it probably fits
12:15 < pasky> yes
12:15 < pasky> which is what I expected to find in data/ :)
12:17 <@kanzure> looks like there's an alignment metadata format
12:17 <@kanzure> http://samtools.sourceforge.net/
12:17 <@kanzure> read the section called "Alignment Process" in README.alignment_data
12:18 <@kanzure> gah they have encoding errors in that file
12:18 <@kanzure> also they seem to be running java with 22 GB of RAM
12:19 < pasky> yep :)
12:20 < pasky> well, isn't java a wonderful choice for data crunching in bioinformatics
12:20 < ParahSailin> bowtie's shitty
12:20 <@kanzure> ParahSailin: can't be worse than the shit your company writes :)
12:21 < ParahSailin> bwa is better than bowtie
12:21 <@kanzure> oh
12:21 <@kanzure> yeah those READMEs reference bwa
12:21 < ParahSailin> i think bowtie still doesnt handle insertions or deletions?
12:21 < juri_> java is a communicable disease usually contracted through exposure to CS courses. ;)
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12:22 <@kanzure> when will this guy learn
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12:22 < juri_> :P
12:25 <@kanzure> ParahSailin: do you guys use bwa?
12:25 < ParahSailin> yes
12:27 < ParahSailin> you can map a read set fairly quickly to human genome with bwa
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12:52 < abetusk> why'd you kick juri_?
12:53 < ParahSailin> arbitrary dislike i think
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12:54 < chris_99> the main problem with java imo is its stupid use of utf-16
12:54 < ThomasEgi> hm.. main problem is that it is used at all^
12:54 < chris_99> i personally don't think its that bad
12:54 < ThomasEgi> i mean. it was designed rather well but the implementation pretty much went wrong
12:55 <@kanzure> chris_99: elaborate on this utf-16 thing?
12:55 <@kanzure> chris_99: i might have had a bug related to that
12:55 <@kanzure> i think android/java defaults to utf-8, but if you know better let me know?
12:55 < chris_99> it means all ascii characters are stored in memory as two bytes
12:56 < chris_99> i'm not sure about android java though
12:56 < synacktic> Redundant mRedundant = new Redundant(redundancy);
12:56 < chris_99> i only know about std. java
12:57 < juri_> arbitrary dislike comes along with the shiney '@'. :)
12:58 < juri_> don't worry, i'll get my revenge. Im thinking "dedicated to everyone except kanzure on freenode, because he is truely a shit.".
12:58 < juri_> sounds fair. :)
12:58 < chris_99> and at least java has real threads unlike python ;)
13:00 < ThomasEgi> the infamous GIL
13:00 < chris_99> that really annoys me
13:00 < ThomasEgi> indeed. one big bomer.
13:00 < chris_99> i use python a lot too, and wish that'd go away
13:00 < ParahSailin> jython
13:01 < chris_99> don't wanna use that particulary
13:01 < ParahSailin> or wait for pypy
13:01 < chris_99> ooh hadn't heard of pypy
13:01 < chris_99> is that any good
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13:08 < ParahSailin> imo if you're worrying about gil in python, you're doing something wrong
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13:22 < chris_99> why?
13:22 < chris_99> what's wrong with trying to do real multiprocessing, without the overhead of fork
13:24  * nmz787 just write everything in a deterministic manner and you're set
13:24 < nmz787> :P
13:26 < ParahSailin> if you need better performance try a different language?
13:29 < juri_> or bigger computers. </shameless_linuxPMI_plug>
13:29 < chris_99> oh interesting juri
13:29 < chris_99> is that like what openmosix used to do
13:30 < juri_> its derived from openmosix.
13:30 < chris_99> aha
13:30 < chris_99> cool
13:30 < chris_99> are you one of the devs?
13:30 < juri_> last one left. ;)
13:31 < chris_99> what do you personally use it for?
13:32 <@kanzure> chris_99: you could use gevent or eventlet if you want to emulate threadyness
13:32 <@kanzure> i used to have a boner for openmosix until i failed to run a browser on it
13:32 < juri_> Importing image databases to my image recognition system, and simulating heat. ;)
13:32 < chris_99> haven't heard of those, do they create an actual pthread, or just simulate context switching
13:32 <@kanzure> they simulate context switching
13:32 < chris_99> ah
13:33 < chris_99> i'm after real multiprocessing
13:33 <@kanzure> http://gevent.org/
13:33 <@kanzure> you shouldn't take my word for it. i mean, they use libev/libevent.
13:33 < juri_> just takes more work on the API.
13:38 <@kanzure> fenn: it looks like humanityplus is invading langton for an event next weekend
13:38 <@kanzure> :/
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13:47 <@kanzure> ParahSailin: what other things besides bwa are you guys using?
13:47 < ParahSailin> velvet is the standard assembler for short reads
13:48 <@kanzure> i'm pretty sure there's a million and one alignment tools by now
13:48 < ParahSailin> we do use bowtie for one thing
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13:48 <@kanzure> is an assembler different from an aligner?
13:48 < ParahSailin> yes
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15:35 < jrayhawk> DXHR is five bucks on steam for the next 48 hours
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16:41 < curt1s> http://www.newscientist.com/blogs/shortsharpscience/2012/11/micro-pyramid.html
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17:18 <@kanzure> anselma
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19:00 <@kanzure> didn't qdot finish the emokit software that we started in here?
19:00 <@kanzure> kinda funny to see him doing this https://github.com/qdot/librealtouch
19:01 <@kanzure> seems to be a library for http://realtouch.com/
19:01 <@kanzure> (nsfw)
19:03 <@kanzure> oh weird. he says: "I actually started slashdong as somewhat of a joke 8 years ago, and now I travel internationally speaking on the subject. Life is weird."
19:03 <@kanzure> welp the more you know
19:10 < brownies> hah
19:12 < juri_> http://scanlime.org/2012/11/hacking-my-vagina/
19:24 <@kanzure> yawn obvious hn reader is obvious
19:24 < juri_> i don't know what hn is.
19:25 <@kanzure> juri_: it's http://news.ycombinator.com/item?id=4826561
19:32 < ParahSailin> second-hand hn reader i see
19:32 < ParahSailin> feeding off the scraps on some third tier spam site
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22:07 <@kanzure> today i did a good thing and told a programmer about github https://github.com/ayanamire
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22:12 < fenn> hrm. today i spent 6 hours trying to change the background color in solidworks
22:12 <@kanzure> and you're complaining about /my/ timewarping skills?
22:12 < juri_> no gitorious?
22:12 < fenn> i succeeded. but only on the "property manager" panel :(
22:12 <@kanzure> gitorious has a terrible ui and is evil
22:12 <@kanzure> i much prefer cgit to gitorious
22:13 < juri_> gitorious is free software. github is not.
22:13 <@kanzure> cgit is also free software, fuck off and die
22:13 < juri_> mm. never heard of it.
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22:13 < juri_> URL?
22:13 <@kanzure> http://diyhpl.us/cgit
22:14 < fenn> http://hjemli.net/git/cgit/about/
22:16 <@kanzure> bah
22:16 <@kanzure> fenn: what are you doing in solidworks?
22:17 < fenn> nothing much, just trying to larn me a sldprt
22:17 <@kanzure> sldasm in da house?
22:17 < fenn> somehow windows managed to corrupt its filesystem in the 6 hours i was using it
22:18 < fenn> it never ceases to amaze me
22:18 <@kanzure> i use solidworks from a vm and i just reset the vm from a backup each time
22:19 <@kanzure> it's my super-awesome vm image with solidworks, autocad, catia, pro/engineer and other wonders of the world crammed into a few gigabytes
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22:19 <@kanzure> gah freenode
22:21 < fenn> how is the performance of said VM?
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22:22 <@kanzure> fenn: eh it takes a while to boot up the cad programs but it works
22:22 <@kanzure> i am upgrading to 32 GB RAM so soon i wont be able to tell the difference
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--- Log closed Sun Nov 25 00:00:28 2012