| --- Log opened Sat Nov 24 00:00:25 2012 | ||
| --- Day changed Sat Nov 24 2012 | ||
| yashgaroth | well surely you could take the pathway out of neurons and then couple their downstream effect to whatever you'd like | 00:00 |
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| nmz787 | i think i saw one system in saccharomyces that was recajiggerable | 00:01 |
| nmz787 | or kluyveromyces | 00:01 |
| 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 | 00:02 |
| yashgaroth | and I assume by TLC you mean thin layer chromatography? | 00:03 |
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| nmz787 | yashgaroth: yes, thin layer chromatography | 00:25 |
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| nmz787 | GPCR reporters would be useful for pharma development, or some sort of directed evolution feedback... | 00:31 |
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| abetusk | http://www.indiegogo.com/DrinkSavvy . Any ideas on how they do this? | 04:08 |
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| @kanzure | merged.. https://github.com/kanzure/pokecrystal/pull/44 | 06:25 |
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| strangewarp | kanzure: I know you occasionally do weird pokemans hacking. You might find this impressive: http://www.youtube.com/watch?v=p5T81yHkHtI | 08:15 |
| @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 | 08:17 |
| strangewarp | No | 08:18 |
| strangewarp | It's a TAS hack where you can inject new code directly into the RAM | 08:18 |
| @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) | 08:19 |
| chris_99 | TAS=? | 08:20 |
| Mariu | oh | 08:20 |
| @kanzure | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/ | 08:20 |
| 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 :) | 08:21 |
| 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 | 08:22 |
| chris_99 | hmm, does it attach? | 08:23 |
| chris_99 | i wrote this to hack around with the JVM via ptrace, https://github.com/anfractuosity/procmod | 08:24 |
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| @kanzure | i don't want to attach to the emulator, i want to attach to the running instance | 08:32 |
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| pasky | kanzure: i have been trying to make sense out of the 1000genomes data but without much luck... | 12:07 |
| @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 | 12:09 |
| @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 | 12:11 |
| @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 | 12:12 |
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| 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 | 12:13 |
| pasky | yes | 12:15 |
| pasky | which is what I expected to find in data/ :) | 12:15 |
| @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 | 12:17 |
| @kanzure | gah they have encoding errors in that file | 12:18 |
| @kanzure | also they seem to be running java with 22 GB of RAM | 12:18 |
| pasky | yep :) | 12:19 |
| 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 :) | 12:20 |
| 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. ;) | 12:21 |
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| @kanzure | when will this guy learn | 12:22 |
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| juri_ | :P | 12:22 |
| @kanzure | ParahSailin: do you guys use bwa? | 12:25 |
| ParahSailin | yes | 12:25 |
| ParahSailin | you can map a read set fairly quickly to human genome with bwa | 12:27 |
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| abetusk | why'd you kick juri_? | 12:52 |
| ParahSailin | arbitrary dislike i think | 12:53 |
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| 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 | 12:54 |
| @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 | 12:55 |
| 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 | 12:56 |
| juri_ | arbitrary dislike comes along with the shiney '@'. :) | 12:57 |
| 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 ;) | 12:58 |
| 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 | 13:00 |
| 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 | 13:01 |
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| ParahSailin | imo if you're worrying about gil in python, you're doing something wrong | 13:08 |
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| chris_99 | why? | 13:22 |
| chris_99 | what's wrong with trying to do real multiprocessing, without the overhead of fork | 13:22 |
| * nmz787 just write everything in a deterministic manner and you're set | 13:24 | |
| nmz787 | :P | 13:24 |
| ParahSailin | if you need better performance try a different language? | 13:26 |
| 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 | 13:29 |
| 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. ;) | 13:30 |
| chris_99 | what do you personally use it for? | 13:31 |
| @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 | 13:32 |
| 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. | 13:33 |
| @kanzure | fenn: it looks like humanityplus is invading langton for an event next weekend | 13:38 |
| @kanzure | :/ | 13:38 |
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| @kanzure | ParahSailin: what other things besides bwa are you guys using? | 13:47 |
| ParahSailin | velvet is the standard assembler for short reads | 13:47 |
| @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 | 13:48 |
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| @kanzure | is an assembler different from an aligner? | 13:48 |
| ParahSailin | yes | 13:48 |
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| jrayhawk | DXHR is five bucks on steam for the next 48 hours | 15:35 |
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| curt1s | http://www.newscientist.com/blogs/shortsharpscience/2012/11/micro-pyramid.html | 16:41 |
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| @kanzure | anselma | 17:18 |
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| @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 | 19:00 |
| @kanzure | seems to be a library for http://realtouch.com/ | 19:01 |
| @kanzure | (nsfw) | 19:01 |
| @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 | 19:03 |
| brownies | hah | 19:10 |
| juri_ | http://scanlime.org/2012/11/hacking-my-vagina/ | 19:12 |
| @kanzure | yawn obvious hn reader is obvious | 19:24 |
| juri_ | i don't know what hn is. | 19:24 |
| @kanzure | juri_: it's http://news.ycombinator.com/item?id=4826561 | 19:25 |
| ParahSailin | second-hand hn reader i see | 19:32 |
| ParahSailin | feeding off the scraps on some third tier spam site | 19:32 |
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| @kanzure | today i did a good thing and told a programmer about github https://github.com/ayanamire | 22:07 |
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| 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 | 22:12 |
| 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. | 22:13 |
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| juri_ | URL? | 22:13 |
| @kanzure | http://diyhpl.us/cgit | 22:13 |
| fenn | http://hjemli.net/git/cgit/about/ | 22:14 |
| @kanzure | bah | 22:16 |
| @kanzure | fenn: what are you doing in solidworks? | 22:16 |
| 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 | 22:17 |
| 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 | 22:18 |
| @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 | 22:19 |
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| @kanzure | gah freenode | 22:19 |
| fenn | how is the performance of said VM? | 22:21 |
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| @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 | 22:22 |
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| --- Log closed Sun Nov 25 00:00:28 2012 | ||
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