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| kanzure | Hey ybit. | 01:01 |
|---|---|---|
| ybit | hi kanzure | 01:03 |
| ybit | i've been busy preparing to be productive :) | 01:05 |
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| xp_prg | hi kanzure you here? | 01:09 |
| gene_ | is your skin glowing under a blacklight? | 01:11 |
| xp_prg | ya | 01:19 |
| kanzure | ybit: preparing to be? | 01:19 |
| ybit | yup, sadly | 01:19 |
| ybit | but, it's only for a week | 01:20 |
| ybit | the preparation | 01:20 |
| xp_prg | kanzure I am trying to present about my embryology experiment tomorrow night, can you be thinking of good papers I could reference please? | 01:22 |
| kanzure | you haven't been reading any papers? | 01:34 |
| xp_prg | kanzure well I want to, was hoping you could guide me to some is all :( | 01:41 |
| kanzure | yay, I get to pick out some hardware for the lab | 01:41 |
| * kanzure wonders if he can get a 16 GB RAM server rack.. | 01:42 | |
| ybit | 16gb of ram, lame. you don't know what power is until you've experienced my 768mb server farm | 01:47 |
| ybit | :) | 01:48 |
| ybit | brb | 01:48 |
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| katsmeow-afk | why ram? | 01:48 |
| katsmeow-afk | altho, if that HP memory works out, server farms may be giving away their harddrives | 01:49 |
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| gene_ | so kanzure, I've been thinking | 02:11 |
| gene_ | a 128X128 digital picture frame cost $10, this has 16384 pixels | 02:12 |
| gene_ | if you can use maskless array gene synthesis to do 8 nucleotides per pixel | 02:13 |
| gene_ | you get 131072 nucleotides or 131 KB | 02:14 |
| gene_ | that's a lot | 02:15 |
| gene_ | 131 kbp I mean | 02:17 |
| gene_ | http://www.biochem.wisc.edu/courses/biochem660/Reading/Singh-Gasson_NatureBiotech_DNAarrays.pdf | 02:23 |
| gene_ | $60 in chemicals | 02:23 |
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| kanzure | http://howto.wired.com/wiki/Open_Up_Government_Data | 09:38 |
| kanzure | an editor at Wired has asked me to contribute to their article/wiki on the topic | 09:38 |
| kanzure | http://groups.google.com/group/Austin-Hacking-Society?lnk=li&hl=en | 10:01 |
| kanzure | seems to be the James Choate mailing list | 10:01 |
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| kanzure | http://www.opencascade.org/support/products/advsamples/ " | 10:30 |
| kanzure | The Advanced Samples Pack is provided with the full source code and is only available to our support clients." | 10:30 |
| kanzure | blah. Two of those screenshots are of a gear and one of a gear + camshaft. | 10:30 |
| kanzure | fenn, have you seen this? http://www.pythonocc.org/ | 10:47 |
| kanzure | "pythonOCC is a set of open-source Python bindings for OpenCascade, a 3D modeling & numerical simulation library. It currently wraps more than 7000 OpenCascade classes, that is, about 50% of the whole library content. pythonOCC may be distributed under the terms the CeCILL Licence." | 10:47 |
| kanzure | seems to have an odd license | 10:47 |
| kanzure | when I saw watchmen the other night, there was a line in the movie along the lines of ".. because anything free must be socialism, right?~~~ ", and the audience laughed. Shows that all hope is not, in fact, lost. | 11:09 |
| * kanzure compiles OpenCASCADE. | 11:10 | |
| kanzure | apt-get install bibutils | 11:12 |
| kanzure | http://heybryan.org/books/Manufacturing/campbell/bibliography/ | 11:16 |
| kanzure | http://code.google.com/p/simplybibtex/ | 11:18 |
| kanzure | bibutils: http://www.refbase.net/index.php/Bibutils | 11:40 |
| kanzure | http://www.me.utexas.edu/~adl/bibliography/SimplyBibTeX/index.php?db=data%2Fcampbell.bib | 11:40 |
| kanzure | hm, OpenCASCADE is still compiling. | 12:14 |
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| kanzure | ok, finally done compiling opencascade | 13:09 |
| fenn | wtf did you do that for | 13:09 |
| kanzure | http://heybryan.org/books/Manufacturing/campbell/bibliography/ via bibutils. | 13:10 |
| kanzure | http://www.me.utexas.edu/~adl/bibliography/SimplyBibTeX/index.php?db=data%2Fcampbell.bib | 13:10 |
| kanzure | fenn, have you seen this? http://www.pythonocc.org/ | 13:10 |
| fenn | looking at it now, highly awesome | 13:11 |
| fenn | i can't believe that guy who wrote pythonizer sat on it for six years | 13:11 |
| kanzure | I thought he was still sitting on it? | 13:11 |
| xp_prg | kanzure I have used opencascade | 13:12 |
| fenn | he is | 13:12 |
| xp_prg | it is a full scenegraph | 13:14 |
| xp_prg | it works on top of opengl and abstracts many 3d construction details | 13:14 |
| fenn | since you can use .dll's for the windows version i bet you can just use the libopencascade6.2-dev package | 13:16 |
| fenn | sorry, libopencascade-dev | 13:16 |
| xp_prg | kanzure how do you hope to use it just curious? | 13:18 |
| xp_prg | what is pythonizer sat? | 13:18 |
| kanzure | fenn: shit. | 13:19 |
| kanzure | now I feel silly | 13:19 |
| kanzure | hm, I can't apt-get it because libopencascade-foundation-6.3.0 does not exist | 13:20 |
| fenn | aroo? | 13:20 |
| xp_prg | fenn what does he hope to use it for? | 13:20 |
| kanzure | xp_prg: why are you asking. | 13:21 |
| kanzure | go away. | 13:21 |
| xp_prg | just curious, maybe I can help :> | 13:21 |
| fenn | sudo apt-get install libopencascade-dev | 13:21 |
| kanzure | fenn: right. | 13:21 |
| kanzure | does it work for you? | 13:21 |
| fenn | apt-get does, about to run pythonocc | 13:21 |
| xp_prg | you can compile from source, I know how to do that kanzure | 13:22 |
| kanzure | xp_prg: why are you unable to read? | 13:22 |
| kanzure | I specifically said that I have compiled it from source. | 13:22 |
| kanzure | jeebus. | 13:22 |
| xp_prg | well your doing apt-get install, you don't do that if you install from source | 13:23 |
| kanzure | do you know why fenn suggested apt-get install? | 13:23 |
| kanzure | it's because I was compiling from source | 13:23 |
| kanzure | so he suggested apt-get. | 13:23 |
| kanzure | what's so hard to understand about this? | 13:23 |
| xp_prg | ok :> | 13:24 |
| fenn | ah i'm so glad i finally turned on ignore | 13:24 |
| fenn | oh great another fucking weird-ass french license | 13:26 |
| kanzure | ah, I had backports in my sources.list, so I've fixed it now | 13:27 |
| kanzure | http://www.me.utexas.edu/~adl/links.htm heh' we have a twitter feed | 13:35 |
| kanzure | fenn, how did you run pythonocc? | 13:36 |
| kanzure | I went into src/ and ran python setup.py, but then it doesn't find "module_builder' | 13:36 |
| xp_prg | kanzure usually it is python setup.py install | 13:37 |
| fenn | yeah i can't find Utils/ | 13:38 |
| kanzure | hm, I can't find 'swig' | 13:38 |
| fenn | i dont know what CAS_ROOT is supposed to be either | 13:38 |
| kanzure | apt-get install swig. | 13:38 |
| kanzure | okay, now it's working, except g++ has now exited. blah. | 13:39 |
| kanzure | I need to go. will fight with this later. | 13:39 |
| fenn | *facepalm* out of disk space | 13:48 |
| ybit | nice find kanzure: pythonocc | 14:40 |
| ybit | or was it fenn... i'll read the log, still nice find | 14:41 |
| fenn | i think debian's package is missing a number of files pythonocc expects | 14:42 |
| fenn | Standard_ThreadId.hxx for example | 14:42 |
| fenn | hey it's only 3 files that's not bad | 14:44 |
| fenn | Standard_PCharacter.hxx and Standard_PExtCharacter.hxx | 14:45 |
| fenn | oh. those are in 6.3 | 14:47 |
| * fenn tries again with opennovation.org packages | 15:06 | |
| ybit | 13:10 < fenn> since you can use .dll's for the windows version i bet you can just use the libopencascade6.2-dev package | 15:06 |
| ybit | 13:13 < kanzure> fenn: shit. | 15:06 |
| ybit | 13:10 < fenn> since you can use .dll's for the windows version i bet you can just use the libopencascade6.2-dev package | 15:06 |
| ybit | 13:13 < kanzure> fenn: shit. | 15:06 |
| ybit | 13:13 < kanzure> now I feel silly | 15:06 |
| fenn | ybit: yes? | 15:06 |
| ybit | hehe, i did the same thing nearly two weeks ago | 15:06 |
| fenn | it turns out i was wrong | 15:07 |
| ybit | really? | 15:07 |
| ybit | why so? | 15:07 |
| fenn | pythonocc is meant to be used with 6.3 | 15:07 |
| ybit | ah | 15:07 |
| fenn | now i'm trying a different set of packages | 15:07 |
| fenn | if i have to compile OCC it's "the wrong way" | 15:07 |
| fenn | well i'm stumped | 15:26 |
| fenn | it seems to mostly work, then fails on some obscure swig python error handling thing | 15:26 |
| fenn | undefined reference to `PyExc_MemoryError' PyExc_IOError PyExc_RuntimeError PyExc_IndexError | 15:27 |
| fenn | and so on for about a thousand lines | 15:27 |
| kanzure-_ | fenn: what are you stumped at in particular? did you get the 6.3 package from opennovation.org's repository? | 15:51 |
| kanzure-_ | occ 6.3 successfully compiled, but then cd src/ ; make install hangs for a while. I suppose I should go run that in the background while I'm not actually at home sitting around. | 15:52 |
| fenn | well it seems to get past all the opencascade stuff and now i'm just stuck on some silly python/swig error | 15:53 |
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| fenn | and yes 6.3 is from opennovation | 15:53 |
| fenn | http://pastebin.ca/1356801 is what i did, more or less | 15:55 |
| kanzure-_ | is your server still broken? | 15:56 |
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| heath_ | sorry for the nick changes | 15:57 |
| fenn | apparently | 15:57 |
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| ybit | bah, i'll stick w/ the original | 15:58 |
| kanzure-_ | You don't have write acces to /usr/local/inc directory. Please use 'sudo python setup.py build'. | 15:59 |
| kanzure-_ | OopenCascade CAS_ROOT environment variable not set. | 15:59 |
| kanzure-_ | hrm. | 15:59 |
| fenn | oh export CASROOT=/usr/share/opencascade/6.3.0/ | 16:00 |
| kanzure-_ | irssi asks you if you want to paste when the lines that you are pasting are more than 6. why isn't a plugin to dump the paste over the web installed by default? | 16:00 |
| kanzure-_ | ah, I think I have to ln -s /usr/local/inc to point over to /usr/local/include | 16:00 |
| fenn | you're supposed to change environment.py :\ | 16:01 |
| fenn | and it should be /usr/include/opencascade not /usr/local/include | 16:01 |
| fenn | yes, this is a pain | 16:01 |
| kanzure-_ | error: package directory '/home/bryan/cad/pythonOCC-md0.1/src/../Utils' does not exist | 16:02 |
| kanzure-_ | hrm. | 16:02 |
| kanzure-_ | it's true, Utils does not exist in next to src/ | 16:02 |
| kanzure-_ | I didn't run | 16:07 |
| kanzure-_ | svn co svn://svn.gna.org/svn/pythonocc/trunk pythonOCC though. | 16:07 |
| fenn | i dont think the Utils dir has anything important | 16:09 |
| kanzure-_ | were you able to find the headers? | 16:09 |
| kanzure-_ | oh right. 6.3 | 16:09 |
| kanzure-_ | http://www.opennovation.org/debian/pool/main/opencascade/opencascade_6.3.0.dfsg.1.orig.tar.gz | 16:12 |
| fenn | what about it | 16:12 |
| kanzure-_ | guess I need to install it | 16:12 |
| kanzure-_ | or at least the -dev package. | 16:12 |
| fenn | get libopencascade-visualization-dev and libopencascade-ocaf-dev | 16:12 |
| fenn | that should get everything | 16:12 |
| kanzure-_ | lots of undefined reference errors. | 16:15 |
| fenn | ok so at least it's not just me | 16:16 |
| kanzure-_ | shouldn't there be something in /usr/lib/opencascade/ to represent compiled opencascade libraries that ld is supposed to link to? | 16:17 |
| fenn | i think passing -shared to g++ should do something | 16:18 |
| fenn | (not that i have any clue what the problem is or what the solution is) | 16:18 |
| fenn | eh guess not | 16:20 |
| kanzure-_ | that involves editing setup.py? | 16:20 |
| fenn | nevermind | 16:20 |
| fenn | it already uses -shared | 16:21 |
| kanzure-_ | https://mail.gna.org/public/pythonocc-users/2008-12/msg00000.html | 16:22 |
| kanzure-_ | hm, it already uses g++ though | 16:22 |
| kanzure-_ | https://mail.gna.org/public/pythonocc-users/2009-01/msg00002.html | 16:23 |
| kanzure-_ | hah, there's like overall 2 total linux users of this package. | 16:23 |
| fenn | yeah and i think they're using fedor | 16:25 |
| fenn | unless you count the dev a user | 16:25 |
| kanzure-_ | https://mail.gna.org/public/pythonocc-users/2009-02/msg00011.html " | 16:26 |
| kanzure-_ | https://mail.gna.org/public/pythonocc-users/2009-02/msg00011.html " | 16:26 |
| kanzure-_ | On my Linux Ubuntu 8.04 system, this generator fails to parse AdvApp2Var_* | 16:26 |
| kanzure-_ | headers and to generate the AdvApp2Var.i SWIG file. However, this file is | 16:26 |
| kanzure-_ | part of the /SWIG_src_modular_linux_darwin'. How is it possible? The answer: | 16:26 |
| kanzure-_ | I just copied/pasted the Windows AdvApp2Var.i file to this directory! And the | 16:26 |
| kanzure-_ | compilation works on Ubuntu 8.04 (in a sense, it's a miracle, that's why I'm | 16:26 |
| kanzure-_ | not surprised by the issue you mention)." | 16:26 |
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| bkero | lolswig | 16:27 |
| fenn | swig is such a pain in the ass for being "simple" | 16:28 |
| fenn | spent two days trying to get it to work on my own example file, following tutorials | 16:29 |
| kanzure-_ | https://mail.gna.org/public/pythonocc-users/2009-03/msg00000.html | 16:31 |
| kanzure-_ | so Thomas says that the problem is fixed in the latest svn version as of six days ago, but I disagree | 16:31 |
| fenn | god dammit kanzure | 16:37 |
| fenn | it's MY ERROR REPORT | 16:37 |
| fenn | MINE MINE MINE | 16:37 |
| fenn | and you shouldnt attach 800kb to a mailing list, it's bad manners | 16:38 |
| fenn | one of these days i'll get an email address that doesn't make me wait 45 minutes for everything | 16:46 |
| kanzure-_ | fenn: it's not a mailing list. | 16:52 |
| kanzure-_ | I mean, I sent that off-list. | 16:52 |
| kanzure-_ | also, it's 600kb. | 16:53 |
| kanzure-_ | hm, ADL uses 61 MB of the 2 GB hdd that runs www.me.utexas.edu. | 16:55 |
| kanzure-_ | in total, 120 MB is used from /home/ on that machine. | 16:55 |
| kanzure-_ | fenn: thomas suggests 'scons' | 17:14 |
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| fenn | sigh.. -lpython2.5 | 18:05 |
| fenn | i hate build scripts | 18:06 |
| kanzure-_ | what computer should we get for the lab, fenn? any thoughts? we have a bunch of dell optiplex 755s ("intel core duo"s) | 18:07 |
| fenn | i have no idea | 18:08 |
| kanzure-_ | bkero: you spend lots of monies on computers, what's hot these days? | 18:08 |
| bkero | kanzure-_: In terms of what? | 18:08 |
| kanzure-_ | lab needs a server, and money isn't much of an issue, so something with 2 or 4 GB of RAM and lots of yummy storage space would be nice | 18:08 |
| kanzure-_ | ooh, maybe I'll go with the hdd that linus reviewed on his blog | 18:09 |
| kanzure-_ | uh, so I have an 18 GB perl file and it has a systematic parse error that can be fixed by replacing all ] by ], | 18:13 |
| kanzure-_ | however, this is not something that I want to open up vim for. | 18:13 |
| kanzure-_ | is this a job for sed or awk or something? | 18:13 |
| bkero | Heh | 18:27 |
| bkero | Go with some Intel SSDs, 16gb RAM, dual xeons | 18:27 |
| bkero | or dual shanghais | 18:27 |
| bkero | kanzure-_: sed in place | 18:27 |
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| fenn | 18GB perl file.. WTF | 18:39 |
| bkero | sed -e /\[/[,/g file.pl | 18:40 |
| bkero | sed -e '/\[/[,/g' file.pl | 18:41 |
| fenn | don't you want -i instead of -e? | 18:43 |
| fenn | anyway the problem is the 18GB perl file | 18:43 |
| bkero | Whatever the in place sed flag is | 18:46 |
| bkero | Yea, -i too | 18:46 |
| fenn | wow no more french license | 20:03 |
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| gene_ | >http://www.biochem.wisc.edu/courses/biochem660/Reading/Singh-Gasson_NatureBiotech_DNAarrays.pdf | 20:44 |
| fenn | surprising they used masks instead of LCD | 20:46 |
| fenn | that's one mask per base pair per array | 20:46 |
| fenn | == a lot of masks! | 20:46 |
| fenn | apparently LCD projectors use 0.7" diagonal LCD panels | 20:48 |
| gene_ | what they used masks? | 20:49 |
| gene_ | they show how to synthesize the photocapper I think | 20:50 |
| gene_ | it requires phosgene... | 20:50 |
| fenn | sounds scary | 20:50 |
| fenn | (and unnecessary) | 20:50 |
| gene_ | Synthesis of photolabile phosphoramidites. The MeNPOC-HEG-cyanoethylphosphoramidite | 20:50 |
| gene_ | (CEP) and MeNPOC-base-CEPs were synthesized | 20:50 |
| gene_ | according to the protocol described by McGall and colleagues8. Briefly, 3,4- | 20:50 |
| gene_ | (methylenedioxy)acetophenone (Aldrich Chemical Co., Milwaukee, WI) was | 20:50 |
| gene_ | reacted with glacial acetic acid and 70% (vol/vol) HNO3 to produce methyl | 20:50 |
| gene_ | 3,4-(methylenedioxy)-6-nitrophenyl ketone. This molecule was reacted with | 20:50 |
| gene_ | sodium borohydride to produce (R,S)-1-(3,4-(methylenedioxy)-6-nitrophenyl) | 20:50 |
| gene_ | ethanol, which was then reacted with phosgene to produce (R,S)-1- | 20:51 |
| gene_ | (3,4-(methylenedioxy)-6-nitrophenyl)ethyl chloroformate (MeNPOC-Cl). | 20:51 |
| gene_ | This molecule was attached to hexaethylglycol and A(PAC), C(ibu), and | 20:51 |
| gene_ | G(ibu). These molecules were then converted to phosphoramidites by reacting | 20:51 |
| gene_ | with 2-cyanoethyl N,N,N’,N’-tetraisopropylphosphorodiamidite and | 20:51 |
| gene_ | diisopropyl ammonium tetrazolide to produce the final products. | 20:51 |
| gene_ | fenn I like scary things | 20:51 |
| gene_ | anyway the chemicals cost $60 | 20:51 |
| gene_ | but think about it fenn | 20:51 |
| gene_ | an 128^2 lcd screen cost ~$10 | 20:52 |
| gene_ | 116 384 pixels | 20:52 |
| gene_ | 16 384 pixels | 20:52 |
| gene_ | 18 nucleotides per pixel | 20:52 |
| gene_ | 294 912 nucleotides | 20:53 |
| gene_ | 294 kbp | 20:54 |
| gene_ | that's a lot | 20:54 |
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| gene_ | dang that method needs a standard DNA synthesizer | 21:01 |
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| gene_ | what exactly is a standard dna synthesis? | 21:10 |
| gene_ | synthesizer | 21:10 |
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| xp_prg | guys I need help a PHD in protein folding is coming over in 30 minutes he wants to see some papers on embryonic forming in xenopus, can you guys help me find some real quick? | 23:38 |
| gene_ | www.pharyngula.com | 23:40 |
| gene_ | enjoy | 23:40 |
| xp_prg | where would you recommend me putting up a wiki for my project? | 23:42 |
| gene_ | yes | 23:48 |
| fenn | gah | 23:55 |
| kanzure | you fail at life | 23:55 |
| fenn | "we will ensure that our government never opens the door to the use of cloning for human reproduction. it is dangerous, profoundly wrong, and has no place in our society or any society." -barak obama | 23:56 |
| fenn | in his stem cell speech | 23:56 |
| kanzure | fuuuck. | 23:57 |
| * kanzure hides his artificial womb under his bed. | 23:57 | |
| xp_prg | kanzure will you please help me find some good papers on embryonic dna programming of xenopus eggs? | 23:58 |
| kanzure | xp_prg: so you're trying to do a project that you haven't read any papers on? | 23:58 |
| kanzure | you previously said that you were afraid that you don't understand anything | 23:58 |
| xp_prg | I bought a book man! | 23:58 |
| kanzure | so let me get this straight | 23:58 |
| kanzure | you're afraid of information and knowledge | 23:58 |
| kanzure | and not only that, but, | 23:58 |
| xp_prg | a guy with a phd in protein folding is coming over in 8 minutes help! | 23:58 |
| kanzure | you didn't even read through any papers? | 23:58 |
| xp_prg | he is going to help me | 23:58 |
| gene_ | Umm kanzure, can you find a nice safe place for me to hide my micromanipulator? | 23:59 |
| gene_ | xp_prg | 23:59 |
| gene_ | think faster | 23:59 |
| xp_prg | I bought coming to life by Christiane Nusslein-Volhard | 23:59 |
| kanzure | why did you buy a book? | 23:59 |
| xp_prg | so I could learn | 23:59 |
| kanzure | how does that help learn? | 23:59 |
| xp_prg | kanzure seriously I don't have a lot of time just give me a few papers I beg of you!!! | 23:59 |
| kanzure | you won't read them. | 23:59 |
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