--- Day changed Mon Mar 09 2009
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01:01 < kanzure> Hey ybit.
01:03 < ybit> hi kanzure
01:05 < ybit> i've been busy preparing to be productive :)
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01:09 < xp_prg> hi kanzure you here?
01:11 < gene_> is your skin glowing under a blacklight?
01:19 < xp_prg> ya
01:19 < kanzure> ybit: preparing to be?
01:19 < ybit> yup, sadly
01:20 < ybit> but, it's only for a week
01:20 < ybit> the preparation
01:22 < 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?
01:34 < kanzure> you haven't been reading any papers?
01:41 < 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
01:42  * kanzure wonders if he can get a 16 GB RAM server rack..
01:47 < ybit> 16gb of ram, lame. you don't know what power is until you've experienced my 768mb server farm
01:48 < ybit> :)
01:48 < ybit> brb
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01:48 < katsmeow-afk> why ram?
01:49 < katsmeow-afk> altho, if that HP memory works out, server farms may be giving away their harddrives
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02:11 < gene_> so kanzure, I've been thinking
02:12 < gene_> a 128X128 digital picture frame cost $10, this has 16384 pixels
02:13 < gene_> if you can use maskless array gene synthesis to do 8 nucleotides per pixel
02:14 < gene_> you get 131072 nucleotides or 131 KB
02:15 < gene_> that's a lot
02:17 < gene_> 131 kbp I mean
02:23 < gene_> http://www.biochem.wisc.edu/courses/biochem660/Reading/Singh-Gasson_NatureBiotech_DNAarrays.pdf
02:23 < gene_> $60 in chemicals
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09:38 < 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
10:01 < kanzure> http://groups.google.com/group/Austin-Hacking-Society?lnk=li&hl=en
10:01 < kanzure> seems to be the James Choate mailing list
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10:30 < 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.
10:47 < 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
11:09 < 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.
11:10  * kanzure compiles OpenCASCADE.
11:12 < kanzure> apt-get install bibutils
11:16 < kanzure> http://heybryan.org/books/Manufacturing/campbell/bibliography/
11:18 < kanzure> http://code.google.com/p/simplybibtex/
11:40 < 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
12:14 < kanzure> hm, OpenCASCADE is still compiling.
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13:09 < kanzure> ok, finally done compiling opencascade
13:09 < fenn> wtf did you do that for
13:10 < 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/
13:11 < 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?
13:12 < xp_prg> kanzure I have used opencascade
13:12 < fenn> he is
13:14 < xp_prg> it is a full scenegraph
13:14 < xp_prg> it works on top of opengl and abstracts many 3d construction details
13:16 < 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
13:18 < xp_prg> kanzure how do you hope to use it just curious?
13:18 < xp_prg> what is pythonizer sat?
13:19 < kanzure> fenn: shit.
13:19 < kanzure> now I feel silly
13:20 < 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?
13:21 < 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
13:22 < 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.
13:23 < 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?
13:24 < xp_prg> ok :>
13:24 < fenn> ah i'm so glad i finally turned on ignore
13:26 < fenn> oh great another fucking weird-ass french license
13:27 < kanzure> ah, I had backports in my sources.list, so I've fixed it now
13:35 < kanzure> http://www.me.utexas.edu/~adl/links.htm  heh' we have a twitter feed
13:36 < 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'
13:37 < xp_prg> kanzure usually it is python setup.py install
13:38 < 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.
13:39 < kanzure> okay, now it's working, except g++ has now exited. blah.
13:39 < kanzure> I need to go. will fight with this later.
13:48 < fenn> *facepalm* out of disk space
14:40 < ybit> nice find kanzure: pythonocc
14:41 < ybit> or was it fenn... i'll read the log, still nice find
14:42 < fenn> i think debian's package is missing a number of files pythonocc expects
14:42 < fenn> Standard_ThreadId.hxx for example
14:44 < fenn> hey it's only 3 files that's not bad
14:45 < fenn> Standard_PCharacter.hxx and Standard_PExtCharacter.hxx
14:47 < fenn> oh. those are in 6.3 
15:06  * 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
15:07 < 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"
15:26 < fenn> well i'm stumped
15:26 < fenn> it seems to mostly work, then fails on some obscure swig python error handling thing
15:27 < fenn> undefined reference to `PyExc_MemoryError' PyExc_IOError PyExc_RuntimeError PyExc_IndexError
15:27 < fenn> and so on for about  a thousand lines
15:51 < kanzure-_> fenn: what are you stumped at in particular? did you get the 6.3 package from opennovation.org's repository?
15:52 < 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.
15:53 < fenn> well it seems to get past all the opencascade stuff and now i'm just stuck on some silly python/swig error
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15:53 < fenn> and yes 6.3 is from opennovation
15:55 < fenn> http://pastebin.ca/1356801 is what i did, more or less
15:56 < kanzure-_> is your server still broken?
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15:57 < heath_> sorry for the nick changes
15:57 < fenn> apparently
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15:58 < ybit> bah, i'll stick w/ the original
15:59 < 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.
16:00 < 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
16:01 < 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
16:02 < 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/
16:07 < kanzure-_> I didn't run 
16:07 < kanzure-_> svn co svn://svn.gna.org/svn/pythonocc/trunk pythonOCC though.
16:09 < 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
16:12 < 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
16:15 < kanzure-_> lots of undefined reference errors.
16:16 < fenn> ok so at least it's not just me
16:17 < kanzure-_> shouldn't there be something in /usr/lib/opencascade/ to represent compiled opencascade libraries that ld is supposed to link to?
16:18 < 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)
16:20 < fenn> eh guess not
16:20 < kanzure-_> that involves editing setup.py?
16:20 < fenn> nevermind
16:21 < fenn> it already uses -shared
16:22 < kanzure-_> https://mail.gna.org/public/pythonocc-users/2008-12/msg00000.html
16:22 < kanzure-_> hm, it already uses g++ though
16:23 < 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.
16:25 < fenn> yeah and i think they're using fedor
16:25 < fenn> unless you count the dev a user
16:26 < 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)."
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16:27 < bkero> lolswig
16:28 < fenn> swig is such a pain in the ass for being "simple"
16:29 < fenn> spent two days trying to get it to work on my own example file, following tutorials
16:31 < 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
16:37 < fenn> god dammit kanzure
16:37 < fenn> it's MY ERROR REPORT
16:37 < fenn> MINE MINE MINE
16:38 < fenn> and you shouldnt attach 800kb to a mailing list, it's bad manners
16:46 < fenn> one of these days i'll get an email address that doesn't make me wait 45 minutes for everything
16:52 < kanzure-_> fenn: it's not a mailing list.
16:52 < kanzure-_> I mean, I sent that off-list.
16:53 < kanzure-_> also, it's 600kb.
16:55 < 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.
17:14 < kanzure-_> fenn: thomas suggests 'scons'
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18:05 < fenn> sigh.. -lpython2.5
18:06 < fenn> i hate build scripts
18:07 < kanzure-_> what computer should we get for the lab, fenn? any thoughts? we have a bunch of dell optiplex 755s ("intel core duo"s)
18:08 < 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
18:09 < kanzure-_> ooh, maybe I'll go with the hdd that linus reviewed on his blog
18:13 < 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?
18:27 < 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
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18:39 < fenn> 18GB perl file.. WTF
18:40 < bkero> sed -e /\[/[,/g file.pl
18:41 < bkero> sed -e '/\[/[,/g' file.pl
18:43 < fenn> don't you want -i instead of -e?
18:43 < fenn> anyway the problem is the 18GB perl file
18:46 < bkero> Whatever the in place sed flag is
18:46 < bkero> Yea, -i too
20:03 < fenn> wow no more french license
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20:44 < gene_> >	http://www.biochem.wisc.edu/courses/biochem660/Reading/Singh-Gasson_NatureBiotech_DNAarrays.pdf
20:46 < 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!
20:48 < fenn> apparently LCD projectors use 0.7" diagonal LCD panels
20:49 < gene_> what they used masks?
20:50 < 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)
20:51 < 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
20:52 < 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
20:53 < gene_> 294 912 nucleotides
20:54 < gene_> 294 kbp
20:54 < gene_> that's a lot
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21:01 < gene_> dang that method needs a standard DNA synthesizer
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21:10 < gene_> what exactly is a standard dna synthesis?
21:10 < gene_> synthesizer
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23:38 < 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?
23:40 < gene_> www.pharyngula.com
23:40 < gene_> enjoy
23:42 < xp_prg> where would you recommend me putting up a wiki for my project?
23:48 < gene_> yes
23:55 < fenn> gah
23:55 < kanzure> you fail at life
23:56 < 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
23:57 < kanzure> fuuuck.
23:57  * kanzure hides his artificial womb under his bed.
23:58 < 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
23:59 < 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.