--- Day changed Mon Sep 01 2008
00:01 < fenn> i mean why bother with modular robotics if you're going to use a one-off process
00:01 < fenn> its like making a one-off RV camper
00:02 < kanzure> wait, he's using squirted goo to make his modular robotics?
00:02 < fenn> the molecubes are squired ABS
00:02 < kanzure> ABS?
00:02 < fenn> a plastic
00:03 < fenn> but the shapes are like perfect for standard plastic injection moulding
00:05 < kanzure> I guess as you add stuff to your inventory you just have to be kicked in the ass to write up the sutff to some extent
00:06 < kanzure> but then how do you standardize across different people coming across the same stuff
00:06 < kanzure> argh
00:06 < kanzure> stupid objects
00:06 < kanzure> stupid turtles.
00:06 < fenn> if you're smart, you look before you leap (i.e. dont start writing code when there's already good code out there)
00:07 < fenn> in industry the standard way of connecting two electrical things is with flat headed screws pressing on bare wire :\
00:07 < fenn> you have to hook them up by hand individually each time
00:07 < kanzure> well sure, but don't you look at the data sheets first ?
00:07 < fenn> we should be able to prevent this from happening to software
00:08 < fenn> the problem in industry is that each manufacturer has their own purposefully incompatible system
00:09 < fenn> so you have to stick with that particular megacorp's system, or else use the lowest common denominator (bare wires)
00:09 < kanzure> stupid.
00:10 < fenn> in software though, a special adaptor plug is free so it shouldnt be a big deal
00:10 < kanzure> but it's software about the manufacturing stuff
00:10 < kanzure> it would be nice if they did what they're supposed to do
00:12 < fenn> eric wilhelm has this 'file format hub' idea which makes a lot of sense, where basically you find and translate all the common factors rather than the lowest common denominator
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00:12 < fenn> the hub has all the factors
00:13 < kanzure> huh?
00:13 < fenn> nevermind.
00:13 < kanzure> http://www.linux.com/feature/48944
00:13 < kanzure> 'Xara announced in late September that it was sponsoring the development of an open source Uber-Converter -- a universal vector graphics translator that is designed to overcome longstanding issues in converting vector graphics files from format to format.'
00:13 < fenn> yes, that
00:14 < kanzure> 'After looking at the Xar format, which Corel used in the Xara Studio software it licensed from Xara, Harrington said Wilhelm felt it was within the scope of an "uber-converter" he had been working on for about a year for CAD software file formats. Harrington put Wilhelm in touch with Moir in hopes of solving the Inkscape-to-Xara conversion problems.'
00:14 < fenn> so, for example inkscape supports stars and xara supports quintic splines (or whatever) so the hub would have to support both stars and quintic splines
00:15 < fenn> then when you translate from inkscape to xar you either lose the star information or downgrade it into a generic path
00:16 < fenn> and you have to sample the quintic spline to represent it with the cubic spline that inkscape supports
00:16 < kanzure> 'hub' just sounds code for saying "converter"
00:16 < fenn> the difference is that you can go from hub to hub
00:16 < kanzure> the hub isn't the converter?
00:16 < fenn> whereas if you only had existing file formats, information would be lost
00:17 < fenn> the hub is an intermediary file format, like all the factors of two numbers multiplied together
00:17 < kanzure> oh
00:17 < kanzure> wait, you were assuming that the 'industry stuff' gives you file formats in the first place
00:18 < kanzure> from what I've seen, that's only if you open up a contract agreement or something
00:18 < fenn> well, if you dont know how it works, you have to reverse engineer it or just give up
00:18 < kanzure> right
00:18 < fenn> not my fault people are assholes
00:18 < kanzure> but we don't even have the files
00:18 < kanzure> let's pick a website, uhm, give me a few moments
00:19 < fenn> do you understand how this applies to two different representations of a design? say, a chair
00:20 < fenn> same chair, just described with two different cad systems
00:21 < kanzure> http://www.atsautomation.com/automation/automation.asp
00:21 < kanzure> sure
00:21 < kanzure> but not only that, but two different companies giving me a chair or knife and neither of them are giving me their CAD files or XML stuffs
00:21 < fenn> so what
00:22 < fenn> that's like complaining MS won't give away the windows source code
00:24 < fenn> postscript started out proprietary, but it was elegant and worked well, so many free reimplementations were created
00:24 < kanzure> I guess you can do something like bugmenot and just have a repo with a "ghost overlay" where people throwup their writeups for others to use
00:25 < fenn> ah i see.. too bad ghost overlays have never really caught on
00:25 < fenn> probably because they are all obnoxious and finicky
00:25 < kanzure> also because it's a terrible hack
00:26 < fenn> its the old patch/fork problem, without any fork option :(
00:26 < kanzure> can we stab them with a fork?
00:27 < fenn> stab away, jacques
00:27 < kanzure> who?
00:28 < fenn> communist revolution has been tried over and over, it doesn't work
00:28 < kanzure> how is this the communist revolution?
00:28 < fenn> because they won't give us the means to production
00:28 < fenn> get it?
00:28 < kanzure> this wasn't the communist revolution :)
00:29 < kanzure> maybe metaphorically
00:30 < fenn> bbl
00:30 < kanzure> well, wait
00:30 < kanzure> not even debian expects you to download all of the packages from the programmer teams
00:30 < kanzure> so it's kinda the same .. aggregate into large repositories
00:31 < fenn> you have the source though, and the option of forking into your own project
00:31 < fenn> with proprietary commercial stuff you don't have that option, even if you are allowed to distribute all the patches you want
00:33 < fenn> it all works great until the company goes belly up and you can't get your stock un-modded widgets
00:33 < fenn> or they decide to change some miniscule detail that screws everything up
00:33 < fenn> or they do a total redesign and call it the same thing
00:34 < fenn> or they send black hatted storm troopers to bust down your door
00:37 < kanzure> wait, is there anything good about the system?
00:38 < fenn> gives you a head start so you dont have to dig in the dirt for a thousand years
00:38 < fenn> also, the system can be subverted occasionally
00:38 < fenn> like blender, bought the IP rights from a dying software company
00:39 < fenn> usually though you just get some gnarly military-industrial-government fallout like opencascade
00:39 < fenn> useless for mere mortals
00:44 < kanzure> also, I'm talking about more than just software
00:44 < kanzure> "here's the specifications for the materials we offer"
00:44 < Phreedom> fenn: comunist revolution was tried, and of course it doesn't work because people aren't willing to share their physical labor freely... however with information it's somewhat different. people still don't share it as much as we'd want to, but due to the low cost of making copies, the few that do share are enough
00:44 < kanzure> or "here's the tools we make"
00:44 < kanzure> Phreedom: it seems to be just a lack of understanding
00:45 < kanzure> I don't think they see how it works .. normal people don't need to see an operating system, for instance
00:45 < kanzure> uhm, s/normal/typical users/
00:57 < kanzure> wtf
00:57 < kanzure> http://en.wikipedia.org/wiki/Hole_in_the_Wall_(US_game_show) 'Two teams of three people play, usually male versus female, with a hobby or occupation as the team name. The studio evokes a Japanese game show with the audience having loud noisemakers. Two lifeguards, one male and one female, sit poolside. The contestants are dressed in the familiar silver spandex and wear red or blue helmets, elbow pads, and knee pads depending on the team color.'
00:57 < kanzure> 'After each team (usually male vs female) is announced, the team captain is then instructed to enter the play area, after a countdown the wall is shown, if the contestant makes it through the wall, they earn 1 point for the team, failure equals no points. Then the opposing team tries their luck on a different wall.'
00:57 < kanzure> oh, it's Fox
01:00 < kanzure> http://www.actlab.utexas.edu/pedagogy.shtml 'When the Yale School of Architecture asked what we called our discipline, all the actlabbies sat down and wrote random syllables on pieces of paper. We put those in a box and shook it up, to the accompaniment of tribal noises. Sandy drew two slips out of the box, and on the basis of that she went to New Haven and told them what we did was called Fu Qui.'
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01:03 < kanzure> Hey.
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03:08 < bkero> Wow, I have some stupid friends.
03:08 < bkero> *had some stupid friends, in high school
03:09 < bkero> She started talking and said that one of her favorite subjects is evolution versuse creationaism(she's very fundy)
03:09 < bkero> She started talking and said that one of her favorite subjects is evolution versuse creationaism(she's very fundy)
03:09 < bkero> damn it
03:09 < bkero> Crazy girl from Montana called me again.
03:09 < bkero> and said that one of the flaws in evolution is that amino acids can't develop in the presence of oxygen.
03:10 < fenn> tell her we came from the stars
03:11 < fenn> panspermia.org explains it all
03:11 < bkero> haha
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03:13 < kanzure> they're all crazy
03:13 < fenn> girls?
03:14 < kanzure> yeah.
03:14 < fenn> mostly just the ones named Kate
03:14 < bkero> This one is named emily.
03:15 < bkero> She's a worthless human being with dilusions of becoming ana uthor.
03:15 < kanzure> Ana Uthor?
03:15 < fenn> ana uthor, the bott from sweden?
03:15 < bkero> An author
03:16 < fenn> http://uk.youtube.com/watch?v=rHvMZnWVOvs
03:16 < bkero> She does nothing but work at safeway, sit at home and readmanga all day, and get fat off junk food.
03:17 < bkero> *read manga
03:17 < kanzure> Something wrong with manga?
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03:18 < fenn> oops that one has no english subtitles, you guys probably dont know swedish eh
03:19 < kanzure> http://heybryan.org/meetings.txt rawr
03:21 < kanzure> hm, have to schedule dr. campbell in there somewhere
03:21 < kanzure> maybe i'll go yell at him for using c#
03:21 < fenn> what's wrong with C#?
03:22 < kanzure> the 800 pound gorilla told me to use it
03:22 < kanzure> I've been suspicous ever since
03:22 < fenn> fair enuf
03:24 < bkero> Uh
03:24 < bkero> The problem with C# is that it compiles into .net code
03:24 < kanzure> the 800 pound gorilla?
03:24 < fenn> i havent really looked at it, i just assumed it was C with OOP extensions
03:25 < kanzure> Microsoft written all over it IIRC
03:25 < fenn> maybe i'm thinking of something else
03:26 < bkero> It's just a dotnet bytecode interpreter
03:27 < bkero> Or rather dotnet bytecode compiler
03:27 < kanzure> hm, it wouldn't be terribly hard to write a crawler for digikey and mouser and seedpot the 'ghost overlay' thingy
03:27 < bkero> So it produces the same code as visual basic .net
03:27 < fenn> kanzure: and provide sort by price function? you could sell that for millions
03:27 < kanzure> they don't sort by price?
03:27 < kanzure> wtf?
03:28 < kanzure> I'm assuming there's some sort of technical metadata for each item
03:28 < fenn> no i emailed several years ago and they promised they were working on it
03:28 < kanzure> "yes sir, right away ... " > /dev/null
03:28 < fenn> you can sort every conceivable property except price
03:28 < kanzure> bwahah
03:28 < bkero> price changes depending on quantity ordered
03:29 < kanzure> bah
03:30 < kanzure> how hard could it be to steal their catalog
03:30 < bkero> It's easier to tell people to fuck off rather than explain things to them.
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03:30 < kanzure> no, I'm sure fenn knows about bulk pricing options
03:30 < kanzure> also sure he doesn't care that much
03:30 < kanzure> bulk resistors or something maybe
03:30 < bkero> Going to make some elctroncics?
03:31 < kanzure> http://digi-key.dirxion.com/default.asp
03:31 < bkero> electronics
03:31 < kanzure> fenn has a lair
03:31 < kanzure> haha
03:31 < kanzure> requires flash
03:31 < kanzure> wtf is this bullshit
03:31 < kanzure> 'Download Interactive Catalog for PCs (.exe - 457MB)'
03:32 < kanzure> on a crappy connection
03:32 < fenn> hmm i whined about that too when it was introduced, there should still be links to individual pdf pages
03:33 < kanzure> http://pdfcatalog.digikey.com/T083/digikey.pdf 100 MB wtf
03:33 < fenn> well you dont download the catalog..
03:33 < kanzure> hm?
03:33 < bkero> I got 2 giant digikey catalog books
03:33 < bkero> I can send them to you if you want.
03:33 < kanzure> in print?
03:35 < bkero> http://www.gametrailers.com/player/39284.html
03:35 < bkero> Yes
03:35 < kanzure> why
03:36 < fenn> i read an article about that, it sounded pretty neat
03:36 < fenn> every nut and bolt on every object in the game has some real engineering purpose for how that object is built
03:38 < bkero> Come on, it's a gritty future where the only form of currency is BOTTLE CAPS
03:39 < fenn> hmm my laptop sucks too much to play that
03:39 < fenn> wmv
03:39 < kanzure> me too
03:39 < bkero> I got 2 8800GTs in preparation.
03:39 < bkero> SLI
03:39 < bkero> It's the only reason I'm bringing my computer to new york.
03:41 < fenn> i almost bought a "real" video card two days ago, then i decided i would never use it
03:41 < bkero> Depends on if you think of using OpenCL or GPGPU stuff.
03:41 < kanzure> CL?
03:42 < bkero> http://en.wikipedia.org/wiki/OpenCL
03:42 < kanzure> not another typo?
03:42 < fenn> is there any discernable difference between 8800GT and 8800GS?
03:42 < bkero> Yes
03:43 < willPow3r> yes
03:44 < bkero> Shader count, clockspeed, slower memory
03:44 < fenn> but, can you actually see any difference?
03:44 < fenn> i mean, i dont know how these numbers really affect anything
03:44 < willPow3r> depends on the game
03:44 < bkero> Yes
03:45 < bkero> Really depends on the ersolution and rendering options you want
03:45 < willPow3r> its the difference between low and medium graphics on crysis
03:45 < bkero> I run 1920x1080 with high options in crysis
03:45 < bkero> On an 8800gs it would be below 5fps
03:46 < willPow3r> i've read that sli doesn't make much difference
03:47 < willPow3r> but on my 8800gs i can run it on 1920x1200 on medium and get 30 fps
03:50 < bkero> on crysis?
03:50 < willPow3r> yea
03:50 < bkero> That sounds a bit high.
03:51 < willPow3r> oh, sorry
03:51 < willPow3r> i have a 8800gts
03:51 < willPow3r> not gs
03:51 < bkero> Yea
03:52 < willPow3r> but you're running sli right?
03:52 < bkero> http://en.hardspell.com/doc/showcont.asp?news_id=2159
03:52 < bkero> Yes
03:53 < willPow3r> do you notice a significant performance improvement over non-sli?
03:53 < bkero> Some games
03:53 < bkero> It's usually transparent to games though since I run most of my games in WINE.
03:54 < willPow3r> crysis? in wine?
03:54 < bkero> Heh no
03:54 < bkero> Not crysis
03:54 < bkero> Most games
04:06 < bkero> JESUS CHRIST
04:06 < willPow3r> tourettes?
04:06 < bkero> In Fallout 3 you can build weapons.  One of which is called a "railway rifle"
04:06 < bkero> It shoots railroad spikes
04:07 < bkero> You decapitate people with railroad spikes.
04:07 < willPow3r> that's very innovative
04:13 < willPow3r> not as cool as wolfenstein 3d, however
04:13 < bkero> I dunno
04:13 < bkero> I've played both
04:13 < bkero> and I've enjoyed this more.
04:14 < willPow3r> http://upload.wikimedia.org/wikipedia/en/6/69/Wolf3d_pc.png
04:14 < willPow3r> can't really compete against these graphics
04:14 < bkero> Yea I've played it
04:14 < bkero> One has nazis
04:14 < bkero> and one has 50s american art deco in apocalypse.
04:21 < faceface> is the email thing still working?
04:27 < faceface> http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000167
04:36  * bkero watches some TED videos.
04:36 < bkero> You all have seen those before, yes?
04:37 < faceface> yes
04:37 < faceface> (some)
04:38 < willPow3r> ted nugent right?
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11:32 < kanzure> http://www.phlatboyz.com/
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11:46 < kanzure> Where the hell is XPP?
11:46 < kanzure> It's a computational neuroscience software package.
11:46 < kanzure> Hm, new list to join - http://visionscience.com/pipermail/visionlist/2007/002438.html
11:46 < kanzure> Hm, new list to join - http://www.neuro-it.net/pipermail/general/2004-April/000070.html
11:47 < kanzure> Aha
11:47 < kanzure> http://www.hirnforschung.net/cneuro/cneuro_software.htm
11:54 < kanzure> http://heybryan.org/mediawiki/index.php/Computational_neuroscience <-- Updated
11:55 < kanzure> Dumping just half of those into "brain on a disc" would work.
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12:58 < kanzure> http://www.chiark.greenend.org.uk/~douglasr/prize/ <-- I was just linking Charlie to this. I saw under my eye a mention of Hod Lipson on the page ..
12:59 < kanzure> http://custom.nimblex.net/ AJAX-like live CD generator? end of the world
13:00 < kanzure> regolith challenge ended earlier today - the lunar excavation challenge competition
13:00 < kanzure> nobody won
13:01 < kanzure> 'Live-xmaker is a command line front-end to live-helper, inspired by morphix-mmaker[4][5] (written by Alex de Landgraaf). This allows all the configurations for a liveCD build to be specified in one XML file. [...]'
13:01 < kanzure> http://git.debian.net/?p=live-helper.git
13:04 < kanzure> http://www.livedistro.org/resources/documentation/howtos/building-your-own-scientific-linux-livecd
13:12 < kanzure> http://wiki.debian.org/DebianLive/Howto/ISO <-- surprisingly simple
13:12 < kanzure> hahah
13:12 < kanzure> Somebody just searched for "homemade transcutaneous electrical neural stimulation download"
13:12 < kanzure> Got my bookmarks.
13:13 < kanzure> 88.192.33.38
13:13 < kanzure> Fedora user.
13:13 < kanzure> sic him
13:33 < kanzure> http://www.mcell.cnl.salk.edu/ <-- Ho hum, a good diagram.
13:41 < kanzure> Charlie made it to boingboing http://www.boingboing.net/2008/09/01/howto-make-a-3d-prin.html#comments
13:56 < kanzure> http://www.psics.org/forum/index.php?topic=5.0 <-- small forum but lightning fast response :)
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14:07 < kanzure> http://www-2.cs.cmu.edu/~dst/HHsim/ <-- Why is the linux download 200 MB ?
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14:57 < kanzure> http://www.cse.unr.edu/brain/FILES_HTML/welcome_frame.html 'NCS3 enables neuroscientists to design, execute, and analyze large-scale, biologically realistic brain simulations using the supercomputing Beowulf network of the University of Nevada, Reno. Our goal is to emulate a multicolumnar brain of up to 1 million compartmental neurons by the year 2003. NCS3 is intended to augment laboratory experimentation to yield a depper understanding of brain phys
14:57 < kanzure> This sounds familiar ...
15:02 < kanzure> http://brain.unr.edu/ncsDocs/
15:02 < kanzure> ^ that may or may not be Markram's neocortical simulator
15:03 < kanzure> http://cortex.cse.unr.edu:8000/ganglia/ <-- cortex cluster report
15:03 < kanzure> http://ganglia.sf.net/
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15:37 < kanzure> hrm
15:37 < kanzure> http://www.mormonism-engineering.org/
15:38 < kanzure> so 'cosmoforming' is what they call it now, eh
15:49 < kanzure> alright, so about 400 MB of software
15:49 < kanzure> and it's all terribly documented (of course)
16:05 < kanzure> hm, I'm kind of surprised that somebody is technically competent enough to be able to pull "live news" off these days
16:05 < kanzure> on television.
16:29 < kanzure> http://www.eyeondna.com/2008/05/10/dna-video-pimp-my-genome-google-tech-talk-with-andrew-hessel/
16:29 < kanzure> oh shit, Andrew did a Google TechTalk
16:29 < kanzure> this isn't the presentation he gave at BioBarCamp 
16:29 < kanzure> but close enough
16:34 < bkero> http://blogoscoped.com.nyud.net/google-chrome/
16:35 < ybit> http://www.theaustralian.news.com.au/story/0,25197,24279207-30417,00.html
16:36 < kanzure> http://blogoscoped.com.nyud.net/archive/2008-09-01-n47.html
16:36 < kanzure> I don't get it.
16:36 < kanzure> what does this Google Chrome actually *do*
16:37 < bkero> lol
16:38 < kanzure> http://blogoscoped.com.nyud.net/google-chrome/3 <-- multithreaded browser?
16:38 < kanzure> ok, that's worthwhile
16:38 < kanzure> http://blogoscoped.com.nyud.net/google-chrome/4
16:38 < kanzure> bah
16:38 < kanzure> multiple threads running on the proc
16:38 < kanzure> sure, but just try running a few hundred instances of firefox
16:40 < bkero> child processes :P
16:40 < kanzure> isn't this like my konqueror idea
16:41 < kanzure> http://heybryan.org/projects/browsehack/tabtabtab.html
16:41 < kanzure> http://blogoscoped.com.nyud.net/google-chrome/7 <-- is it really safe to be instantiating the whole damn rendering engine each time ? just saying ..
16:42 < kanzure> #9 <-- haha, masochists :)
16:43 < kanzure> oh, 20 minutes into that video I linked to
16:43 < kanzure> is what you want to see.
16:46 < kanzure>  http://blogoscoped.com.nyud.net/google-chrome/13 javascript vm ?
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17:01 < kanzure> it's weird, Andrew is much less coherent in the 2007 video
17:01 < kanzure> I'm guessing he had practice up to August '08
17:01 < kanzure> 40 min - 'Drew Endy has been going around talking about bio fabs' eh, he rarely mentions bio fabs
17:02 < kanzure> (Drew, I mean)
17:23 < kanzure> oh
17:23 < kanzure> http://richardjschueler.com/wp-gallery2.php?g2_itemId=57070
17:23 < kanzure> that's a much better video about what he's doing
17:37 < kanzure> http://www.arl.org/sparc/
17:37 < kanzure> for open access stuffs
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18:24 < procto> kanzure: I think it's likely that rather than instantiating a wholly new renderer, they will copy one into the new process memory
18:25 < kanzure> isn't it a large struct anyway though ?
18:25 < kanzure> eh
18:25 < kanzure> I suppose it's okay anyway though
18:25 < kanzure> because of guys like at openmosix
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18:25 < kanzure> or the kernel modules to save procs to hdd
18:25 < procto> you can't optimally maximize ALL variables, you maximize some mole than other- :>
18:25 < kanzure> so when you get up to 500 tabs, I won't have to worry
18:25 < procto> in this case, compartmentalization is mole important than memory use
18:26 < procto> because though use will be high, reuse will also be high
18:26 < procto> and for power users of tabs like you, it's heaven sent
18:26 < procto> where heaven == google :>
18:27 < procto> I've been using a rough equiv of their UI by using vimperator
18:31 < kanzure> vimperator for vim ?
18:31 < kanzure> also, their ui seems to suck
18:31 < kanzure> why not a vertical tab list?
18:31 < kanzure> hopefully they thought about that and have it extendable or something
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18:43 < kanzure> Phreedom: one page writeup or just /part now
18:43 < kanzure> :p
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18:44 < kanzure> haha
18:44 -!- Phreedom [n=freedom@ip-194-50-167-184.mir.dn.ua] has joined #hplusroadmap
18:44 < kanzure> :)
18:44 < Phreedom> everywhere I go somebody wants me to do something
18:44 < kanzure> rawr
19:24 < fenn> "google - placing blame where blame belongs"
20:08 < kanzure> on the browser?
20:09 < kanzure> but really Phreedom, it'd be nice
20:09 < kanzure> even wild ranting :)
20:09 < Phreedom> kanzure_: I know I know
20:09 < Phreedom> I'd like to share it too
20:09 < kanzure> ?
20:09 < kanzure> Can't ?
20:10 < Phreedom> need time as always :(
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20:49 < kanzure> hm
20:49 < kanzure> Any ideas on ripping partsregistry.org ?
20:50 < kanzure> I'm thinking that it might be a good dataset to play with on graph-demo/graph-easy, the javascript graphviz implementation
20:50 < kanzure> but I need to download the "parts"
21:33 < kanzure> Argh. This site is annoying too.
21:33 < kanzure> What happened to the good old days when people just threw up files in directories?
21:34 < kanzure> I feel like I'm herding turtles.
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21:45 < fenn> you could just ask them for a .zip of all the files
21:46 < kanzure> hackers don't have to ask
21:46 < kanzure> am I leet hax0r yet?
21:46 < kanzure> maybe I will
21:46 < kanzure> not now though, I was kinda hoping to only spend 10 minutes on this stupid problem
21:47 < fenn> ask now so you have what you need next time you feel like working on it
21:47 < kanzure> http://partsregistry.org/Registry_Software:PERL_Modules:PlateImage.pm hrm
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21:49 < kanzure> wah, I don't feel like being social right now
21:49 < kanzure> who do I have to yell at
21:49 < kanzure> is it Bill Flanagan?
21:49 < kanzure> I know he does openwetware
21:49 < kanzure> does he do partsregistry too?
21:50 < kanzure> http://partsregistry.org/Registry:Feature_requests <-- old stuff .. Endy's #2 is pretty easy .. if I had what I wanted here
21:52 < fenn> this is really a prime candidate for git-ification
21:52 < fenn> or at least some kind of distributed archiving
21:53 < kanzure> no kidding ..
21:53 < kanzure> and it's something that can be forked
21:53 < kanzure> ;-)
21:53 < kanzure> I was going to see if I could throw this into the graph-easy/graph-demo pages that had the javascript + graphviz stuff
21:54 < kanzure> as an alternative route to turtleworkers from the fabrication industries just for the moment :)
21:54 < kanzure> as in, just for the night
21:54 < kanzure> but again another stupid technical decision on their end, so..
21:54 < kanzure> http://heybryan.org/~bbishop/docs/biobricks.js is their javascript from the view page
21:54 < kanzure> http://partsregistry.org/wiki/index.php/Part:BBa_J01080
21:55 < kanzure> now, it looks like they're making an invisible form somehow
21:55 < kanzure> <INPUT type='hidden' id='new_dna_format' name='new_dna_format' value='' /> <INPUT type='hidden' id='selection_start' name='selection_start' value='14' /> <INPUT type='hidden' id='selection_end'   name='selection_end'   value='0' />
21:55 < fenn> that's a common way of preserving user variables, like view mode
21:55 < kanzure> that might be all .. but if it was, wouldn't that be in the GET rather than POST ?
21:56 < kanzure> I don't see any form element telling the browser to post
21:56 < kanzure> there's also nothing in the js saying to do a post and not a get
21:56 < fenn> GET url's with lots of variables are ugly, or something
21:56 < kanzure> sure they are, but I don't see how they're making it not do a GET here
21:56 < kanzure> oh, also, the INPUT vars there are not enough - there must be something else hidden here that I'm missing
21:57 < fenn> form.method = 'POST';
21:57 < kanzure> that tells it the id of the page that I'm coming from
21:57 < kanzure> you see that in the js ?
21:57 < kanzure> stupid vim search function .. (yes, I escape quoted the period)
21:57 < fenn> the period?
21:57 < kanzure> aha
21:57 < kanzure> got it
21:57 < kanzure> yes
21:57 < kanzure> line 1164 ?
21:57 < fenn> i use / for searches
21:57 < kanzure> me too
21:58 < kanzure> primaryPartId .. excellent.
21:59 < fenn> shouldnt that say something like BBa_J01080
21:59 < kanzure> yes
22:00 < fenn> is there some way to translate other languages into javascript?
22:00 < kanzure> like what?
22:01 < kanzure> don't we have some java-to-c stuff out there ?
22:01 < kanzure> or the other way around ?
22:01 < fenn> it just seems weird that javascript is the only language you can run in a browser
22:02 < kanzure> VB Script
22:02 < kanzure> don't know why everyone is fascinated with javascript
22:02 < kanzure> apt-get is perfectly fine for giving your clients some programs
22:02 < kanzure> heck, they're basically using it when they type in the address each time I guess
22:03 < kanzure> hm, http://partsregistry.org/cgi/partsdb/puttext.cgi?primaryPartId=BBa_J01080 is not enough
22:03 < kanzure> although I'm making the assumption that it accepts GET as well
22:03  * kanzure checks with wget
22:03 < kanzure> same thing
22:05 < kanzure> why is no sequence specified?
22:05 < kanzure> isn't that what should be in the db?
22:06 < fenn> http://partsregistry.org/cgi/partsdb/puttext.cgi?primaryPartId=BBa_J01080&seqHidden=Hi%20Bryan!
22:06 < kanzure> wtf
22:06 < kanzure> what is the purpose of this cgi script
22:07 < fenn> is there a way to intercept the POST variables?
22:07 < kanzure> perhaps with a firefox extension
22:08 < kanzure> I was toying around with that in lynx to no avail
22:08 < kanzure> (did not exist)
22:10 < kanzure> clearly there's some information being drawn out from somewhere on this page
22:11 < kanzure> if you press 'view source' it's not there
22:11 < kanzure> oh
22:11 < kanzure> it's an extension
22:11 < kanzure> to mediawiki.
22:12 < kanzure> by 'view source' I mean the link on the page
22:16 < kanzure> how do I use mysqladmin to investigate foreign hosts
22:16 < kanzure> I thought it would just be mysqladmin --host=partsregistry.org
22:19 < fenn> would they leave the db open to random connections?
22:19 < fenn> is that standard practice?
22:19 < kanzure> when you install mysql your username and password is like "root" and ""
22:19 < fenn> hmm
22:20 < fenn> i should hope they changed that
22:20 < kanzure> which is probably the stupidest thing ever
22:20 < fenn> this gives new meaning to biohacker :)
22:22 < kanzure> http://partsregistry.org/Assembly:Robotic_Assembly:Files buh ?
22:22 < kanzure> http://partsregistry.org/DAS_-_Distributed_Annotation_System
22:22 < kanzure> ah
22:22 < kanzure> I am saved
22:22 < kanzure> I love Randy.
22:22 < kanzure> http://partsregistry.org/das/protein_annotations/dna?selection=PartName:firstbase,lastbase
22:22 < kanzure> XML 
22:23 < kanzure> http://partsregistry.org/das/parts/entry_points/
22:24 < kanzure> bahhahah
22:24 < kanzure> is that it?
22:24 < kanzure> hm
22:24 < kanzure> I wish I could make NY Times with only <300 items in a db
22:25 < fenn> well they do actually do something (so i hear)
22:27 < fenn> are all the parts proteins?
22:27 < kanzure> http://partsregistry.org/das/parts/features/?segment=BBa_R0050:0,500000
22:27 < kanzure> is this usable ?
22:27 < kanzure> I mean, the data looks .. like little
22:27 < kanzure> hm
22:27 < kanzure> no, some of them are promoter sequences for example
22:28 < fenn> thats just the annotation, but you still need the actual sequence right?
22:29 < fenn> looks like a plasmid
22:30 < fenn> ah here's the sequence http://partsregistry.org/das/parts/dna/?segment=BBa_R0050:0,500000
22:31 < fenn> s/features/dna/
22:31 < kanzure> okay, so takin the other features/ page, 
22:31 < kanzure> *taking
22:31 < kanzure> how is this usable if I was to throw this into a giant pot
22:31 < kanzure> for designing circuits ?
22:31 < kanzure> I mean, it doesn't look all that useful ..
22:31 < fenn> well, i have no idea
22:31 < kanzure> there's a start and end portion of the 'features' in the fle there it seems
22:31 < fenn> wtf is BBa_R0050 for example
22:31 < kanzure> feature id
22:31 < kanzure>    <FEATURE id='2018' label='putative'>
22:31 < kanzure>     <TYPE id='start' category='translation'>start</TYPE>
22:32 < kanzure> is that literally meaning ' the start of translation ' ?
22:33 < kanzure> http://partsregistry.org/wiki/index.php/Part:BBa_R0050
22:33 < kanzure> it's a promoter
22:34 < fenn> hmm what's the start codon again?
22:35 < fenn> ATG = start
22:35 < fenn> at 35 i see an ATG
22:36 < fenn> at 41 there's CAT which is the complement
22:36  * fenn counts again
22:37 < fenn> er, right, so going backwards on the other strand starting at 43 would be the start codon (start translation)
22:39 < kanzure> count? char count in vim ..
22:40 < kanzure> CAT is not the complement of ATG
22:40 < kanzure> ATG & TAC
22:40 < kanzure> fuck
22:40  * kanzure hangs his head in shame
22:40 < kanzure> I don't understand how there's "on the other strand"
22:40 < kanzure> this is all one strand, no?
22:42 < fenn> it's double stranded DNA
22:42 < kanzure> so, {strand1}{complement} ?
22:42 < fenn> the arrow on their annotation is going the wrong way for my idea to be right
22:43 < fenn> i dont remember or know what pM and pR mean
22:43 < kanzure> haven't heard of those variables either
22:43 < kanzure> why would they tell you the complementary strand anyway?
22:43 < kanzure> that's easily computed
22:44 < fenn> because humans are looking at it
22:44 < fenn> The pL, pR and pM promoters of lambdoid phages direct the transcription of early phage genes and the prophage repressor gene.
22:45 < fenn> i'm going to name my son lambdoid
22:48 < kanzure> then where is the complementary strand beginning/ending in the features/ page ?
22:49 < fenn> sorry i think i confused you
22:50 < fenn> the features page only has annotation for one direction
22:50 < fenn> one strand
22:50 < kanzure> so it applies to exactly 50% of the nucleotides on the dna/ page 
22:50 < kanzure> oh wait
22:50 < kanzure> is there a newline in there?
22:50 < fenn> no, the dna page only gives you one direction
22:50 < kanzure> hm, nope
22:50 < kanzure> oh
22:51 < fenn> newlines are just to make it fit into 100 columns
22:51 < fenn> if the seq length is > 100
22:52 < fenn> one would think there might be human readable comments in the DTD explaining wtf each field means
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22:55 < kanzure> hm
22:55 < kanzure> http://partsregistry.org/das/parts/features/?segment=BBa_F2622:0,500000
22:55 < kanzure> it doesn't seem to have much of a difference really
22:55 < kanzure> this is a 'sender device'
22:55 < kanzure> whatever that means
22:56 < fenn> oo that's a bit more complex
22:58 < fenn> c3hsl appears to be some kind of inter-bacterial communication molecule
22:59 < fenn> erm, c6 = hexanoyl homoserine lactone
23:00 < fenn> i have this feeling like when starting at an electrical schematic written in russian
23:01 < fenn> staring*
23:01 < kanzure> I'm not even sure this tells us anything useful
23:02 < fenn> the annotation shows you how it's put together
23:02 < fenn> there doesn't appear to be any formalized usage information though, like 'whats it good for'
23:02 < fenn> what does PoPs mean?
23:03 < fenn> polymerase per second
23:03  * fenn looks around for an axe
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23:04 < kanzure> newgenome just found me a meeting with Dr. Mauk :-)
23:04 < kanzure> the "Building Brains" guy
23:04 < kanzure> http://heybryan.org/buildingbrains.html
23:05 < newgenome> you going to the singularity summit?
23:06 < kanzure> Can't afford the flight.
23:06 < kanzure> I have people that would put me up, but not the cash to get up there.
23:06 < fenn> which Dr Mauk?
23:06 < kanzure> fenn: he's teaching a freshman-only first-semester-only class on "building brains"
23:08 < kanzure> http://clm.utexas.edu/CLMsite/Mauk.html
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23:08 < kanzure> 'The cerebellum is especially amenable to analysis using computer simulations, due to the relatively simple way it is engaged by motor learning and to it’s well known and simple synaptic organization. We use large-scale simulations designed to reflect as accurately as possible key properties of the cerebellum to 1) test hypotheses regarding network properties of the cerebellum, 2) identify key experiments, and 3) as an overall index of our understan
23:09 < kanzure> basically it's probably some guys sitting around doing pGENESIS or O'Reilly's PDP++
23:10 < kanzure> the class is fairly simple
23:11 < kanzure> http://heybryan.org/~bbishop/docs/Building Brains Syllabus.pdf
23:11 < kanzure> I missed the first two days of class since I didn't know of its existence
23:11 < newgenome> you got into building brains?
23:11 < kanzure> yes
23:11 < newgenome> what do you do?
23:11 < kanzure> I haven't attended yet :-)
23:12 < newgenome> oh
23:12 < kanzure> I was surprised to find a class with the same name as http://heybryan.org/buildingbrains.html
23:12 < kanzure> obviously he's talking about digital brains
23:12 < kanzure> but meh
23:12 < newgenome> the cerebellum
23:12 < newgenome> that's motor coordination
23:12 < newgenome> right?
23:13 < newgenome> this might be useful for ninja reflexes
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23:13 < kanzure> Yes, or it might be useful so that I don't go insane not talking with anybody who knows what it is that I play around with at home
23:13 < fenn> hear hear
23:14 < newgenome> do you have any tissue cultures going yet?
23:15 < kanzure> No supplies.
23:15 < newgenome> I hear they are easy to do
23:15 < kanzure> hahah
23:15 < kanzure> How so? 
23:15 < fenn> there sure is a lot of AI stuff on the syllabus (more "cognitive science" than neuro)
23:15 < kanzure> I know :-(
23:15 < kanzure> but it's Building Brains, not Building Minds
23:15 < newgenome> almost the same thing
23:15 < fenn> not at all
23:15 < kanzure> wtf is a mind?
23:16 < fenn> one is philosophical wankery, the other is pure empirical observation
23:16 < kanzure> well, also with some occassional wankery
23:16 < fenn> naturally
23:17 < kanzure> "computer simulation project approved by instructor"
23:17 < fenn> i'm more inclined to the philosophical wankery of cog-sci than neuro myself
23:17 < kanzure> "my plan is to convert jupiter into a brain"
23:17 < kanzure> what do you mean?
23:17 < newgenome> heh
23:17 < fenn> talking to me?
23:17 < kanzure> mm
23:17 < kanzure> yes
23:17 < fenn> well, if you figure out how a human brain works, you'll end up being able to make human-level intelligence (naughty word)
23:18 < newgenome> could you send me the syllabus
23:18 < kanzure> newgenome: I linked you to it
23:18 < newgenome> the page you set up is 404 error
23:18 < fenn> but i think nature has already optimized just about everything as usual, and it will be very hard to improve on the existing brain design
23:18 < kanzure> http://heybryan.org/~bbishop/docs/Building%20Brains%20Syllabus.pdf
23:18 < kanzure> try that
23:19 < fenn> so, cog-sci breaks it down into pure first principles, from which we can come up with new cognitive architectures
23:19 < newgenome> much better
23:19 < kanzure> what do you mean by first principles
23:19 < kanzure> because right now it sounds like wankery
23:19 < fenn> the problem is that there's really no way to test the first principles in reality, they're sort of like religious beliefs
23:19 < kanzure> unless you actually refer to something here
23:19 < kanzure> epistemology?
23:20 < fenn> at least at the current point in time, we dont have any kind of test bed
23:20 < kanzure> test bed of what
23:21 < kanzure> Wed. 10th of Sept: "Class discussion: How would we know a computer was intelligent?"
23:21 < kanzure> "Counter question, professor: How would we know that YOU are intelligent?"
23:21 < fenn> well, the problem seems to be figuring out how we do what we do
23:21 < fenn> but we dont know what exactly it is that we do
23:21 < kanzure> fenn: most programmers do little
23:21 < newgenome> I don't think I'll take that class
23:21 < newgenome> not this semester at least
23:21 < kanzure> it's this semester only
23:21 < kanzure> freshmen only
23:21 < newgenome> I here elective classes like this can be prttty hard
23:21 < newgenome> dang
23:21 < kanzure> This isn't going to be hard
23:22 < newgenome> that's a hard choice
23:22 < kanzure> ai stuff and cog sci is still opinion-oriented
23:22 < fenn> freshmen only? thats weird
23:22 < newgenome> that is usually indicative of paper writing
23:22 < kanzure> he tells us to send him email about our philosophical problems 
23:22 < kanzure> in the syllabus
23:22 < kanzure> so
23:22 < kanzure> I'm thinking something odd is going on here
23:22 < fenn> its a CULT!!!!!11
23:23 < kanzure> gasp
23:23 < fenn> rofl
23:23 < newgenome> oh noes
23:23 < kanzure> no, I refer to the fact that he wants us to send him email
23:23 < kanzure> who does that? :p
23:23 < fenn> well, i suppose it makes more sense than typing up a MS-word document and printing it out
23:24 < fenn> its not like all professors are just trying to get their own research done and have to teach some stupid freshman class
23:24 < kanzure> wouldn't he rather teach some serious comp neurosci to grad students?
23:25 < fenn> dunno, maybe he's in the wrong field and would rather be doing philosophy or cog-sci
23:25 < kanzure> mm
23:25 < newgenome> or maybe he is using it as a filler
23:25 < kanzure> s/filler/filter/
23:26 < newgenome> or just to attract some liberal arts students
23:28 < newgenome> the computer simulation part sounds cool
23:28 < kanzure> yeah, and it's basically something you could do right now
23:28 < kanzure> just open up NEURON or GENESIS or better yet, O'Reilly's "emergence"
23:28 < kanzure> and start playing around with some data sets or something
23:28 < kanzure> I say better yet because he has deb and rpm files on the wiki
23:28 < kanzure> with pretty screenshots
23:29 < newgenome> links to pretty screen shots?
23:29 < kanzure> hold on
23:30 < newgenome> btw anyone heard from percent?
23:30 < fenn> not for 2-3 days
23:31 < kanzure> he doesn't want me giving out his AIM nickname
23:31 < kanzure> but if you need me to yell at him, just ask
23:31 < kanzure> and he's not on anyway
23:33 < newgenome> wondering some things about nanotubes
23:34 < newgenome> like is it possible to make tiny trusses made from nanotubes?
23:34 < fenn> what do you mean by 'possible' exactly?
23:37 < newgenome> as in take some nanotubes, and join them together into some sort of 3d structure without require implausible molecular assemble technology
23:37 < newgenome> to make a material much stronger than steel
23:37 < kanzure> biotinylate the ends of them and you might be able to do something, but where are you getting your precision from?
23:37 < kanzure> erm, the manipulation
23:37 < newgenome> that's the point
23:38 < kanzure> just use macroscale clumps of them
23:38 < kanzure> i.e.,
23:38 < kanzure> if you poured nanotubes into a pot of cement
23:38 < kanzure> wouldn't this reinforce the cement ?
23:38 < kanzure> would it?
23:38  * kanzure wonders.
23:38 < newgenome> yeah I was thinking that too
23:38 < newgenome> may be just use centimeter long nanotubes
23:39 < newgenome> put them in bundles and weld them together some how
23:40 < fenn> there's a lot of development of side chains to grab the matrix (for space elevator cable)
23:40 < newgenome> what do you mean
23:40 < fenn> if it's just the nanotubes, they'll pull apart as if they weren't connected (because they aren't)
23:40 < fenn> so you want some kind of cross linking, or at least sticky side chains
23:41 < newgenome> I know, but nanotubes can be 'welded' using some sort of e-beam
23:42 < fenn> i guess you are talking about something like this http://news.rpi.edu/update.do?artcenterkey=319
23:43 < fenn> The difficulty was finding nanotubes that cross and touch, which are critical for the initiation of intertube links. “Unfortunately, we can’t control this type of alignment just yet,”
23:43 < newgenome> yeah
23:44 < fenn> i dont get the whole browser tab thing, what's the point
23:45 < kanzure> hm?
23:45 < kanzure> well, that's why I wanted to put it on the task bar
23:45 < newgenome> they also have to find a way to get nanotubes of the same length and chirality to make the type of structures I am talking about
23:45 < kanzure> or do you mean google's comic portrayal of
23:45 < kanzure> oh wait
23:45 < kanzure> you mean tabs on the tubes :)
23:46 < fenn> i'm still reading the google chrome comic
23:46 < fenn> this just strikes dread into my heart: http://blogoscoped.com.nyud.net/google-chrome/18
23:47 < kanzure> it's not loading well for me
23:47 < kanzure> ah
23:49 < kanzure> OH
23:49 < kanzure> http://www.google.com/googlebooks/chrome/
23:49 < kanzure> (caps)
23:49 < kanzure> 'We will be launching the beta version of Google Chrome tomorrow in more than 100 countries.'
23:50 < kanzure> 'All of us at Google spend much of our time working inside a browser. We search, chat, email and collaborate in a browser. ' wtf
23:50 < kanzure> *that* scares me
23:50 < kanzure> http://googleblog.blogspot.com/2008/09/fresh-take-on-browser.html
23:50 < newgenome> why?
23:55 < kanzure> programmers running a multibillion dollar company
23:55 < kanzure> using chat programs
23:55 < kanzure> in a browser
23:55 < newgenome> that is scary because?
23:56 < newgenome> they could listen to you?
23:56 < fenn> because it's moronic, and they should know better
23:56 < kanzure> safety isn't the issue
23:56 < fenn> rather than encouraging stupid behavior
23:58 < fenn> it's scary because google is supposed to be the best of the best
23:58 < newgenome> yeah that is very moronic
23:59 < newgenome> they should make something new 
23:59 < newgenome> like neural interfaces
23:59 < fenn> like.. a better browser! wah
23:59 < newgenome> that are free
23:59 < kanzure> newgenome: http://heybryan.org/projects/browsehack/tabtabtab.html is my browser improvement project
23:59 < newgenome> but of course send ads directly into your brain