2008-09-01.log

--- Day changed Mon Sep 01 2008
fenni mean why bother with modular robotics if you're going to use a one-off process00:01
fennits like making a one-off RV camper00:01
kanzurewait, he's using squirted goo to make his modular robotics?00:02
fennthe molecubes are squired ABS00:02
kanzureABS?00:02
fenna plastic00:02
fennbut the shapes are like perfect for standard plastic injection moulding00:03
kanzureI guess as you add stuff to your inventory you just have to be kicked in the ass to write up the sutff to some extent00:05
kanzurebut then how do you standardize across different people coming across the same stuff00:06
kanzureargh00:06
kanzurestupid objects00:06
kanzurestupid turtles.00:06
fennif you're smart, you look before you leap (i.e. dont start writing code when there's already good code out there)00:06
fennin industry the standard way of connecting two electrical things is with flat headed screws pressing on bare wire :\00:07
fennyou have to hook them up by hand individually each time00:07
kanzurewell sure, but don't you look at the data sheets first ?00:07
fennwe should be able to prevent this from happening to software00:07
fennthe problem in industry is that each manufacturer has their own purposefully incompatible system00:08
fennso you have to stick with that particular megacorp's system, or else use the lowest common denominator (bare wires)00:09
kanzurestupid.00:09
fennin software though, a special adaptor plug is free so it shouldnt be a big deal00:10
kanzurebut it's software about the manufacturing stuff00:10
kanzureit would be nice if they did what they're supposed to do00:10
fenneric 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 denominator00:12
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fennthe hub has all the factors00:12
kanzurehuh?00:13
fennnevermind.00:13
kanzurehttp://www.linux.com/feature/4894400:13
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
fennyes, that00:13
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
fennso, for example inkscape supports stars and xara supports quintic splines (or whatever) so the hub would have to support both stars and quintic splines00:14
fennthen when you translate from inkscape to xar you either lose the star information or downgrade it into a generic path00:15
fennand you have to sample the quintic spline to represent it with the cubic spline that inkscape supports00:16
kanzure'hub' just sounds code for saying "converter"00:16
fennthe difference is that you can go from hub to hub00:16
kanzurethe hub isn't the converter?00:16
fennwhereas if you only had existing file formats, information would be lost00:16
fennthe hub is an intermediary file format, like all the factors of two numbers multiplied together00:17
kanzureoh00:17
kanzurewait, you were assuming that the 'industry stuff' gives you file formats in the first place00:17
kanzurefrom what I've seen, that's only if you open up a contract agreement or something00:18
fennwell, if you dont know how it works, you have to reverse engineer it or just give up00:18
kanzureright00:18
fennnot my fault people are assholes00:18
kanzurebut we don't even have the files00:18
kanzurelet's pick a website, uhm, give me a few moments00:18
fenndo you understand how this applies to two different representations of a design? say, a chair00:19
fennsame chair, just described with two different cad systems00:20
kanzurehttp://www.atsautomation.com/automation/automation.asp00:21
kanzuresure00:21
kanzurebut 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 stuffs00:21
fennso what00:21
fennthat's like complaining MS won't give away the windows source code00:22
fennpostscript started out proprietary, but it was elegant and worked well, so many free reimplementations were created00:24
kanzureI guess you can do something like bugmenot and just have a repo with a "ghost overlay" where people throwup their writeups for others to use00:24
fennah i see.. too bad ghost overlays have never really caught on00:25
fennprobably because they are all obnoxious and finicky00:25
kanzurealso because it's a terrible hack00:25
fennits the old patch/fork problem, without any fork option :(00:26
kanzurecan we stab them with a fork?00:26
fennstab away, jacques00:27
kanzurewho?00:27
fenncommunist revolution has been tried over and over, it doesn't work00:28
kanzurehow is this the communist revolution?00:28
fennbecause they won't give us the means to production00:28
fennget it?00:28
kanzurethis wasn't the communist revolution :)00:28
kanzuremaybe metaphorically00:29
fennbbl00:30
kanzurewell, wait00:30
kanzurenot even debian expects you to download all of the packages from the programmer teams00:30
kanzureso it's kinda the same .. aggregate into large repositories00:30
fennyou have the source though, and the option of forking into your own project00:31
fennwith proprietary commercial stuff you don't have that option, even if you are allowed to distribute all the patches you want00:31
fennit all works great until the company goes belly up and you can't get your stock un-modded widgets00:33
fennor they decide to change some miniscule detail that screws everything up00:33
fennor they do a total redesign and call it the same thing00:33
fennor they send black hatted storm troopers to bust down your door00:34
kanzurewait, is there anything good about the system?00:37
fenngives you a head start so you dont have to dig in the dirt for a thousand years00:38
fennalso, the system can be subverted occasionally00:38
fennlike blender, bought the IP rights from a dying software company00:38
fennusually though you just get some gnarly military-industrial-government fallout like opencascade00:39
fennuseless for mere mortals00:39
kanzurealso, I'm talking about more than just software00:44
kanzure"here's the specifications for the materials we offer"00:44
Phreedomfenn: 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 enough00:44
kanzureor "here's the tools we make"00:44
kanzurePhreedom: it seems to be just a lack of understanding00:44
kanzureI don't think they see how it works .. normal people don't need to see an operating system, for instance00:45
kanzureuhm, s/normal/typical users/00:45
kanzurewtf00:57
kanzurehttp://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
kanzureoh, it's Fox00:57
kanzurehttp://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.'01:00
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kanzureHey.01:03
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bkeroWow, I have some stupid friends.03:08
bkero*had some stupid friends, in high school03:08
bkeroShe started talking and said that one of her favorite subjects is evolution versuse creationaism(she's very fundy)03:09
bkeroShe started talking and said that one of her favorite subjects is evolution versuse creationaism(she's very fundy)03:09
bkerodamn it03:09
bkeroCrazy girl from Montana called me again.03:09
bkeroand said that one of the flaws in evolution is that amino acids can't develop in the presence of oxygen.03:09
fenntell her we came from the stars03:10
fennpanspermia.org explains it all03:11
bkerohaha03:11
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kanzurethey're all crazy03:13
fenngirls?03:13
kanzureyeah.03:14
fennmostly just the ones named Kate03:14
bkeroThis one is named emily.03:14
bkeroShe's a worthless human being with dilusions of becoming ana uthor.03:15
kanzureAna Uthor?03:15
fennana uthor, the bott from sweden?03:15
bkeroAn author03:15
fennhttp://uk.youtube.com/watch?v=rHvMZnWVOvs03:16
bkeroShe does nothing but work at safeway, sit at home and readmanga all day, and get fat off junk food.03:16
bkero*read manga03:17
kanzureSomething wrong with manga?03:17
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fennoops that one has no english subtitles, you guys probably dont know swedish eh03:18
kanzurehttp://heybryan.org/meetings.txt rawr03:19
kanzurehm, have to schedule dr. campbell in there somewhere03:21
kanzuremaybe i'll go yell at him for using c#03:21
fennwhat's wrong with C#?03:21
kanzurethe 800 pound gorilla told me to use it03:22
kanzureI've been suspicous ever since03:22
fennfair enuf03:22
bkeroUh03:24
bkeroThe problem with C# is that it compiles into .net code03:24
kanzurethe 800 pound gorilla?03:24
fenni havent really looked at it, i just assumed it was C with OOP extensions03:24
kanzureMicrosoft written all over it IIRC03:25
fennmaybe i'm thinking of something else03:25
bkeroIt's just a dotnet bytecode interpreter03:26
bkeroOr rather dotnet bytecode compiler03:27
kanzurehm, it wouldn't be terribly hard to write a crawler for digikey and mouser and seedpot the 'ghost overlay' thingy03:27
bkeroSo it produces the same code as visual basic .net03:27
fennkanzure: and provide sort by price function? you could sell that for millions03:27
kanzurethey don't sort by price?03:27
kanzurewtf?03:27
kanzureI'm assuming there's some sort of technical metadata for each item03:28
fennno i emailed several years ago and they promised they were working on it03:28
kanzure"yes sir, right away ... " > /dev/null03:28
fennyou can sort every conceivable property except price03:28
kanzurebwahah03:28
bkeroprice changes depending on quantity ordered03:28
kanzurebah03:29
kanzurehow hard could it be to steal their catalog03:30
bkeroIt's easier to tell people to fuck off rather than explain things to them.03:30
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kanzureno, I'm sure fenn knows about bulk pricing options03:30
kanzurealso sure he doesn't care that much03:30
kanzurebulk resistors or something maybe03:30
bkeroGoing to make some elctroncics?03:30
kanzurehttp://digi-key.dirxion.com/default.asp03:31
bkeroelectronics03:31
kanzurefenn has a lair03:31
kanzurehaha03:31
kanzurerequires flash03:31
kanzurewtf is this bullshit03:31
kanzure'Download Interactive Catalog for PCs (.exe - 457MB)'03:31
kanzureon a crappy connection03:32
fennhmm i whined about that too when it was introduced, there should still be links to individual pdf pages03:32
kanzurehttp://pdfcatalog.digikey.com/T083/digikey.pdf 100 MB wtf03:33
fennwell you dont download the catalog..03:33
kanzurehm?03:33
bkeroI got 2 giant digikey catalog books03:33
bkeroI can send them to you if you want.03:33
kanzurein print?03:33
bkerohttp://www.gametrailers.com/player/39284.html03:35
bkeroYes03:35
kanzurewhy03:35
fenni read an article about that, it sounded pretty neat03:36
fennevery nut and bolt on every object in the game has some real engineering purpose for how that object is built03:36
bkeroCome on, it's a gritty future where the only form of currency is BOTTLE CAPS03:38
fennhmm my laptop sucks too much to play that03:39
fennwmv03:39
kanzureme too03:39
bkeroI got 2 8800GTs in preparation.03:39
bkeroSLI03:39
bkeroIt's the only reason I'm bringing my computer to new york.03:39
fenni almost bought a "real" video card two days ago, then i decided i would never use it03:41
bkeroDepends on if you think of using OpenCL or GPGPU stuff.03:41
kanzureCL?03:41
bkerohttp://en.wikipedia.org/wiki/OpenCL03:42
kanzurenot another typo?03:42
fennis there any discernable difference between 8800GT and 8800GS?03:42
bkeroYes03:42
willPow3ryes03:43
bkeroShader count, clockspeed, slower memory03:44
fennbut, can you actually see any difference?03:44
fenni mean, i dont know how these numbers really affect anything03:44
willPow3rdepends on the game03:44
bkeroYes03:44
bkeroReally depends on the ersolution and rendering options you want03:45
willPow3rits the difference between low and medium graphics on crysis03:45
bkeroI run 1920x1080 with high options in crysis03:45
bkeroOn an 8800gs it would be below 5fps03:45
willPow3ri've read that sli doesn't make much difference03:46
willPow3rbut on my 8800gs i can run it on 1920x1200 on medium and get 30 fps03:47
bkeroon crysis?03:50
willPow3ryea03:50
bkeroThat sounds a bit high.03:50
willPow3roh, sorry03:51
willPow3ri have a 8800gts03:51
willPow3rnot gs03:51
bkeroYea03:51
willPow3rbut you're running sli right?03:52
bkerohttp://en.hardspell.com/doc/showcont.asp?news_id=215903:52
bkeroYes03:52
willPow3rdo you notice a significant performance improvement over non-sli?03:53
bkeroSome games03:53
bkeroIt's usually transparent to games though since I run most of my games in WINE.03:53
willPow3rcrysis? in wine?03:54
bkeroHeh no03:54
bkeroNot crysis03:54
bkeroMost games03:54
bkeroJESUS CHRIST04:06
willPow3rtourettes?04:06
bkeroIn Fallout 3 you can build weapons.  One of which is called a "railway rifle"04:06
bkeroIt shoots railroad spikes04:06
bkeroYou decapitate people with railroad spikes.04:07
willPow3rthat's very innovative04:07
willPow3rnot as cool as wolfenstein 3d, however04:13
bkeroI dunno04:13
bkeroI've played both04:13
bkeroand I've enjoyed this more.04:13
willPow3rhttp://upload.wikimedia.org/wikipedia/en/6/69/Wolf3d_pc.png04:14
willPow3rcan't really compete against these graphics04:14
bkeroYea I've played it04:14
bkeroOne has nazis04:14
bkeroand one has 50s american art deco in apocalypse.04:14
facefaceis the email thing still working?04:21
facefacehttp://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.100016704:27
* bkero watches some TED videos.04:36
bkeroYou all have seen those before, yes?04:36
facefaceyes04:37
faceface(some)04:37
willPow3rted nugent right?04:38
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kanzurehttp://www.phlatboyz.com/11:32
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kanzureWhere the hell is XPP?11:46
kanzureIt's a computational neuroscience software package.11:46
kanzureHm, new list to join - http://visionscience.com/pipermail/visionlist/2007/002438.html11:46
kanzureHm, new list to join - http://www.neuro-it.net/pipermail/general/2004-April/000070.html11:46
kanzureAha11:47
kanzurehttp://www.hirnforschung.net/cneuro/cneuro_software.htm11:47
kanzurehttp://heybryan.org/mediawiki/index.php/Computational_neuroscience <-- Updated11:54
kanzureDumping just half of those into "brain on a disc" would work.11:55
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kanzurehttp://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 ..12:58
kanzurehttp://custom.nimblex.net/ AJAX-like live CD generator? end of the world12:59
kanzureregolith challenge ended earlier today - the lunar excavation challenge competition13:00
kanzurenobody won13:00
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
kanzurehttp://git.debian.net/?p=live-helper.git13:01
kanzurehttp://www.livedistro.org/resources/documentation/howtos/building-your-own-scientific-linux-livecd13:04
kanzurehttp://wiki.debian.org/DebianLive/Howto/ISO <-- surprisingly simple13:12
kanzurehahah13:12
kanzureSomebody just searched for "homemade transcutaneous electrical neural stimulation download"13:12
kanzureGot my bookmarks.13:12
kanzure88.192.33.3813:13
kanzureFedora user.13:13
kanzuresic him13:13
kanzurehttp://www.mcell.cnl.salk.edu/ <-- Ho hum, a good diagram.13:33
kanzureCharlie made it to boingboing http://www.boingboing.net/2008/09/01/howto-make-a-3d-prin.html#comments13:41
kanzurehttp://www.psics.org/forum/index.php?topic=5.0 <-- small forum but lightning fast response :)13:56
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kanzurehttp://www-2.cs.cmu.edu/~dst/HHsim/ <-- Why is the linux download 200 MB ?14:07
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kanzurehttp://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 phys14:57
kanzureThis sounds familiar ...14:57
kanzurehttp://brain.unr.edu/ncsDocs/15:02
kanzure^ that may or may not be Markram's neocortical simulator15:02
kanzurehttp://cortex.cse.unr.edu:8000/ganglia/ <-- cortex cluster report15:03
kanzurehttp://ganglia.sf.net/15:03
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kanzurehrm15:37
kanzurehttp://www.mormonism-engineering.org/15:37
kanzureso 'cosmoforming' is what they call it now, eh15:38
kanzurealright, so about 400 MB of software15:49
kanzureand it's all terribly documented (of course)15:49
kanzurehm, I'm kind of surprised that somebody is technically competent enough to be able to pull "live news" off these days16:05
kanzureon television.16:05
kanzurehttp://www.eyeondna.com/2008/05/10/dna-video-pimp-my-genome-google-tech-talk-with-andrew-hessel/16:29
kanzureoh shit, Andrew did a Google TechTalk16:29
kanzurethis isn't the presentation he gave at BioBarCamp 16:29
kanzurebut close enough16:29
bkerohttp://blogoscoped.com.nyud.net/google-chrome/16:34
ybithttp://www.theaustralian.news.com.au/story/0,25197,24279207-30417,00.html16:35
kanzurehttp://blogoscoped.com.nyud.net/archive/2008-09-01-n47.html16:36
kanzureI don't get it.16:36
kanzurewhat does this Google Chrome actually *do*16:36
bkerolol16:37
kanzurehttp://blogoscoped.com.nyud.net/google-chrome/3 <-- multithreaded browser?16:38
kanzureok, that's worthwhile16:38
kanzurehttp://blogoscoped.com.nyud.net/google-chrome/416:38
kanzurebah16:38
kanzuremultiple threads running on the proc16:38
kanzuresure, but just try running a few hundred instances of firefox16:38
bkerochild processes :P16:40
kanzureisn't this like my konqueror idea16:40
kanzurehttp://heybryan.org/projects/browsehack/tabtabtab.html16:41
kanzurehttp://blogoscoped.com.nyud.net/google-chrome/7 <-- is it really safe to be instantiating the whole damn rendering engine each time ? just saying ..16:41
kanzure#9 <-- haha, masochists :)16:42
kanzureoh, 20 minutes into that video I linked to16:43
kanzureis what you want to see.16:43
kanzure http://blogoscoped.com.nyud.net/google-chrome/13 javascript vm ?16:46
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kanzureit's weird, Andrew is much less coherent in the 2007 video17:01
kanzureI'm guessing he had practice up to August '0817:01
kanzure40 min - 'Drew Endy has been going around talking about bio fabs' eh, he rarely mentions bio fabs17:01
kanzure(Drew, I mean)17:02
kanzureoh17:23
kanzurehttp://richardjschueler.com/wp-gallery2.php?g2_itemId=5707017:23
kanzurethat's a much better video about what he's doing17:23
kanzurehttp://www.arl.org/sparc/17:37
kanzurefor open access stuffs17:37
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proctokanzure: I think it's likely that rather than instantiating a wholly new renderer, they will copy one into the new process memory18:24
kanzureisn't it a large struct anyway though ?18:25
kanzureeh18:25
kanzureI suppose it's okay anyway though18:25
kanzurebecause of guys like at openmosix18:25
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kanzureor the kernel modules to save procs to hdd18:25
proctoyou can't optimally maximize ALL variables, you maximize some mole than other- :>18:25
kanzureso when you get up to 500 tabs, I won't have to worry18:25
proctoin this case, compartmentalization is mole important than memory use18:25
proctobecause though use will be high, reuse will also be high18:26
proctoand for power users of tabs like you, it's heaven sent18:26
proctowhere heaven == google :>18:26
proctoI've been using a rough equiv of their UI by using vimperator18:27
kanzurevimperator for vim ?18:31
kanzurealso, their ui seems to suck18:31
kanzurewhy not a vertical tab list?18:31
kanzurehopefully they thought about that and have it extendable or something18:31
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kanzurePhreedom: one page writeup or just /part now18:43
kanzure:p18:43
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kanzurehaha18:44
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kanzure:)18:44
Phreedomeverywhere I go somebody wants me to do something18:44
kanzurerawr18:44
fenn"google - placing blame where blame belongs"19:24
kanzureon the browser?20:08
kanzurebut really Phreedom, it'd be nice20:09
kanzureeven wild ranting :)20:09
Phreedomkanzure_: I know I know20:09
PhreedomI'd like to share it too20:09
kanzure?20:09
kanzureCan't ?20:09
Phreedomneed time as always :(20:10
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kanzurehm20:49
kanzureAny ideas on ripping partsregistry.org ?20:49
kanzureI'm thinking that it might be a good dataset to play with on graph-demo/graph-easy, the javascript graphviz implementation20:50
kanzurebut I need to download the "parts"20:50
kanzureArgh. This site is annoying too.21:33
kanzureWhat happened to the good old days when people just threw up files in directories?21:33
kanzureI feel like I'm herding turtles.21:34
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fennyou could just ask them for a .zip of all the files21:45
kanzurehackers don't have to ask21:46
kanzuream I leet hax0r yet?21:46
kanzuremaybe I will21:46
kanzurenot now though, I was kinda hoping to only spend 10 minutes on this stupid problem21:46
fennask now so you have what you need next time you feel like working on it21:47
kanzurehttp://partsregistry.org/Registry_Software:PERL_Modules:PlateImage.pm hrm21:47
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kanzurewah, I don't feel like being social right now21:49
kanzurewho do I have to yell at21:49
kanzureis it Bill Flanagan?21:49
kanzureI know he does openwetware21:49
kanzuredoes he do partsregistry too?21:49
kanzurehttp://partsregistry.org/Registry:Feature_requests <-- old stuff .. Endy's #2 is pretty easy .. if I had what I wanted here21:50
fennthis is really a prime candidate for git-ification21:52
fennor at least some kind of distributed archiving21:52
kanzureno kidding ..21:53
kanzureand it's something that can be forked21:53
kanzure;-)21:53
kanzureI was going to see if I could throw this into the graph-easy/graph-demo pages that had the javascript + graphviz stuff21:53
kanzureas an alternative route to turtleworkers from the fabrication industries just for the moment :)21:54
kanzureas in, just for the night21:54
kanzurebut again another stupid technical decision on their end, so..21:54
kanzurehttp://heybryan.org/~bbishop/docs/biobricks.js is their javascript from the view page21:54
kanzurehttp://partsregistry.org/wiki/index.php/Part:BBa_J0108021:54
kanzurenow, it looks like they're making an invisible form somehow21:55
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
fennthat's a common way of preserving user variables, like view mode21:55
kanzurethat might be all .. but if it was, wouldn't that be in the GET rather than POST ?21:55
kanzureI don't see any form element telling the browser to post21:56
kanzurethere's also nothing in the js saying to do a post and not a get21:56
fennGET url's with lots of variables are ugly, or something21:56
kanzuresure they are, but I don't see how they're making it not do a GET here21:56
kanzureoh, also, the INPUT vars there are not enough - there must be something else hidden here that I'm missing21:56
fennform.method = 'POST';21:57
kanzurethat tells it the id of the page that I'm coming from21:57
kanzureyou see that in the js ?21:57
kanzurestupid vim search function .. (yes, I escape quoted the period)21:57
fennthe period?21:57
kanzureaha21:57
kanzuregot it21:57
kanzureyes21:57
kanzureline 1164 ?21:57
fenni use / for searches21:57
kanzureme too21:57
kanzureprimaryPartId .. excellent.21:58
fennshouldnt that say something like BBa_J0108021:59
kanzureyes21:59
fennis there some way to translate other languages into javascript?22:00
kanzurelike what?22:00
kanzuredon't we have some java-to-c stuff out there ?22:01
kanzureor the other way around ?22:01
fennit just seems weird that javascript is the only language you can run in a browser22:01
kanzureVB Script22:02
kanzuredon't know why everyone is fascinated with javascript22:02
kanzureapt-get is perfectly fine for giving your clients some programs22:02
kanzureheck, they're basically using it when they type in the address each time I guess22:02
kanzurehm, http://partsregistry.org/cgi/partsdb/puttext.cgi?primaryPartId=BBa_J01080 is not enough22:03
kanzurealthough I'm making the assumption that it accepts GET as well22:03
* kanzure checks with wget22:03
kanzuresame thing22:03
kanzurewhy is no sequence specified?22:05
kanzureisn't that what should be in the db?22:05
fennhttp://partsregistry.org/cgi/partsdb/puttext.cgi?primaryPartId=BBa_J01080&seqHidden=Hi%20Bryan!22:06
kanzurewtf22:06
kanzurewhat is the purpose of this cgi script22:06
fennis there a way to intercept the POST variables?22:07
kanzureperhaps with a firefox extension22:07
kanzureI was toying around with that in lynx to no avail22:08
kanzure(did not exist)22:08
kanzureclearly there's some information being drawn out from somewhere on this page22:10
kanzureif you press 'view source' it's not there22:11
kanzureoh22:11
kanzureit's an extension22:11
kanzureto mediawiki.22:11
kanzureby 'view source' I mean the link on the page22:12
kanzurehow do I use mysqladmin to investigate foreign hosts22:16
kanzureI thought it would just be mysqladmin --host=partsregistry.org22:16
fennwould they leave the db open to random connections?22:19
fennis that standard practice?22:19
kanzurewhen you install mysql your username and password is like "root" and ""22:19
fennhmm22:19
fenni should hope they changed that22:20
kanzurewhich is probably the stupidest thing ever22:20
fennthis gives new meaning to biohacker :)22:20
kanzurehttp://partsregistry.org/Assembly:Robotic_Assembly:Files buh ?22:22
kanzurehttp://partsregistry.org/DAS_-_Distributed_Annotation_System22:22
kanzureah22:22
kanzureI am saved22:22
kanzureI love Randy.22:22
kanzurehttp://partsregistry.org/das/protein_annotations/dna?selection=PartName:firstbase,lastbase22:22
kanzureXML 22:22
kanzurehttp://partsregistry.org/das/parts/entry_points/22:23
kanzurebahhahah22:24
kanzureis that it?22:24
kanzurehm22:24
kanzureI wish I could make NY Times with only <300 items in a db22:24
fennwell they do actually do something (so i hear)22:25
fennare all the parts proteins?22:27
kanzurehttp://partsregistry.org/das/parts/features/?segment=BBa_R0050:0,50000022:27
kanzureis this usable ?22:27
kanzureI mean, the data looks .. like little22:27
kanzurehm22:27
kanzureno, some of them are promoter sequences for example22:27
fennthats just the annotation, but you still need the actual sequence right?22:28
fennlooks like a plasmid22:29
fennah here's the sequence http://partsregistry.org/das/parts/dna/?segment=BBa_R0050:0,50000022:30
fenns/features/dna/22:31
kanzureokay, so takin the other features/ page, 22:31
kanzure*taking22:31
kanzurehow is this usable if I was to throw this into a giant pot22:31
kanzurefor designing circuits ?22:31
kanzureI mean, it doesn't look all that useful ..22:31
fennwell, i have no idea22:31
kanzurethere's a start and end portion of the 'features' in the fle there it seems22:31
fennwtf is BBa_R0050 for example22:31
kanzurefeature id22:31
kanzure   <FEATURE id='2018' label='putative'>22:31
kanzure    <TYPE id='start' category='translation'>start</TYPE>22:31
kanzureis that literally meaning ' the start of translation ' ?22:32
kanzurehttp://partsregistry.org/wiki/index.php/Part:BBa_R005022:33
kanzureit's a promoter22:33
fennhmm what's the start codon again?22:34
fennATG = start22:35
fennat 35 i see an ATG22:35
fennat 41 there's CAT which is the complement22:36
* fenn counts again22:36
fenner, right, so going backwards on the other strand starting at 43 would be the start codon (start translation)22:37
kanzurecount? char count in vim ..22:39
kanzureCAT is not the complement of ATG22:40
kanzureATG & TAC22:40
kanzurefuck22:40
* kanzure hangs his head in shame22:40
kanzureI don't understand how there's "on the other strand"22:40
kanzurethis is all one strand, no?22:40
fennit's double stranded DNA22:42
kanzureso, {strand1}{complement} ?22:42
fennthe arrow on their annotation is going the wrong way for my idea to be right22:42
fenni dont remember or know what pM and pR mean22:43
kanzurehaven't heard of those variables either22:43
kanzurewhy would they tell you the complementary strand anyway?22:43
kanzurethat's easily computed22:43
fennbecause humans are looking at it22:44
fennThe pL, pR and pM promoters of lambdoid phages direct the transcription of early phage genes and the prophage repressor gene.22:44
fenni'm going to name my son lambdoid22:45
kanzurethen where is the complementary strand beginning/ending in the features/ page ?22:48
fennsorry i think i confused you22:49
fennthe features page only has annotation for one direction22:50
fennone strand22:50
kanzureso it applies to exactly 50% of the nucleotides on the dna/ page 22:50
kanzureoh wait22:50
kanzureis there a newline in there?22:50
fennno, the dna page only gives you one direction22:50
kanzurehm, nope22:50
kanzureoh22:50
fennnewlines are just to make it fit into 100 columns22:51
fennif the seq length is > 10022:51
fennone would think there might be human readable comments in the DTD explaining wtf each field means22:52
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kanzurehm22:55
kanzurehttp://partsregistry.org/das/parts/features/?segment=BBa_F2622:0,50000022:55
kanzureit doesn't seem to have much of a difference really22:55
kanzurethis is a 'sender device'22:55
kanzurewhatever that means22:55
fennoo that's a bit more complex22:56
fennc3hsl appears to be some kind of inter-bacterial communication molecule22:58
fennerm, c6 = hexanoyl homoserine lactone22:59
fenni have this feeling like when starting at an electrical schematic written in russian23:00
fennstaring*23:01
kanzureI'm not even sure this tells us anything useful23:01
fennthe annotation shows you how it's put together23:02
fennthere doesn't appear to be any formalized usage information though, like 'whats it good for'23:02
fennwhat does PoPs mean?23:02
fennpolymerase per second23:03
* fenn looks around for an axe23:03
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kanzurenewgenome just found me a meeting with Dr. Mauk :-)23:04
kanzurethe "Building Brains" guy23:04
kanzurehttp://heybryan.org/buildingbrains.html23:04
newgenomeyou going to the singularity summit?23:05
kanzureCan't afford the flight.23:06
kanzureI have people that would put me up, but not the cash to get up there.23:06
fennwhich Dr Mauk?23:06
kanzurefenn: he's teaching a freshman-only first-semester-only class on "building brains"23:06
kanzurehttp://clm.utexas.edu/CLMsite/Mauk.html23:08
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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 understan23:08
kanzurebasically it's probably some guys sitting around doing pGENESIS or O'Reilly's PDP++23:09
kanzurethe class is fairly simple23:10
kanzurehttp://heybryan.org/~bbishop/docs/Building Brains Syllabus.pdf23:11
kanzureI missed the first two days of class since I didn't know of its existence23:11
newgenomeyou got into building brains?23:11
kanzureyes23:11
newgenomewhat do you do?23:11
kanzureI haven't attended yet :-)23:11
newgenomeoh23:12
kanzureI was surprised to find a class with the same name as http://heybryan.org/buildingbrains.html23:12
kanzureobviously he's talking about digital brains23:12
kanzurebut meh23:12
newgenomethe cerebellum23:12
newgenomethat's motor coordination23:12
newgenomeright?23:12
newgenomethis might be useful for ninja reflexes23:13
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kanzureYes, 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 home23:13
fennhear hear23:13
newgenomedo you have any tissue cultures going yet?23:14
kanzureNo supplies.23:15
newgenomeI hear they are easy to do23:15
kanzurehahah23:15
kanzureHow so? 23:15
fennthere sure is a lot of AI stuff on the syllabus (more "cognitive science" than neuro)23:15
kanzureI know :-(23:15
kanzurebut it's Building Brains, not Building Minds23:15
newgenomealmost the same thing23:15
fennnot at all23:15
kanzurewtf is a mind?23:15
fennone is philosophical wankery, the other is pure empirical observation23:16
kanzurewell, also with some occassional wankery23:16
fennnaturally23:16
kanzure"computer simulation project approved by instructor"23:17
fenni'm more inclined to the philosophical wankery of cog-sci than neuro myself23:17
kanzure"my plan is to convert jupiter into a brain"23:17
kanzurewhat do you mean?23:17
newgenomeheh23:17
fenntalking to me?23:17
kanzuremm23:17
kanzureyes23:17
fennwell, if you figure out how a human brain works, you'll end up being able to make human-level intelligence (naughty word)23:17
newgenomecould you send me the syllabus23:18
kanzurenewgenome: I linked you to it23:18
newgenomethe page you set up is 404 error23:18
fennbut i think nature has already optimized just about everything as usual, and it will be very hard to improve on the existing brain design23:18
kanzurehttp://heybryan.org/~bbishop/docs/Building%20Brains%20Syllabus.pdf23:18
kanzuretry that23:18
fennso, cog-sci breaks it down into pure first principles, from which we can come up with new cognitive architectures23:19
newgenomemuch better23:19
kanzurewhat do you mean by first principles23:19
kanzurebecause right now it sounds like wankery23:19
fennthe problem is that there's really no way to test the first principles in reality, they're sort of like religious beliefs23:19
kanzureunless you actually refer to something here23:19
kanzureepistemology?23:19
fennat least at the current point in time, we dont have any kind of test bed23:20
kanzuretest bed of what23:20
kanzureWed. 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
fennwell, the problem seems to be figuring out how we do what we do23:21
fennbut we dont know what exactly it is that we do23:21
kanzurefenn: most programmers do little23:21
newgenomeI don't think I'll take that class23:21
newgenomenot this semester at least23:21
kanzureit's this semester only23:21
kanzurefreshmen only23:21
newgenomeI here elective classes like this can be prttty hard23:21
newgenomedang23:21
kanzureThis isn't going to be hard23:21
newgenomethat's a hard choice23:22
kanzureai stuff and cog sci is still opinion-oriented23:22
fennfreshmen only? thats weird23:22
newgenomethat is usually indicative of paper writing23:22
kanzurehe tells us to send him email about our philosophical problems 23:22
kanzurein the syllabus23:22
kanzureso23:22
kanzureI'm thinking something odd is going on here23:22
fennits a CULT!!!!!1123:22
kanzuregasp23:23
fennrofl23:23
newgenomeoh noes23:23
kanzureno, I refer to the fact that he wants us to send him email23:23
kanzurewho does that? :p23:23
fennwell, i suppose it makes more sense than typing up a MS-word document and printing it out23:23
fennits not like all professors are just trying to get their own research done and have to teach some stupid freshman class23:24
kanzurewouldn't he rather teach some serious comp neurosci to grad students?23:24
fenndunno, maybe he's in the wrong field and would rather be doing philosophy or cog-sci23:25
kanzuremm23:25
newgenomeor maybe he is using it as a filler23:25
kanzures/filler/filter/23:25
newgenomeor just to attract some liberal arts students23:26
newgenomethe computer simulation part sounds cool23:28
kanzureyeah, and it's basically something you could do right now23:28
kanzurejust open up NEURON or GENESIS or better yet, O'Reilly's "emergence"23:28
kanzureand start playing around with some data sets or something23:28
kanzureI say better yet because he has deb and rpm files on the wiki23:28
kanzurewith pretty screenshots23:28
newgenomelinks to pretty screen shots?23:29
kanzurehold on23:29
newgenomebtw anyone heard from percent?23:30
fennnot for 2-3 days23:30
kanzurehe doesn't want me giving out his AIM nickname23:31
kanzurebut if you need me to yell at him, just ask23:31
kanzureand he's not on anyway23:31
newgenomewondering some things about nanotubes23:33
newgenomelike is it possible to make tiny trusses made from nanotubes?23:34
fennwhat do you mean by 'possible' exactly?23:34
newgenomeas in take some nanotubes, and join them together into some sort of 3d structure without require implausible molecular assemble technology23:37
newgenometo make a material much stronger than steel23:37
kanzurebiotinylate the ends of them and you might be able to do something, but where are you getting your precision from?23:37
kanzureerm, the manipulation23:37
newgenomethat's the point23:37
kanzurejust use macroscale clumps of them23:38
kanzurei.e.,23:38
kanzureif you poured nanotubes into a pot of cement23:38
kanzurewouldn't this reinforce the cement ?23:38
kanzurewould it?23:38
* kanzure wonders.23:38
newgenomeyeah I was thinking that too23:38
newgenomemay be just use centimeter long nanotubes23:38
newgenomeput them in bundles and weld them together some how23:39
fennthere's a lot of development of side chains to grab the matrix (for space elevator cable)23:40
newgenomewhat do you mean23:40
fennif it's just the nanotubes, they'll pull apart as if they weren't connected (because they aren't)23:40
fennso you want some kind of cross linking, or at least sticky side chains23:40
newgenomeI know, but nanotubes can be 'welded' using some sort of e-beam23:41
fenni guess you are talking about something like this http://news.rpi.edu/update.do?artcenterkey=31923:42
fennThe 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
newgenomeyeah23:43
fenni dont get the whole browser tab thing, what's the point23:44
kanzurehm?23:45
kanzurewell, that's why I wanted to put it on the task bar23:45
newgenomethey also have to find a way to get nanotubes of the same length and chirality to make the type of structures I am talking about23:45
kanzureor do you mean google's comic portrayal of23:45
kanzureoh wait23:45
kanzureyou mean tabs on the tubes :)23:45
fenni'm still reading the google chrome comic23:46
fennthis just strikes dread into my heart: http://blogoscoped.com.nyud.net/google-chrome/1823:46
kanzureit's not loading well for me23:47
kanzureah23:47
kanzureOH23:49
kanzurehttp://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.'23:49
kanzure'All of us at Google spend much of our time working inside a browser. We search, chat, email and collaborate in a browser. ' wtf23:50
kanzure*that* scares me23:50
kanzurehttp://googleblog.blogspot.com/2008/09/fresh-take-on-browser.html23:50
newgenomewhy?23:50
kanzureprogrammers running a multibillion dollar company23:55
kanzureusing chat programs23:55
kanzurein a browser23:55
newgenomethat is scary because?23:55
newgenomethey could listen to you?23:56
fennbecause it's moronic, and they should know better23:56
kanzuresafety isn't the issue23:56
fennrather than encouraging stupid behavior23:56
fennit's scary because google is supposed to be the best of the best23:58
newgenomeyeah that is very moronic23:58
newgenomethey should make something new 23:59
newgenomelike neural interfaces23:59
fennlike.. a better browser! wah23:59
newgenomethat are free23:59
kanzurenewgenome: http://heybryan.org/projects/browsehack/tabtabtab.html is my browser improvement project23:59
newgenomebut of course send ads directly into your brain23:59

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