--- Day changed Wed Nov 26 2008 00:00 < gene> http://www.newscientist.com/article/dn16119-invention-microscopic-biorobot-slaves.html 00:00 < gene> check it out 00:00 < gene> "But like more normal-sized robots, biobots could be entertaining too, the patent says. People could race them around tracks, mazes, or obstacles. They might even compete in biobot war games, trying to track each other down and making a kill by secreting antibiotics." 00:00 < gene> we might want to try this... 00:01 < kanzure_> using light to guide them is pretty slow 00:01 < kanzure_> I mean, they're slow 00:01 < kanzure_> guiding mechanism (light) is as fast as possible of course 00:01 < kanzure_> but their movement isn't that quick really 00:02 < gene> kanzure move your hand 00:02 < kanzure_> I'm not bacteria 00:02 < gene> do you see it? 00:02 < gene> yeah 00:02 < gene> you aren't 00:02 < gene> but you can see stuff pretty fast 00:02 < kanzure_> http://heybryan.org/mediawiki/index.php/In_vitro_liquid_wars <- was one of my projects that I was designing over the summer 00:02 < kanzure_> right, I wasn't saying that 00:02 < kanzure_> bacteria aren't the fastest little swimmers around 00:03 < gene> I know 00:03 < gene> hey that dude probably stole from you 00:03 < gene> TEST YOUR MIGHT, CHALLENGE THAT PATENT! 00:05 < kanzure_> what, it's a patent? 00:05 < kanzure_> why.. 00:12 < kanzure_> fenn: Paul wants me to start publishing logs of the channel 00:13 < kanzure_> I'm concerned that I might not recall everything I've ever written in the channel 00:13 < kanzure_> so I don't know whether a full log spurt on the internet would be appropriate. 00:13 < kanzure_> What's the protocol in these situations? 00:14 < kanzure_> nsh: public channel logging? yes/no? 00:14 < kanzure_> procto: if we want to log, would your bot be willing? 00:16 * nsh doesn't mind 00:17 < kanzure_> I'm concerned that I might not recall everything I've ever written in the channel 00:17 < kanzure_> so I don't know whether a full log spurt on the internet would be appropriate. 00:20 < procto> kanzure_: yeah, I can throw a bot up 00:20 < procto> kanzure_: you can host it if you want 00:20 < procto> the code is super simple 00:20 < kanzure_> I supposedly have all logs ever in txt format 00:21 < xp_prg> kanzure did you meet with him? 00:21 < kanzure_> Sanjay? yes 00:22 < xp_prg> how did it go? 00:22 < kanzure_> quite well, he was surprisingly knowledgable of some of the software packages I've already been using 00:22 < xp_prg> cool, does he like synth bio? 00:23 < kanzure_> uh, I went to talk to him about CFD 00:23 < kanzure_> don't know why I should have mentioned synthetic biology .. 00:25 < kanzure_> http://heybryan.org/~bbishop/docs/logs/ 00:29 < Maattt> hey people 00:29 < kanzure_> Hey Maattt. 00:29 < Maattt> I'm back home in Houston and it feels WEIRD 00:29 < kanzure_> Heh. Just found this: http://gonzolabs.org/dance/contestants/ "Dance your PhDs". Seems to be an interpretative dance. From Amara Graps. 00:30 < Maattt> what... haha 00:32 < kanzure_> Hrm. GTA3 or visualization programming. 00:39 < Maattt> I'm pretty sure whatever that girl is doing is not what vitamin D does :p 00:47 < kanzure_> Don't be so sure. 10 years from now. Every party you go to. Just wait. You'll see. 01:20 < kanzure_> http://www.opencfd.co.uk/openfoam/doc/README.html 'Run the first example case of incompressible laminar flow in a cavity:' 01:53 < kanzure_> hm 01:53 < kanzure_> "A team in the US has brought the world one step closer to cheap, mass- 01:53 < kanzure_> produced, perfect diamonds. The improvement also means there is no 01:53 < kanzure_> theoretical limit on the size of diamonds that can be grown in the 01:53 < kanzure_> lab. 01:53 < kanzure_> CVD for diamond growth? 01:53 < kanzure_> http://www.newscientist.com/article/dn16036 01:53 < kanzure_> http://www.pnas.org/content/105/46/17620 Enhanced optical properties of chemical vapor deposited single crystal 01:53 < kanzure_> diamond by low-pressure/high-temperature annealing. 01:54 < kanzure_> ultra high strength microspheres or 01:54 < kanzure_> microfibers would be able to solve the problem of finding lightweight 01:54 < kanzure_> storage tanks for the hydrogen fuel on the VentureStar reusable launch 01:54 < kanzure_> vehicle: http://groups.google.com/group/sci.astro/msg/4bddfa864aa04056?hl=en 01:55 < fenn> spheres? 01:56 < kanzure_> I guess it's the same reasoning in geodiscs 01:59 < kanzure_> fenn: for context, I've forwarded an email to openvirgle with where I found it 01:59 < kanzure_> it's an interesting email from arocket, the rocketry mailing list with Cormack and XCOR and Henry Spencer (the guy with all usenet postings ever), etc. 02:01 < kanzure> Carmack? hrm. 02:01 < kanzure> CVD is popping up in a lot of places. CVD, these diamonds. Wonder what's up with that. 02:02 < kanzure> maybe it's because it does homogeneous distribution of the chemical vapor in high temperature and high pressure environments, and this is somehow special across the board? 02:02 < fenn> also it doesnt take for-fucking-ever like most processes 02:04 < fenn> well i guess i have to tear myself away from the internet to go drive for 14 hours 02:04 < kanzure> delivery job? 02:04 < kanzure> oh, turkey 02:15 < kanzure_> http://www.ayanda-biosys.com/mea_biochips.html Ayanda MEAs. scooped from mea-users mailing list. 02:15 < kanzure_> ' 02:15 < kanzure_> Electrode material: platinum; Electrode geometry: 3D tip-shaped (electrode height: 25 - 35 um); Electrode dimensions: 30 um circular electrodes; Electrode spacing: 100 um (centre to centre); Electrode impedance at 1 kHz: 600 - 900 k?; Noise level: 15 - 20 uV; Applications: Acute slice preparations or organotypic slice cultures (brain tissue, spinal cord, etc.); Re-use: acute slices up to 100 times, organotypic cultures several times.' 02:34 < kanzure> fenn: What's wrong with using igloos again? Besides having to live in a cold environment. 02:47 < kanzure_> http://heybryan.org/bioreactor/membraneless_filtration/gnuplot_spiral_parametric.txt <- yay, it works. 02:47 < kanzure_> http://heybryan.org/bioreactor/membraneless_filtration/2008-11-25_gnuplot.png 03:12 < kanzure> Maattt: Ever play with spirals? 03:13 < kanzure> http://heybryan.org/bioreactor/membraneless_filtration/2008-11-25_gnuplot.png 03:13 < kanzure> http://heybryan.org/bioreactor/membraneless_filtration/gnuplot_spiral_parametric.txt 03:13 < Maattt> you mean those things where you put one circle inside another and they go around and around? 03:13 < kanzure> One circle inside of another? Nah, not quite. 03:13 < Maattt> oh, never mind 03:13 < Maattt> you mean actual spirals 03:13 < kanzure> Heh. 03:13 < Maattt> what about them? 03:14 < Maattt> i was just in a car with a guy who drove at 130 mph 03:14 < kanzure> I'm just playing around with a 3D spiral generator. 03:14 < kanzure> Drag racer? 03:14 < Maattt> 3d spirals? 03:14 < kanzure> right 03:14 < kanzure> So I have some cross sections and such, and am splicing them together with some varying delta h from 0 to max height, that sort of thing. 03:14 < Maattt> cool 03:14 < kanzure> uh, well, not zero, but some initial height 03:15 < kanzure> Will be throwing it into a fluids simulator later I guess. 03:15 < Maattt> you have some very diverse interests. 03:15 < kanzure> Braaiiins! 03:15 < Maattt> mine are mostly confined to art and bacon. 03:15 < kanzure> tasty bacon? 03:58 < kanzure> Hrm, visualization first or vtk compatability 03:58 < kanzure> compatibility 04:01 < kanzure_> 'XCOR Aerospace to announce ticket sales for suborbital flights' 04:44 < kanzure_> Somebody should show gene the vtk sonification toolkit. 04:52 < kanzure_> http://openfoamwiki.net/index.php/Contrib_PyFoam 04:55 < kanzure_> ah, here we go. vtkBox: http://www.creatis.univ-lyon1.fr/~jpr/PUBLIC/Doc_VTK_5.0.4/html/a01187.html 05:05 < kanzure_> http://vtkblog.blogspot.com/search/label/vtkCubeSource <--- Check this out. Where precisely are coords mentioned for each of these objects? :/ 05:05 < kanzure_> (in the compressed archive there's a .cpp) 05:08 < kanzure_> Ah: http://www.vtk.org/pipermail/vtkusers/2008-February/094235.html polygonPoints 05:28 < kanzure_> http://www.vmtk.org/ "Vascular Modeling Toolkit" 05:28 < kanzure_> "The Vascular Modeling Toolkit is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels." 05:39 < kanzure_> https://svn.cscs.ch/pv-meshless/trunk/VTK/Examples/DataManipulation/Python/BuildUGrid.py perhaps this is it instead. 09:36 < UtopiahGHML> I wonder if any work in stigmergy has been applied to logistic and the human factor (like floor marking and such) 15:03 < kanzure> oh 15:03 < kanzure> I'm so happy 15:03 < kanzure> people are starting to email me as "Dr. Bryan Bishop" 15:09 < kanzure_> http://heybryan.org/books/Manufacturing/origami/Origami%20fold%20as%20algebraic%20graph%20rewriting.pdf <- The origami webEOS / webOrigami people sent me this paper. 15:09 < kanzure_> They're also addressing me as Dr. :-) 15:23 < kanzure> gene: Almost done. 15:24 < gene> excellent 15:24 < gene> I mean excellent.... 15:26 < kanzure> Woah. Hold on a sec. 15:26 < kanzure> I've been talking with Aaron Swartz? Really? 15:26 < kanzure> Was it anyone in here that was saying he was a jerk a few months ago? 15:27 < kanzure> Something about living with a certain somebody in NY. 15:27 < kanzure> Maybe I was talking with Jef. 15:27 < gene> huh? 15:28 < gene> NOW, NO ONE CAN STOP US FROM VISUALIZING DATA! NO ONE, MWAHAHAHAHAHAHA 15:30 < gene> Who is this Aaron person? 15:30 < kanzure> Aaron did RSS when he was 14. 15:30 < kanzure> and contributes to the W3C groups, etc. 15:31 < gene> wow 15:32 < gene> I have true admiration for the people who served in the Robot Smashing Service 15:37 < gene> you might be right about BASIC 15:37 < gene> http://www.marriedtothesea.com/090608/10-PRINT-SHIT-FUCK-CRAP-20-GOTO-10.gif 15:39 < gene> the URL gives it awaythough 15:40 < kanzure> BASIC is good for learning, and good for simple prototyping, but prototyping in later scripting languages like perl, python, tcl, bash, whatever, is more likely to 'stick' (as in, be useable). 15:40 < kanzure> Now, as it turns out, Visual Basic has a few tricks up its sleeves because it's by Microsoft. 15:40 < kanzure> They're doing some compiler tricks to make it run slightly more quickly than otherwise :-) because they know their own source code to Windows and so on (supposedly). 15:41 < kanzure> gene: Actually, I know it might sound corny, but if you want to see an interesting form of basic, check out Dark Basic. 15:41 < kanzure> They have a demo version online 15:41 < kanzure_> http://darkbasic.thegamecreators.com/ 15:41 < kanzure_> "DarkBASIC allows you to create your own games, demos, slideshows, even business applications using the easy to understand BASIC programming language. Even if you've never coded before, just follow the in-depth tutorials and you'll be generating results in minutes! Harness the power of Direct X and make 3D objects come to life in just a few simple commands." 15:41 < gene> well it has the word dark in it, it's bound to be interesting 15:43 < kanzure> I was writing a few games with it, like "Super Monkey Balls" (a 3D platformer game with annoying music) and a 2D RPG (a continuation of some work I was doing in Visual Basic called "DBZ Insane", which was a slightly functional DBZ RPG, with ki blasts and everything :-)) 15:44 < gene> was that first one based off another game? 15:44 < wrldpc> heh: http://digg.com/music/Scientific_Rap_Museum 15:45 < gene> well I have to leave within -1 seconds 15:45 < gene> so bye 15:46 < kanzure> First one was not based off of another game. 15:46 < kanzure> It consisted of this giant yellow sphere with a terribly large grin, jumping around on way-too-large platforms. 15:48 < kanzure> Hrm. One of the demos that I remember doing was this 'game' where you had a giant glove-hand floating in the sky (the mouse) and you were isometric to a hilly terrain on which there were a few thousand red spheres spawned. As you clicked and moved, the balls would move over the terrain in that general direction. Can't remember why I bothered doing that.. 16:05 < wrldpc> I really can't stand sinecures. 16:06 < wrldpc> The do-nothing produce-nothing get-EVERYTHING people. 16:12 < kanzure> Anything in particular ? 16:44 < wrldpc> snowcm.com/ 16:44 < wrldpc> http://www.snowcm.com/ 16:56 < wrldpc> there are thousands of these firms. 17:36 < kanzure> Heh, I like how professors call at the most inconvenient times. 17:37 < kanzure> "Bryan! Hey, are you coming to the lab today?" *laundry* 17:43 < kanzure> Hi elias`. 18:03 < gene> You know that game does sound like another game a lot 18:05 < gene> well, it looks like I have to go linux 18:05 < gene> to use open foam 18:12 < kanzure> if you tried really, really hard, we're talking superhuman effort, you might be able to get openfoam to work with cygwin. But that's just asking for trouble. 18:12 < kanzure> also, the ME dept www server is running webmin on port 10000 but I can't figure out from where to access it. I need to figure out the mysql username so that I can deploy a wiki on ~adl :-/ 18:14 < kanzure_> http://bitesizebio.com/2008/11/25/diy-electrocompetent-e-coli/ <- like it says, getting comp cells 18:23 < kanzure_> http://www.heppnetz.de/projects/goodrelations/ <- B2B alternative? I wonder how many companies are using it. 18:24 < procto> wrldpc: you were asking about biotech cooking. here's an idea I just read on one of my cooking blogs 18:24 < procto> wrldpc: it's just so simple it's barely biotech, but at the same time, it's very refreshing and innovative 18:25 < procto> wrldpc: basically, what this dude did is he made noodles by adding xanthan to a liquid and using a syringe to push it into a plastic tube, and then let it set 18:25 < procto> wrldpc: he made the same thing with chicken broth, and you get delicious chicken broth noodles 18:26 < procto> and the science is of course the experimentation with different gelatinous substances 18:26 < procto> etc. 18:26 < procto> (before him, only agar agar and the like were used, which resulted in noodles that were too weak) 18:28 < kanzure> xanthan? 18:34 < xp_prg> kanzure you using that script at all? 18:35 < kanzure> yeah, I thought we were talking the other day about this? 18:35 < kanzure> did you forget our conversation? 18:36 < procto> kanzure: xanthan gum 18:37 < kanzure> so a gum noodle? 18:37 < kanzure> I'm not familiar enough with xanthan gum I guess. 18:40 < kanzure_> http://www.tri-conference.com/ molecular medicine tri-conference, 2009. 18:41 < procto> kanzure: it's a gelling agent 18:41 < procto> kanzure: you've most likely eaten it at least twice this week 18:41 < procto> they put it in just about everything 18:42 < procto> xanthan gum and gum arabic are the two most popular stabilizers 18:42 < procto> the noodle is just this gelatinous thing 18:43 < kanzure> gum arabic I've heard of, yes :) 18:43 < procto> the point of his research was to make it more noodly than gely 18:43 < procto> so he experimented, etc. 18:43 < kanzure> it's also used in nanoparticle synthesis as it turns out, but I only remember that because I linked to the eznanoparticle-synthesis subdir in an email earlier today 18:52 < gene> what your not familiar with Xanthan gum? 18:56 < gene> or at least guar gum? 18:57 < gene> buy a big bag of the stuff from a health food store 18:57 < gene> I hear it is quite useful 19:22 < gene> http://www.a-vital-life.com/page.php?p=sbga-harvest 19:22 < gene> how about that for algae harvesting? 19:22 < gene> A HUGE BOAT 19:22 < gene> not driven with propellors, but fricking paddlewheels 19:22 < kanzure> I wonder if you can make algae replicate linearly, in a constrained space. 19:22 < kanzure> like in a very tiny capillary 19:23 < gene> heh 19:23 < gene> that would be funny 19:23 < kanzure> then you just smash it all out. 19:23 < kanzure> or blow it out 19:23 < gene> I think one company is doing(or done that) 19:23 < gene> they grow it inside mats 19:24 < kanzure> that's the basic scheme for single (or near single) layer tissue growth, giant sheets. 19:24 < gene> with exhaust from a coal plant 19:25 < kanzure> anyway, the spiral generator is almost working. At the moment I'm making cross-sections out of four voxels, w 19:25 < kanzure> which you can imagine as a hollowed out rectangular polygon. 19:25 < kanzure> annoyingly, the coords for voxel creation aren't labeled, so there's 8 points and 3 numbers per point, 19:26 < kanzure> and the mapping isn't obvious, so I've been painstakingly trying to figure out how to deform the typical cube voxel into the rectangular shape 19:26 < gene> I know what a voxel is 19:26 < kanzure> blah documentation. 19:26 < gene> you can't 19:26 < gene> it's a voxel 19:26 < kanzure> nope, you can :) 19:26 < gene> oh 19:26 < kanzure> Hi fenn. 19:27 * kanzure goes down to eat and then off to the lab .. apparently the ME dept has "quarantined" a machine in my lab because it was "infected by a virus" 19:27 < kanzure> I suspect they were watching port 6667 19:27 < gene> speaking of voxels, one of the people here on campus made an MRI machine with 0.5 mm cube voxels 19:27 < gene> THE MOST EVIL PORT OF THEM ALL 19:27 < kanzure> is that resolution of the machine, or is that the resolution of the visualization? 19:28 < kanzure> because I can make up a normal cube out of a trillion voxels, but that doesn't mean that the original data that was scanned had a resolution of a trillion 19:28 * kanzure really leaves now 19:30 < gene> of the machine 19:30 < gene> bye 20:34 < gene> http://ovablastic.blogspot.com/2008/11/rats-neurons-in-dish-learn-how-to-fly.html 20:38 < procto> ah yes, that 21:20 < kanzure> I am gone for the weekend. 22:22 < gene> hey guess what I on H+ on a bus