2009-03-05.log

--- Day changed Thu Mar 05 2009
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kanzurehttp://www.dna-rainbow.org:8000/dna-radio.mp3.m3u   <-- why did this make slashdot.08:11
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fennmicrothermal whatsit actuator paper is 162 pages - don't tell me to read all of it, what should i be looking at?10:25
fennoh i see it's like optical tweezers but low tech10:32
fennso that should be fairly simple to make with standard circuit etching techniques10:34
fennnot that i have any idea what to do with it10:35
fennPCR i guess10:35
fennit would be interesting to move bits of melted wax around and let them solidify, as a 3d printer mechanism10:37
fennor some kind of two part epoxy10:37
fenni like the grid idea where they move individual droplets around better than the channel ideas10:41
fennseems like it would be faster at smaller scales and higher gravity (in a centrifuge)10:47
fenn20 seconds per move is too long10:47
kanzurefenn: one of the appendices has the diagrams or something. so, near the end. there's a paragraph that effectively describes it.11:03
fenn"it's kind of like virtualization" isn't going to help a non-programmer11:04
kanzurenone of my explanations are11:04
kanzureI should have just done a linkdump11:04
fennyou should have just kept your trap shut :)11:05
kanzureis it that bad?11:05
fennsave those two emails and read it again in a month11:06
kanzuremoving bits of solidifying wax around does sound like fun.11:06
fennthe neat part about that technique is it's massively parallel11:07
fennthe problem with digital rapid prototyping has been getting the resolution down because serial methods take so long11:07
kanzurealso the whole "program a lab on a chip" and analogies to FPGAs blah blah blah11:07
kanzureoh, that would be a method of fabrication, that's true11:07
fenn"lab on a chip" is bullshit as far as i can tell11:07
kanzure(there was also a paper I came across recently talking about fabricating inside a microchannel, though I don't know why or what results they got)11:07
fenni could believe "micropipettor on a chip"11:07
kanzurewhat do you think is bullshit about it?11:08
kanzurebesides it being a buzzword11:08
fennit's just pure hype11:08
kanzurewhat about people who have put individual lab tools on a chip?11:08
fenni want to see experiments being done with them11:08
fennnobody calls DNA arrays "lab on a chip"11:09
kanzureso, "select one experiment from a random biology journal recently, and run that on a standard 'lab on a chip' platform" ?11:09
kanzurehell, even an experiment from high school / college intro biology labs11:09
fennor just do the experiment in a microfluidics environment in the first place.. which i dont see happening (i havent looked either)11:10
kanzureI've found that it is common for experiments to sometimes place new equipment demands on a researcher11:10
kanzurei.e., the lab doesn't have xyz11:10
kanzurefenn: wait, what?11:10
fennif they are so cool and awesome how come nobody is using them11:10
fennanything microfluidics11:11
kanzureI think you're asking "why don't I have one / why weren't they used in my bio labs"11:11
kanzurebecause I have not seen anything discussing adoption rates or lack thereof11:11
kanzureI'm sure the standard complaints are at play: IP bullshit, fabrication costs (hah), other crap.11:12
fennthe only "real" experiments on the front page of lab-on-a-chip.com are DNA microarrays11:12
fennthe rest is the same hype that's been around since 200011:13
fennportable DNA analysis etc11:13
kanzurehttp://www.rsc.org/publishing/journals/LC/11:13
fenni guess that doesn't even mean anything11:13
kanzurehm.11:13
kanzurewhat about the in vitro protein expression experiments?11:16
fennlink11:17
kanzurehah, "11:18
kanzureLong-term and room temperature operable bioactuator powered by insect dorsal vessel tissue"11:18
kanzureone moment.11:18
fennok this is a "real experiment" http://www.nature.com/nmeth/journal/v6/n1/abs/nmeth.1289.html11:18
kanzurehttp://heybryan.org/books/papers/microfluidics/Lecithin-Based%20Water-In-Oil%20Compartments%20as%20Dividing%20Bioreactors%20-%20in%20vitro%20protein%20synthesis.pdf11:19
kanzurehttp://heybryan.org/books/papers/microfluidics/Protein%20fabrication%20automation.pdf11:19
kanzureah, your link is better than those two.11:20
fennthere should be some kind of 96 well plate to microfluidic chip adapter11:21
kanzure"11:22
kanzureLaser trapping and Raman spectroscopy of single cellular organelles in the nanometer range"11:22
kanzurehow can that not be SCIENCE? :)11:23
fennthe grid-based grab droplets and move them around strategy seems much more flexible and useful as an actual "lab on a chip" than all this combinatorial stuff11:24
fennit's like FPGA vs ASIC11:25
fennwell, sort of11:25
kanzurehm. I never heard about ASIC. looks like it's basically "really truly hardcoding" ?11:26
fennyep11:27
fennthink FPGA without the "field programmable" part11:27
fennbut they are used for analog and power too11:28
fennit's almost a buzzword11:28
kanzurewhat's the advantage of mf cell-free protein expression? it doesn't (yet) make it easy to acquire the special chemicals you need to make that happen.11:30
kanzureguess it just lets you use smaller volumes.11:31
kanzureI wonder if your parallel wax droplet fabrication method could be layered.11:34
kanzureas long as you can move the microheater array upwards a specific distance, apply your new wax droplets by micropipetters or something11:35
* kanzure thinks this is starting to sound a lot like a goo squirter11:35
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fennmaybe, but you can decrease the drop size to something ridiculously small since it's parallelizable11:47
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xp_prgtell me how to do electrphloresis with microfluidics12:59
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nshwho about?13:00
nshnevermind, found it. (was trying to remember the word "stigmergy")13:03
fennlots of fun cyborg dystopian explosions in this comic http://www.onemanga.com/BLAME/13:05
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genehttp://hi.eecg.toronto.edu/wearhow-split0/index.html13:27
geneHow to make a wearable from Steve Mann himself13:27
fennuh.. $560 on batteries alone?13:29
fenndead bug construction? no thanks13:30
fennwhile steve may be obsessed, it doesn't mean he knows what he's doing13:30
geneyeah13:32
geneI just need a head mounted display with a camera that can hook up to my laptop13:32
geneI wonder how small a computer my laptop would be sans screen and keyboard13:33
fenni'm going to use a beagleboard, if i havent already repeated myself too many times13:33
fenngumstix overo is interesting as well, but ultimately costs more for less oomph13:33
genecan it run crysis?13:35
geneand cad applications13:35
geneI care more about cad13:35
genewell I'm going to go see a very large high res display13:35
fennit has openGL ES but last i checked the software wasn't ready13:37
fennso, probably not crysis, ever13:37
fennbut probably CAD13:38
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elias`I've been thinking of using Pandora for something like that.13:43
fennit's the same chip13:43
elias`seems the final version is going to have 256 MB RAM13:43
fennyeah i'm considering using an SSD for swap13:44
elias`A USB webcam would probably be sufficient for a head mounted camera, but display seems more trickier (if you don't consider the potential trouble with getting a relatively discreet camera).13:47
elias`Someone hacked a monocle-like thing out of myvu crystal to mount to glasses, but seemed cumbersome since he had to focus on the side of his vision to actually see it properly13:48
ybitin apt-get construct <hardware>, what's the automation process of getting all the minerals again? i forget14:10
ybitah14:11
ybityes, i remember now. it's for a fablab, not home use.14:12
fennnobody ever said that14:12
ybiteric drexler's mol. assembler would be for home use14:12
fennyou have running water, don't you?14:13
ybit14:13
fennlikewise, you buy commodities at stores, right?14:13
ybit14:13
fennanyway, it's not just for space probes, or just for high tech centres14:14
fennyou get to choose any level of logistical autonomy14:14
geneI'd want some accelerometers and a compass installed in mine 14:16
geneEric drexler hasn't made much progress...14:16
genehttp://www.iherb.com/ProductDetails.aspx?pid=11876&at=014:18
gene"Silicon, a component if silica, gives structure to all living things throughout the plant and animal kingdoms. It is essential to the human body and is found in the lungs, intestines and blood. Silicon gives strength and support to nails, hair, skin, connective tissue, tendons, and ligaments . *"14:18
geneholy cow, we're silicon based!14:18
genetrying to find me some colloidal silica, for making shear thickening fluid...14:19
fennlike cab-o-sil? thickener for airplane body work14:19
fenninteresting note of caution re: cab-o-sil http://www.rcuniverse.com/forum/m_2715206/tm.htm14:20
geneI can't believe it, people are selling it as a supplement!14:21
fennwhat, it's just dirt14:21
genenext thing I know I'll find quacks selling DNA polymerase and restriction enzymes as a supplement14:22
fenni hope so14:22
geneno, it's not dirt14:22
fennit will only make things easier14:22
geneit's been so highly processed it can't be considered dirt14:22
geneheh, well colloidal silica is quite small particles range from 5nm-405nm14:25
kanzurefenn: one of these days I'd like you to go over http://www.wired.com/images/article/full/2009/02/laser2_630x.jpg with me. It would be nice to figure out what all of the components are, or whether or not there's enough information here that Ed Boyden otherwise hasn't published on the OpenStim wiki14:30
kanzurethe rest can probably be pieced together from heybryan.org/~bbishop/docs/open-rtms/ (a partial collection of Superkuh's bibliography on the subject)14:30
genewhat's that?14:31
kanzurerTMS.14:31
genewhoever that is, they go to radioshack14:31
kanzureis that valid english?14:31
kanzurewhat are you trying to say?14:31
genemost of those components in that picture look like they are from radioshack14:32
kanzureright :)14:32
kanzurealthough the coil might be something weird14:32
fennparallel IGBT test 440A14:32
genehome depot14:32
kanzureah, it's "IGBT"14:32
fennpresumably 440A refers to the current in the coils14:32
kanzure I had my neck so messed up for the longest time trying to figure out wtf that said14:32
geneoriginal article14:33
gene?14:33
kanzureoriginal article is worthless: http://www.wired.com/science/discoveries/news/2009/03/neuroengineering214:33
kanzure(more or less)14:33
kanzurelook up openstim and transcenmentalism (ed's site)14:33
fennthe big fat black boxes on the right are the IGBT's, the little squares are probably mosfet's that drive the igbt's, and the thingies on the breadboard are probably voltage regulators or something14:34
geneoh that one14:34
fennblue box = capacitor? black box on cardboard = batteries?14:34
genewait just one second here, I don't believe it14:35
fennwhy dont you just ask them14:35
kanzureI guess.14:35
kanzurehrm, I have ed's number on my cell phone14:35
kanzureguess I finally have a use for it?14:35
geneMIT students use radioshack components?14:35
kanzuregene: what else would they use?14:35
fenngene: are you that clueless?14:35
fennradioshack didn't invent electronics14:36
geneare there no good electronics stores in the MIT area14:36
kanzuregene: what difference does it make whether or not parts are distributed through vendors?14:36
fennthey have electronics labs stuffed to the brim with every possible chip you could want, and rush delivery from companies eager to get their product into the hands of MIT engineers14:36
geneok14:36
xp_prgkanzure I want to do electrophloresis with microfluidics tell me how14:36
genejust buy some agar14:37
kanzurexp_prg: I want to take over the galaxy tell me how or else I fuck your mom14:38
xp_prgI don't know here is my mom14:39
kanzure..14:39
genewhy?14:41
kanzurexp_prg: what have you done to answer your question?14:41
xp_prglearned why hydrophobic means, understood the sharpie experiment, watched youtube videos showing on a microfluidic lab is done, done gel electrophloresis with agar etc...14:43
xp_prgwhy what14:43
xp_prgwhat = what14:43
kanzurexp_prg: but you haven't even read any papers on electrophoresis in microfluidics?14:43
kanzurewhat the hell man?14:43
xp_prgno, I am afraid I won't understand them :(14:44
ybitsorry to have been out of it for awhile btw, i'm no longer distracted with open money. there are some neat underlying concepts, but i finally concluded that it wasn't one of my goals set out last year, and so it's been set aside.14:44
kanzurexp_prg: then why are you asking how to do it14:45
kanzureif you're afraid you won't understand how to do it14:45
kanzureybit: congrats? :)14:45
ybitkanzure: indeed :)14:46
xp_prgcuz I understand the fundamental principles and I thought it would be easy for you to tell me14:46
kanzureyou do not understand the fundamental principles.14:46
xp_prgand I am excited to do it :>14:46
kanzurebecause you are afraid of them14:46
ybithttp://heybryan.org/mediawiki/index.php/Microfluidics + the interwebs is a start14:46
fennxp_prg: it's not easy to explain things to people; it's so painful and awful a thing to do that we pay university professors hundreds of thousands of dollars a year14:46
kanzureyay for ybit.14:46
ybitxp_prg ^14:47
xp_prgok I will try14:47
* xp_prg hates that at work he can't browse the web to do this kind of stuff :(14:47
xp_prgthat is one of the reasons I ask in here sorry14:47
kanzurejust tunnel home.14:47
fennwget -rk -np -nc http://heybryan.org/books/papers/microfluidics/14:48
kanzureor better yet:14:48
fennOH WAIT you're one of those windows idiots14:48
kanzurehttp://heybryan.org/books/papers/microfluidics_2009.zip14:48
fennguess you're screwed14:48
xp_prgfenn I am on macosx14:48
fennthen why is your nick xp_prg14:48
xp_prgkanzure do you think it is doable by diybio person?14:48
xp_prgor will it be way too complicated?14:48
xp_prgfenn exteme programming *sigh*14:49
kanzurewow.14:49
fennwhat's the word for that..14:50
fennlike "ABS brakes" or "API interface"14:50
kanzureredundant acronym?14:50
kanzurerecursive acronym?14:51
geneI think diybio's going nowhere15:37
geneeveryone just wants to GFP e.coli15:38
geneI mean at least be creative and GFP human tissue or a plant15:38
fennoo very creative.. that's never been done before15:39
fennbacterial culture is so much easier that there's no compelling reason to do tissue culture15:40
genewell of course it's been done before, it's just that no one has tattoos that change with circadian rhythms15:41
geneperhaps mood tattoos...15:41
fennthis is quite possibly dumber than the magnet in the fingertip idea15:42
geneit is, but it's creative15:44
genehttp://hackedgadgets.com/2006/07/08/wearable-wrist-computer-from-1984/15:44
genewearable computers15:44
geneone might use a gene gun to do the tattooing15:45
genehttp://www.skynetresearch.com/15:45
fennhah i stumbled across that the other day15:46
genehmm.. looks like an alternate reality game to me, I say we pester them like they're a real company15:46
genehey could you give me a quote on improving our self-replicating automaton's replication rate?15:47
genehttp://twitter.com/skynetresearch15:47
generecent activity, hmmm...15:47
genehow's the fablab going along fenn?15:48
fennnot much activity.. les and i aren't synchronized15:50
fenni made some step pulleys for the lathe, that's about it15:51
genehow?15:51
genedoes the fab have a cnc machine?15:51
genewe don't have one right?15:52
fennglued four squares of plywood together, turn them down, then i made a 35 degree vee bit with an angle grinder out of m2 square steel stock15:52
fennnothing functional yet15:52
genemachine shop here says it will take 3 weeks to make a part I need...15:52
fennthe pulleys are for the lathe which will be CNC'd eventually15:53
fennwhat part do you need made?15:53
* fenn looks at #reprap15:53
genemy weird spiral thing15:53
genethat has the people from the machine shop baffled15:54
fennidiots15:54
fennaren't you in ME? are you telling me they have no CNC machines?15:57
fennobviously you had access to an FDM15:57
genefenn, they're trying to program the machine manually...16:04
geneyeah, I know16:05
fenni have a spiral generator if you want it16:05
fennspits out gcode16:05
fennhttp://fenn.freeshell.org/lengthspiral.py16:06
geneI don't care about that, I need a program to convert 3d models to gcode16:07
* fenn wonders why the only copy of that was in irc/16:07
fennoh ffs16:07
fenngo spend 9 million dollars then16:07
fenndon't pay attention to anything i've been ranting about for the last year16:07
genewait a second fenn, in that program is angle the pitch angle?16:07
fennno it's like the hands of a clock16:08
geneI have mastercam16:08
geneI don't know how to use it16:08
fennthen use mastercam16:08
fenni'm not going to VNC into your laptop and do your homework for you16:08
genehahahaha16:09
genehttp://www.physorg.com/news155494040.html16:10
* fenn searches for the news in that article16:11
geneit's in there believe me16:12
geneit wasn't using GFP16:12
fennbig deal - fluorescent labeled sugars16:14
geneyeah16:15
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kanzurefenn: you might want to post about lengthspiral.py in the diybio sharpie mf discussion re: protein separations and mass spec for nano-scale devices thingies.18:23
fennuh, why?18:23
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kanzureto be helpful?18:24
fenni mean why is it relevant?18:24
kanzureSpiral microfluidic nanoparticle separators.pdf18:25
kanzurehttp://heybryan.org/books/papers/microfluidics/Spiral%20microfluidic%20nanoparticle%20separators.pdf18:25
kanzureor is your program still using those jolting edges instead of smooth curves?18:26
katsmeowwow, http://diybio.org/ has a few hundred of these : Warning: array_map()18:26
kanzuresounds like php18:27
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fennkanzure: can't you just use inkscape or whatever to make a spiral?18:30
kanzurewhy are you asking?18:32
fennhttp://fenn.freeshell.org/microfluidic-spiral.png  is a lot faster and easier to do than to figure out wtf to do with g-code and some random python script some dude made that is totally unrelated18:36
kanzurewasn't that from a paper?18:37
fenni just drew it after looking at that pdf you linked to18:37
kanzureoh, there was one where something like that exact image is used18:37
kanzureit might have been that one.18:37
fennhuh i need another turn on the spiral18:38
fennanyway18:38
kanzurein this case, gcode isn't useful if you're just going to print out the pattern on an inkjet printer18:38
kanzureso instead how about an SVG generator? 18:39
fennwell i could do it but why?18:39
kanzureoh, I'm not suggesting you write it18:39
kanzurebut wouldn't that be useful? instead of unsteadily drawing a spiral each time you want to add a few more loops?18:39
kanzure(or a few more turns, I mean)18:39
kanzureor insert some other random parameter that I am neglecting to think about18:40
fennyes of course some parametric cad program would be ideal18:40
kanzurewhy put all of your eggs into one basket?18:41
fennbecause you need some way to add the little dealies on the ends eventually18:41
fennwriting a custom generator for each job is stupid18:41
kanzureI tend to write a lot of scripts for myself these days18:42
kanzureand even build up on previous scripts I've written18:42
kanzurewhat's wrong with that?18:42
fennit's impenetrable18:42
fenncould you write a script to remake that diagram in four minutes?18:42
kanzurehow many parameters?18:43
kanzureor which ones18:43
fennnone18:43
kanzureoh18:43
kanzurethen why make it a script?18:43
fennall hardcoded (if that's easier)18:43
kanzurewtf?18:43
fennbecause you can add parameters if you want18:43
kanzureI think I could do it.18:44
kanzurethe spiral would just be the set of parametric equations.18:44
kanzureand then the i/o dealies would be custom with a partial curve that I'd have to do a regression analysis of.18:44
fennoh of course18:45
fenni suppose an arc is too complicated18:45
kanzureplot t*cos(t), t*sin(t)18:45
kanzureah, an arc :)18:45
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fennthis spiral is just a centrifuge?18:46
fenndon't they know that A = v^2/r18:47
kanzurewell, centrifugal forces aren't supposed to be involved. but that paper claims so.18:47
fennso why the huge radius curves18:47
kanzurehttp://heybryan.org/books/papers/microfluidics/Continuous%20particle%20separation%20in%20spiral%20microchannels%20using%20dean%20flows%20and%20differential%20migration.pdf18:48
kanzurehttp://heybryan.org/books/papers/microfluidics/Membrane-free%20microfiltration%20by%20asymmetric%20inertial%20migration%20-%20spirals%20-%20bifurcations.pdf18:48
kanzurehttp://heybryan.org/books/papers/microfluidics/Membraneless%20microseparation%20by%20asymmetry%20in%20curvilinear%20laminar%20flows.pdf18:48
kanzurethose papers don't rely on centrifugal forces IIRC18:48
fenni hate it when they refer to a phenomenon by the name of the discoverer18:54
fenna Dean force, you dont say18:54
kanzurethey probably don't know better18:54
fennand that's because of a Dean vortex, I see18:54
kanzure(as in, what the force actually is)18:54
kanzureoh, and this one: http://heybryan.org/books/papers/microfluidics/Membraneless%20microseparation%20by%20asymmetry%20in%20curvilinear%20laminar%20flows.pdf18:59
kanzureah, crap, I mentioned that one already.18:59
katsmeowif you don't have the right font for reading Amharic, Khmer, or Thai, they are available at http://idn.icann.org/Fonts  , i mention this only because some new domain stuff reads in english not like it is supposed to,, such as .xn-zckzah19:11
kanzureis that a new TLD?19:11
kanzurewoah. IANA.org says yes.19:12
kanzurehrm19:12
katsmeow.xn--jxalpdlp Greek (.??????) <<-- mirc won't copy/paste the greek19:12
katsmeow.xn--9t4b11yi5a Korean (.???) <<== ditto19:12
katsmeow.xn--hgbk6aj7f53bba Persian (.???????) <<== ditto19:12
katsmeowhell of a situation, i bet windows won't even allow the name to be typed in, nor the page saved19:13
katsmeowi can't get a grip on a domain like www.mydomain..xn--hlcj6aya9esc7a19:13
genenow where did you find that kanzure19:14
kanzuregene: find what?19:14
genefirst paper?19:14
kanzurewhich one?19:14
kanzureContinuous particle separation in spiral microchannels using dean flows and differential migration?19:15
geneyup19:15
kanzureI'm not sure where I found it.19:17
kanzurebut I found it on 2009-02-2719:17
genethere's also some saffman forces too19:17
geneshit, I though this dean vortex thing wasn't that important19:18
genebut I guess it is19:18
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genethat paper helps a lot19:19
kanzure--the last message I got was the one in which you said 'saffman forces' at the end19:20
kanzure--(the desktop has frozen, am tunneling in to fix.)19:20
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kanzureokay, fixed.19:24
kanzureso, eli has now bought and put up crap at lesswrong.org .. too bad notevenwrong.org is taken.19:31
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geneI though that dean vortex thing wasn't that important20:36
genethat's what I said20:37
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kanzurestuff to get: The effect of the variation of surface tension with temperature on the motion of bubbles and drops21:06
kanzureMotion of large bubbles in curved channels21:06
kanzureA note on the existence of wakes behind large, rising bubbles,21:07
kanzureThe motion of large bubbles in horizontal channels,21:07
kanzureOn the ability of drops or bubbles to stick to non-horizontal surfaces of solids21:07
kanzureOn the ability of drops or bubbles to stick to non-horizontal surfaces of solids. Part 2. Small drops or bubbles having contact angles of arbitrary size21:08
kanzureOn the motion of bubbles in capillary tubes21:08
kanzureSelf-propulsion of asymmetrically vibrating bubbles21:08
kanzureThe response of microscopic bubbles to sudden changes in the ambient pressure21:09
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genehuh22:16
genedid you say the propulsion of vibrating bubbles?22:16
genethat's easy22:16
genesomething like a triangle track should work for that22:17
generesponse of microscopic bubbles to changes in ambient pressue, p bubble = p atm22:17
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ybithttp://heybryan.org/folders.html :: i like how the story @ the bottom doesn't have an end ;P23:40
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