2010-11-09.log

--- Log opened Tue Nov 09 00:00:08 2010
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archels< ybit2> i often doubt my ability to save the human race < ybit2> because of time constraints01:49
archelshaha01:49
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archelsShit, there was an ImmInst conference in Belgium?02:03
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kanzureide thingy for openscad/repg/skeinforge http://fabbaloo.com/blog/2010/11/8/rapcad-announced.html08:07
kanzurehillis knowledge database or why wikipedia sucks http://edge.org/3rd_culture/hillis10/hillis10_index.html08:11
kanzureoops i might have meant http://edge.org/3rd_culture/hillis04/hillis04_index.html08:11
industromaticrapcad sounds like a GUI is all.08:12
kanzurealthough he poses it as a learning thing. whatever.08:12
kanzureindustromatic: yeah :/08:12
industromaticBryan, what microfluidic set of parts would sell best to diybio folks?08:18
industromaticI'm thinking of a microscope slide mount with ports and a diverter that works with a piezo driver to push to and fro.08:19
industromaticA diverter would be used with microscope for slow hand sorting, and with emitter detector for fast sorts.08:20
industromaticany of that needs good macro connecting tubing that is very limp.08:20
industromaticI like the idea of simple push fit ports that tubing shoves into for a seal.08:21
industromaticAll out of glass bonded at boiling water temps with sodium silicate.08:21
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kanzureindustromatic: a plug-and-play jigsaw puzzle system08:28
kanzureFast and reliable way to establish fluidic connections to planar microchips http://bio.cc/Bioinformics/papers/microfluidics/Fast%20and%20reliable%20way%20to%20establish%20fluidic%20connections%20to%20planar%20microchips%20-%20straws%20-%20glue%20-%20Snakenborg%20-%202007.pdf08:28
kanzureInterconnectable blocks - a method for providing reusable, rapid, multiple aligned and planar microfluidic interconnections http://bio.cc/Bioinformics/papers/microfluidics/Interconnectable%20blocks%20-%20a%20method%20for%20providing%20reusable,%20rapid,%20multiple,%20aligned%20and%20planar%20microfluidic%20interconnections%20-%20Snakenborg%20-%202009.pdf08:29
kanzureMacro-to-macro interfaces http://bio.cc/Bioinformics/papers/microfluidics/Macro-to-micro%20interfaces%20for%20microfluidic%20devices.pdf08:29
kanzureMicrofluidic assembly blocks http://bio.cc/Bioinformics/papers/microfluidics/Microfluidic%20assembly%20blocks.pdf08:29
kanzureMicrofluidic motherboards and interconnects http://bio.cc/Bioinformics/papers/microfluidics/Microfluidic%20motherboard%20-%20has%20a%20good%20list%20of%20different%20types%20of%20interconnections%20from%20the%20literature.pdf08:29
kanzureanother paper i recall used straws and bubble gum for ports. i imagine rubber cement or something like it would work fine too. straw diameter might be too large.08:30
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industromaticI'm thinking of products that go beyond bubble gum, but are not an array of legos either.08:36
industromaticCan't think of ways to get lego block fluidics.08:37
kanzurethose articles show "lego block" fluidics (sort of)08:37
kanzurewhy are syringe pumps so expensive?08:39
industromatic"lego block" fluidics could be done if you could make a 3D flange accurately line up with edge ports.08:46
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kanzureyou could maybe have the blocks lock together but also on a 2d surface (plexiglass?)08:47
industromaticI'm searching for good teeny tubing.  That could define most of it.08:47
kanzureplexiglass -> put down block pieces into whatever pattern (interconnected) -> sandwhich plexiglass again & tighten it down like hell08:47
kanzure*sandwich08:48
industromaticYeah, the 4mm tall IB interconnect blocks seeems good.08:48
kanzureanother scare article on diybio (well, not entirely) http://www.dodbuzz.com/2010/11/08/seven-terror-tech-trends/08:51
kanzurehaha someone's commentary on that article :) http://www.ph2dot1.com/2010/11/hoo-boy.html08:52
industromaticI like capillary glass tubes for lining up with a port out of a planar surface, but there's no good o-ring method.08:54
kanzurehow are you propelling the liquids?08:54
industromaticSo finding teeny teflon tubing seems the thing.08:54
kanzuresurface tension? margonelli forces? lasers/explosions? hydrualics/pumps? pneumatics? gravity?08:54
industromaticpropelling the liquids?  Oh, haven't gotten that far.08:54
kanzureit greatly influences design decisions08:55
industromaticpos disp. pumps seem best sellers.08:55
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industromaticTheyhave to be micro smooththough.08:55
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industromaticMaybe an ethernet syringe pump would be a good first product -- not even microfluidic, just Luer lock.09:03
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kanzuremiriam leis again.. skdb = Repo(owner=kanzure, name="skdb")09:30
kanzureer09:30
kanzurehttp://www.synthethics.eu/09:30
dbolserFocus Issue of Chaos: Intrinsic and Designed Computation: Information Processing in Dynamical Systems--Beyond the Digital Hegemony09:33
dbolserhttp://maestro.aip.org/trk/click?ref=zstq4sfk3_0-45ex38bax3183875&09:33
dbolserChaogates: Morphing logic gates that exploit dynamical patterns09:35
dbolserhttp://maestro.aip.org/trk/click?ref=zstq4sfk3_0-45ex38bfx3183875&09:35
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industromaticAfter reading the paper on IBs, I'm sold.  Glass "chips" could be edge ground and polished just as the PMMA boded ones they used.09:38
kanzure:)09:38
kanzuresnakenborg's paper?09:38
industromaticYep.  snakenborg.09:39
kanzurewhat an awesome name09:39
industromaticWonder if that is legally locked anywhere?09:39
kanzure?09:39
industromaticEven Snakenborg's methods don't attempt a grid of building block microfluidics, just a standardized edge connect for most any "chip".09:41
industromaticSnakenborg's needle attach block is so close together they used one port at a time.  Limiting.09:44
dbolserwhat is the limit of protein quantification 'on-a-chip'?09:45
kanzureyou mean chromatography or what ?09:45
dbolseri.e. can you make a chip to detect cancer marker proteins?09:45
kanzureyes09:45
kanzurebut it would involve some extra hardware :P09:45
dbolserah...09:45
kanzurefor instance, there was a chromatography-on-a-chip setup i saw09:45
dbolserso the chip would do separation?09:45
dbolserright09:45
kanzurethere's also other ways though09:46
kanzurelike if you used antibodies or aptamers09:46
dbolserI'm wondering what the limit of protein identification is 09:46
dbolserin terms of miniaturization09:46
kanzurei'm sorry but what do you mean "the limit"09:46
industromaticAn attach block that fans out to luerlocks would be good.09:47
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kanzureindustromatic: also check out http://bio.cc/Bioinformics/papers/microfluidics/Fast%20and%20reliable%20way%20to%20establish%20fluidic%20connections%20to%20planar%20microchips%20-%20straws%20-%20glue%20-%20Snakenborg%20-%202007.pdf09:48
dbolserkanzure: sorry, bad way of trying to summarise 09:48
industromaticdbolser:  Some mass spec by MEMS beam mass change detectors could do somethinng if they had zones that would attract proteins on the vibrating beams.09:48
dbolserwhat is the cheapest way to do protein identification?09:48
dbolseric09:49
kanzureyou could also separate proteins by mass via gravity09:50
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kanzuregravity: http://bio.cc/Bioinformics/papers/microfluidics/A%20Gravity-Driven%20Microfluidic%20Particle%20Sorting%20Device%20with%20Hydrodynamic%20Separation%20Amplification.pdf09:50
kanzuregravity: http://bio.cc/Bioinformics/papers/microfluidics/Hydrodynamic%20filtration%20for%20on-chip%20particle%20concentration%20and%20classification%20utilizing%20microfluidics.pdf09:50
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kanzureagain: http://bio.cc/Bioinformics/papers/microfluidics/In-channel%20focusing%20of%20flowing%20microparticles%20utilizing%20hydrodynamic%20filtration.pdf09:51
dbolserhmmm09:51
t_siamendesproteins have novel shapes/folds so it shouldnt be too hard to id them from that09:51
dbolsert_siamendes: indeed, they are clearly distinguishable when xtalized and blasted with x-rays ;-)09:51
kanzurei like aptamers/antibodies because you can have a binding event involving, say, light/glowing09:51
kanzureand then you just take a picture09:51
dbolserkanzure: so we just need a biomarker ab array09:52
kanzurespiral microfluidic nanoparticle separator http://bio.cc/Bioinformics/papers/microfluidics/Spiral%20microfluidic%20nanoparticle%20separators.pdf09:52
dbolserkanzure: can I s/particle/protein/ in all these tools?09:53
dbolserwhy does bio.cc sound familiar...09:53
kanzureheh09:53
kanzureuh09:53
kanzuredon't tell please :(09:54
kanzurei hid the files on there09:54
dbolserbtw, are you here: http://groups.google.com/group/biocc-server-interface/pendmsg?hl=en-GB_GB&pli=109:54
dbolser;-)09:54
dbolseroh... bad link09:54
dbolserhttp://groups.google.com/group/biocc-server-interface?hl=en-GB_GB09:54
kanzurepresumably i have an account there but i don't know where to ssh into09:55
dbolserkanzure: they set up an ip based ssh filter09:55
kanzurelovely :(09:55
dbolseryou can get an account on ssh.biomama.org09:55
dbolserwhich is for all IPs09:55
dbolser(you can ssh bio.cc from biomama09:56
kanzuressh.biomama.org doesn't resolve09:56
dbolsersorry, .com09:56
kanzureconnection refused on port 2209:56
dbolser202209:56
kanzurepicky.09:56
kanzurehmm my old password doesn't work09:57
dbolserright, you'll need a new one. Please ask jongbhak@yahoo.com and cc whtndks81@gmail.com09:57
kanzurek09:57
dbolserhe said they just ordered 'hundreds' of Tb disks...09:58
dbolsershould be fun ;-)09:58
dbolsernight09:58
kanzuredbolser: have you seen library genesis?09:58
kanzurehttp://free-books.dontexist.com/09:58
kanzureit's a couple TB torrent09:58
dbolsercool09:58
dbolserdidn't look in detail yet09:58
dbolserUtopiah: pointed me at it09:59
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industromaticI read the older Snakenborg paper and searched for patent fluidic interconnection block and no hits.10:50
industromaticWhat if you molded thick "gaskets" like his IBs so the through holes could be molded around wires that are shorter?10:52
industromaticThat might make it less laborious to mold.10:53
kanzuredid you search for patents in the .dk or where-ever he's authoring from? 10:54
kanzure(not that it matters)10:54
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industromaticjust googled "patent fluidic interconnection block".10:59
kanzureoh, you should google patent and snakenborg instead10:59
industromaticSnakenborg used 250 um POFbier as mold for the channels in his IBs -- that's the size of some wire also.11:01
kanzurehere:11:01
kanzurehttp://www.dtu.dk/English/Service/Phonebook.aspx?lg=showcommon&id=25156&type=publications11:01
kanzurethere's a few patents11:01
kanzurenothing relevant11:02
kanzureOne-step fabrication of microfluidic chips with in-plane, adhesive-free interconnections"11:02
kanzurethat was http://www.dtu.dk/English/Service/Phonebook.aspx?lg=showcommon&id=26181611:02
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industromatic>nothing relevant  that I saw wither11:07
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kanzurehmm i do not feel good about this11:16
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kanzurein order to be more "relevant" humanity+ is thinking about an "H+ stamp of approval" for tech projects11:16
kanzurenamely, other people who are doing work get the "privledge" of adding the Humanity+ stamp of approval11:17
kanzureimho this is a disasterous idea11:17
kanzurepersonally i wouldn't want the Humanity+ stamp on any of my projects11:17
kanzuresince the organization is such an embarrassing failure11:17
industromaticyou'r e in a funk over   "H+ stamp of approval"?11:22
industromaticI looked at the patents and thought aboutthe papers and the IB concept is so like a gasket it proably won't patent.11:23
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industromaticIBs also have integral o-rings, which also is prior art.11:23
kanzurenot a funk- just some email exchanges going on. doesn't matter11:24
kanzureare these PMMA or PDMA?11:24
kanzureybit had an SU8 lithography setup a while back11:24
kanzurewonder if he still uses that11:24
industromaticThe IBs are molded of silicone11:24
industromaticSU8 == ?11:25
industromaticSU8 is a photoresist?11:26
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industromaticThe edges of 2-layer bonded microfluidics they connect to are PMMA, but glass will work fine also.11:27
industromaticI could see developing some glass parts that are autoclavable, reused, and micromachined molds for silicone sealer gaskets that are many uses.11:28
industromaticInstead of the needle attach blocks of silicone, I would make those of hard plastic or glass/epoxied asesmblies to luer locks or something smaller for tubes.11:30
kanzurewith a luer lock multiple blocks wouldn't be flesh next to each other, would they?11:31
kanzureflush11:32
kanzurenot flesh :)11:32
industromaticluer lock is 4mm. and big syringes plug into or connectors with about 8mm size, so that would need fan out.11:32
kanzurebig syringes can have different i/o ports on the blocks (like on the top/bottom surfaces)11:32
kanzurei was thinking the blocks themselves would connect to other blocks by the edges (the surface that has the depth of the block/chip)11:33
industromaticWithout making a sketch, start from syringe driven tube, then luer to a lbock that fans in four paths, then a IB, then glass with anything, and optionally another set of IB and luer or just drains or ??11:34
industromatic"big syringes can have different i/o ports"  I would skip anything like that, and keep all multiport stuff in the micro size range.11:35
industromaticI think you can buy luer to tube where the tube is .5mm ID  500 um.  11:36
kanzureindustromatic: http://diyhpl.us/~bryan/irc/microfluidic_interconnectable_blocks.png crude diagram11:45
kanzurenothing to scale :P11:50
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industromaticBryan:  your diagram looks like a thing that Snakenborg DID patent.  A holder for many chips and interconnects.12:28
kanzurehmm12:28
kanzurelink to the patent?12:28
industromaticI'll look.12:28
industromatichere:  http://www.europatentbox.com/patent/EP2108452A1/abstract/190659.html12:28
industromaticTo get some of the images that tell you what I mean, use the link to full doc .pdf12:29
kanzurehmm if the image on that link is to be believed, then my idea is different12:30
kanzurenamely the concept of having a platform on which to plug the chips on to the surface, in any generic order12:30
kanzureor whatever pattern.12:30
industromaticIt is just an app, not a patent.  It covers adjustability and clamping is about all...12:30
kanzurethe image (Fig. 2) looks more like a jig12:30
industromaticyes, jig and clamp.12:30
industromaticyours has clear plate clamp also, just as his.12:31
kanzurehmm i see12:32
kanzureclaim 13 is p. nice 12:32
industromaticA lego method could work.  The pegs would need to be deep, so alignment could happen as you lower blocks in place with gaskets between.12:32
kanzureright12:33
industromaticHow many could you connect at once?  Depends on their interconnects...toomany fingers required...12:33
kanzurehuh? i'm hoping a final system ilke this would be exactly like a jigsaw puzzle except with standardized pieces12:35
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kanzureindustromatic: the snakenborg patent seems different from my idea in many ways; he basically has "an adjustable external hard drive enclosure" for chips12:36
kanzurewhereas i'm thinking of a sort of.. "breadboard" where components connect (except when they are flush or otherwise connected)12:36
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industromatic"breadboard" has hurdles I know not how to scale.12:44
industromaticUnless they connect underneath?12:45
industromaticBut then the bottom plate is complex and can plug, and how to make snake holes in it?12:46
kanzurei was just using the word breadboard- rapid prototyping board on which you plug things into (or on top of), i don't think connecting the devices to the board/plate itself is necessary (except for clamping)12:47
industromaticedge connections need side pressure to work, so how the jigsaw puzzle?12:47
kanzurealthough the bottom board could have pegs on which the chips would fall in place to (as a way to "lock" them into place so they don't move around while you work)12:47
kanzurehmm12:47
kanzurewell12:48
kanzurei was hoping there might be a way to tighten them down enough for that :/12:48
industromaticAre yo thinking seals that are at most 1 atm + .2 ATM differential?12:48
kanzurei wouldn't know the pressure ratings yet12:48
industromaticThe ohters were getting 5 ATM12:48
kanzurethis is pretty easy to test i think12:49
industromaticIf you really wanted lego-like, and accepted .2 ATM pressures, and large dead volumes, maybe...12:50
kanzurewhere would the dead volumes be?12:50
kanzurewhat's the pressure on lego snap-fits anyway12:50
industromaticdead V is at each connect, where you have the human tolerable slop of +/-400 um.12:50
industromaticlego side pressure can be big.12:51
kanzuresuppose the bottom plate had an array of pegs, on which the blocks could be dropped on to, which would lower the placement margin error12:51
industromaticeasy to test i think....  nothing ever is...  test is the hard work.12:52
kanzurealthough i don't know if i like that approach (board with pegs on it for each blog)12:52
kanzure*block12:52
industromaticsnakenborg et al used pins -- same thing.12:53
industromaticpins located for the squeeze action to create seals.12:53
industromaticlego pegs same thing.12:53
industromaticHere's a simpler connect goal using IB concept:   http://ecosensory.com/diybio/microfluidic-blocks-1.jpg12:56
industromaticIn that I only squeeze in one dir, not jigsaw possibilities.12:56
industromaticIf not adjacent you could design pin plate for connect squeeze in 2 dirs.12:57
industromaticThe selling points for such a sys are:  reuse the luer connect, luer transition, and output buckets across experiments.12:59
industromaticAlso reuse the IBs mostly...  design "chips" on grids and they will reuse well.13:00
industromaticports on grids like 1mm13:00
industromaticgotta work on income generating....13:01
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kanzurehi jmil 13:19
jmilyo yo ma13:20
jmilwhat's up13:20
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UtopiahIEEE International Symposium on Rapid System Prototyping (RSP) http://www.rsp-symposium.org 15:57
kanzurea study on etsy/instructables/"DIY" http://staceyk.org/hci/KuznetsovDIY.pdf15:57
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QuantumGNASA's CTO Bobby Braun will be on The Space Show on Friday. Send your questions to DrSpace@thespaceshow.com 16:16
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joshcryerhttp://www.worldenergyoutlook.org/docs/weo2010/weo2010_london_nov9.pdf16:35
joshcryerWEO -> peak oil upon us16:36
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joshcryerMain site btw: http://www.worldenergyoutlook.org/ (if not obvious)16:41
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QuantumGyawn16:43
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joshcryerThis is the first time the IEA has predicted production falloff.16:48
joshcryerEven if you don't think Peak Oil is an issue (and I personally don't, to the extent that we won't be able to find other ways to extract resources, eg oil shale), it's sobering.16:49
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kanzureftp://free-books.dontexist.com/scimagz/16:59
superkuhOh my.17:00
kanzurewow they have the full tetrahedron letters17:00
superkuhThanks for the heads up, kanzure.17:00
joshcryerLooks like it's about 4 gigs for that.17:01
joshcryerWhat's Tetrahedron letters?17:01
kanzuresuperkuh: there's a torrent on free-books.dontexist.com17:01
kanzureit's a few terabytes in total17:01
joshcryerHow many seeders? Haha17:02
kanzurejoshcryer: tetrahedron letters is a lot of scientific papers about molecular biology, RNA, DNA, self-replication, theoretical organic chemistry, etc.17:02
kanzurehttp://www.elsevier.com/wps/find/journaldescription.cws_home/233/description17:03
QuantumGwow, this site is awesome17:05
joshcryerQuantumG, http://i48.photobucket.com/albums/f234/Melanchthon/OilECoyote.jpg17:05
joshcryer:P17:05
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joshcryerYeah, it's slow as fuck though, I'm trying to find the terabyte torrent but there's no... descriptions that I see.17:06
kanzureuh one sec17:06
kanzureit's probably being raped by the entire free world17:06
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joshcryerHaha17:06
joshcryerHow'd you find it?17:07
kanzureeugen leitl17:07
kanzurehttp://eugen.leitl.org/17:07
joshcryerEpic collection, I assume it's just a collection of collections.17:07
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QuantumGFrancis_C._Moon-The_Machines_of_Leonardo_Da_Vinci_and_Franz_Reuleaux__Kinematics_of_Machines_from_the_Renaissance_to_the_20th_Century_(History_of_Mechanism_and_Machine_Science)-Springer(2007).pdf17:08
QuantumGHerbert_Goldstein_et_al.-Classical_Mechanics-Addison-Wesley.pdf17:08
QuantumGwas just looking at these two books this morning and thinking "I should really read that stuff" and now I can download em17:09
kanzurejoshcryer: all of the relative torrents are in here:17:09
kanzureftp://free-books.dontexist.com/repository_torrent/0-319.rar17:09
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kanzurehaha that's a 23 MB file.17:10
joshcryerHaha17:10
joshcryerI download a hundred gigs a month typically.17:10
joshcryerIt would take me two years to get this thing.17:11
joshcryerUnless I set up a wifi AP swarm and leech from my neighbors.17:11
kanzurehm wait that's not what i want17:11
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joshcryerI wanted to get "The elements of computing systems: building a modern computer from first principles"17:12
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kanzurehttp://gen.lib.rus.ec/ might be faster17:13
kanzurekolkhoz17:13
joshcryerThanks17:14
joshcryerThat actually loads, heh.17:14
joshcryerThey don't have it. :/ Aww.17:14
kanzuremaybe this is the torrent:17:15
kanzurehttp://gen.lib.rus.ec/files/torrents_0-256.rar17:15
joshcryerAww, they don't have "The Hidden Language of Computer Hardware and Software"17:16
joshcryerHow dare them not have what I want.17:16
kanzuretorrents_0-256.rar is a tarbomb17:18
JayDuggerGood evening, everyone.17:29
kanzurewhat is this? http://torrent.rus.ec/tracker.php?f=41417:29
kanzuremaybe a generic tracker17:29
kanzurehttp://home-lib.net/17:30
kanzurehttp://lib.ololo.cc/libdb/LibraryGenesis110k-torrents.7z17:36
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kanzureoh well. i was hoping to check up on the health of those torrents.17:42
JayDuggerWhat do you use to translate the pages?17:42
kanzurehow will i learn if i translate?17:42
JayDuggerHow's your Russian? :P17:42
JayDuggerBetter than mine, obviously.17:43
kanzure????? ??????17:43
JayDuggerShow off.17:43
JayDuggerI withdraw the question. 17:44
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kanzurei could just go with ??@??~H????@??~H????@??~H????@??~H????@??~H??17:44
kanzureand pretend your client is broken17:44
joshcryerWhy learn Russian?17:44
joshcryerUnless you plan to acquire a Russian bride.17:44
JayDuggerOr have Russian co-workers.17:45
kanzureJayDugger: i think i meant something closer to "3to ??????"17:50
* kanzure grumbles something about key bindings17:50
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JayDuggerAfter all...where else than Library Genesis would one find such useful titles as Naylor's "The Busy Brides Essential Wedding Checklists"?18:31
RedeemerKanzure, have ya figured out anything regarding hotel stuff?18:38
RedeemerCorrection, any ideas rather?18:38
kanzurenope18:43
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kanzurehttp://openpcr.org/2010/11/igem-2010-synthetic-biology-and-more/20:10
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kanzurehi egeste_ 21:15
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fennomfg becoming root on my phone (nexus one) voids the warranty21:55
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fennso if i want to do something like, oh, wget some mp3's from my server i can't get it repaired when the battery explodes21:56
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fennhttps://github.com/martynhaigh/Tiny-Open-Source-Violin22:16
fennseems like there is hardly any open source stuff for android22:24
superkuhhttp://superkuh.ath.cx/violin_slightly-more-tiny-and-slightly-less-opensource.jpg (33kB vs 179kB)22:24
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--- Log closed Wed Nov 10 00:00:07 2010

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