2014-06-02.log

--- Log opened Mon Jun 02 00:00:08 2014
--- Day changed Mon Jun 02 2014
kanzurehere's one... "A high numerical aperture, polymer-based, planar microlens array" http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-17-22-1990800:00
kanzure"We present a novel microfabrication approach for obtaining arrays of planar, polymer-based microlenses of high numerical aperture. The proposed microlenses arrays consist of deformable, elastomeric membranes that are supported by polymer-filled microchambers. Each membrane/microchamber assembly is converted into a solid microlens when the supporting UV–curable polymer is pressurized and cured. By modifying the microlens diameter (40-60 ...00:00
kanzure... μm) and curing pressure (7.5-30 psi), we demonstrated that it is possible to fabricate microlenses with a wide range of effective focal lengths (100–400 μm) and numerical apertures (0.05-0.3)."00:00
kanzureand:00:02
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kanzurehttp://infoscience.epfl.ch/record/178092/files/charbon11omex.pdf "Hybrid polymer microlens arrays with high numerical apertures fabricated using simple ink-jet printing technique"00:02
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kanzure"Direct-writing of complex liquid crystal patterns" http://www.opticsinfobase.org/oe/fulltext.cfm?uri=oe-22-10-12691&id=28631400:07
kanzure"Downloading of the abstract is permitted for personal use only."00:07
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kanzuregene_hacker: that nasa paper sounds like they want an excuse to blast up a large vat of photoresist00:21
kanzurecool paper00:22
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poppingtonicpaperbot: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1539-6924.2007.00960.x03:34
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/479617625f547c822610788969f661fa.txt03:35
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poppingtonicpaperbot: http://www.onlinelibrary.wiley.com/doi/10.1111/j.1539-6924.2007.00960.x/pdf03:38
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/11b2fce3dfede6790e1d3e1b5b843299.txt03:38
poppingtonicpaperbot: http://onlinelibrary.wiley.com/store/10.1111/j.1539-6924.2007.00960.x/asset/j.1539-6924.2007.00960.x.pdf03:39
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/ed0346d10cdb475d53eff1327a9016c1.txt03:39
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kanzurefda banned easter eggs: http://en.wikipedia.org/wiki/Kinder_Surprise07:31
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kanzure23:50 < narmno> sorry kanzure but i ended up using lua07:53
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kanzure"These lenses often appear on the surplus market, many of which were made for cathode-ray ("tube type") big screen televisions but are often sold as "fire starters" or solar ovens.  Typically made using flexible optical plastic, many of these lenses measure around 1 meter diagonally.  To use these lenses effectively they must be mounted in a rigid frame as it is imperative that they remain as flat as possible in order to accurately focus.  In ...08:13
kanzure... other words, you cannot "hand-hold" them and expect any reasonable performance - they must be mounted in a frame!"08:13
kanzure"Flexible lenses.  Stamped in clear vinyl, these are flexible and are usually mounted in some sort of flexible plastic frame to allow them to be kept in a 3-ring binder."08:13
kanzure"One potential source of Fresnel lenses for experimenters have been overhead projectors.  Typically, these lenses are built into the plate onto which the transparency is laid, with the Fresnel lens being used to direct the light upwards toward the right-angle mirror or lens assembly and onto the screen. Unfortunately, these lenses are NOT usually suitable for purposes of collimation or the focusing of a distant light source onto a detector as ...08:14
kanzure... they may not be designed to focus at infinity.  Since their main purpose is usually that of concentrating the light from the projection bulb and not forming an image directly, they do not function as needed and often blur and/or scatter light should they be attempted to be used.."08:15
kanzurehttp://modulatedlight.org/optical_comms/fresnel_lens_comparison.html08:15
kanzureoh hm.... " As noted before, the imprecise nature of a Fresnel lens precludes their efficient use to efficiently collimate coherent light (such as that from a laser) as an inexpensive, molded Fresnel lens may not practically be made to be accurate enough to be diffraction-limited.  In other words, attempts to use a Fresnel lens for laser light will likely result in a significant percentage of that light being scattered rather than being ...08:16
kanzure... collimated."08:16
kanzurethis is an unusual site08:19
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kanzure"In 1984, Robert Forward suggested another conceptual technique to improve the performance of an interstellar laser sail. As shown in figure 7.7, Forward would position a thin-film refractive optical element - a Fresnel lens - between the laser and the starship. If the position of these three optical elements (laser, lens and starship) can be accurately maintained for decades or centuries (no mean task!), the light-years distant starship ...08:26
kanzure... could be presented with a very well collimated beam, at a distance measured in liht years.... If the lens radius is 500 km and the lens focal length is 15 AU, about 110,000 Fresnel zones are required for 1 micron laser light. A well-collimated beam from the lens would completely fill the 500 km radius sail of a very distant starship if the laser were to be positioned 15 AU from the lens, as shown."08:26
kanzure"Exercise 7.4: Jones (1985) proposed a maser propelled light sail pushed by a well-collimated 3 m wavelength microwave beam. How many Fresnel lens zones would be required for this wavelength if the maser lens separation (lens focal length) is 15 AU and the lens radius is 3000 km?"08:26
kanzurethis is from "Deep Space Probes: To the outer solar system and beyond"08:26
kanzure*distance measured in light years08:28
kanzureinterventional astronomy08:40
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eudoxia>...a very distant starship08:44
eudoxiahow distant? over how many AU would you be able to maintain constant acceleration?08:44
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kanzurepublicknowledge.org emailed a pdf to openmanufacturing re: patent system reform, https://groups.google.com/d/msg/openmanufacturing/vS4ju1VqXb0/e3AB5NvvgsAJ10:02
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kanzure.title http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm399335.htm10:28
yoleauxFDA launches openFDA to provide easy access to valuable FDA public data10:28
kanzurehmm http://open.fda.gov/10:28
gradstudentbotOh that's interesting, do you want to write a paper together?10:29
chris_99sure gradstudentbot, what on10:30
gradstudentbotI am sponsored by the Beijing Genomics Institute.10:30
kanzurelist of us government api endpoint thingies http://18f.github.io/API-All-the-X/data/developer_hubs10:30
chris_99"Bureau of Alcohol, Tobacco, Firearms, and Explosives" interesting combination10:32
eudoxiabureau of fun things10:32
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chris_99haha10:32
kanzurei'm skeptical of curved optics now10:39
kanzurewhat's all that matter for10:39
kanzure"The Gran Telescopio Canarias is a 10.4 m (410 in) reflecting telescope... The GTC began its preliminary observations on 13 July 2007, using 12 segments of its primary mirror, made of Zerodur glass-ceramic by the German company Schott AG. Later the number of segments was increased to a total of 36 hexagonal segments fully controlled by an active optics control system, working together as a reflective unit.[4][7]"10:43
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sheenakanzure: i pm'd you10:46
kanzurei see it10:46
kanzure.title https://www.youtube.com/watch?v=PVXQUItNEDQ10:48
yoleauxRay Kurzweil: Get ready for hybrid thinking10:48
kanzureblah nevermind10:48
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kanzurehuh, didn't know about photoresist tape11:01
kanzure"I think you are refering to what is called Dry Film Resist. Dry film resist is commonly used in printed circuit board industry and can cover a much larger area than spin photoresist. However, thickness is needed to hold the film together so film photoresist typically comes in thickness of around 50 microns, and is applied to a planar area by hot roll lamination. Resolution is also lower. The smallest line/space that a state of the art PCB ...11:02
kanzure... company can mass produce are 100 micron/100 micron."11:02
kanzurehttp://www.dupont.com/pcm/techinfo/laminate/optimize.html11:02
kanzurehttp://www.dupont.com/pcm/techinfo/laminate/hotroll.html11:02
nmz787_i1yep11:02
nmz787_i1you can get it on ebay too11:02
kanzuresounds easier than spincoating all the time11:03
chris_99you can get a spray apparently11:03
kanzurehow would you guarantee thickness with the spraw?11:03
kanzure*spray11:03
chris_99no idea, probably not v. well11:03
kanzureor surface finish, rather11:03
chris_99mm11:05
kanzurenmz787_i1: it would be nice to not need bulky lenses for everything (photolithography, micromachining, spectroscopy, etc)11:06
||0_-_0||paperbot http://brain.oxfordjournals.org/content/early/2014/04/22/brain.awu107.abstract11:08
paperbotXMLSyntaxError: None (file "/home/bryan/code/paperbot/phenny/modules/scihub.py", line 51, in _go)11:09
kanzurehmm11:11
kanzure||0_-_0||: file bug reports https://github.com/kanzure/paperbot/issues11:11
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delinquentmehttp://www.genomeweb.com//sequencing/roche-acquires-nanopore-sequencing-firm-genia-technologies-350m11:24
delinquentmedamn. biotech everywhere.11:24
kanzurei have a mole there.. i should ask him for things.11:25
delinquentme"Genia, based in Mountain View, Calif., has been developing a single-molecule sequencing-by-synthesis technology that uses nanopore-based electrical detection and employs a semiconductor integrated circuit."11:25
kanzureyeah it's this one:11:26
kanzurehttp://211.144.68.84:9998/91keshi/Public/File/49/30-4/pdf/nbt.2147.pdf11:26
kanzure"An emerging DNA sequencing technique uses protein or solid-state pores to analyze individual strands as they are driven in single-file order past a nanoscale sensor1–3. However, uncontrolled electrophoresis of DNA through these nanopores is too fast for accurate base reads4. Here, we describe forward and reverse ratcheting of DNA templates through the α-hemolysin nanopore controlled by phi29 DNA polymerase without the need for active ...11:28
kanzure... voltage control. DNA strands were ratcheted through the pore at median rates of 2.5–40 nucleotides per second and were examined at one nucleotide spatial precision in real time. Up to 500 molecules were processed at ~130 molecules per hour through one pore. The probability of a registry error (an insertion or deletion) at individual positions during one pass along the template strand ranged from 10% to 24.5% without optimization. This ...11:28
kanzure... strategy facilitates multiple reads of individual strands and is transferable to other nanopore devices for implementation of DNA sequence analysis."11:28
kanzureand then it's a matter of using a dsp and doing lots of funky stats to figure out the right sequence for molecules going through a large nanopore array11:29
kanzure.tell gene_hacker the valveless microfluidic dna synthesizer is also interesting because it shoves all of the complicated equipment outside the realm of microfluidics (like the valve train). in fact, with a large enough array and micromirror array, you could have a 1024x1024 well microfluidic dna synthesizer that you could even operate manually (using manual dna synthesis), which although time-consuming has the advantage of building a million ...11:34
yoleauxkanzure: I'll pass your message to gene_hacker.11:34
kanzure... separate dna fragments simultaneously.11:34
kanzureblah yoleaux probably doesn't do multi-line .tell does it?11:35
kanzure.tell gene_hacker http://diyhpl.us/~bryan/papers2/DNA/Syringe%20method%20for%20stepwise%20chemical%20synthesis%20of%20oligonucleotides.pdf11:35
yoleauxkanzure: I'll pass your message to gene_hacker.11:35
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nmz787_i1kanzure: diffractive optics via self-assembled nanostructures would probably be pretty nice11:59
nmz787_i1otherwise they're expensive if not made in bulk11:59
@fennhttps://en.wikipedia.org/wiki/Magnetic_refrigeration  neat stuff12:03
delinquentmenmz787, what material are you suggesting to use for the assembly?12:03
delinquentmefenn, that sounds like the "Cells alive system"12:04
kanzurefenn, why were we thinking of a bluray led micromachiner cutter thing instead of dmd? was there a good reason?12:04
kanzurewas it something about avoiding lenses?12:05
kanzureiirc i was annoyed about curing times, but that's not a good enough reason12:05
delinquentmeYou know about these freezers right? magnetic agitation of fluids while dropping the temperature12:05
@fenncontinuous channel length is higher with a continuous process like a single laser12:05
@fennalso smoother side walls because no aliasing12:05
kanzurethat's a marginally okay reason12:06
@fennalso it could be used as a laser cutter?12:06
@fennalso i've never actually used a DMD chip and the unknowns associated with that12:07
kanzureso with a photolithography system you get dna synthesis (partially), microelectronics, microfluidics, and 3d printing12:07
kanzurefwiw dmd documentation from texas instruments is reasonably thorough, i mean the instruction set looked like something usable, and they probably have application notes about throwing it into an apparatus/device/thing12:07
@fenni wouldn't use a bare chip if at all possible12:08
@fennthings that take digital video as input are somewhat scarce tho12:08
@fennbanned by RIAA12:09
kanzurewhat scarcity are you referring to12:09
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@fennit's hard to find a simple DVI to parallel adapter12:09
@fenni recently found a chinese LED panel with HDMI in for $4012:10
kanzurei thinkthe lack of optics required for micro led cutting/curing is a neat benefit, but ultimately spatial light modulation or micromirrors sound better.. argh.12:10
@fennit still needs optics, no?12:11
kanzurei think it just needs a pinhole slit?12:11
@fenni mean, someone has done all the hard work to make the optics to read bumps on a DVD12:11
@fennand DMD projectors have the optics needed to use the chip12:12
kanzureif that was true then why does everyone make hilariously complex setups with microscopes and micromirror arrays12:12
@fennbecause they are looking at the newport catalog with specs and cad drawings12:13
kanzuretake a gander at figure 1,12:14
kanzurehttp://diyhpl.us/~bryan/papers2/optics/photolithography/A%20maskless%20photolithographic%20prototyping%20system%20using%20a%20low-cost%20consumer%20projector%20and%20a%20microscope.pdf12:14
@fenndo i have to12:14
gradstudentbotWasn't that a Nature paper?12:14
kanzureit's a projector taped to a microscope with a bunch of other optical elements12:14
kanzurehm maybe that's not so bad12:15
@fennnotice the ~5 degree angle the projector is mounted at on the bracket12:16
kanzureargh what a terribly stupid picture. where's your diagrams..12:17
@fennanyway yes, that would be one way to do photolithography12:17
@fenndo microscopes commonly have numerically controlled stages?12:17
@fenni've heard of "motorized stage" but that could mean anything12:18
delinquentmeSouth Korea’s Electronics and Telecommunications Research Institute (ETRI)12:18
kanzurethese guys used linuxcnc so i assume yes http://diyhpl.us/~bryan/papers2/optics/photolithography/Low%20cost%20UV%20laser%20direct%20write%20photolithography%20system%20for%20rapid%20prototyping%20of%20microsystems.pdf12:18
delinquentmehas done something like what you're talking about ... with a maskless curing of photo resists at microscales12:18
delinquentmeLCD based12:18
@fenni dont understand what is going on in that image12:20
@fennwhy is the monitor mounted on a micometer slide?12:21
@fenni guess the objective is connected to the monitor by a big bracket12:22
kanzureon a related note, this one claims something about 20 million separate dna fragments built in parallel with a micromirror array projector glued to a microscope:12:24
kanzurehttp://diyhpl.us/~bryan/papers2/optics/photolithography/Step-and-scan%20maskless%20lithography%20for%20ultra%20large%20scale%20DNA%20chips.pdf12:24
@fennif you have a belt of magnetocaloric material and feed it through a magnetized region, it will give off heat. does it require force to feed the belt in? and does that mean a heat differential can cause the belt to turn?12:25
gradstudentbotThat's beyond the scope of my research.12:25
kanzurei wonder if laser cutting and micromirror array modulation could be interchanged on the same device. i mean, the xy stage is certainly the same component in both cases. (i think a micromirror array is the way to go since it's cheap and an lcd is slightly more hacky?)12:26
kanzureand it sounds like these guys are just shining a uv led through a regular microscope12:26
@fennyes a micromirror array lets you tune the wavelength, is higher power, and is smaller12:26
@fennsmaller is important when dealing with precision optics12:27
kanzureand shining a regular micromirror array through a regular microscope too12:27
kanzurein the low cost direct uv led write paper, there's no line item in the BOM for "crazy optics"12:27
kanzureoh, lens $5012:27
kanzurehm.12:27
@fennit's worth mentioning that you can do "spatial dithering" with a high resolution stage, to smooth out pixel aliasing12:28
kanzurewell that's not bad. if you know which lens.12:28
@fennthe pixel center can be moved around12:28
@fennyeah i'm not at all impressed with their level of documentation12:29
@fennthis is not even instructables grade12:29
@fennit's a talk abstract?12:29
@fenn"Honolulu PRiME 2012" the 222nd meeting of the electrochemical society12:30
kanzure"the 310th meeting of weird wizards nobody will ever hear of"12:31
@fennseems like there is a lot of optics stuff in hawaii12:31
kanzurei'm curious why i don't see microscope setups for microelectronics photolithography reasons12:32
cpopellI'm pretty sure that's how azonenberg does it12:33
cpopellbut I don't remember that much detail on his lab12:33
kanzurehe's in hibernation mode12:33
kanzure(spending his time elsewhere)12:33
cpopellyeah, he's trying to wrap up his PhD12:33
cpopelland got a girlfriend :V12:33
kanzurewhat a loser12:33
kanzureabout the phd thing, i mean12:33
gradstudentbotI wasn't able to find any references.12:33
kanzurealso, i'm concerned about how cheap this system is ($1k in parts) compared to how few have bothered12:34
kanzuremicroelectronics, microfluidics, dna synthesis, and 3d lithography-printing-something, for the price of one, and nobody is doing it??12:35
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@fenn"A major breakthrough came 2002 when a group at the University of Amsterdam demonstrated the giant magnetocaloric effect in MnFe(P,As) alloys that are based on earth abundant materials."12:41
kanzurenmz787_i: i would be willing to do continuous-flow valveless microfluidic dna synthesis12:41
@fennpaperbot: http://www.nature.com/nature/journal/v415/n6868/full/415150a.html12:42
paperbothttp://libgen.org/scimag/get.php?doi=10.1038%2F415150a12:42
kanzurefenn, did you look at gene_hacker's nasa link? http://www.nasa.gov/sites/default/files/files/Quadrelli_2012_PhI_OrbitingRainbows_.pdf12:45
kanzureactually, i mean, it is an interesting thing to look at12:48
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kanzure"Forty six clumps [from Project West Ford] are known to remain in orbit as of 2013.[13]"12:55
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justanotheruserkanzure: please describe your attack on maidsafe13:05
kanzurethe attack is just an accumulation of their currency/money/tokens- you can do a sybil attack, host only a single version of the file, and earn a disproportionately larger amount of credit than the well-behaving actors13:06
kanzure*single copy of the file13:07
justanotheruseryeah, I assumed PoR (really Trust in Resource because there is no such thing as a proof of resource) either needed a central authority or was vulnerable to sybil13:08
kanzurei think my attack only works if they are storing redundant copies of data13:09
kanzurenot sure13:09
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kanzureParahSailin: are there any dna synthesis bead-based protocols where you use light to attach/detach beads (perhaps even selectively with maskless light arraying)13:14
kanzureor, some other method of starting strands in particular regions on a well array, and later decoupling them to wash them into a collection chamber13:15
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nmz787_ikanzure: if you've seen a support-free synthesis method (for any kind of polymer) I'm looking for refs13:16
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dbolseranyone want a post doc in Korea working on biomedical engineering?13:18
dbolserMy friend is hireing13:18
kanzurei'll take one, but i'm only paying $25k/year at the moment13:19
dbolserthe university teaches all courses in english13:19
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kanzurenmz787_i: dbolser might know13:19
kanzuredbolser: oh, you're not offering me a postdoc person?13:19
dbolserkanzure: no, sorry13:19
dbolser'support free'?13:20
kanzurenmz787_i: yeah wait, be more specific.. obv. there are in-solution synthesis methods.13:20
dbolserJong is hiring post-doc's here:13:21
dbolserhttp://www.unist.ac.kr/index.sko13:22
[nsh]<--- free money goes here kthx13:22
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nmz787_imost in-solution are liquid-phase supports... i.e. grown on PEG13:27
kanzurewelp you can always look through the dark corner http://diyhpl.us/~bryan/papers2/DNA/13:29
dbolsernmz787_i: are you looking for something like emulsion PCR?13:29
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heathhttps://github.com/heath/treemap13:33
heathnow onto the frontend13:34
kanzureoh i forgot about this paper,13:34
kanzurehttp://diyhpl.us/~bryan/papers2/DNA/Light-directed%20synthesis%20of%20high-density%20oligonucleotide%20arrays%20using%20semiconductor%20photoresists%20-%201996.pdf13:34
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nmz787_idbolser: nope, no PCR, it would all be in solution, so not emulsion13:36
kanzure"Once the resist has been applied to the substrate and patterned, a nucleotide is added to the surface in the exposed areas using standard solid-phase oligonucleotide synthesis protocols. The glass surface is initially derivatized with hydroxyl-terminated linker molecules protected with acid-labile DMT (or "trityl") groups. In the image-transfer step, exposed regions of the substrate are selectively deprotected ("detritylated") by treatment ...13:37
gradstudentbotI am busy researching.13:37
kanzure... with acid, revealing hydroxyl groups that are then reacted with a 5'-DMT-protected deoxynucleoside phosphoramidite. By repeating this sequence of steps in conjuniction with an appropriate series of masking patterns and nucleotide additions, a large matrix of oligonucleotide sequences can be constructed in a relatively small number of steps (18, 19)."13:37
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nmz787_ii found a paper using water-resistant chemistry, using modified 5'-DMT group chemistry13:38
nmz787_ithe keyword was NBS n-bromo-succinimide13:38
nmz787_ithat is also worth looking further into13:38
nmz787_iwater is a major PITA for any of this13:39
kanzuredoes your car have a valve train13:39
nmz787_iyes13:42
nmz787_iall except electric would13:42
kanzurei really like gene_hacker's idea of not including the valves in the microfluidic device13:42
nmz787_iwhich specifically?13:43
kanzureand we can get away with not having any at first (manual insertion of liquids by syringe pump or syringe)13:43
kanzurewell he was referencing that picoarray dna snythesizer paper.. they were doing continuous flow-through valveless microfluidics with a micromirror array for photogenerated acid dna synthesis. they had it plugged into a column on a conventional dna synthesizer (expedite 8909) to use its existing valve train.13:44
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kanzurevalveless means less parts means less engineering effort13:45
nmz787_ibut that's only part of the problem13:45
nmz787_iyou need to then cleanup the dna and insert it13:45
kanzurefragment selection?13:45
nmz787_iwhich, I'm pretty sure, you're going to want some valves for13:45
nmz787_iyeah basically13:46
kanzurewasn't there at least one version of dna synthesis that had cleavable fluorophores13:46
kanzureor was that only in sequencing.. ugh.13:46
nmz787_iand if you use a solid support, or even a liquid-phase support, you're going to have to cleave the constructs from the supports every time you want to purify13:46
nmz787_iyeah13:46
nmz787_ii think that was  the single molecule guys13:46
nmz787_ii always forget their name, even though their process is kickass13:47
nmz787_iHelicos13:47
nmz787_ihttp://www.google.com/patents?id=TfEAAgAAEBAJ13:47
nmz787_ibut yeah who knows what their chemistry is13:47
nmz787_ithat's why i figure its easier to do valves than chemistry13:47
kanzurehow would the valves do sequencing?13:48
kanzurewhat?13:48
nmz787_i(i've been thinking lately about how to manage getting a chem PhD)13:48
nmz787_iyou sequence the order they open/close13:48
kanzureif you're going to go for a phd you should study with gene_hacker or jmil13:48
kanzureyeah but you still have to verify and sequence eventually either way13:49
nmz787_ijmil isn't a polymer chem guy afaik13:49
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nmz787_ii've been planning on simply having a reporter that i always synthesize13:49
nmz787_ito work as a  sort of CRC13:49
gradstudentbotThat's not really surprising since they did it ex vivo.13:49
nmz787_iGFP or something 'if it glows it goes' or the banana smell gene 'if it gasses it passes13:50
nmz787_i'13:50
kanzurehow long is gfp anyway?13:50
kanzure500 amino acids?13:50
nmz787_inah13:50
nmz787_iprob 300ish13:50
kanzure238 amino acids according to wikipedia13:51
nmz787_i23813:51
kanzurehm13:51
kanzurenot the smallest13:51
kanzureoh that would be worth looking up, directed evolution of shorter gfp molecules13:51
kanzure*gfp sequences13:51
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kanzureclose..13:53
kanzure.title http://peds.oxfordjournals.org/content/22/5/313.short13:53
yoleauxDirected evolution of an extremely stable fluorescent protein13:53
kanzure"eCGP123 could not be denatured by a standard thermal melt, preserved almost full fluorescence after overnight incubation at 80°C and possessed a free energy of denaturation of 12.4 kcal/mol. It was created from CGP by a recursive process involving the sequential introduction of three destabilizing heterologous inserts, evolution to overcome the destabilization and finally ‘removal’ of the destabilizing insert by gene synthesis. We ...13:53
kanzure... believe that this approach may be generally applicable to the stabilization of other proteins."13:53
gradstudentbotAnyone else think pol II looks like a butt?13:53
@fennpaperbot: http://www.opticsinfobase.org/ao/viewmedia.cfm?uri=ao-28-5-976&seq=013:53
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/93514aa9aede1d8ae0a80250a240a40.txt13:53
@fennpaperbot: http://www.opticsinfobase.org/DirectPDFAccess/AF98D35B-DA55-98A8-EAC0DE8800362C8D_32231/ao-28-5-976.pdf?da=1&id=32231&seq=0&mobile=no13:54
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/141d3bf3c08a1cd0f424219ebc3e032d.pdf13:54
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kanzurewho the hell names their folder "Direct PDF Access"13:54
kanzurealso: i wonder if that nasa paper considered orbital clouds of protein for their electromagnetic aerosol devices13:55
@fennlots of hieroglyphics in this paper13:55
kanzureit seems to be some kind of code13:56
@fenni just want to know what a kinoform is13:56
kanzure.d kinoform13:56
yoleauxSorry, I couldn't find a definition for 'kinoform'.13:56
@fenn"Kinoform lenses, a type of refractive lens similar to those found in lighthouses  are being considered by researchers for their ability to efficiently focus x-ray light down to very small spots. This feature is vital to the study of molecules, atoms, and advanced materials at the nanoscale"13:57
@fennblah blah diamond heat conduction synchrontron etc13:57
kanzurei thought lighthouses use fresnel lenses13:57
@fennno13:58
@fennthey look similar13:58
kanzureParahSailin: minimum viable sequence of a fluorescent protein?14:02
kanzureso that nasa paper wants granular clouds of dust with micron-sized particles.. proteins could probably be made that large if necessary.14:05
kanzureor even dna14:05
dbolserfocus xrays?14:09
dbolserif you can do that, you can look at atoms14:09
dbolserhow big is a micron in Angstroms?14:09
kanzuredbolser: hm? the paper is about using orbital optical tweezers to manipulate clouds of dust to form kilometer-scale telescopes14:11
kanzuredbolser: http://www.nasa.gov/sites/default/files/files/Quadrelli_2012_PhI_OrbitingRainbows_.pdf14:11
dbolserInteresting14:11
dbolseryeah, big viruses are only a few hundred angstroms, and a micron is 10,000 angstrom14:12
nmz787_ikanzure: those kinoforms look like a specific ruling style for a diffractive optic14:12
dbolserit's not easy to engineer a protein that big14:12
kanzureit was fenn asking about kinoforms btw14:12
kanzuredbolser: i think some of the larger viruses are much bigger14:13
dbolseryou can get fibers on that scale, but they prolly aint the right shape14:13
dbolserkanzure: I'd be surprized14:13
nmz787_ibut yeah diffraction is how fabs are doing sub-wavelength these days14:13
dbolserbased on the physics of protein folding14:13
kanzuremimivirus has a capsid of 0.6 microns14:13
kanzurecapsid diameter14:13
kanzuresometimes 0.8 microns14:14
dbolserpretty awesome14:14
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dbolserthe biggest virus structure solved is .2 microns14:18
dbolserhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC137492/14:18
kanzuresolved = seen in a microscope?14:18
dbolseryes14:18
dbolserseen at atomic resolution14:19
kanzureoh i see. well that doesn't seem necessary? heh14:19
dbolserI guess you can literally see things on that scale14:19
kanzurei think it should be possible to use directed evolution to get a virus of larger size if necessary14:19
dbolserno, not at all :-)14:19
kanzurefor some reason i think virus capsids would be a better substrate than dried dead bacteria or dna for interstellar telescopes14:19
dbolseryes14:20
kanzuredead bacteria will probably collapse in unpredictable ways14:20
dbolserI bet the structures hold up in space better14:20
kanzurei assume a virus capsid stays a virus capsid much longer14:20
dbolserkanzure: if you could stableize em like above14:20
kanzuresure, optical tweezers etc14:20
kanzureother advantage is you could embed stuff into the capsid14:20
dbolserhowever, there is a trade off between stability and folding efficiency14:20
dbolserindeed... but not sure if they'd fall apart in a vacuum14:21
kanzurei guess if you really wanted a dead substrate you could also just use emulsions or microspheres14:21
dbolserproteins unfold under pressure14:21
dbolseryeah14:21
dbolserhttp://www.ncbi.nlm.nih.gov/pubmed/23251035 <- folding vs. stability14:21
paperbothttp://libgen.org/scimag/get.php?doi=10.1073%2Fpnas.121018011014:21
* kanzure pets paperbot14:22
kanzure"Pandoraviruses have a size approaching 1 micrometer and a blob-like shape resembling some types of bacteria. The genome of the larger variant, Pandoravirus salinus, was reported to contain 2556 putative protein-coding sequences, of which only 6% had recognizable relationships with genes from other known organisms."14:23
kanzuredoh i forgot about this one. mimivirus isn't the largest.14:23
dbolsersome viruses are just weird14:23
dbolsersame with bacteria14:24
dbolserfungi14:24
dbolserplants14:24
dbolserparis japonicus has a genome the size of a small village of humans14:24
kanzuredoes jong have a complete backup of all the ncbi-hosted genomes?14:26
kanzurei am concerned about redactions from ncbi genbank and proteinwhatever14:29
dbolserkanzure: he built a korean version of NCBI in his previous job14:33
dbolserENA mirror genbank14:34
kanzurebut just genbank?14:34
dbolserthere is also soemething called biomirror14:34
dbolsergenbank, sra, gca, etc14:34
dbolsereuropean nucleotide archive14:34
kanzurei haven't tracked the data but i think that companies might be forcing ncbi to do redactions of certain proteins or genes14:34
dbolserit's possible, but against their guidelines...14:35
kanzure"Fig 28: A simulated raw image of an exo-earth at 10 light years, using a 150 apertures regularly distributed over 150 km."14:41
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kanzure.wik optical lift14:49
yoleaux"Optical lift is an optical analogue of aerodynamic lift, in which a cambered refractive object with differently shaped top and bottom surfaces experiences a stable transverse lift force when placed in a uniform stream of light." — http://en.wikipedia.org/wiki/Optical_lift14:49
kanzure"The experiment began as computer models that suggested when light is incident on a tiny object shaped like a wing, a stable lift force is applied to the particle. Then the researchers decided to do physical experiments in the laboratory, and they created tiny, transparent, micrometer-sized rods that were flat on one side and rounded on the other, rather like airplane wings. They immersed the lighfoils in water and bombarded them with 130 mW ...14:51
kanzure... infrared laser light from underneath the chamber. Radiation pressure pushes the particles along the direction of propagation, this is called the scatter force, but the excitement came when the particles were forced to the side in a direction perpendicular to the direction of propagating light. The transverse force on the particles is the lift force. The researchers discovered not only that the rods experienced stable lift, but that, ...14:51
kanzure... depending on refractive index, the rod could have up to two stable angles of attack it rotated to when exposed to the laser light. Symmetrical spheres tested did not exhibit this same lift effect.[2] In optical lift, created by a "lightfoil", the lift is created within the transparent object as light shines through it and is refracted by its inner surfaces. In the lightfoil rods a greater proportion of light leaves in a direction ...14:51
kanzure... perpendicular to the beam and this side therefore experiences a larger radiation pressure and hence, lift.[2] The 2010 discovery of stable optical lift is considered by some physicists to be "most surprising".[3] Unlike optical tweezers, an intensity gradient is not required to achieve a transverse force. Many rods may therefore be lifted simultaneously in a single quasi-uniform beam of light. Swartzlander and his team propose using ...14:51
kanzure... optical lift to power micromachines, transport microscopic particles in a liquid, or to help on self-alignment and steering of solar sails,[3] a form of spacecraft propulsion for interstellar space travel. Solar sails are generally designed to harness light to "push" a spacecraft, whereas Swartzlander designed their lightfoil to lift in a perpendicular direction; this is where the idea of being able to steer a future solar sail spacecraft ...14:51
kanzure... may be applied.[4] Swartzlander said the next step would be to test lightfoils in air and experiment with a variety of materials with different refractive properties, and with incoherent light.[2]"14:51
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dbolser28 c is nice14:56
delinquentmeAs far as cellular aging is concerned. We need only to worry about two things: nuclear DNA + mitochondrial DNA right?15:03
delinquentmeAs far as a *cell* is concerned. Thats everything.  Right?15:03
dbolserno15:03
dbolsercells accumulate mis-folded proteins in 'granules'15:03
dbolserthat accumulate with age15:03
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kanzure"Palmer [60] considered using the nonlinear optical index of glass beads or aerosol droplets to organize the particles and trap them into fresnel-like three-dimensional holographic gratings."15:05
delinquentmeAh ok so cytoplasmic junk15:05
delinquentmedbolser, thoughts on how to locate and remove those?15:06
delinquentmeReally specific binding proteins.15:06
gradstudentbotDude, you contaminated my experiment.15:06
kanzuredefeat of cellular aging will most likely take longer than whole head life support could theoretically take (why are people always more interested in cryonics? there are perfectly good brains still living that could continue to live if you etc.. etc..)15:07
kanzurei forgot what i was typing about15:07
delinquentmekanzure, you're saying chop the head off and stick it on a robot ... feed it with proper nutrients15:10
kanzureyou don't need the robot part15:10
||0_-_0||delinquentme if you want to remove lipofuscins first you'll need to target the aggregates and then you'll need to do some sort of molecular work to un-clot them15:13
||0_-_0||problem is they really like being clotted15:13
||0_-_0||so you've got a fair high barrier to overcome there15:13
kanzurelipofuscins are not the only problem in aging, sigh15:14
delinquentmeliterally we could just jam probes with the correct antigens for known aggregates and yank them out15:15
||0_-_0||kanzure we're aware but the discussion was part of "cytoplasmic junk"15:15
kanzureno, he only said that because he doesn't know15:16
||0_-_0||and delinquentme sure we could try that, but getting an antibody into a cell is not exactly easy and you've still got the problem of induced toxicity when the aggregates break up or you fuck the membrane trying to yank them out15:16
delinquentmeAlso we've got the whole breeding thing as a way to clean all damage.  Which makes me REALLY take a second look at this:  http://guardianlv.com/2012/10/jd-stem-cell-discovery-will-allow-gay-men-to-create-their-own-eggs-for-surrogate-birth/15:19
delinquentmeI'm trying to find the associated paper15:21
EnLilaSkoMB + centrophenoxine for dat dere lipo15:21
EnLilaSkoAlthough centro is questionable15:21
delinquentmeSo these guys are taking somatic cells and coaxing them into eggs.15:22
||0_-_0||wtf delinquentme biology is not legos; what works in one very limited and simplified system is not the truth15:22
delinquentme||0_-_0||, specific example?15:23
||0_-_0||all of it15:23
delinquentmeI mean I understand DNA isn't a lego.  But what caused the 'wtf'15:23
||0_-_0||breeding to clear damage isn't going to rejuvenate anyone15:23
||0_-_0||I don't know how you've drawn that conclusion15:23
gradstudentbotMy project sucks.15:24
kanzuregene_hacker: optical lift is pretty neat15:25
gradstudentbotBlah, I'm going to quit.15:25
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delinquentme||0_-_0||, Ok so we know that everytime someone makes a whole human from a new embryo ... there is no damage ( per aging is concerned ) IN that organism.15:27
delinquentmeyes? Yes. Ok. So in looking at the research statements above they're essentially coaxing asexual reproduction .15:28
||0_-_0||if epigenetics weren't also a factor, I'd find that possible15:28
delinquentmeCells derived from that cluster ... could be immunologically the same15:28
delinquentmespecifics ||0_-_0|| what epigenetic events are giving you reservations here?15:29
kanzurelots of embryos die for all sorts of reasons, including damage15:30
||0_-_0||stress markers, preserved transcription factors, chromatin patterns15:30
gradstudentbotMy labview crashed.15:30
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delinquentmekanzure, sure but we've got a totally novel way of getting cellular material to that pristine state.  With the possibility of them being genetically identical15:32
kanzurewhat about it15:33
delinquentme||0_-_0||, so these are all part of that intergenerational process ... but it remains to be determined if any of that matters if all we want are less damaged cells15:33
Mokstarbasically he's trying to recreate the system described in A Brave New World15:33
Mokstarand/or solve the Japanese underpopulation problem15:33
delinquentmeIf the thing identifies the cell as self , thats a step in the right direction15:33
||0_-_0||Brovansky groups, yes15:33
||0_-_0||you're aware that there's no real immune system to speak of for quite a while in gestation, right?15:34
delinquentmeSorry ||0_-_0||  Im talking about taking those cells and jamming them into adult persons as therapy15:34
||0_-_0||OK can we please work on making parameters and context clearer lest we appear to be spouting out our collective anal manifolds?15:35
justanotheruser||0_-_0||: I don't like your name15:36
delinquentmeI think there are a total of like 6 things necessary for total acceptance within the body. 2 of those are MHCs15:36
justanotheruserI don't have any authority here, i'm just stating that15:36
||0_-_0||justanotheruser it's pronounced "THWB"15:36
justanotheruserthwub?15:36
delinquentmethumpin15:37
||0_-_0||I should probably reclaim my main nick15:37
||0_-_0||your feedback has been noted justanotheruser thank you for caring15:37
justanotheruserlol15:38
nmz787_itubthumper15:39
nmz787_ikanzure: optical lift is indeed neat15:39
||0_-_0||do you get knocked down nmz787_i ?15:39
nmz787_ii will have to look for some shapes15:39
nmz787_iyes, but I get up again15:39
nmz787_iI have a bad tendency to piss the night away sometimes, though last night I was pretty productive with kicad!15:40
kanzurenmz787_i: pick out a microscope for doing dmd things15:41
gradstudentbotCan I defend with just one aim done?15:42
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justanotheruserkanzure: I assume youve heard of http://www.swarmcorp.com/16:10
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kanzureugh16:14
kanzurethat sounds awful16:14
justanotheruserkanzure: great camera work and dramatic music16:16
kanzureah, didn't look at the video, because why would i16:17
@fennwhy is "optical lift" surprising at all? it's just conservation of momentum, and it's how solar sails work16:17
kanzureno, solar sails work by a different mechanism16:18
@fennactually no, you're wrong16:20
* kanzure pouts16:20
kanzurebut the author said so16:20
@fenneither way it's force caused by the momentum of light being reflected in some direction or other16:21
@fennthe fact that they used glass rods doesn't change the physics16:21
nmz787_ikanzure: I've got a microscope that is trinocular and supposedly has some fluorescense filters... but if i were to buy one, I've been eyeing the new ones on ebay and/or microscopenet.com16:21
kanzurehook up the dmd projector to the microscope16:21
nmz787_ikanzure: my microscope is ~50 years old though (has good optics)... so its dusty and all the oil is gelled up now so action is hard on control knobs... also power supply/light bulb is gone16:22
gradstudentbotThe grant got rejected.16:22
kanzureso why were we doing the lasre cutter xy slide if you already had one16:23
kanzurei guess something repeatable that can be made multiple times is better16:23
nmz787_ikanzure: I had trouble thinking of how to connect the two, and adjust the hell so planes were parallel16:23
nmz787_iyep16:23
@fenni wish people would stop making terrible websites16:24
kanzureadjust the hell?16:24
nmz787_iwell cause if the planes aren't parallel, results could be shitty16:24
nmz787_iso how do you finely adjust the projector relative the the scope16:24
kanzurei think a certain amount of shit is acceptable, ya?16:24
kanzurewell according to these articles you don't have to16:24
nmz787_iuntil you need to start iteratively debugging16:24
kanzureor you get one $50 lense or osmething.. very confused.16:24
@fennyou keep the plane in focus like a camera autofocus16:25
nmz787_iare you looking at DMD photolithography exposure of the photo generated acid?16:25
nmz787_ifenn: that doesn't work for getting them all focused at once16:25
nmz787_ifenn: that also doesn't take into account the adjustment hardware16:25
kanzuredmd photolithography for 3d lithography, microelectronics fabrication, dna synthesis, and microfluidics16:25
@fennyes it does, the projection plane is short so it can all be in focus (as long as your optics dont suck)16:26
@fennsome optics have spherical abberation or whatever16:26
nmz787_isure autofocus algos are great, and work if you only need one area in focus at a time, but with that autofocus algo/data you can then feed it back to some adjustment screws or something16:26
nmz787_ibut the projector was a few lbs16:26
nmz787_iand I'm apparently bad with fabricating mechanical stuff16:26
nmz787_ikanzure: i'm kinda not so interested in DMD photolith after I saw interpixel noise in some photoresist in one of the pro DMD photolith companies research articles they had posted16:27
nmz787_i(I believe Heidelberg)16:28
gene_hackeryou can calibrate for that16:28
yoleaux18:35Z <kanzure> gene_hacker: the valveless microfluidic dna synthesizer is also interesting because it shoves all of the complicated equipment outside the realm of microfluidics (like the valve train). in fact, with a large enough array and micromirror array, you could have a 1024x1024 well microfluidic dna synthesizer that you could even operate manually (using manual dna synthesis), which although time-consuming has the  …16:28
yoleauxadvantage of building a million ...16:28
yoleaux18:35Z <kanzure> gene_hacker: http://diyhpl.us/~bryan/papers2/DNA/Syringe%20method%20for%20stepwise%20chemical%20synthesis%20of%20oligonucleotides.pdf16:28
kanzurewhat is an acceptable amount of noise for you?16:28
@fennugh i hate everyone /me goes away16:28
kanzurefenn: what's wronnnnng16:29
@fennPMS16:29
gene_hackerthere is noise and you have to deal with the fact that the illumination isn't uniform16:29
kanzurefenn: the pixels?16:29
nmz787_itracing around with a laser seems to get around interpixel noise totally16:29
nmz787_ibut then you have to have a nice smooth tracing machine16:30
@fenninertia smooths out steps16:30
gene_hackerthen you have laser tracking noise16:30
nmz787_ifenn: idk about that at such microscales16:30
@fennwhat "noise" are you all talking about?16:31
nmz787_ifenn: i'm talking about leadscrew variation16:31
gene_hackeroh tracing16:31
@fennperiodic error doesn't matter if it's repeatable; absolute error doesn't matter because hopefully your feature size is small16:31
gene_hackerwell whatever works.16:31
seba-hm16:32
seba-i could do sous vide16:32
gene_hackeryou could also use use an array of LEDs for a synthesizer, from what i understand a picoarray doesn't have very many pixels16:32
seba-in my incubator16:32
@fennhow do you release the dna once you've synthesized it?16:32
seba-lol16:32
kanzurefenn: probably solid phase support release.. wash away the beads, etc16:33
kanzureor you could have pressure applied to the whole device so that beads are held in place16:33
@fennbut you want to release one well at a time or it will cross contaminate16:33
nmz787_ifenn: i've been planning on a support-free or at least liquid-phase support16:33
@fennotherwise what's the point of the "array" at all?16:33
kanzureyes you will probably not have single bead release in that design16:33
gene_hackeror use frickin' magnets!16:33
kanzurewell you can synthesize lots of dna fragments that are meant to be assembled together16:33
gene_hackerand magnetic beads16:33
kanzureoh yeah, magnetic beads exist16:33
gradstudentbotWho used the last of the buffer?16:33
@fennthis plan doesn't make any sense16:34
kanzuregene_hacker: i dunno why the pico array didn't have lots of pixels, i see no reasons why not16:34
gene_hackerthe point of the array is to keep the photogenerated acid separate16:34
gradstudentbotI think I just cured cancer. Wow.16:34
kanzurefenn: you synthesize your library, then you put your library in a pot and you make your super-long protein sequence16:34
@fennwhat's the error rate of "picowell photosynth" or whatever they're calling it16:34
gene_hackerwell one should start simple first to work out any kinks16:34
@fennlet's say you have one picowell16:35
@fennthere are a million dna strands in it16:35
@fennwhat percentage of those strands are "perfect"16:35
@fennlet's say it's 100 bases long16:35
kanzurethe picoarray one is 67% yield per 40mer ? http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf16:36
kanzurelol 67%16:36
@fenn.wa e^40 = 0.67 solve for e16:36
yoleauxe⁴⁰ = 0.67 e: False16:36
@fennbah16:36
@fenn.c 0.67^(1/40)16:36
yoleaux0.67^(1/40) = 0.99003801...16:36
@fennso you gotta get a lot of 9's16:37
@fennor you gotta sequence each strand and then you are cambrian genomics16:37
kanzurewell, hm16:38
@fennoh they were talking about targeting picowells, not etching them16:40
nmz787_ior you have a saner synthesis process16:42
nmz787_ithat keeps track for you16:42
kanzureoh yeah, fluorescence-based things that tell you if the reaction happened at all16:42
kanzurebut it's not a single strand if it's on a bead- it's probably a few million strands16:42
kanzuremaybe you could get single strands to grow in each area16:42
nmz787_inah there's plenty of interogation methods16:43
kanzureand then make the fluorescence event bright enough16:43
nmz787_iscanned frequency voltammetry is what i want to investigate16:43
kanzurewell if some % of your strands on the bead are wrong you're going to get propagating pcr errors16:43
nmz787_ithen dont use a bead16:43
nmz787_iso you can get rid of the erroneous (even if length check is the only metric)16:43
kanzurei wonder what the source of the yield problem is in this case16:46
kanzuremaybe it's the chemistry16:47
nmz787_icorners that don't get mixed well (microwells dont have this problem)16:47
kanzurewhat's the point of having a chemical process that only works 1% of the time16:47
nmz787_ichemistry that hurts existing syntecons16:47
nmz787_ior whatever you call the already-synthesized stuff16:47
kanzurei wonder if dna gets tangled on beads and makes certain strands miss out on individual cycles16:48
nmz787_ilike the acid can either activate.... OR it can depurinate a sidechain16:48
nmz787_iprobably16:48
kanzurethere should be a journal of theoretical dna synthesis16:54
kanzure(not just "journal of nucleic acids research")16:54
kanzure*of practical dna synthesis16:55
kanzurepaperbot: http://www.mdpi.com/1420-3049/18/1/1063/pdf?y=116:56
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/b2d710d98a9d3d35094b393ac7161a84.pdf16:56
kanzure"Frontiers and Approaches to Chemical Synthesis of Oligodeoxyribonucleotides"16:56
nmz787_ithat is one i will have to read when i leave work16:57
nmz787_ibut maybe find some similar that don't "focusing on large-scale methods"16:57
nmz787_ithat is the opposite optimization we want16:58
nmz787_i(solution to the problem could overlap, but my thinking is the end-goals are sufficiently different)16:58
nmz787_ii.e. if you think their target is some small RNA for FDA human trials of some RNA interference crap16:59
nmz787_i(i know it says deoxy)16:59
nmz787_ibbl16:59
nmz787_itry to find that nbs (n-bromo-succinimide) paper17:00
kanzurei'm curious about other complex chemical reactions with yield problems17:00
kanzuresurely chemists have done this before in other areas17:00
kanzurei'd be very disappointed if dna synthesis is the most complicated sequence of reactions we've bothered to make17:01
kanzurebut also, presumably more complex chemistries would require clever solutions that can be backported, erm, sidewayported17:01
@fennsymported!17:01
kanzureyou can't just make up words, you have to use someone's name17:02
@fennsymbionese liberported17:03
kanzurei should go find a chemist and bug them about this17:04
@fennchemists get to use crystallization17:04
kanzurehm17:04
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@fennafaik crystallization doesnt  work so well wrt strand mismatch17:04
@fennit does work but it's tricky17:04
@fennyou linked a paper about it some years ago17:05
kanzurewas this dna related?17:05
@fennyes, maybe it was george church?17:05
kanzuregreat i'll just look it up in my non-existing tagging system17:05
@fennslow cooling of pcr products17:05
@fennthe strands with no mismatches would anneal first17:06
@fennbut it was like 0.0001C17:06
kanzure(i'm not digging this up, i have no audible bells ringing)17:07
kanzurei wonder if people really think they're hearing bells whenever they remember things17:07
kanzure(must be loud in there)17:07
kanzure(or silent in my case..)17:08
kanzurehm, i think nate has a point here, "oh we have terrible yields? let's just parallelize it!" is probably not a good idea17:09
@fenntoday i was woken up by the doorbell, i roll around and go back to sleep. i'm woken again by the doorbell a couple hours later. whoever's at the door must be back, guess i have to get up and answer it. go to the door, nobody's there. turns out it was the printer making its "paper jam" noise17:10
kanzureduring your napyear did you see the printer device that moves itself around on top of the stack of blank paper17:10
@fennwhy would i want that17:10
kanzurewell i didn't want it17:11
@fenndoes it have a laser cutter or something17:11
@fennor is it just a turtle LOGO bot17:11
kanzurei think inkjet or laser toner transfer (probably inkjet, knowing the world..)17:11
@fennok whatever, don't care17:11
@fenni remember a "paint roller" with a mouse sensor to track position and a print head, you could "roll" a pattern onto a wall17:12
ThomasEgifenn,  http://theoatmeal.com/comics/printers17:13
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@fennwhy are there no open source printers?17:14
@fennhow hard could it be to drill a tiny hole in something17:14
kanzuretiny hole?17:15
gradstudentbotI remember the paper, I just don't remember the details.17:16
@fennwow the paranoid schizophrenics are going to love this http://www.technologyreview.com/news/527561/military-funds-brain-computer-interfaces-to-control-feelings/17:16
@fennalso it uses the same electrode layout as my piezo sonar array sketch17:17
kanzurean open source printer is worth doing17:17
kanzureand bypassing fingerprinting would be nice17:18
@fennfingerprinting?17:19
kanzuremost inkjet printers have a specific id they make apparent on each printed page17:19
kanzuresomething about the government17:19
kanzure.title http://boingboing.net/2008/10/23/howto-read-the-secre.html17:20
yoleauxHOWTO read the secret forensic dots in your laser-printer output17:20
@fennthat's only laser printers i guess17:20
kanzure"These dots were long-rumoured, but it wasn't until EFF discovered them that their existence was verified and their code was cracked."17:20
kanzurehuh the electronic frontier foundation had to do it? wtf?17:20
kanzureother results from same search include:17:22
kanzure.title http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/c0nr00593b#!divAbstract17:22
yoleauxIn situ growth of gold nanoparticles on latent fingerprints—from forensic applications to inkjet printed nanoparticle patterns17:22
kanzure"Latent fingerprints are made visible in a single step by in situ growth of gold nanoparticles on ridge patterns. The chemicals, among the essential components of human sweat, found responsible for the formation and assembly of gold nanoparticles are screened and used as ink to write invisible patterns, using common ball pen and inkjet printer, which are then developed by selectively growing gold nanoparticles by soaking them in gold salt ...17:23
kanzure... solution."17:23
kanzure.title http://pubs.rsc.org/en/content/articlehtml/2013/cc/c3cc42451k17:30
yoleauxSolid phase click ligation for the synthesis of very long oligonucleotides17:30
kanzure"owever, it remains challenging to achieve clean and efficient chemical ligation of oligonucleotides. An alternative strategy is to design a chemical linkage that mimics the natural phosphodiester and which can be formed efficiently and selectively. This has been achieved through a click chemistry approach4 in which the CuI-catalysed [3+2] azide–alkyne cycloaddition (CuAAC) reaction5,6 is used to synthesise DNA containing biocompatible ...17:30
kanzure... artificial linkages (Fig. 1a) ....  We now report a solid-phase strategy for ligating oligonucleotides using the CuAAC and SPAAC reactions. This approach has several desirable features; it is simple to carry out, the reaction can be forced to completion by adding an excess of the solution-phase reactant, there is no requirement for a template oligonucleotide, and excess reagents can be conveniently removed and recovered."17:30
kanzurethe review paper "DNA-associated click chemistry" says that people have tried this click chemistry technique in vivo. that seems like an unusual thing to do..17:40
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kanzurealso, you don't really need dna, you just need something that a polymerase enzyme will recognize correctly, or that a polymerase enzyme can be modified to recognize correctly17:41
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kanzurethis link redirects to a weird place: http://onlinelibrary.wiley.com/doi/10.1002/ijch.201300032/full17:54
kanzureit redirects over to http://onlinelibrary.wiley.com/doi/10.1002/ijch.201300032/abstract?systemMessage=Wiley+Online+Library+will+be+disrupted+Saturday%2C+7+June+from+10%3A00-15%3A00+BST+%2805%3A00-10%3A00+EDT%29+for+essential+maintenance&userIsAuthenticated=false&deniedAccessCustomisedMessage=17:54
kanzurei wonder if that's an xss vulnerability17:55
kanzureeither chrome is stripping my injected html or the server is smart enough to not use it as input17:55
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nmz787kanzure: have you seen the HELP synthesis articles?18:13
nmz787that overview mentioned it18:13
kanzureno18:15
nmz787I think its High Efficieny Liquid Phase18:15
kanzurehm i forgot about this one,18:20
kanzurehttp://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Optical%20tweezers%20directed%20one-bead%20one-sequence%20synthesis%20of%20oligonucleotides.pdf18:20
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kanzureyashgaroth: have you visited azco biotech yet?18:35
yashgarothno, are they affiliated with aztechnology?18:36
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kanzureyashgaroth: they do dna synthesizer equipment refurbishing18:49
kanzureyashgaroth: in san diego18:49
yashgarothwell, san diego county18:51
yashgaroththey have a strange website18:51
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nmz787they make new ones too19:10
nmz787they make the one cambrian uses19:10
kanzurecambrian genomics didn't build their own equipment?19:19
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nmz787well, they put them all in a row and interfaced them with robot arms or something, their big thing is sorting them once they seqquence them19:43
kanzurecaruthers historical review of the context of oligonucleotide and dna synthesis http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543024/?report=classic19:56
kanzureuhh "I also found myself in the middle of this revolution both in research and as a cofounder of two biotechnology companies, Amgen and Applied Biosystems."20:01
kanzurecaruthers co-founded applied biosystems.. so i guess that explains why they have always been one of the few to bother to make dna synthesizers.20:01
kanzure"At our first meeting in Thousand Oaks, Lee and I proposed that this new company, which was to be called Applied Molecular Genetics, should have an instrument division that would sell protein sequencers and DNA synthesizers based upon Lee's and my work, respectively. However, the other scientists were concerned that Applied Molecular Genetics would become primarily an instrumentation company rather than one focused on genetic engineering and ...20:02
kanzure... molecular biology. As a result, the proposal was dropped, but later that same morning, Lee and I, in discussion with the venture capitalists who were starting Applied Molecular Genetics, decided to move forward with the formation of a new instrument-focused company, which became known as Applied Biosystems."20:02
kanzure"We located Applied Biosystems in Foster City, California, and hired Sam Eletr as our first chief executive officer (spring 1981). Sam proved to be an excellent entrepreneurial choice. We started with only three million dollars but were able to convince a large number of pharmaceutical and biotechnology companies and academic laboratories to advance large deposits (half of the proposed sale price) on future protein sequencers and DNA ...20:03
kanzure... synthesizers (that had yet to be designed, let alone manufactured) simply so they would be in the queue for the first machines. With this capital, Sam hired two or three scientists each from Lee's and my laboratories to design and build our first instruments. From my laboratory, Bill Efcavitch and Curt Becker were among the first employees (later, Lincoln McBride as well). Bill and Curt started with a series of valves, tubing, small ...20:03
kanzure... HPLC-grade silica columns, a tank of liquid nitrogen, and a large piece of plywood. Within a few months, they were synthesizing DNA on this platform. Sam asked John Bridger, an engineer hired from Hewlett-Packard, to design a DNA synthesizer, which became known as our 380A machine. By December 1982, Bill installed the first commercial synthesizer in my laboratory (Fig. 5), and Applied Biosystems began shipping the instruments in 1983."20:03
kanzure"Meanwhile, Winston Salser and Bill Bowes recruited George Rathmann as the first chief executive officer of Applied Molecular Genetics, and they raised 18.9 million dollars, which, at that time, was the largest initial private placement ever put together to start a new venture capital-funded company"20:04
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kanzure.title http://www.thingiverse.com/thing:15905220:41
yoleauxLaboratory Pipette by lewisite20:41
kanzuregoogle scholar search results for "intitle:theoretical phosphoramidite": 4821:06
kanzurenot promising21:06
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aristarchusi got my dna sequenced!21:38
jrayhawk_post it!21:39
aristarchusi will after i augment it21:40
aristarchuslol21:40
||0_-_0||whelp, guys21:41
||0_-_0||today we lost a hero21:41
||0_-_0||Alexander Shulgin passed away today21:41
kanzureroman lygin replied21:43
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heathhttp://docs.python-guide.org/en/latest/scenarios/admin/21:44
heathnot sure the part about fabric really makes sense21:45
kanzureyou know, i've found that fabric is really quite weird21:47
kanzurei don't usually think in the way that fabric expects me to be thinking21:48
kanzureheath: i've been liking fig lately, http://orchardup.github.io/fig/21:51
kanzureservice discovery is still a pain though21:51
kanzureand it makes livereload slightly more confusing21:52
gradstudentbotProtip: the lab's attic hasn't been used since 1966. Pretty nice.21:52
kanzure"Peter Glaser died on May 29, 2014. I knew him through SSI because he pioneered the concept of Solar Power Satellites, and was associated with Gerry O'Neill and Bill Brown on beamed power and space settlements. He also worked on Apollo and Space Station missions." http://en.wikipedia.org/wiki/Peter_Glaser21:54
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kanzure.title https://pag.confex.com/pag/xxi/webprogram/Paper6977.html22:14
yoleauxAbstract: true-Single Molecule Sequencing Illuminates the Sequencing of Ancient DNA Molecules (Plant and Animal Genome XXI Conference)22:14
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kanzure"Pleistocene horse bones preserved in permafrost"22:15
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heathhrm, wonder why the hitchhiker's guide doesn't mention httpie22:19
kanzurebecause you should be using httpretty instead22:20
heathi don't really mock stuff22:21
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* heath needs to sleep22:22
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gene_hackersleep is for slackers22:30
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kanzurehttps://archive.org/details/HackerNewsStoriesAndCommentsDump23:15
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--- Log closed Tue Jun 03 00:00:23 2014

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