--- Log opened Tue Jul 21 00:00:17 2015
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03:14 < archels> "Acoustic triangulation is possible via accelerometers on upper stage"
03:14 < archels> https://www.reddit.com/r/spacex/comments/3dyvta/rspacex_crs7_failure_investigation_teleconference/
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03:53 < indiebio> hi all, do you know about this publication? http://www.oreilly.com/biocoder/?imm_mid=0d5585&cmp=em-na-na-info-na_biocoder_issue8
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06:11 < kanzure> indiebio: latest issue looks pretty lame compared to the others. sad.
06:11 < indiebio> I've not actually had time to read any of them..
06:12 < indiebio> but 'lame' is how I think of this area in general - looooaaaads of hype, very little substance. but maybe just me.
06:15 < kanzure> yep
06:15 < kanzure> but that's what oreilly biocoder is- it's a magazine, from the assholes that brought you "make magazine" and other catastrophes
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07:12 < FourFire> ...
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09:11 < delinquentme> ASDF
09:15 < kanzure> agreed
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09:56 < kanzure> .title https://www.youtube.com/watch?v=eKM4dqNnkLI
09:56 < yoleaux> Stabbing an LCD screen experiment - YouTube
09:57 < kanzure> .title https://www.youtube.com/watch?v=_zoeeR3geTA
09:57 < yoleaux> DIY Custom LCD - YouTube
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10:48 < juri_> AOEU
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11:21 < kanzure> optoelectrowetting using a laser and a 40x objective lens, 17 micron spot size, moves ecoli cells towards center of laser spot within a 20 micron radius through dielectrophoresis and virtual electrode created by photoconductor http://nanophotonics.eecs.berkeley.edu/research/oet/Eric%20-%20MEMS%202004.pdf
11:21 < chris_99> .title https://www.youtube.com/watch?v=2vaf1w101cg
11:21 < yoleaux> Magnasee - magic goop that allows you to see the invisible magnetic patterns on recorded media - YouTube
11:22 < kanzure> "We have shown that optical power as low as 1 microwatt is sufficient to move a 25 micron latex bead at a speed of 4.5 microns/sec."
11:23 < kanzure> s/optoelectrowetting/optoelectronic
11:32 < juri_> nice.
11:33 < juri_> is that on a surface, or embedded in oil?
11:35 < kanzure> well there was the youtube video yesterday that demonstrated droplet movement by light in open-air, does that count as not oil?
11:40 < kanzure> uv led mixing http://pubs.acs.org/doi/abs/10.1021/ja311837r
11:40 < kanzure> hmph "A fast and switchable microfluidic mixer based on ultrasound-induced vaporization of perfluorocarbon"
11:42 < kanzure> uv switchable microvalves http://iopscience.iop.org/0957-4484/25/12/125301 (something like this, once working, would convince me that microfluidics projects with valves might be ok)
11:44 < kanzure> more of the same http://iopscience.iop.org/0960-1317/25/3/035032
11:45 < kanzure> "optopneumatic piston" in pdms http://pubs.rsc.org/en/content/articlelanding/2015/lc/c4lc01389a#!divAbstract
11:56 < kanzure> an okay review http://diyhpl.us/~bryan/papers2/microfluidics/Photo-actuation%20of%20liquids%20for%20light-driven%20microfluidics:%20state%20of%20the%20art%20and%20perspectives%20-%202012.pdf
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11:58 < kanzure> but doesn't mention lcd stuff
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13:52 < kanzure> group blood testing for syphilis http://blog.shriphani.com/2015/07/21/a-new-weapon-in-the-fight-against-syphilis/
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14:42 < delinquentme> kanzure,
14:43 < delinquentme> does you know anything about FDA not allowing scale up to be done in human cell lines?
14:44 < drethelin> what do you mean by scaleuip
14:46 < delinquentme> drethelin, I mean for production of therapeutics
14:47 < drethelin> I mean it's not "not allowing" so much as having huge barriers to entry
14:47 < drethelin> you have to trials and prove efficacy
14:47 < drethelin> and manufacture in a GMP facility whatnot
14:47 < drethelin> 9 figure+ costs
14:47 < drethelin> unless you're talking about something other than what I think
14:52 < drethelin> http://lesswrong.com/r/discussion/lw/mi3/open_thread_jul_20_jul_26_2015/cla1
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15:09 < kanzure> drewbot_: hmm, not entirely true
15:09 < kanzure> "De novo sequencing that many people would be much more human DNA sequence data than has ever been produced in the history of the world, would clog up the current world complement of high throughput sequencers for a long time, would be no more useful for legal purposes, and probably cost $40 billion + (probably more to develop infrastructure)."
15:09 < kanzure> this analysis assumes no development of sequencing technology
15:10 < kanzure> by the time that they use up even half their $400M, perhaps better dna sequencing tech will be out on the market
15:10 < kanzure> at any rate, i'm not sure why it should matter whether they are collecting whole genomes or not. snps is pretty damning....
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16:33 < kanzure> yashgaroth: hi
16:34 < yashgaroth> yo
16:41 < kanzure> yashgaroth: new plan https://www.youtube.com/watch?v=8PeYwGDnt7I
16:45 < kanzure> actually i'm starting to think ping pong balls...
16:45 < yashgaroth> looks like a bit of a pain to automate, also how small can you get a laser point?
16:45 < CaptHindsight> anyone know the ball rates for testing to meet Biocompatibility; ISO 10993?
16:45 < CaptHindsight> heh ball/ballpark
16:45 < kanzure> don't know
16:46 < kanzure> yashgaroth: depends on your optical setup, but uh, pretty small. i would expect to be able to manipulate 30 micron diameter droplets with a telescope or typical microscope.
16:47 < yashgaroth> I wonder if you could overlay that on some quad-HD LCD screen and move em around with that instead
16:48 < kanzure> yep...
16:48 < kanzure> apparently the answer is yes
16:49 < kanzure> but i wouldn't know where to put the magnet.
16:49 < juri_> neat.
16:49 < yashgaroth> because having a microscope on top of every droplet is gonna be, eurgh
16:49 < kanzure> well, i think you still need a microscope anyway because water doesn't always behave the same way in this environment methinks
16:49 < kanzure> e.g. optical detection of failed droplet movements
16:50 < juri_> use a stereo microscope, and use one feed to a camera.
16:50 < kanzure> juri_: um, that's what all the papers already show
16:50 < juri_> this way you can adjust out imprecision in the head.
16:50 < juri_> oh, OK. :)
16:50 < yashgaroth> aww I wanted to shoot a laser out of my eyeball
16:50  * juri_ is a few papers behind.
16:51 < kanzure> juri_: no really, have you ever seen a paper where they were like "we found the thor catalog incomprehensible and we don't know what an optical train is"
16:51 < kanzure> yashgaroth: yea but it's lots of equipment. and plus you need a magnet for the laser one as well as the lcd one (to keep beads in place when you wash).
16:51 < kanzure> if you used giant ping pong balls though.....
16:52 < juri_> I haven't read many papers in the last few years. been busy inventing. ;)
16:52 < kanzure> what's the wink for?
16:54  * juri_ shrugs.
16:54 < kanzure> yashgaroth: i've been thinking of large beads instead, like golf balls or ping pong balls... https://www.youtube.com/watch?v=VD85c6tlbz4&t=53s
16:54 < juri_> i guess i'm still proud of my work last summer.
16:54 < kanzure> you can just store those in a giant bin next to the equipment
16:55 < mgin> what's this?
16:55 < kanzure> mgin: http://diyhpl.us/wiki/dna/synthesis/notes/
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16:58 < yashgaroth> bowling balls would provide a significant advantage in momentum, as well as easy manipulation via the fingerholes
16:58 < kanzure> you can't store as many bowling balls though
16:58 < yashgaroth> these are minor technical concerns
16:59 < yashgaroth> I checked and wolfram alpha doesn't know the volume of ping pong balls, or golf balls
16:59 < yashgaroth> anyway bowling alleys have already solved the storage issue, I'll see if I can dig up some of their patents
17:00 < kanzure> oh, i was only going to use their surface area, not their volume
17:00 < kanzure> or they could be cut in half if necessary
17:00 < CaptHindsight> hollow bowling balls
17:01 < yashgaroth> golf balls do have the advantage in surface area, what with the dimples
17:01 < CaptHindsight> you can get them hollow as well
17:01 < CaptHindsight> if you buy enough
17:01 < yashgaroth> ah as always with wolfram alpha it's a matter of phrasing
17:01 < yashgaroth> .wa volume of a ping pong ball * one million
17:01 < yoleaux> table tennis ball: volume×1000000: 3.351×10⁷ cm³ (cubic centimeters); Unit conversions: 33.51 m³ (cubic meters); 33510 L (liters); 8852 gallons; 1183 ft³ (cubic feet); Comparisons as volume: ~0.93 × volume of a 1C-series freight container (1266 to 1272 ft³); ~1.1 × volume of a humpback whale (Megaptera novaeangliae) (~31 m³); ~(0.8 to 1.7) × 20-foot equivalent unit (680 to 1520 ft³)
17:02 < kanzure> 33 kL hehe
17:02 < kanzure> oh they even tell you the volume in units of freight containers, perfect
17:04 < kanzure> i also appreciate that they compute the volume in units of humpback whales.
17:04 < yashgaroth> just in case you want to store them inside a whale instead of a shipping container
17:05 < kanzure> prolly bottle caps would work better and be cheaper
17:07 < yashgaroth> ping pong ball material is much more amenable to chemical activation and cross-linking
17:10 < kanzure> hm but then you'd have to figure out how to re-attach things to ping pong balls after cleaving, doing your reactions and wanting to store the results until later. hmph.
17:10 < kanzure> at least cleaning is easier with them.
17:10 < kanzure> and storage.
17:12 < kanzure> if you use microcentrifuge tubes, then your wash steps have to involve silly things like gel extraction (unless, again, you can figure out how to selectively re-link)
17:14 < kanzure> maybe there's a photopolymer linker that instantly links back to the surface under a certain light, or similar but with an electric field.
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17:17 < kanzure> perhaps you could do a layered photopolymer surface where you could shine a light to cause the next layer of linker chemistry to be exposed to the oligos, then you wait for them to bind, then you run your wash step.
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17:18 < kanzure> what was the problem with magnets again?
17:20 < yashgaroth> applying them accurately enough that they don't move the drop around when you go to immobilize the bead? I guess
17:24 < kanzure> i thought they were a common solid support
17:25 < kanzure> .title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828674/
17:25 < yoleaux> Direct oligonucleotide synthesis onto super-paramagnetic beads
17:25 < kanzure> "To mainstream the process, we describe a novel procedure of direct oligonucleotide synthesis onto the surface of SPMBs (e.g. MyOne Dynabeads). With the many challenges surrounding containment of paramagnetic beads (≤ 1 μm) during automated oligonucleotide synthesis, we show that by applying a magnetic force directly to the SPMBs we prevent their loss caused by high-pressure drain steps during synthesis"
17:25 < kanzure> no shit?
17:25 < kanzure> i thought that was the whole point
17:27 < yashgaroth> heh
17:28 < kanzure> oh weird they made this compatible with ABI equipment. how nice of them.
17:31 < kanzure> perhaps there's a way to attach oligos to a bead (their attachment method is only for er.. pre-synthesis precursors).
17:31 < kanzure> unless you don't need wash steps during assembly.
17:32 < yashgaroth> we're talking ligase assembly right? not phosphoramidite assembly
17:34 < kanzure> right... yes. or other assembly methods. i also don't know how to do phosphoramidite assembly.
17:36 < yashgaroth> well like synthesis but I didn't know if we were calling that assembly too
17:36 < yashgaroth> might not need a wash step for oligo/ligase assembly, I mean it wouldn't hurt but any incorrect/missed additions shouldn't continue to extend anyway
17:36 < kanzure> the phosphoramidite approach to oligonucleotide synthesis needs a wash step
17:37 < kanzure> (many wash steps)
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17:59 < delinquentme> kanzure, I know I've shown you this https://www.youtube.com/watch?v=WKuzhIQ_wNE
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18:07 < kanzure> .title
18:07 < yoleaux> MorsPrincipium Est - The Unborn - YouTube
18:07 < kanzure> yes...
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18:57 < ParahSailin_> dont magnets move pretty slow when theyre small?
18:57 < ParahSailin_> like good for pulling down stuff in a tube, but not really for real time manipulation
19:04 < kanzure> only for pulling things down
19:05 < kanzure> droplet/water is moved, magnets go along for the ride
19:05 < kanzure> *magnetic particles
19:05 < kanzure> (unless the magnet is activated. in which case, they should not move.)
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20:02 < CaptHindsight> http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.5b02491
20:02 < CaptHindsight>     Previous Article
20:02 < CaptHindsight>     Next Article
20:02 < CaptHindsight>     Articles ASAP
20:02 < CaptHindsight> Lasing within Live Cells Containing Intracellular Optical Microresonators for Barcode-Type Cell Tagging and Tracking
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21:20 < kanzure> weird.
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22:12 < justanotheruser> http://pdos.csail.mit.edu/scigen/
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23:05 < delinquentme> kanzure,
23:05 < delinquentme> i need troll help
23:05 < delinquentme> stat
23:05 < delinquentme> fenn,
23:05 < delinquentme> nmz787,
23:05 < delinquentme> how do obfuscate URL for url without having facebook show preview
23:17 < delinquentme> I think there is a need for obfuscated rickrolls
23:20 < justanotheruser> Is this a good utilization of ##hplusroadmap resources?
23:23 < delinquentme> justanotheruser, who are you
23:23 < delinquentme> identify
23:23 < delinquentme> kthanksbai
23:25 < justanotheruser> delinquentme: I'm justanotheruser
23:35 < xrr> Hmm. ##nutrition is silent. Perhaps someone here can help me with this
23:35 < xrr> I took a blood test with a bunch of minerals 10 months ago and again now
23:35 < xrr> Now I'm comparing the reference ranges given by the lab then and now
23:35 < xrr> They were previously given in mmol/l and now in mg/l
23:35 < xrr> I would think that the conversion is just multiplication by a constant, so low/high ratio of the range should remain the same
23:35 -!- rigel [~yourmom@c-24-21-52-83.hsd1.or.comcast.net] has quit [Read error: Connection reset by peer]
23:35 < xrr> Is that correct?
23:35 < xrr> These ratios don't actually match for the ranges given by the lab. For example, potassium, 3.5/5.0 (in mmol/l) is way off from 1750/1850 (in mg/l)
23:36 < xrr> Calcium, magnesium and iron are also way off
23:36 -!- rigel [~yourmom@c-24-21-52-83.hsd1.or.comcast.net] has joined ##hplusroadmap
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--- Log closed Wed Jul 22 00:00:18 2015