2015-07-21.log

--- Log opened Tue Jul 21 00:00:17 2015
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archels"Acoustic triangulation is possible via accelerometers on upper stage"03:14
archelshttps://www.reddit.com/r/spacex/comments/3dyvta/rspacex_crs7_failure_investigation_teleconference/03:14
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indiebiohi all, do you know about this publication? http://www.oreilly.com/biocoder/?imm_mid=0d5585&cmp=em-na-na-info-na_biocoder_issue803:53
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kanzureindiebio: latest issue looks pretty lame compared to the others. sad.06:11
indiebioI've not actually had time to read any of them..06:11
indiebiobut 'lame' is how I think of this area in general - looooaaaads of hype, very little substance. but maybe just me.06:12
kanzureyep06:15
kanzurebut that's what oreilly biocoder is- it's a magazine, from the assholes that brought you "make magazine" and other catastrophes06:15
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FourFire...07:12
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delinquentmeASDF09:11
kanzureagreed09:15
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kanzure.title https://www.youtube.com/watch?v=eKM4dqNnkLI09:56
yoleauxStabbing an LCD screen experiment - YouTube09:56
kanzure.title https://www.youtube.com/watch?v=_zoeeR3geTA09:57
yoleauxDIY Custom LCD - YouTube09:57
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juri_AOEU10:48
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kanzureoptoelectrowetting 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.pdf11:21
chris_99.title https://www.youtube.com/watch?v=2vaf1w101cg11:21
yoleauxMagnasee - magic goop that allows you to see the invisible magnetic patterns on recorded media - YouTube11:21
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."11:22
kanzures/optoelectrowetting/optoelectronic11:23
juri_nice.11:32
juri_is that on a surface, or embedded in oil?11:33
kanzurewell there was the youtube video yesterday that demonstrated droplet movement by light in open-air, does that count as not oil?11:35
kanzureuv led mixing http://pubs.acs.org/doi/abs/10.1021/ja311837r11:40
kanzurehmph "A fast and switchable microfluidic mixer based on ultrasound-induced vaporization of perfluorocarbon"11:40
kanzureuv 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)11:42
kanzuremore of the same http://iopscience.iop.org/0960-1317/25/3/03503211:44
kanzure"optopneumatic piston" in pdms http://pubs.rsc.org/en/content/articlelanding/2015/lc/c4lc01389a#!divAbstract11:45
kanzurean okay review http://diyhpl.us/~bryan/papers2/microfluidics/Photo-actuation%20of%20liquids%20for%20light-driven%20microfluidics:%20state%20of%20the%20art%20and%20perspectives%20-%202012.pdf11:56
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kanzurebut doesn't mention lcd stuff11:58
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kanzuregroup blood testing for syphilis http://blog.shriphani.com/2015/07/21/a-new-weapon-in-the-fight-against-syphilis/13:52
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delinquentmekanzure,14:42
delinquentmedoes you know anything about FDA not allowing scale up to be done in human cell lines?14:43
drethelinwhat do you mean by scaleuip14:44
delinquentmedrethelin, I mean for production of therapeutics14:46
drethelinI mean it's not "not allowing" so much as having huge barriers to entry14:47
drethelinyou have to trials and prove efficacy14:47
drethelinand manufacture in a GMP facility whatnot14:47
drethelin9 figure+ costs14:47
drethelinunless you're talking about something other than what I think14:47
drethelinhttp://lesswrong.com/r/discussion/lw/mi3/open_thread_jul_20_jul_26_2015/cla114:52
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kanzuredrewbot_: hmm, not entirely true15:09
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
kanzurethis analysis assumes no development of sequencing technology15:09
kanzureby the time that they use up even half their $400M, perhaps better dna sequencing tech will be out on the market15:10
kanzureat any rate, i'm not sure why it should matter whether they are collecting whole genomes or not. snps is pretty damning....15:10
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kanzureyashgaroth: hi16:33
yashgarothyo16:34
kanzureyashgaroth: new plan https://www.youtube.com/watch?v=8PeYwGDnt7I16:41
kanzureactually i'm starting to think ping pong balls...16:45
yashgarothlooks like a bit of a pain to automate, also how small can you get a laser point?16:45
CaptHindsightanyone know the ball rates for testing to meet Biocompatibility; ISO 10993?16:45
CaptHindsightheh ball/ballpark16:45
kanzuredon't know16:45
kanzureyashgaroth: 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.16:46
yashgarothI wonder if you could overlay that on some quad-HD LCD screen and move em around with that instead16:47
kanzureyep...16:48
kanzureapparently the answer is yes16:48
kanzurebut i wouldn't know where to put the magnet.16:49
juri_neat.16:49
yashgarothbecause having a microscope on top of every droplet is gonna be, eurgh16:49
kanzurewell, i think you still need a microscope anyway because water doesn't always behave the same way in this environment methinks16:49
kanzuree.g. optical detection of failed droplet movements16:49
juri_use a stereo microscope, and use one feed to a camera.16:50
kanzurejuri_: um, that's what all the papers already show16:50
juri_this way you can adjust out imprecision in the head.16:50
juri_oh, OK. :)16:50
yashgarothaww I wanted to shoot a laser out of my eyeball16:50
* juri_ is a few papers behind.16:50
kanzurejuri_: 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
kanzureyashgaroth: 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
kanzureif you used giant ping pong balls though.....16:51
juri_I haven't read many papers in the last few years. been busy inventing. ;)16:52
kanzurewhat's the wink for?16:52
* juri_ shrugs.16:54
kanzureyashgaroth: i've been thinking of large beads instead, like golf balls or ping pong balls... https://www.youtube.com/watch?v=VD85c6tlbz4&t=53s16:54
juri_i guess i'm still proud of my work last summer.16:54
kanzureyou can just store those in a giant bin next to the equipment16:54
mginwhat's this?16:55
kanzuremgin: http://diyhpl.us/wiki/dna/synthesis/notes/16:55
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yashgarothbowling balls would provide a significant advantage in momentum, as well as easy manipulation via the fingerholes16:58
kanzureyou can't store as many bowling balls though16:58
yashgaroththese are minor technical concerns16:58
yashgarothI checked and wolfram alpha doesn't know the volume of ping pong balls, or golf balls16:59
yashgarothanyway bowling alleys have already solved the storage issue, I'll see if I can dig up some of their patents16:59
kanzureoh, i was only going to use their surface area, not their volume17:00
kanzureor they could be cut in half if necessary17:00
CaptHindsighthollow bowling balls17:00
yashgarothgolf balls do have the advantage in surface area, what with the dimples17:01
CaptHindsightyou can get them hollow as well17:01
CaptHindsightif you buy enough17:01
yashgarothah as always with wolfram alpha it's a matter of phrasing17:01
yashgaroth.wa volume of a ping pong ball * one million17:01
yoleauxtable 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)17:01
kanzure33 kL hehe17:02
kanzureoh they even tell you the volume in units of freight containers, perfect17:02
kanzurei also appreciate that they compute the volume in units of humpback whales.17:04
yashgarothjust in case you want to store them inside a whale instead of a shipping container17:04
kanzureprolly bottle caps would work better and be cheaper17:05
yashgarothping pong ball material is much more amenable to chemical activation and cross-linking17:07
kanzurehm 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
kanzureat least cleaning is easier with them.17:10
kanzureand storage.17:10
kanzureif 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)17:12
kanzuremaybe there's a photopolymer linker that instantly links back to the surface under a certain light, or similar but with an electric field.17:14
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kanzureperhaps 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.17:17
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kanzurewhat was the problem with magnets again?17:18
yashgarothapplying them accurately enough that they don't move the drop around when you go to immobilize the bead? I guess17:20
kanzurei thought they were a common solid support17:24
kanzure.title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828674/17:25
yoleauxDirect oligonucleotide synthesis onto super-paramagnetic beads17:25
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
kanzureno shit?17:25
kanzurei thought that was the whole point17:25
yashgarothheh17:27
kanzureoh weird they made this compatible with ABI equipment. how nice of them.17:28
kanzureperhaps there's a way to attach oligos to a bead (their attachment method is only for er.. pre-synthesis precursors).17:31
kanzureunless you don't need wash steps during assembly.17:31
yashgarothwe're talking ligase assembly right? not phosphoramidite assembly17:32
kanzureright... yes. or other assembly methods. i also don't know how to do phosphoramidite assembly.17:34
yashgarothwell like synthesis but I didn't know if we were calling that assembly too17:36
yashgarothmight 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 anyway17:36
kanzurethe phosphoramidite approach to oligonucleotide synthesis needs a wash step17:36
kanzure(many wash steps)17:37
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delinquentmekanzure, I know I've shown you this https://www.youtube.com/watch?v=WKuzhIQ_wNE17:59
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kanzure.title18:07
yoleauxMorsPrincipium Est - The Unborn - YouTube18:07
kanzureyes...18:07
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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 manipulation18:57
kanzureonly for pulling things down19:04
kanzuredroplet/water is moved, magnets go along for the ride19:05
kanzure*magnetic particles19:05
kanzure(unless the magnet is activated. in which case, they should not move.)19:05
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CaptHindsighthttp://pubs.acs.org/doi/abs/10.1021/acs.nanolett.5b0249120:02
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CaptHindsight    Articles ASAP20:02
CaptHindsightLasing within Live Cells Containing Intracellular Optical Microresonators for Barcode-Type Cell Tagging and Tracking20:02
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kanzureweird.21:20
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justanotheruserhttp://pdos.csail.mit.edu/scigen/22:12
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delinquentmekanzure,23:05
delinquentmei need troll help23:05
delinquentmestat23:05
delinquentmefenn,23:05
delinquentmenmz787,23:05
delinquentmehow do obfuscate URL for url without having facebook show preview23:05
delinquentmeI think there is a need for obfuscated rickrolls23:17
justanotheruserIs this a good utilization of ##hplusroadmap resources?23:20
delinquentmejustanotheruser, who are you23:23
delinquentmeidentify23:23
delinquentmekthanksbai23:23
justanotheruserdelinquentme: I'm justanotheruser23:25
xrrHmm. ##nutrition is silent. Perhaps someone here can help me with this23:35
xrrI took a blood test with a bunch of minerals 10 months ago and again now23:35
xrrNow I'm comparing the reference ranges given by the lab then and now23:35
xrrThey were previously given in mmol/l and now in mg/l23:35
xrrI would think that the conversion is just multiplication by a constant, so low/high ratio of the range should remain the same23:35
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xrrIs that correct?23:35
xrrThese 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)23:35
xrrCalcium, magnesium and iron are also way off23:36
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