--- Log opened Tue Jul 05 00:00:48 2016
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02:16 < ebowden> Did anyone here have anything whatever to do with recent advancements in microfluidic oligonucleotide synthesisers, or were they just beaten to the punch?
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02:26 < kanzure> ebowden: which recent advances?
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02:45 < maaku> audio project update: I've gotten now dozens of hours of recording from that little wrist microphone
02:46 < chris_99> maaku, which wrist mic was it?
02:46 < chris_99> is the quality decent
02:46 < maaku> the quality is pretty good. I want to use it as example input for whatever project I do in the future, but there are some real annoyances with respect to uploading, charging, etc.
02:46 < maaku> for daily use at least
02:46 < maaku> hang on
02:47 < maaku> this one : https://www.amazon.com/Weefun-Wristband-Rechargeable-Reduction-Interview/dp/B01B79K0ZW/ref=sr_1_1?ie=UTF8&qid=1467712027&sr=8-1&keywords=wrist+voice+recorder
02:48 < maaku> i suspect the reason the recording is so noise free is good filters + high compression
02:48 < maaku> the output is 4-bit telephony
02:48 < maaku> which is something like 85MB/hr, which is just barely bearable
02:49 < maaku> from a data collection standpoint
02:49 < maaku> only holds about ~1 day of charge
02:49 < chris_99> 4 bit? you mean 4 byte or..?
02:49 < maaku> 4 bit per sample
02:49 < chris_99> eek
02:49 < chris_99> that's v. low
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02:49 < maaku> it's exactly the same thing your cell phone does
02:50 < maaku> https://en.wikipedia.org/wiki/Adaptive_differential_pulse-code_modulation
02:50 < maaku> .wik https://en.wikipedia.org/wiki/Adaptive_differential_pulse-code_modulation
02:50 < yoleaux> maaku: Sorry, that command (.wik) crashed.
02:50 < maaku> Adaptive differential pulse-code modulation (ADPCM) is a variant of differential pulse-code modulation (DPCM) that varies the size of the quantization step, to allow further reduction of the required data bandwidth for a given signal-to-noise ratio.
02:51 < maaku> the variant used in the device is 48kHz, 4-bit per sample, which is typical for use in telephony with a high-noise line
02:51 < chris_99> can you use a higher number of bits?
02:52 < maaku> this thing has zero configurability :P
02:52 < maaku> you have to run some binary blob to set the local time, and that's it
02:52 < chris_99> oh heh
02:52 < maaku> I've seen student projects that have better UX
02:53 < chris_99> lol
02:53 < maaku> but for the purpose of -voice recording- it's spot on in their codec choices I think
02:53 < maaku> I would like to get a Pebble TIme 2 though, when they come out.
02:54 < maaku> It would be nice to run on a more powerful device, and do smart codec switching
02:54 < maaku> As well as pipe the mic out through bluetooth.
02:55 < maaku> purvaisive surveillance is still some years away though, even for 3 letter agencies
02:56 < chris_99> alternatively, get a bowler hat, mount this on top - https://www.amazon.co.uk/R%C3%98DE-VideoMic-Directional-On-Camera-Microphone/dp/B0007U9SOC
02:56 < chris_99> (i've got that mic for video stuff, works pretty nicely, i plug into my slr)
02:58 < ebowden> kanzure: http://www.the-scientist.com/?articles.view/articleNo/45760/title/Gen9-Announces-Next-Generation-of-the-BioFab--DNA-Synthesis-Platform-/
03:03 < archels> maaku: so that's >4 bits effectively of resolution per sample, compressed to 4 bits per sample on average using some cleverness, right?
03:03 < maaku> right
03:04 < maaku> er, information science wise it is absolutly <=4 bits
03:04 < maaku> but it's a pretty damn good 4 bits
03:04 < maaku> with much better quality than one might expect "4 bit audio" to have
03:04 < maaku> it does decompress to either 8- or 12-bit audio stream (I forget which)
03:06 < maaku> chris_99: i could use a bowler hat
03:06 < chris_99> heh
03:06 < archels> neat
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03:08 < TMA> an easy transformation on audio is to measure the intensity in logarithmic scale -- human ear perceives logarithmically. you get more faithful sound with 16 points logarithmically spaced than 16 points linearly spaced
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03:10 < maaku> TMA: my understanding of the compression codec used here is that the next 16 points (4 bits) is logarithmically spaced, but also dependent on the last N samples in some way
03:10 < maaku> so as to provide better coverage for where the next sample is likely to be, on typical (voice) inputs
03:12 < chris_99> how does that work then out of interest, as ADCs would be producing linearly spaced output wouldn't they?
03:12 < maaku> i don't know details :( see wiki link above
03:15 < ebowden> Does anyone here have any idea how common cancer cells that don't produce more lactate than their non-cancerous counterparts are?
03:30 < TMA> in the same way digital images would benefit from logarithmic scale of the samples - the difference between say (1,1,1) and (2,2,2) is (perceived) much greater than between (254,254,254) and (255,255,255)
03:33 < TMA> (that's why the "better" image manipulation programs use 16 bit per channel or a floating point number -- the artifacts from quantization are less visible then)
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03:49 < chris_99> TMA, but i still don't get how it's better if the ADC is producing say 16 bit linear output, how does converting to 16 bit logarithmic improve things?
03:51 < TMA> chris_99: 16 bit linear -> 4 bit logarithmic
03:51 < chris_99> aren't you throwing away data then?
03:52 < TMA> chris_99: I am. but the result is arguably better (from the human perception point) than 16->8 linear
03:54 < chris_99> ah i think i get you now
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05:00 < nsh> what does hplus think of Persinger? (God helmet chap)
05:01 < nsh> https://neurocogconsultants.app.box.com/s/l9f7tld3yjny4b00eqbq
05:01 < nsh> .wik Thixotropic
05:01 < yoleaux> "Thixotropy is a time-dependent shear thinning property. Certain gels or fluids that are thick (viscous) under static conditions will flow (become thin, less viscous) over time when shaken, agitated, or otherwise stressed (time dependent viscosity)." — https://en.wikipedia.org/wiki/Thixotropic
05:01 < nsh> Thixotropic Phenomena in Water: Quantitative Indicators of Casimir-Magnetic Transformations from Vacuum Oscillations (Virtual Particles)
05:01 < nsh> is he onto something that isn't braincrack?
05:02 < nsh> what's the O-H distance?  oxygen hydrogen bond spacing?
05:02 < nsh> i guess
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08:51 < pasky> http://www.theregister.co.uk/2016/07/03/mri_software_bugs_could_upend_years_of_research/?mt=1467666616578
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11:01 < kanzure> maaku: yeah we can do some custom wearable electronics for audio recording. i think we should aim for a general framework for adding lots of microphones and accelerometers to the different microphones. and some stupidly long battery life (even if it increases weight).
11:01 < nmz787> .tell ebowden 3 cents a bp is nice compared to prior years prices... but I wouldn't call it breakthrough... we still don't have genomes or operons at a disposable cost
11:01 < yoleaux> nmz787: I'll pass your message to ebowden.
11:01 < nmz787> I thought they were referring to this: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149774
11:01 < nmz787> .title
11:01 < yoleaux> PLOS ONE: Rapid Synthesis of a Long Double-Stranded Oligonucleotide from a Single-Stranded Nucleotide Using Magnetic Beads and an Oligo Library
11:01 < nmz787> looks quite like something we talked about in here
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11:03 < kanzure> i also think we should put some (small) amount of thought into full-conference audio recording (for all the chatter) even if not all of the participants are wearing the device (i suppose the first conference to deploy this at would be one that discusses this concept, ha ha)
11:03 < kanzure> re: audio codec questions, i suggest asking gmaxwell
11:04 < kanzure> nmz787: soo i mentioned your proposal and there was no specific response to that. i think that it's a good idea. i think that HGP could fund projects like that (and others). but things are early stage at the moment.
11:04 < kanzure> nmz787: and we have a good opportunity to define a big chunk of how that works.
11:09 < kanzure> fenn: i have offered to pay maaku to work on some machine learning audio transcription stuff.   if you have ideas on that, i am sure maaku will listen.  (mostly i think the bottleneck is the machine learning portion for now.)
11:09 < nmz787> kanzure: ok, keep me posted as new things arise
11:09 < kanzure> and, as i said, some electronics would make sense at some point, although i'm more interested in the bottleneck
11:09 < kanzure> nmz787: well i also need ideas i think.
11:09 < nmz787> kanzure: more ways to approach the same problem, or other aspects?
11:09 < kanzure> fenn: btw we should schedule a time for you to meet with andrew and me while i am here.
11:10 < nmz787> or like, how to actually get it done?
11:10 < kanzure> nmz787: i mean "here is a few hundred million dollars, how do you want to run HGP?"
11:11 < kanzure> there is a meeting at georgia tech in a few weeks for semisynbio
11:12 < nmz787> I wouldn't mind attending
11:12 < nmz787> I could probably use my employer's name to get in... if needed
11:30 < kanzure> you might have more luck than me on that front
11:39 < nmz787> kanzure: are you talking about this one: https://www.src.org/calendar/e006096/
11:40 < nmz787> says by invitation only
11:40 < nmz787> we have lots of tie-in with GA Tech, so I might be able to figure something out
11:42 < kanzure> yes that's the one (he said invite only which is why i thought maybe you would have more luck)
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11:42 < kanzure> (or i can probe more)
11:42 < kanzure> what's a good way to geotag location on audio recordings without access to a phone
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11:44 < kanzure> nmz787: fenn: also, it has been requested that we provide a one-paragraph writeup of why "controlled enzymatic dna synthesizer" is the most amazing thing ever from a technical perspective (e.g. to give to semisynbio or other groups)
11:45 < kanzure> i was pointing out that iteration cycles need to get pretty short, gutenberg press (except better because gutenberg press was not widely distributed or usable by anyone other than a handful of people), and the importance of literacy both read and write. i think there are some other good reasons probably.
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11:49 < nmz787> well it seems amazing to me in its apparent technical feasibility: relatively straightforward fabrication and analytics; significantly reduced dependence on synthetic chemistry, preferring instead enzyme-based 'green chemistry'.
11:50 < kanzure> yes, should probably mention something about how absurdly low cost it is
11:50 < nmz787> cycle times seem like a 'given' for reducing something from a 4-car-garage space requirement to a finger-size (of course things take longer to get across the garage than from finger to finger)
11:50 < kanzure> and how assembly is a really inefficient step which is better to avoid
11:50 < nmz787> well that device still has an assembly portion
11:51 < nmz787> but it probably need'nt with optimization (things like deleting over-addition)
11:51 < kanzure> the idea behind controlled polymerase is that you should be able to print out a billion bp with only a handful of errors. i think this is an achievable target, without sequencing.
11:51 < kanzure> did you read the 2010 proposal?
11:51 < kanzure> pasted as link yesterday
11:51 < nmz787> but the assembly portion doesn't particularly concern me either, since it seems most of the problems arise when the DNA interacts with itself, screwing up ligase's gluing action
11:51 < kanzure> (not the 2011 proposal re: RNA polymerase)
11:52 < nmz787> so constraining the DNA so it can't fold onto itself should help a lot
11:52 < nmz787> the two page thing? that mentioned electronic polymerase control?
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11:55 < kanzure> yes
11:55 < nmz787> the electronic stop-polymerase paper? seems reasonable enough... I almost said it could be reasonable to think polymerase was 'security hardened' such that it wouldn't be susceptible to electronic interference... but then I realized of course they are susceptible, otherwise specific buffers wouldn't change the behaviour/incorporation-rate/fidelity
11:56 < nmz787> so I'd look at those kind of papers to try and get an idea of how to do the same with a signal generator
11:56 < kanzure> http://www.theatlantic.com/magazine/archive/2012/11/hacking-the-presidents-dna/309147/
11:56 < kanzure> nmz787: oh good point re: buffers. yeah.... probably a lot of weird buffer mixtures have been found by now.
11:58 < kanzure> at $1M for 1M bp, you really can't do anything.   you require thousands or millions of genome-length dna fragments before you can do regular programming and experimentation. "right the first time" should not be the expectation.
11:58 < kanzure> i think the demand for short dna is actually going to be always less than the demand for superlong genome-length dna
11:59 < nmz787> also particularly beautiful I think about what I proposed (or other enzymatic methods) is that it is all water based meaning we don't have to worry about moisture-free gas and solvents and other pain in the ass to keep track of shit
11:59 < kanzure> (hence, you need not the ability to print one genome, but thousands or millions worth of genomes of bp)
11:59 < nmz787> kanzure: actually short DNA is big-biz for diagnostics and shit
11:59 < nmz787> PCR assays
11:59 < kanzure> meh
11:59 < nmz787> probably tons of short DNA going into medical trials
11:59 < nmz787> I think the tide will turn soon enough though
11:59 < nmz787> price-dependent
11:59 < kanzure> well, what do you consider to be short, though
12:00 < kanzure> primers? sure they are useful.   but polymerase can copy long fragments of dna for a good reason :).
12:00 < nmz787> for medical trials I'd guess less than 200 bp
12:00 < nmz787> gene or operon length is still pretty short to me
12:01 < kanzure> if everything is "one shot and you're done" then nobody is going to try unique constructions without having someone else front the cost of the experimentation
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12:04 < nmz787> kanzure: are you just talking rhetorically? isn't this obvious to anyone wanting to hack synbio?
12:06 < kanzure> it's not obvious to them
12:06 < kanzure> it's a request to write down painfully obvious things like that, yeah
12:06 < nmz787> huh
12:06 < nmz787> fucking engineers
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12:08  * kanzure shrugs
12:17 < nmz787> the reality of engineering industry is definitely not what I expected as a tech-enamored teenager
12:19 < kanzure> you didn't read dilbert?
12:20 < nmz787> I thought he was an office worker, I assumed they were not the same as tech workers
12:25 < kanzure> note taking tool thingy https://github.com/rolandshoemaker/theca https://news.ycombinator.com/item?id=12035431
12:27 < xentrac> nmz787: I wonder if we can make a better engineering industry
12:27 < chris_99> kanzure, looks cool, do you use Rust out of interest?
12:27 < kanzure> no
12:28 < kanzure> but andytosh1 does, you could bug him about rust stuff
12:28 < chris_99> aha cool, i've been playing a bit with it for some simple RPC network stuff, and a GTK interface
12:28 < nmz787> xentrac: probably we can only 'do our part' there are millions of other people in this system... and I don't expect to be able to radically shift this too much... maybe if anything we could lead a company that sets an example or something
12:29 < xentrac> yeah, I think it's feasible to start or take over a company
12:29 < xentrac> there might be other approaches that are more effective
12:30 < xentrac> education, say
12:35 < nmz787> it could also simply be a side-effect of human intelligence/memory being limited
12:35 < nmz787> AI managers might turn things around, idk
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12:55 < nmz787> .title http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156905
12:55 < yoleaux> PLOS ONE: Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach
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13:34 < kanzure> "Time for another human genome project?" (2012) http://www.huffingtonpost.com/andrew-hessel/human-genome_b_1345842.html
13:36 < kanzure> https://en.wikipedia.org/wiki/Human_Genome_Project_-_Write
14:04 < CaptHindsight> kanzure: since that project you mentioned from China wants to print long oligos 100K-millions are they planning on swapping several genes at a time or just doing it to do it?
14:06 < kanzure> there should be a traveling microscopy zoo
14:06 < kanzure> CaptHindsight: well, human genome project is doing it to synthesize just 1 genome (one dna molecule), but yes the idea is that we want lots of dna because we have many many projects to try
14:07 < CaptHindsight> kanzure: there a lot of junk in there that doesn't have to be printed every time
14:08 < kanzure> "human" genome synthes is because it gets people interested
14:08 < kanzure> there's lots of things to print dna for
14:08 < CaptHindsight> yeah I know
14:08 < CaptHindsight> I'm just saying why clone the whole drive if you're just swapping a few files?
14:08 < kanzure> in those cases, you can use crispr for gene editing or gene surgery
14:09 < CaptHindsight> I think it makes sense even if you're swapping out several chromosomes
14:10 < CaptHindsight> unless we discover that there's more to the junk that meets the eye
14:11 < kanzure> yes there's a use to the junk
14:12 < CaptHindsight> a femtoliter inkjet will print sub micron drops
14:12 < kanzure> cool.
14:12 < kanzure> btw someone mentioned that electrowetting of micron-sized drops doesn't work
14:13 < kanzure> customarray went out of business
14:13 < kanzure> and twist biosciences is doing my flooding idea, apparently
14:13 < CaptHindsight> so you'll be able to to get about a full genome on one slide
14:16 < CaptHindsight> the inkjet is kind of klunky in my opinion but it will be a good gen1-2 demo
14:17 < CaptHindsight> I'm setting up a new lab now just for DNA
14:19 < CaptHindsight> I see there being more work in building some of the tools to mass produce vs just printing an entire genome
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14:27 < kanzure> CaptHindsight: sure.  i think assembly is a big problem.
14:27 < kanzure> from each individual fragment
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14:53 < kanzure> fenn do you want to visit autodesk pier9
15:00 < kanzure> hgp-write website http://engineeringbiologycenter.org/
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15:51 < nmz787> kanzure: do they really want to try and condense all the chromosomes into 1 megachromosome?
15:53 < nmz787> kanzure: as far as I knew, twist isn't doing basic-synthesis
15:53 < nmz787> I thought they were only doing microwell gibson or something
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16:05 < kanzure> they are doing synthesis and maybe some assembly
16:06 < ebowden> That 3 cents per bp team?
16:06 < yoleaux> 18:01Z <nmz787> ebowden: 3 cents a bp is nice compared to prior years prices... but I wouldn't call it breakthrough... we still don't have genomes or operons at a disposable cost
16:07 < ebowden> I call them team 3 cent.
16:08 < ebowden> GOD having them at disposable cost would be awesome.
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17:18 < fenn> yes i would like to visit autodesk
17:19 < fenn> i think i have been to their old location on market street
17:19 < fenn> anyway it would be fun to meet up
17:24 < kanzure> what is your sleep schedule
17:25 < fenn> got up around 2 pm but i'm having trouble sleeping for stupid reasons
17:27 < fenn> "someone mentioned that electrowetting of micron-sized drops doesn't work" did they say why?
17:28 < fenn> btw 1 micron diameter drop is like 0.25 femtoliters
17:28 < fenn> i was imagining somewhat larger drops
17:30 < fenn> say 50 micron (65 picoliter)
17:38 < fenn> i thought it was common knowledge that fMRI was mostly bunk
17:44 < kanzure> evaporation
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18:02 < streety> Doesn't electrowetting work beneath oil as well as air? Wouldn't that resolve the evaporation issue?
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18:47 < kanzure> er... yes. probably.
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21:20 < nmz787> fenn: something kanzure posted (I think) said more like 0.5 fL
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21:48 < kanzure> autodesk bought eagle?
22:01 < kanzure> jcorgan is "am trying to find out the current state of the art for homebrew IR and NMR"
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22:02 < night> huh
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--- Log closed Wed Jul 06 00:00:49 2016