--- Log opened Tue Jan 30 00:00:38 2018
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01:32 < ebowden_> https://twitter.com/thelateempire/status/957527371221028865
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02:01 < brujo_biologica>  . /usr/bin/byobu-reconnect-sockets
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07:12 < kanzure> .tw
07:12 < yoleaux> a shitcoin startup called Prodeum just exitscammed with millions of investor dollars and left them the following message on their site https://pbs.twimg.com/media/DUnR8ffXkAAnsHM.jpg (@thelateempire)
07:12 < kanzure> meh
07:16 < mrdata> um, no
07:16 < mrdata> i heard they raised a total of $11
07:17 < mrdata> but they are gone like gonorrhea
07:26 < kanzure> http://www.sciencemag.org/news/2018/01/naked-mole-rats-defy-biological-law-aging "More—and older—mole rats are needed to be sure that the risk of dying really is flat, Finch argues"
07:42 < kanzure> .tw https://twitter.com/chiefynduom/status/958330649001291776
07:42 < yoleaux> @rtzmrmn @jimmysong this is 10,000 words on medium. however, listen to @kanzure perspective here: https://soundcloud.com/heryptohow/andrew-poelstra-bryan-bishop-and-brian-deery he gets it - serious people don't sit back and wait even though we predict something will happen on its own. you work to ensure that it happens (@chiefynduom, in reply to tw:958328541870833664)
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08:23 < ebowden_> https://twitter.com/thelateempire/status/957753017893302272
08:24 < kanzure> boring
08:24 < kanzure> don't be boring
08:27 < JayDugger> We can't all be famous on Twitter and Soundcloud. It would cheapen the distinction for those who are.
08:31 < kanzure> i'm not looking at his fame i'm looking at his boring irc messages and they are boringn
08:32 < ebowden_> I dared post about something bad happening with a shitcoin startup.
08:33 < JayDugger> Ah.
08:34 < kanzure> there's lots of bad shitcoin stuff out there
08:34 < kanzure> it shouldn't be surprisin that there's a high amount of fraud and malevolence in the world
08:34 < kanzure> or malware
08:36 < ebowden_> I heard a moronic "economist" say that cryptocurrencies provided no value, when I know for a fact that there are things that can only be purchased with them due to banks dumping people for their business being judged "risky".
08:37 < ebowden_> And they can be very fast ways of actually completing transactions.
08:37 < kanzure> uh why are you listening to economists?
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08:47 < ebowden_> (She believed that their only use was for crime.)
08:47 < ebowden_> It was on the television, and I was in the room.
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08:54 < fenn> dangerous crimethink
08:55 < fenn> better not add those numbers the wrong way
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10:32 < pasky> anyone in bay area up for a lunch?
10:36 < bluebear_> which bay? :-)
10:39 < pasky> the san francisco bay :)
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11:02 < bluebear_> sorry... too far away for me at this moment :'(
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11:10 < MrHindsight> https://www.nature.com/articles/nbt.4060
11:11 < MrHindsight> Nanopore sequencing and assembly of a human genome with ultra-long reads
11:12 < MrHindsight> asking in #Bioinformatics was near useless ...
11:13 < MrHindsight> what are the most popular applications and in what format do DNA sequencers use for their data?
11:18 < kanzure> fasta
11:19 < MrHindsight> https://en.wikipedia.org/wiki/List_of_open-source_bioinformatics_software
11:19 < kanzure> ya
11:20 < MrHindsight> a ton but how many are active projects
11:20 < kanzure> a lot of bioinformatics tools aren't active anymore
11:20 < kanzure> you could go look at the rotting remains of bioperl and biopython
11:21 < MrHindsight> is there some standard format for the data that most sequencers use?
11:22 < kanzure> fasta
11:23 < MrHindsight> https://en.wikipedia.org/wiki/FASTA_format
11:23 < kanzure> you could also look at formats used by e.g. protein databank (pdb) or https://reactome.org/
11:24 < kanzure> or genbank
11:25 < MrHindsight> nanopore ---> analog ----> A/D ---- a bit of signal processing ---> buffer, here's your string
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11:27 < kanzure> yes, that's how nanopore sequencing works
11:28 < kanzure> thought you knew
11:28 < MrHindsight> I do
11:28 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Cheap%20third-generation%20sequencing%20-%20nanopores%20-%20cyclodextrin%20-%20hemolysin%20-%202009.pdf
11:28 < MrHindsight> I'm just looking at formats
11:28 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Challenges%20in%20DNA%20motion%20control%20and%20sequence%20readout%20using%20nanopore%20devices%20-%202015.pdf
11:28 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Identification%20of%20single%20nucleotides%20in%20MoS2%20nanopores%20-%202015.pdf
11:28 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Nanopore%20Unzipping%20of%20Individual%20DNA%20Hairpin%20Molecules%20-%202004.pdf
11:28 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Reading%20DNA%20at%20single-nucleotide%20resolution%20with%20a%20mutant%20MspA%20nanopore%20and%20phi29%20DNA%20polymerase.pdf
11:28 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Sequence-specific%20detection%20of%20individual%20DNA%20strands%20using%20engineered%20nanopores%20-%20Howorka%20-%202001.pdf
11:28 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Slowing%20DNA%20translocation%20through%20a%20nanopore%20using%20a%20functionalized%20electrode%20-%202014.pdf
11:28 < kanzure> http://diyhpl.us/~bryan/papers2/bio/The%20potential%20and%20challenges%20of%20nanopore%20sequencing%20-%20Schloss.pdf
11:30 < MrHindsight> block of DNA data is in memory, what format should it be in or do I even bother
11:31 < kanzure> they just use strings
11:31 < kanzure> unless you mean the nanopore readings
11:32 < kanzure> in which case it's just capacitance measurements or something
11:32 < MrHindsight> after conversion to digital
11:33 < MrHindsight> wow, attitude from someone with no hands on
11:33 < MrHindsight> welcome to IRC
11:34 < kanzure> huh?
11:34 < kanzure> i've never reverse engineered a nanopore, not sure what these companies are actually doing
11:34 < MrHindsight> taking forever
11:35 < MrHindsight> it's almost like nobody is trying to get anything done except keep their old business models
11:40 < MrHindsight> REing what they do would probably cause brain damage
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13:34 < spurserh> @kanzure "10–20Gb per 48 hours"
13:34 < spurserh> @kanzure isn't that several thousand bases per second?
13:35 < spurserh> oh but this is sequencing, so that's not a big deal
13:43 < kanzure> yes, you can actually run dna through nanopores even faster but you can't probe it fast enough
13:44 < kanzure> "One way of framing an ambitious goal that involves doing it over and over again is to say let’s make every agricultural species, every industrial and microbial organism and every human transplant be resistant to every virus. Then you could do the same thing over and over again once you got good at it." - george church
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14:59 < kanzure> "A non-surgical approach for male germ cell mediated gene transmission through transgenesis" https://www.nature.com/articles/srep03430
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15:52 < FourFire> kanzure, did the calico study reveal *anything* we didn't already know?
15:55 < FourFire> I hate podcasts, reliable voice to text NNs which annotate seperate speakers when?
16:12 < maaku> certainly nanopores can be combined with micro fluidic chips into a sorting network
16:13 < maaku> wouldn't that allow arbitrary assembly by tossing random DNA (or RNA?) sequences through nanopores, and switching based on transcription such that two parts that need to join are placed together
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16:17 < maaku> I imagine probabilities make this annoying after a few thousand base pairs, but then you'd switch to sequence-specific ligation of DNA
16:19 < MrHindsight> maaku: either nobody is really trying to get any of this working beyond glacial speeds or they aren't sharing their research
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16:29 < kanzure> maaku: sorry what problem are you trying to solve? there have been proposals for droplet microfluidic devices for nanoscale droplets that carry around dna and liagate them with regular old chemistry.
16:29 < maaku> kanzure: full genome sequencing
16:29 < maaku> gah, synthesis
16:29 < kanzure> ok so your technique (of ligating small molecules together) is called a library approach
16:30 < kanzure> if you have a library of 8mers that's only 4^n n=8 items etc and then you ligate themm togteher in a certain order
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17:18 < nmz787> main reason you need to limit nanopore translocation today is the electrode placement, and lack of on-chip amplifiers and (maybe) signal conditioning
17:30 < nmz787> MrHindsight: gzip or 7zip is a format that is likely used...
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17:42 < MrHindsight> https://en.wikipedia.org/wiki/FASTQ_format since the quality is a concern since it's typically been so low
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17:46 < MrHindsight> nmz787: ^^
17:47 < MrHindsight> I guess I should patent nanopore and amp in one before the tech stalls for another 20 years
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19:23 < kanzure> blort
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20:10 < CaptHindsight> https://arstechnica.com/science/2018/01/pocket-sized-dna-reader-used-to-scan-entire-human-genome-sequence/
20:11 < CaptHindsight>  On its own, the nanopore sequence had an accuracy rate of only 92 percent.
20:11 < CaptHindsight> having multiple reads of the same sequence from the same machine boosted the accuracy above 97 percent
20:12 < CaptHindsight> Adding in the high-quality short reads to this boosted accuracy to 99.96 percent.
20:12 < nmz787> CaptHindsight: I can say some academics are already working on solid-state nanopore + nearby amp
20:12 < nmz787> CaptHindsight: that doesn't mean it's also patented tho
20:14 < nmz787> CaptHindsight: not sure what you're saying about FASTQ... you can still gzip/7zip that data. There's even a section in that wiki page on compression
20:14 < CaptHindsight> sure you can compress it
20:14 < CaptHindsight> the Q is for quality
20:15 < nmz787> CaptHindsight: also, that Oxford Nanopore isn't a solid-state nanopore, it's a bio-pore
20:15 < CaptHindsight> which to me is odd that all the sequencers did such a bad job that quality had to be factored in
20:15 < nmz787> well, it's more like the type of noise or errors that are intrinsic to the specific device
20:15 < CaptHindsight> yeah, they posted all the pores they tried in some story
20:16 < nmz787> the Oxford Devices for example, get better quality with newer firmware
20:16 < nmz787> so you can literally hope that they update the software/firmware before you start your experiment, and you might get better results after
20:16 < nmz787> they're using neural nets these days for Oxford
20:16 < nmz787> and or markov chains
20:17 < CaptHindsight> I'm just building my own
20:17 < nmz787> (I think and)
20:17 < nmz787> your own basecaller?
20:17 < CaptHindsight> pores on up to the USB connector
20:17 < nmz787> me too
20:18 < CaptHindsight> think you'll be done by 2030?  :)
20:18 < nmz787> yeah
20:19 < nmz787> I hope to get to POC in the next few years at least
20:20 < nmz787> further if I can convince my job to let me run some experiments internally, or get funding elsewhere to do it startup-mode
20:21 < nmz787> this is one of the approaches I'm considering starting with replication dx.doi.org/10.1039/c3nr06723h
20:22 < nmz787> via one of these http://diyhpl.us/~nmz787/pdf/Cost-Effective_Systems_for_Atomic_Layer_Deposition.pdf
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20:22 < nmz787> need to figure out materials compatibility though for the various layers
20:22 < nmz787> i.e. coefficient of thermal expansion
20:23 < nmz787> but also chemical compatibility with processing steps
20:25 < nmz787> i.e. if you deposit aluminum for nanochannels, grow oxide up, planarize, then add ITO for clear electrodes... will that all work at the various temps without cracking one or another... or when you go to dissolve the aluminum, will that also etch the ITO?
20:25 < nmz787> writing that constraint solver is a decent hurdle
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20:36 < CaptHindsight> https://www.nature.com/articles/nbt.4060
20:36 < CaptHindsight> Nanopore sequencing and assembly of a human genome with ultra-long reads
20:43 < CaptHindsight> https://nanoporetech.com/products/smidgion  <$1k ?
20:44 < CaptHindsight> not bad IF it works
20:44 < CaptHindsight> will it be crippled in some way?
20:44 < CaptHindsight> has been taking forever to be released
20:47 < nmz787> just less pores I think
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20:58 < CaptHindsight> https://store.nanoporetech.com/flowcells/spoton-flow-cell-mk-i-r9.html  they are selling the flow cells separately
20:59 < CaptHindsight> SDS : POTASSIUM FERROCYANIDE
20:59 < CaptHindsight> 5-10%
21:00 < CaptHindsight> in the 60's-70's that was still shipped in Chemistry sets
21:11 < nmz787> yeah, super small but ionic I think?
21:11 < nmz787> ionic/charged
21:12 < nmz787> I definitely remember that compound name
21:13 < nmz787> CaptHindsight: I was told by a user that the company originally requested the flowcell to be returned
21:13 < nmz787> not sure if by requested they meant they signed some agreement
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21:47 < CaptHindsight> nmz787: maybe that was just for the early production units
21:47 < CaptHindsight> it looks like they want this to be fairly high volume
21:48 < CaptHindsight> 100k's per year
21:49 < CaptHindsight> a much better pore and analog could easily be swapped in
21:49 < CaptHindsight> I wonder how hackable the controller is or in the case of the cell phone accessory version how open the interface is
21:51 < CaptHindsight> end goal loks like DNA ID for everyone and the end of privacy/anonymity
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22:29 < nmz787> my guess is the controller could be replicated easily, in addition to pore+analog you'd probably want some multiplexers/analog-switches so you reduce the pinout signal count and route things to off the shelf ICs
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--- Log closed Wed Jan 31 00:00:39 2018