--- Log opened Sat Sep 30 00:00:32 2017
00:16 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
00:20 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-cnliafhqrovfiafg] has quit [Quit: Connection closed for inactivity]
01:50 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection]
02:03 -!- rpifan [~rpifan@73.106.75.66] has joined ##hplusroadmap
02:15 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap
02:26 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap
02:39 -!- rpifan [~rpifan@73.106.75.66] has quit [Ping timeout: 248 seconds]
02:49 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap
03:37 < kanzure> https://scholar.google.com/scholar?as_ylo=2016&hl=en&as_sdt=5,44&sciodt=0,44&cites=7419634282531968460&scipsc=
03:39 < kanzure> yes the report is missing an enzyme section (it was sort of weird that molecular assemblies inc. was the extent of the discussion around proteins)
04:25 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has joined ##hplusroadmap
04:30 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 248 seconds]
04:48 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds]
04:52 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap
05:51 -!- traumschule [~traumschu@mehl.schokokeks.org] has quit [Quit: Reconnecting]
05:51 -!- traumschule [~traumschu@mehl.schokokeks.org] has joined ##hplusroadmap
05:56 -!- traumschule [~traumschu@mehl.schokokeks.org] has quit [Quit: Reconnecting]
05:56 -!- traumschule [~traumschu@mehl.schokokeks.org] has joined ##hplusroadmap
06:00 -!- traumschule [~traumschu@mehl.schokokeks.org] has quit [Client Quit]
06:00 -!- traumschule [~traumschu@mehl.schokokeks.org] has joined ##hplusroadmap
06:13 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap
06:39 -!- thxffo [SMD@gateway/shell/elitebnc/x-pxftiecwzmrojvcv] has quit [Ping timeout: 264 seconds]
06:40 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap
06:44 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 248 seconds]
06:48 < kanzure> apparently tetrahydrouridine is an inhibitor of cytidine deaminase
06:48 < kanzure> need peptide inhibitor tho
06:50 < kanzure> "Inhibition of α-helix-mediated protein–protein interactions using designed molecules" https://www.nature.com/nchem/journal/v5/n3/full/nchem.1568.html (2013)
06:50 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap
06:51 < kanzure> "Designing photoswitchable peptides using the AsLOV2 domain" http://www.sciencedirect.com/science/article/pii/S1074552112000798
06:52 < kanzure> coooool "Caged versions of the ipaA and SsrA peptides, LOV-ipaA and LOV-SsrA, bind their targets with 49- and 8-fold enhanced affinity in the light, respectively"
06:52 < kanzure> 48x is pretty good
06:56 < kanzure> "... Here, we set about to systematically benchmark the properties of four optical dimerizer systems, CRY2/CIB1, TULIPs, phyB/PIF3, and phyB/PIF6." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4277767/   although they didn't study timing (ugh)
07:00 < kanzure> hm the switching time of this LOV stuff does not seem to match the 100 ms/bp scroll rate through a slowed nanopore
07:01 < kanzure> seems closer to ~1 sec switching time
07:12 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 248 seconds]
07:47 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap
08:15 -!- NikopolSohru [~NSohru@5.79.76.32] has joined ##hplusroadmap
08:16 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 248 seconds]
08:17 -!- thxffo [SMD@gateway/shell/elitebnc/x-egnouibaknsmmdzr] has joined ##hplusroadmap
08:18 -!- rpifan [~rpifan@73.106.75.66] has joined ##hplusroadmap
08:20 -!- rpifan [~rpifan@73.106.75.66] has quit [Client Quit]
08:35 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has quit [Ping timeout: 258 seconds]
08:57 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 260 seconds]
09:01 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=1aca83b6 Bryan Bishop: various other gene editing proteins >> http://diyhpl.us/diyhpluswiki/gene-editing/
09:12 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 255 seconds]
09:24 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap
10:19 < kanzure> what are the numbers on archival tape data storage? want density, write speed, cost per bit written, etc.
10:19 < kanzure> s/what are/where are
10:23 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap
10:25 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap
10:28 < fenn> LTO-6 2.5TB $27 https://www.tapeandmedia.com/sony-lto-6-tape-ultrium-tapes.asp = 1.35e-12 USD/bit
10:28 < fenn> ultrium-7 750MB/s
10:30 < fenn> cartridge size: 102mm x 105.4mm x 21.5mm = 8.65e16 bit/m^3   210g = 9.5e13 bit/kg
10:31 < kanzure> so $0.006/second in terms of total data write capacity and write cost?
10:32 < kanzure> $0.006 per 750MB-second
10:32 < fenn> sorry lto-6 may actually be closer to 400MB/s
10:32 < fenn> it's unclear whether you can use lto-6 tapes in a ultrium-7 drive
10:33 < kanzure> whatever, i only care about rough order of magnitude, that's hardly 50% difference
10:35 < kanzure> trying to figure out what would be competitive cost for 1 kilobit/second write
10:36 < kanzure> hm my $0.006/(750MB-second) is wrong because it does not take into account things like power cost and yearly maintenance (gotta spin the tapes or else they break or something?)
10:37 < fenn> tapes are fine on a shelf
10:38 < fenn> if you want to read them you have to have a robot
10:40 < kanzure> to make 1 kilobit/second competitive on the cost front, you need 750 * 8 * 1e6 lower cost?
10:41 < kanzure> so a factor of 10 million
10:42 < kanzure> and even if that's true, then that's not enough because 1000 kilobits/sec is actually imposing a high temporal cost not just whatever dollar cost your technique has
10:42 < fenn> i'm getting more like 740 million
10:43 < fenn> 222 million with more realistic tape drive numbers
10:44 < kanzure> and that's just barely at cost of data write with tape. soo you need about another order of magnitude if you don't want to be eaten by whatever next year's tape advancements bring in performance..
10:54 -!- thxffo [SMD@gateway/shell/elitebnc/x-egnouibaknsmmdzr] has quit [Ping timeout: 258 seconds]
11:00 < kanzure> polymerase motion stuff http://diyhpl.us/~bryan/papers2/polymerase/Molecular%20events%20during%20translocation%20and%20proofreading%20extracted%20from%20200%20static%20structures%20of%20DNA%20polymerase%20-%202016.pdf
11:07 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 258 seconds]
11:07 < CaptHindsight> why would anyone want to store data in meatspace using one of the components of meat?
11:10 < kanzure> at some point you have to write into physical reality
11:11 < kanzure> virtual pagebuffers don't go on forever, no matter what the OS kernel says
11:14 -!- thxffo [SMD@gateway/shell/elitebnc/x-syerejokxbzjiexb] has joined ##hplusroadmap
11:21 < kanzure> "re: Zador: “While Zador’s group was successful in joining pre- and post- synaptic barcodes as a proof of concept, their initial experiments resulted in a high frequency of false positives. Further dilution of the PCR emulsion reduced this; however, they noted that it would also require scaling up SYNseq beyond practical limits for high throughput applications.”"
11:26 < CaptHindsight> meat is not a good storage medium, unless it's supposed to be edible
11:26 < kanzure> dna is one of the highest density data storage mediums we can actively work with
11:29 < CaptHindsight> gimmick
11:29 < CaptHindsight> look for better options
11:29 < CaptHindsight> is somebody funding this?
11:29 < kanzure> IARPA
11:30 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap
11:30 < CaptHindsight> i saw some articles on this nonsense
11:30 < CaptHindsight> i wonder who's behind it and why
11:30 < kanzure> see pm
11:32 < CaptHindsight> unless you want to store data in living things without anyone noticing
11:32 < kanzure> nah
11:34 < CaptHindsight> oh sure that a pm, but you post my quote on a website after wasting a week of my time  :)
11:34 < kanzure> heh i'm still hopin i can pay you to do cool things
11:35 < CaptHindsight> heh, actually somebody at the NIH saw it and contacted me
11:35 < CaptHindsight> so thank you
11:37 < CaptHindsight> they weren't making oligos in house yet
11:38 < kanzure> cool
11:41 < CaptHindsight> and it spooked some other customers away since they now knew that I knew too much about what they were doing
11:50 < kanzure> let me know what you think about the contents
12:03 -!- NikopolSohru [~NSohru@5.79.76.32] has quit [Ping timeout: 248 seconds]
12:04 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has joined ##hplusroadmap
12:24 -!- eb3c90 [~kvirc@host109-155-47-183.range109-155.btcentralplus.com] has quit [Quit: KVIrc 4.2.0 Equilibrium http://www.kvirc.net/]
12:41 -!- thxffo [SMD@gateway/shell/elitebnc/x-syerejokxbzjiexb] has quit [Ping timeout: 246 seconds]
12:46 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 255 seconds]
12:48 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 260 seconds]
13:02 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap
13:06 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
13:10 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Quit: Leaving.]
13:23 < kanzure> hmph
13:28 < kanzure> how about: ssDNA molecule with lots of functionalized fuzzy hairy stuff hanging off of it. and the chemistry is configured such that you optically induce a reaction that changes the underlying nucleotides. after flashing a light, the nucleotide is modified by the chemistry, which disconnects and floats off. the next nucleotide is protected by a cap. then you flash a light to remove the cap. ...
13:28 < kanzure> ...then you flash a light to choose the next nucleotide in the sequence.  the other bp need to be "non-reactive" until one side of their 'functionalized molecule' is missing an edge. so over time you are progressvely modifying that that single ssDNA molecule.
13:29 < kanzure> and the functionalized extra molecules hanging off of each nucleotide needs to be capable of changing the nucleotide to be any type, based on the light you shine at the reaction.
13:31 < kanzure> also, they don't need to be nucleotides, but they do need to be interpreted as nucleotides by polymerase so that when the molecule is copied it can be converted into a biologically-relevant dna molecule
13:35 -!- y0no_ [y0no@2001:bc8:212d:201:ff01::a] has quit [Ping timeout: 255 seconds]
13:42 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 258 seconds]
14:00 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap
14:27 < heath> i like this idea: 00:23 < kanzure> we need a general library of "string manipulation" methods to modify dna molecules. i thought it would have to be proteins that iteratively scan a molecule and update it, but now i'm not so sure.
14:32 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap
14:36 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap
14:41 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Read error: Connection reset by peer]
14:43 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
15:00 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection]
15:02 -!- y0no [y0no@2001:bc8:212d:201:ff01::a] has joined ##hplusroadmap
15:11 < kanzure> heath: here's the start of such a library http://diyhpl.us/wiki/gene-editing/
15:15 < kanzure> re: $6,000/human genome synthesis costs, "This writing is more focused on Genome editing than de Novo Synthesis. It's worth noting the lead author Raj Chajri  is an expert in Genome editing, but not De novo DNA Synthesis. They are sparse on detail accommodating Scale up of De Novo synthesis, citing an old paper from the lab from 2004 that was not designed to support gigascale synthesis. In  ...
15:15 < kanzure> ...fairness, George has tendency to make wild extrapolations that ignore fundamental limitations of present methodologies. Often this is not from a lack of understanding, but a lack of detail provided sufficient to support such claims/projections. I suspect this is the best explanation."
15:16 < kanzure> ????
15:25 < FourFire> sounds like someone being extremely charitable in order to not burn bridges.
15:26 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 240 seconds]
15:26 < kanzure> steel bridges don't melt bea--- er.. wait i've messed this up.
15:35 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap
15:45 -!- superkuh [~superkuh@unaffiliated/superkuh] has quit [Remote host closed the connection]
15:47 -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap
15:54 -!- y0no [y0no@2001:bc8:212d:201:ff01::a] has quit [Read error: Connection reset by peer]
15:58 -!- y0no [y0no@2001:bc8:212d:201:ff01::a] has joined ##hplusroadmap
16:19 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 248 seconds]
16:32 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 248 seconds]
16:59 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Quit: Leaving.]
17:00 -!- thxffo [SMD@gateway/shell/elitebnc/x-ysnvikkbyyupwhbn] has joined ##hplusroadmap
17:00 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
17:04 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 248 seconds]
17:16 -!- delinquentme [~delinquen@2602:306:ceb7:990:39c4:5d7a:2d39:b4f8] has joined ##hplusroadmap
17:20 < nmz787> $27 for 2.5TB isn't too much better than spinning discs? It seems like a 4-5X difference
17:20 < nmz787> how much are the tape recorders?
17:21 -!- delinquentme [~delinquen@2602:306:ceb7:990:39c4:5d7a:2d39:b4f8] has quit [Ping timeout: 258 seconds]
17:25 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap
17:29 < nmz787> delinquentme: have you seen the FIB docs?
17:30 < nmz787> delinquentme: http://diyhpl.us/~nmz787/pdf/smi3200/
17:30 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has joined ##hplusroadmap
17:36 < delinquentme> nmz787, lovely!  "scanning ion microscope"
17:36 < delinquentme> Yeah I guess you can image with it as well...
17:36 < delinquentme> whats it using for subtractive mfg?  was it berylium?
17:39 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection]
17:47 < nmz787> no, gallium
17:47 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 258 seconds]
17:47 < nmz787> usually used for TEM specimen prep
17:47 < nmz787> but also used in bio for nano microtome, when used with a SEM in the same chamber pointing at the same sample, from a different angle
17:48 < nmz787> oh, he left
18:21 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap
18:29 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Read error: Connection reset by peer]
18:34 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap
18:49 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap
18:57 < kanzure> hrm
19:03 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 258 seconds]
19:12 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap
19:19 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap
19:28 < kanzure> nmz787: this is the helixworks stuff https://openmoss.org/docs/MoSS.pdf
19:28 -!- atrus6 [~atrus6@72.241.82.247] has quit [Ping timeout: 240 seconds]
19:53 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 258 seconds]
19:56 -!- sachy [~sachy@nat.brmlab.cz] has quit [Ping timeout: 252 seconds]
20:21 -!- jaboja [~jaboja@jaboja.pl] has quit [Remote host closed the connection]
20:28 -!- night [~Adifex@unaffiliated/adifex] has quit [Ping timeout: 255 seconds]
20:30 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap
20:37 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap
20:38 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 240 seconds]
20:53 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap
21:08 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Remote host closed the connection]
21:10 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Quit: Leaving...]
21:16 < nmz787> yashgaroth: so the recA-like, how do you load a primer onto it?
21:17 < yashgaroth> it forms a nucleofilament of several monomers onto one primer, each monomer covers I think 4 nucleotides, and you need 5+ to form a stable filament
21:17 < yashgaroth> 5+ monomers that is
21:18 < nmz787> so you have the 5 monomers, and they don't associate unless there is a ssDNA/primer?
21:18 < yashgaroth> yeah
21:19 < nmz787> and then you can move that into a vat of dsDNA, and it will find the match after diffusing enough, right?
21:20 < yashgaroth> not so much diffusing, in the presence of dsDNA it'll process along the dsDNA using ATP
21:21 < nmz787> hmm, 1 ATP per base processed?
21:21 < yashgaroth> I don't think that's been investigated
21:22 < nmz787> so it will cruise inside the dsDNA, not just end-match?
21:22 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 258 seconds]
21:23 < yashgaroth> yeah it melts the strands
21:23 < nmz787> know of anything similar that only end-matches?
21:23 < nmz787> could the disabled/mutated cas9 thing that kanzure mentioned possibly be used?
21:24 < yashgaroth> how do you mean end matching, like something that'll only shove the primer into the end of a dsDNA fragment?
21:24 < nmz787> yeah
21:24 < nmz787> so the end can be used as an address
21:24 < nmz787> and you can quickly retrieve it
21:24 < yashgaroth> I mean, if it has homology to that part, it'll stop there...when we use it to amplify DNA it really only sticks the primer into the end of the amplicon
21:25 < nmz787> otherwise I guess you'd have to require the address to not be present in any other 'data'
21:25 < nmz787> hmm, ok, so it starts from the ends?
21:25 < yashgaroth> I don't think it necessarily starts at the end of a fragment since it's used for homologous recombination between chromosomes
21:26 < nmz787> if that was the case, then an address-like sequence would get chosen still, if it started with a non-matching address fragment
21:26 < nmz787> ah, mm
21:26 < nmz787> that would certainly work well for data-search
21:27 < nmz787> the ATP requirement is a bit questionable as far as overall energy requirements... but that is only because I don't have any idea of them compared to silcon data retrieval
21:27 < yashgaroth> I imagine it's pretty efficient, but note that it will burn ATP even without dsDNA present
21:28 < yashgaroth> could maybe mutate it to suck at dsDNA melting, to bias it toward ends
21:28 < nmz787> what happens if you starve it of ATP?
21:28 < nmz787> just stops twitching?
21:29 < yashgaroth> it dissociates; you can use ATP gamma S to keep it on the strands without performing the scanning I believe
21:30 < nmz787> it'll restart/reassociates with reintroduction of ATP?
21:30 < yashgaroth> mhm
21:31 < nmz787> hmm, how long does ATP gamma S poisoning work?
21:31 < nmz787> permanent or unless salt/ionic conditions change a lot?
21:31 < yashgaroth> until you have an excess of regular ATP, not sure how slowly it gets hydrolyzed by itself
21:33 < yashgaroth> typically you don't have the gamma S in there unless you want structural info, since I imagine it'll fuck with the enzyme at even low concentrations
21:55 -!- night [~Adifex@unaffiliated/adifex] has joined ##hplusroadmap
22:42 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-imdnawvjodvhfxso] has joined ##hplusroadmap
22:56 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has quit [Quit: Leaving]
23:05 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has quit [Ping timeout: 258 seconds]
23:44 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap
--- Log closed Sun Oct 01 00:00:33 2017