--- Log opened Mon Sep 25 00:00:28 2017 00:02 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 252 seconds] 00:21 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 00:44 < nmz787> https://www.nature.com/articles/ncomms7222 00:44 < nmz787> .title 00:44 < yoleaux> Entropic cages for trapping DNA near a nanopore | Nature Communications 00:44 < nmz787> "Figure 8: Enzymatic cutting of trapped DNA." 01:22 < nmz787> .wik electro-olfactogram 01:22 < yoleaux> nmz787: Sorry, that command (.wik) crashed. 01:25 < nmz787> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5154552/ 01:25 < nmz787> Direct Analysis of Gene Synthesis Reactions Using Solid-State Nanopores 01:45 -!- CRM114 [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 02:22 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 252 seconds] 02:29 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has joined ##hplusroadmap 02:38 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap 02:47 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 255 seconds] 02:51 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 02:51 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 02:56 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 252 seconds] 02:58 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 03:00 -!- Traumschule [~traumschu@185.104.184.179] has joined ##hplusroadmap 03:43 -!- preview [~quassel@2407:7000:842d:4000::3] has quit [Ping timeout: 246 seconds] 04:14 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 04:31 -!- cluckj [~cluckj@static-173-59-27-112.phlapa.ftas.verizon.net] has quit [Quit: Leaving] 04:35 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-ngdquxzngijpormq] has joined ##hplusroadmap 04:41 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has quit [Remote host closed the connection] 04:53 -!- TinKode [~TinKode@unaffiliated/tinkode] has joined ##hplusroadmap 05:02 -!- TinKode [~TinKode@unaffiliated/tinkode] has quit [Quit: TinKode] 05:06 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 05:29 -!- TinKode [~TinKode@unaffiliated/tinkode] has joined ##hplusroadmap 05:33 -!- preview [~quassel@2407:7000:842d:4000::3] has joined ##hplusroadmap 05:36 -!- TinKode [~TinKode@unaffiliated/tinkode] has quit [Quit: TinKode] 06:48 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 255 seconds] 06:51 < kanzure> "auto-cycling proximity recording" from peng yin https://wyss.harvard.edu/high-fidelity-recording-of-molecular-geometry-with-dna-nanoscopy/ 06:51 < kanzure> "As proof-of-principle, the team designed multiple DNA probes in silico, and synthesized and attached them to molecular targets contained in the prescribed geometries of DNA origami nanostructures. Through this newly-engineered, DNA-directed biochemical mechanism, a record in the form of a barcoded DNA strand is synthesized on the structure if and only if two of these DNA probes are in close ... 06:52 < kanzure> ...enough proximity to each other (“proximity recording”). Records are released as they are synthesized, and later collected for sequence analysis." 06:52 < kanzure> ".. the approach functions as a ‘DNA nanoscope’, which uses specifically engineered DNA biochemistry to visualize target pairs in a molecular object.. " 06:52 < kanzure> "By using antibodies and other widely used agents to direct DNA probes to molecular targets, we could apply APR technology to decode the components and geometries of biological complexes. ... barcoding may enable us to one day follow, individually, thousands or millions of macromolecules in a biochemical pathway." 07:00 -!- mindsForge [~nak@174-26-65-3.phnx.qwest.net] has joined ##hplusroadmap 07:35 -!- delinquentme [~delinquen@142-254-104-244.dsl.dynamic.fusionbroadband.com] has joined ##hplusroadmap 07:43 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 07:44 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 248 seconds] 08:06 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 08:29 -!- gene-hacker [~tetrapod@CMU-943103.ANDREW.CMU.EDU] has joined ##hplusroadmap 08:29 < gene-hacker> https://livestream.com/viewnow/NIAC2017 08:29 < gene-hacker> NIAC symposium 08:29 < gene-hacker> current topic: flying UAVs into tornados 08:29 < gene-hacker> really cool 08:29 < mindsForge> tnx 08:31 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 248 seconds] 08:32 < kanzure> gene-hacker: here is a weird thing (using dna molecules to report data about the shape of molecular objects) https://wyss.harvard.edu/high-fidelity-recording-of-molecular-geometry-with-dna-nanoscopy/ 08:34 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-ngdquxzngijpormq] has quit [Quit: Connection closed for inactivity] 08:50 -!- mrdata [~mrdata@unaffiliated/mrdata] has joined ##hplusroadmap 08:56 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 09:11 < fltrz> kanzure: very interesting 09:15 -!- mrdata [~mrdata@unaffiliated/mrdata] has quit [Ping timeout: 264 seconds] 09:22 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Quit: Leaving.] 09:28 < gene-hacker> area of effect asteroid mining up now 09:30 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 09:41 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=b3227671 Bryan Bishop: fix link on index page >> http://diyhpl.us/diyhpluswiki/index/ 09:41 -!- mindsForge [~nak@174-26-65-3.phnx.qwest.net] has quit [Quit: Leaving.] 09:48 < kanzure> gene-hacker: let me know which talks i should type/transcribe later 09:58 < kanzure> re: autocyclic proximity recording using dna and barcodes, probably could do synaptic barcoding this way? you could pollute the entire (vitrified?) brain with dna and then sequence the complete connectome, assuming that nearby neurons are close enough that dna molecules can bind together. and that this could somehow bridge between synapses. 09:59 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 10:00 < kanzure> ( https://twitter.com/kanzure/status/912360801444524038 ) 10:01 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 10:04 < kanzure> .tw https://twitter.com/kanzure/status/912360801444524038 10:04 < yoleaux> @wyssinstitute @AdamMarblestone i wonder if this could be used for connectome sequencing. Synapses are large gaps, might need connecting objects? (@kanzure, in reply to tw:912303082356269056) 10:04 < kanzure> .tw https://twitter.com/kanzure/status/912362153004453888 10:04 < yoleaux> @wyssinstitute @AdamMarblestone Also sounds like this has the potential to detect receptors embedded in neuronal membranes.Gets put into giant graph of barcoded objects. (@kanzure, in reply to tw:912360801444524038) 10:14 < kanzure> dna synthesizer -> brain uploading. easy peasy. 10:17 -!- preview [~quassel@2407:7000:842d:4000::3] has quit [Ping timeout: 246 seconds] 10:21 < kanzure> how many barcodes would you need to label every item of interest in the brain? you need at least the number of neurons, synapses, and receptors. 10:26 < kanzure> so say 100 trillion synapses, and 1 million receptors per synapse (which is probably a low estimate?), is 1e20 objects, so at minimum you'd need 34 bp barcodes? let's say 36 bp to be safe. so that would require 4^36 unique dna barcode molecules. about 1e21 custom dna molecules. 10:29 < kanzure> that's about 100 trillion genomes worth of custom dna (assuming 1 Gbp per genome) 10:30 < kanzure> my $1/genome synthesis cost target does not accommodate this 10:31 < kanzure> in connectome sequencing schemes i believe the barcodes are randomly generated everywhere 11:14 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 11:19 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Remote host closed the connection] 11:32 < fltrz> urgh that APL+Win32 shit is one of the most cruft things I have seen 11:35 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 12:04 -!- mindsForge [~nak@174-26-65-3.phnx.qwest.net] has joined ##hplusroadmap 12:10 < nmz787> kanzure: it does appear like assembly software/algorithms have not scaled to GPUs yet... I guess that doesn't mean the existing algos' logic can't be baked into Silicon as-is 12:12 < nmz787> https://f1000researchdata.s3.amazonaws.com/manuscripts/12992/510dad5d-6960-42e6-823d-69d83330ec60_12012_-_carlos_lannoy.pdf?doi=10.12688/f1000research.12012.1 12:12 < nmz787> seems like a decent and recent review of diff programs for assembly, also maybe reviewing the errors nanopore seq produces (for encoding idea generation) 12:14 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 12:14 < kanzure> well it might simply be the case that nobody has formulated the problem into a form that GPUs are good at handling 12:14 < kanzure> there are all sorts of clever ways to force GPUs to do your dirty nasty laundry 12:14 < kanzure> like encoding data into textures 12:16 < kanzure> (it might also be the case that the problem is fundamentally a bad fit for GPUs though) 12:17 < kanzure> http://homolog.us/blogs/blog/2013/05/24/gpu-and-fpga-accelerated-bioinformatics-algorithms/ 12:30 -!- delinquentme [~delinquen@142-254-104-244.dsl.dynamic.fusionbroadband.com] has quit [Ping timeout: 240 seconds] 12:34 < nmz787> http://ieeexplore.ieee.org/document/6617698/?reload=true&arnumber=6617698 12:34 < nmz787> .title 12:34 < yoleaux> CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing - IEEE Journals & Magazine 12:35 < kanzure> ahem, https://scholar.google.com/scholar?cites=3424428260121303502&as_sdt=5,44&sciodt=0,44&hl=en 12:36 < nmz787> FPGA papers could be promising for porting to ASIC 12:36 < nmz787> I might have meant that instead of GPUs 12:37 < nmz787> oops 12:39 < kanzure> i would be surprised if there is no general cuda-to-asic thing 12:39 < kanzure> i guess cuda implementation is proprietary. but still.. 12:46 < nmz787> https://rd.springer.com/chapter/10.1007/978-3-319-56258-2_25 12:46 < nmz787> FPGA Implementation of a Short Read Mapping Accelerator 12:47 < kanzure> my guesstimate is that the bottleneck is on-chip memory. gotta make deal with DRAM manufacturer. 12:47 < kanzure> or do custom board with lots of RAM 12:55 -!- delinquentme [~delinquen@184.250.69.92] has joined ##hplusroadmap 13:21 -!- delinquentme [~delinquen@184.250.69.92] has left ##hplusroadmap ["Leaving"] 13:24 -!- cluckj [~cluckj@static-173-59-27-112.phlapa.ftas.verizon.net] has joined ##hplusroadmap 13:55 -!- traumschule_ [~traumschu@185.104.184.179] has joined ##hplusroadmap 13:59 -!- Traumschule [~traumschu@185.104.184.179] has quit [Ping timeout: 264 seconds] 14:36 -!- CRM114 [~urchin@unaffiliated/urchin] has quit [Remote host closed the connection] 14:37 < kanzure> "FCUDA: Enabling efficient compilations of CUDA kernels onto FPGAs" http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.160.5661&rep=rep1&type=pdf 14:37 < kanzure> cc nmz787, maaku 15:22 < kanzure> fenn: any wish list items for a report to semiconductor industry people about dna and dna synthesis? "author's prerogative" gives me some wiggle room to include whatever as long as it's relevant. and i haven't spent enough time thinking exactly what to include. 15:23 < kanzure> for example, one item that i included is that i mentioned the estimated fabrication costs for the inkjet dna synthesizer that CaptHindsight quoted-- i know it's only a part of the whole project, but i think that sort of number is very interesting to include in this report (note that i also added lots of disclaimers like "hobby scale"). i also mentioned 'permissive licensing' there. 16:11 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 240 seconds] 16:12 -!- gene-hacker [~tetrapod@CMU-943103.ANDREW.CMU.EDU] has quit [Ping timeout: 240 seconds] 16:12 < kanzure> i wonder if genehacker has been indoctrinated into hod lipson's lab yet 16:26 < docl> .title https://arc.aiaa.org/doi/abs/10.2514/1.62412 16:26 < yoleaux> An Error Occurred Setting Your User Cookie 16:27 < kanzure> "Passive Sorting of Asteroid Material Using Solar Radiation Pressure 16:27 < kanzure> " 16:27 < kanzure> "This paper analyzes the feasibility of manipulating asteroid material by means of solar radiation pressure. A novel method is proposed for passively sorting material as a function of its grain size or density, where solar radiation pressure is used as a passive in situ mass spectrometer. A simplified analysis shows that, in principle, this method allows an effective sorting of regolith ... 16:27 < kanzure> ...material. This could have immediate applications for a sample return mission, and for industrial-scale in-situ resource utilization to separate and concentrate regolith according to particle size or composition." 16:27 < kanzure> docl: did you watch the NIAC presentations today? 16:27 < docl> no 16:28 < kanzure> https://livestream.com/viewnow/NIAC2017 16:28 < docl> Thanks 16:28 -!- Aurelius [~cpopell@50.35.79.117] has joined ##hplusroadmap 16:31 < docl> What I was thinking wrt the above paper, if it's possible to use solar light pressure like that in space, why not use it in a vacuum chamber on earth? Rare isotopes are super valuable, and you could possibly meet the energy budget for the separation with passive solar 16:31 < kanzure> really high vacuum is expensive 16:35 < kanzure> also i think you are limited on total mass you can really pump down to high vacuum 16:35 < kanzure> i'm making this up. i haven't checked. 16:49 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 16:57 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has quit [Ping timeout: 240 seconds] 16:59 < JayDugger> Acres and acres of hard vacuum for free. On the Moon. 16:59 < JayDugger> Transportation not covered. 17:00 < fltrz> lol the todarand webpage suggests they intend to license the algorand+todashit frankenstein... how does that work? will it be open source? if not then back to trusted. if yes open source, then what prevents people from forking/reusing the interesting (algorand) bits of the codebase? 17:02 < docl> is hard vacuum really a thing we need for this isotopic sorting scheme? seems like it works at the dust particle level. seems like you could probably steer dust particles through an argon atmosphere 17:03 < fltrz> unless they intend draconian DMCA style intimidation of people reusing their tech 17:04 -!- gene-hacker [~tetrapod@c-24-131-17-249.hsd1.pa.comcast.net] has joined ##hplusroadmap 17:12 < kanzure> gene-hacker: https://arc.aiaa.org/doi/abs/10.2514/1.62412 17:12 < kanzure> gene-hacker: docl was talking about it earlier 17:25 -!- mrdata [~mrdata@unaffiliated/mrdata] has joined ##hplusroadmap 17:51 -!- JayDugger [~jwdugger@47.185.237.246] has quit [Quit: Leaving.] 18:31 -!- mrdata [~mrdata@unaffiliated/mrdata] has quit [Read error: Connection reset by peer] 18:48 -!- gene-hacker [~tetrapod@c-24-131-17-249.hsd1.pa.comcast.net] has quit [Ping timeout: 248 seconds] 18:50 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 19:03 -!- balrog [~balrog@unaffiliated/balrog] has quit [Ping timeout: 248 seconds] 19:14 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 19:37 < heath> it was mentioned today that agilent's patent expires this year 19:37 < heath> not sure which one though 19:37 < heath> quick search for agilent and array 19:37 < heath> https://www.google.com/patents/US6545758 19:37 < heath> http://www.google.sr/patents/US20040101894 19:37 < heath> https://www.google.com/patents/US20060210997 19:38 < heath> https://www.google.com/patents/US9023601 19:45 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:45c5:d001:ce75:13c6] has joined ##hplusroadmap 19:45 < heath> i imagine this isn't what he's talking about, but possibly useful regardless: https://patents.google.com/patent/US5472672A/en?q=dna+synthesis&q=array&sort=old 19:47 < kanzure> their patent for inkjet dna synthesis + array stuff? 19:48 < heath> possibly, i'll followup with him tomorrow if it's not found by then 19:50 < kanzure> heath: yashgaroth: checkout the dna nanoscopy madness in the logs http://gnusha.org/logs/2017-09-25.log 19:59 < yashgaroth> pretty cool 19:59 < yoleaux> 20 Sep 2017 17:20Z yashgaroth: prader-willi syndrome seems to indicate that chromosome 15 is not really necessary 20:00 < yashgaroth> I think that's only part of chromosome 15 20:02 < heath> https://patents.google.com/?assignee=Agilent+Technologies%2c+Inc.&after=19951230&sort=old 20:02 < heath> https://patents.google.com/patent/US6875620B1/ 20:02 < heath> https://patents.google.com/patent/US6183067B1/ 20:07 < heath> https://patents.google.com/patent/US6458583B1/ 20:07 < kanzure> yashgaroth: aww don't burst my bubble like that. hm. 20:08 < kanzure> if we sequence literally everything i'm sure we'll find someone/something that is missing its usual chromosomes and seems to be doing OK 20:08 < kanzure> minus dna extraction errors.... 20:20 -!- ensign [~ensign@2001:41d0:8:d711::1] has quit [Ping timeout: 255 seconds] 20:30 -!- ensign [~ensign@2001:41d0:8:d711::1] has joined ##hplusroadmap 20:40 -!- traumschule_ [~traumschu@185.104.184.179] has quit [Ping timeout: 252 seconds] 21:41 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] 21:55 -!- mrdata [~mrdata@unaffiliated/mrdata] has joined ##hplusroadmap 21:59 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 22:13 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:45c5:d001:ce75:13c6] has quit [Quit: Leaving] 22:22 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 22:23 < fenn> you don't need custom dna sequences for random barcodes, probably 22:24 < fenn> also it would be nice if each individual cell had its own barcode which was appended to each synapse's barcode 22:24 < fenn> much less data crunching after the fact 22:25 -!- andytoshi [~apoelstra@unaffiliated/andytoshi] has quit [Ping timeout: 260 seconds] 22:25 -!- andytoshi [~apoelstra@wpsoftware.net] has joined ##hplusroadmap 22:25 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 252 seconds] 22:27 < fenn> it would also be nice to have time stamping 22:28 < fenn> per day time stamps ought to be good enough for brain backups 22:43 < fenn> docl: silex is better but not the same mechanism, it selectively ionizes only the target isotope https://en.wikipedia.org/wiki/Separation_of_isotopes_by_laser_excitation 22:43 < fenn> seems to be much consternation about silex because it works so well 22:49 < fenn> should i know what toda or algorand are? 22:49 < fenn> seems like yet another altcoin 22:50 < fenn> this time with academic backing 23:16 < fenn> "your chance of being selected for a reward is based on the number of coins (algos) you own or otherwise set aside. The more algos you have, the better chance you have of getting picked. Once you know you are selected as a proposer, you create a block and then propagate it to the network along with a hash proof ... The proposer with the smallest hash proof (again, random) is the one to present 23:16 < fenn> the next candidate block." 23:20 < fenn> so far seems pretty normal 23:20 < fenn> 30 simultaneous patent applications in the US alone seems a bit much 23:55 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap --- Log closed Tue Sep 26 00:00:28 2017