--- Log opened Mon Jun 19 00:00:26 2017 00:04 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 00:09 -!- esmerelda [~mabel@71-212-79-193.tukw.qwest.net] has joined ##hplusroadmap 00:29 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has quit [Ping timeout: 246 seconds] 00:31 -!- augur [~augur@c-67-169-58-9.hsd1.ca.comcast.net] has quit [Remote host closed the connection] 00:37 -!- emeraldgreen [~user@188.227.115.178] has joined ##hplusroadmap 00:52 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 00:52 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap 01:12 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 246 seconds] 01:20 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 01:21 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 240 seconds] 01:28 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection] 01:30 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap 01:33 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 268 seconds] 01:39 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 02:01 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection] 02:03 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap 02:23 -!- jcluck [~cluckj@static-98-114-202-142.phlapa.ftas.verizon.net] has joined ##hplusroadmap 02:25 -!- cluckj [~cluckj@static-98-114-202-142.phlapa.ftas.verizon.net] has quit [Ping timeout: 240 seconds] 03:33 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 03:33 -!- rancyd_ [stryfe@2604:a880:800:10::539:100f] has joined ##hplusroadmap 03:51 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 03:54 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 255 seconds] 04:05 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has joined ##hplusroadmap 04:05 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Read error: Connection reset by peer] 04:06 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 04:10 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has quit [Ping timeout: 240 seconds] 04:22 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection] 04:24 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap 04:38 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 04:44 -!- emeraldgreen [~user@188.227.115.178] has quit [Quit: Leaving.] 04:44 -!- nmz787_i [~ntmccork@134.134.139.83] has quit [Remote host closed the connection] 04:56 < kanzure> nmz787_: nice eye, i had missed that. 04:59 -!- nmz787_i [~ntmccork@134.134.139.77] has joined ##hplusroadmap 05:02 < kanzure> nmz787_i: nice eye, i had missed that. 05:02 < kanzure> .tw https://twitter.com/GeneMods/status/876122174595231745 05:02 < yoleaux> Wonder how much the sDNA prices on this chart have changed since 2014. How cheap are array-built genes? @srikosuri? https://www.nature.com/nmeth/journal/v11/n5/fig_tab/nmeth.2918_F1.html (@GeneMods) 05:02 < kanzure> .tw https://twitter.com/srikosuri/status/876142992041558017 05:02 < yoleaux> @GeneMods About the same ($0.03-0.10/bp). At this point logistics and demand drive pricing more than oligo or process costs. (@srikosuri, in reply to tw:876122174595231745) 05:02 < kanzure> .tw https://twitter.com/kanzure/status/876772041474572288 05:02 < yoleaux> @srikosuri @GeneMods Oligo costs need to drop another 1000x. I want $1/genome synthesis. Relatedly, CC'd you on (H)GP-write tech workgroup email yesterday. (@kanzure, in reply to tw:876142992041558017) 05:04 < kanzure> https://www.genomeweb.com/business-news/twist-bioscience-raises-27m-venture-capital https://twitter.com/TwistBioscience/status/876103141703520256 05:05 -!- Gurkenglas [~Gurkengla@dslb-188-103-222-233.188.103.pools.vodafone-ip.de] has joined ##hplusroadmap 05:05 < kanzure> interplanetary mission instruments http://ipmdatabase.webnode.com/ 05:06 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has joined ##hplusroadmap 05:06 < kanzure> https://eos.org/meeting-reports/instrument-development-enables-planetary-exploration https://twitter.com/uFluidix/status/875020160494645248 05:06 -!- drewbot [~cinch@54.205.161.243] has joined ##hplusroadmap 05:08 < kanzure> .tw https://twitter.com/EricvdHelm/status/875553979031093248 05:08 < yoleaux> Nili Ostrov from the @geochurch lab praising yeast for its excellent DNA assembly properties, to synthesize recoded E. coli #sb7conf (@EricvdHelm) 05:08 < kanzure> .tw https://twitter.com/ajfedorec/status/875551751218184192 05:08 < yoleaux> removing 7 codons from e coli genome with MAGE would require ~as much oligo synthesis as just synthesisng a whole genome #sb7conf (@ajfedorec) 05:09 < kanzure> .tw https://twitter.com/GeneMods/status/875539985818103808 05:09 < yoleaux> #iwill try to help get a community biohacking lab started in Chicago (cc @BiochemPhD) #synbioleap #sb7conf (@GeneMods) 05:10 < kanzure> .title https://www.youtube.com/watch?v=-YRyQqUpPu8 05:10 < yoleaux> Biohacker chat with Hannu Rajaniemi and Josiah Zayner - YouTube 05:11 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has quit [Ping timeout: 246 seconds] 05:11 < kanzure> "Inducible, tunable and multiplex human gene regulation using CRISPR-Cpf1-based transcription factors" http://biorxiv.org/content/early/2017/06/15/150656 https://twitter.com/crispr_de/status/875463519788912640 05:13 < kanzure> .tw https://twitter.com/JoanGabriel/status/875279096460136448 05:14 < yoleaux> #sb7conf By creating oxygen, cyanobacteria killed 90% of life on Earth. Be careful what ideas you take from nature to build synbio systems. (@JoanGabriel) 05:17 < kanzure> .tw https://twitter.com/GeneMods/status/875168932499533824 05:17 < yoleaux> So, enzymatic synthesis not solved just yet (by @molassemblies; @DNAScript?) #sb7conf (@GeneMods) 05:17 < kanzure> .tw https://twitter.com/SynBioJamesH/status/875173181945896960 05:17 < yoleaux> @GeneMods @molassemblies @DNAScript Lots of others solving this challenge too - check out @nuclera and #evonetix. (@SynBioJamesH, in reply to tw:875168932499533824) 05:18 < kanzure> .tw https://twitter.com/maxmundt1/status/875155843372662784 05:18 < yoleaux> "Beijing Genome Institute will be the first to sequence the human genome for 100 dollars 5 years from now" #sb7conf https://pbs.twimg.com/media/DCUtdAPUAAAWN_L.jpg (@maxmundt1) 05:20 < kanzure> .tw https://twitter.com/antonioregalado/status/875045428923949056 05:20 < yoleaux> Nature tags CRISPR 'off target' paper with note on concern after companies demanded action (https://www.technologyreview.com/s/608073/gene-editing-companies-hit-back-at-paper-that-criticized-crispr/) https://pbs.twimg.com/media/DCTIxkxXYAAyi60.jpg (@antonioregalado) 05:20 < kanzure> haha, so if you spam nature.com enough they will put up alerts on their papers. 05:27 < kanzure> .tw https://twitter.com/andrewhessel/status/874461953292345344 05:27 < yoleaux> Couldn't get to Singapore for SB7.0? Watch the livestream here -- http://sb7.info/homepage/sb7-0-live-stream/ #synbio (@andrewhessel) 05:29 < kanzure> something about adamala vesicle fusion, not sure what that is about https://twitter.com/KateAdamala 05:31 -!- sachy [~sachy@nat.brmlab.cz] has joined ##hplusroadmap 05:32 < kanzure> .tw https://twitter.com/srikosuri/status/876775881049505793 05:32 < yoleaux> @kanzure @GeneMods It's not oligo cost. Microarray oligos are already that low. It's assembly, verification, logistics that drive cost. (@srikosuri, in reply to tw:876772041474572288) 05:35 < kanzure> .tw https://twitter.com/kanzure/status/876780323501101056 05:35 < yoleaux> @srikosuri @GeneMods For one-pot assembly, there are likely yeast strains that could help move towards >100 fragment assembly: https://groups.google.com/d/msg/enzymaticsynthesis/uyZqtJO24RE/lApLb4JmCAAJ (@kanzure, in reply to tw:876775881049505793) 05:35 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 240 seconds] 05:36 < kanzure> .tw https://twitter.com/srikosuri/status/876776043834744832 05:36 < yoleaux> @kanzure @GeneMods Also saw that HGP email. Thanks. Let me know if I can help in any way. (@srikosuri, in reply to tw:876772041474572288) 06:00 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has joined ##hplusroadmap 06:07 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has joined ##hplusroadmap 06:12 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has quit [Ping timeout: 246 seconds] 07:06 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:5de1:fb49:9314:ed3a] has joined ##hplusroadmap 07:08 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has joined ##hplusroadmap 07:12 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has quit [Ping timeout: 246 seconds] 07:16 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 07:18 -!- Gurkenglas [~Gurkengla@dslb-188-103-222-233.188.103.pools.vodafone-ip.de] has quit [Ping timeout: 255 seconds] 07:44 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 246 seconds] 07:51 -!- nmz787_i [~ntmccork@134.134.139.77] has quit [Ping timeout: 240 seconds] 08:01 -!- nmz787_i [ntmccork@nat/intel/x-ewstsqwlfzxweces] has joined ##hplusroadmap 08:01 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 08:09 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has joined ##hplusroadmap 08:11 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 08:14 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has quit [Ping timeout: 258 seconds] 08:16 -!- nmz787_i [ntmccork@nat/intel/x-ewstsqwlfzxweces] has quit [Quit: Leaving.] 08:19 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:5de1:fb49:9314:ed3a] has quit [Quit: Leaving] 08:23 -!- sbodin [~sbodin@91.226.140.2] has joined ##hplusroadmap 08:51 < kanzure> .tw https://twitter.com/elonmusk/status/875913504451985411 08:51 < yoleaux> Colonizing Mars (thanks Prof Hubbard for creating this from my talk). Major changes to the plan coming soon. http://online.liebertpub.com/doi/pdf/10.1089/space.2017.29009.emu (@elonmusk) 08:51 < kanzure> so he got a guy named hubbard to write his paper for him, but hubbard is not listed as the author..? 09:01 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection] 09:03 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap 09:08 -!- Gurkenglas [~Gurkengla@dslb-188-103-222-233.188.103.pools.vodafone-ip.de] has joined ##hplusroadmap 09:10 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has joined ##hplusroadmap 09:14 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has quit [Ping timeout: 240 seconds] 09:25 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection] 09:26 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap 09:35 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Remote host closed the connection] 10:10 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has joined ##hplusroadmap 10:15 -!- augur [~augur@2601:643:8400:9b9b:3c05:8a98:cdf7:4cc0] has quit [Ping timeout: 240 seconds] 10:23 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 10:26 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Remote host closed the connection] 10:29 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 10:33 -!- augur [~augur@c-67-169-58-9.hsd1.ca.comcast.net] has joined ##hplusroadmap 10:45 < kanzure> a bunch of people complaining about interrupt-mode working styles https://news.ycombinator.com/item?id=14586390 10:51 -!- esmerelda [~mabel@71-212-79-193.tukw.qwest.net] has quit [Ping timeout: 240 seconds] 10:51 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 10:59 -!- drewbot [~cinch@54.205.161.243] has quit [Remote host closed the connection] 11:05 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 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nmz787_i [~ntmccork@134.134.139.73] has joined ##hplusroadmap 11:50 -!- jcluck is now known as cluckj 11:55 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 255 seconds] 12:02 -!- nmz787_i [~ntmccork@134.134.139.73] has quit [Quit: Leaving.] 12:26 -!- marciogm [~xxxIdent@unaffiliated/marciogm] has quit [Ping timeout: 255 seconds] 12:29 -!- marciogm [~xxxIdent@unaffiliated/marciogm] has joined ##hplusroadmap 12:30 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 12:34 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 12:54 -!- Guest34245 is now known as abetusk 12:55 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 13:25 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 13:26 < kanzure> this company seems to be selling synthetic nucleotides they have labeled "X" and "Y" https://twitter.com/Synthorx 13:26 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 13:40 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 14:06 -!- nmz787_i [ntmccork@nat/intel/x-reiunoxcngublyem] has joined ##hplusroadmap 14:12 < kanzure> haha "AI risk is string theory for computer programmers" 14:21 -!- Netsplit *.net <-> *.split quits: yoleaux, jcorgan, kuldeep, blueskin, hylleddin 14:21 -!- blueskin [~blueskin@2001:41d0:1:9185::1] has joined ##hplusroadmap 14:21 -!- blueskin [~blueskin@2001:41d0:1:9185::1] has quit [Changing host] 14:21 -!- blueskin [~blueskin@unaffiliated/blueskin] has joined ##hplusroadmap 14:22 -!- Netsplit over, joins: hylleddin 14:22 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 14:23 -!- kuldeep [~kuldeep@unaffiliated/kuldeepdhaka] has joined ##hplusroadmap 14:24 -!- jcorgan [~jcorgan@unaffiliated/jcorgan] has joined ##hplusroadmap 14:26 -!- yoleaux [~yoleaux@xn--ht-1ia18f.nonceword.org] has joined ##hplusroadmap 14:29 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 14:43 -!- Netsplit *.net <-> *.split quits: yoleaux 14:45 -!- Netsplit over, joins: yoleaux 15:16 -!- ebowden [~ebowden@2001:8003:1074:bc00:4576:4329:d320:b5ea] has joined ##hplusroadmap 15:16 -!- ebowden [~ebowden@2001:8003:1074:bc00:4576:4329:d320:b5ea] has quit [Changing host] 15:16 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 15:19 -!- TC [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 15:20 -!- TC is now known as Guest3985 15:22 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 240 seconds] 15:40 < nmz787_i> might get one of these on free loan: https://ark.intel.com/products/91317/Intel-Xeon-Processor-E5-2699-v4-55M-Cache-2_20-GHz 15:40 < chris_99> holy moley 15:41 < chris_99> 22 cores 15:41 < chris_99> how much ram would they give you too 15:42 < nmz787_i> I don't really need a desktop at home... but I figured I'd kick myself the first time I needed to compile something that was taking a while... also it gives me a reason to buy a nice video card, which should help watching/editing the GoPro 4k videos I recently recorded 15:43 -!- m4l3z [~m4l3z@2a01cb040226f200404fb17a34e7b369.ipv6.abo.wanadoo.fr] has joined ##hplusroadmap 15:43 < chris_99> neat 15:43 < chris_99> what video editor will you use for that? 15:43 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 15:44 < nmz787_i> hrmm, I was just trying to use AviDemux 15:45 < nmz787_i> no RAM will come with it 15:45 < nmz787_i> they'll just hand me a CPU and smile 15:46 -!- Guest3985 [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 240 seconds] 15:53 < chris_99> heh 15:53 < chris_99> i think i briefly played with https://www.lwks.com/ 15:54 < chris_99> but iirc they disabled the export in the free version except to youtube or something i think 15:54 < chris_99> which is anonoying 15:59 < juri_> I should be soldering together the box nmz787_i broke for me, on thursday. 15:59 < juri_> ;) 16:07 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 16:14 -!- m4l3z [~m4l3z@2a01cb040226f200404fb17a34e7b369.ipv6.abo.wanadoo.fr] has quit [Remote host closed the connection] 16:16 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 16:22 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has quit [Ping timeout: 260 seconds] 16:28 -!- Gurkenglas_ [~Gurkengla@dslb-188-103-222-233.188.103.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 16:28 -!- c0rw1n [~c0rw1n@87.67.247.161] has quit [Quit: Leaving] 16:32 -!- c0rw1n [~c0rw1n@87.67.247.161] has joined ##hplusroadmap 16:33 < nmz787_i> juri_: soldering! a computer case!? 16:35 < juri_> i need to solder a new power supply connector onto it, since the last one caught fire. while executing your code. 16:35 < juri_> ;) 16:52 -!- q4 [~q4@user-94-254-233-58.play-internet.pl] has joined 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for most people 18:32 < nmz787> good summary 18:32 < nmz787> I think that pretty much covered it, in my eyes 18:32 < nmz787> err, from my perspective 18:33 < kanzure> reverse engineering some more head set data https://github.com/openyou/emokit/issues/256#issuecomment-309615242 18:37 -!- Jenda`_ is now known as Jenda` 18:37 -!- Jenda` is now known as Jenda 18:38 -!- genemods [826ce1f8@gateway/web/freenode/ip.130.108.225.248] has joined ##hplusroadmap 18:39 < kanzure> genemods: sup. 18:39 < genemods> Hey! 18:39 < genemods> Your wiki rocks. 18:39 < kanzure> thank you. 18:41 < genemods> I haven't even had the chance to get through the index yet--you don't by any chance maintain a list of biohacking hubs, do you? 18:41 < kanzure> it's a little old http://diyhpl.us/wiki/diybio/groups/ 18:41 -!- delinquentme [~delinquen@2602:306:ceb7:990:b9be:f7b7:ce09:869b] has joined ##hplusroadmap 18:41 < kanzure> personally i am not really fond of that business model, i don't think it works 18:42 < delinquentme> wom wom wom 18:42 < kanzure> usually people who are good at biology and who also want to work on DIY projects are the kind of people that have no money and can't fund a lab 18:42 < delinquentme> academia makes lots of good workers 18:42 < delinquentme> =X 18:42 < genemods> Heh 18:45 < kanzure> i was showing nmz787 and delinquentme some meeting notes i typed from a hgp-write conference call this morning. not sure if you'd be interested in seeing that. 18:45 < genemods> Definitely am, I think I've read some of them already (you posted them on twitter too, right?) 18:46 < kanzure> hgp-write this thing http://diyhpl.us/~bryan/papers2/bio/Synthetic%20human%20genome%20project%20hgp-write%20draft%20timeline%20-%202016.pdf 18:46 < kanzure> on twitter i post transcripts when i'm in the audience and typing, but in this case it was a more private meeting of a tech/infra working group focused on dna synthesis technology development 18:47 < genemods> I'm well aware :P https://www.youtube.com/watch?v=yqwepdrv-NY 18:48 < kanzure> bioethicists are largely evil 18:49 < delinquentme> ^^ 18:49 < genemods> Haha 18:50 < delinquentme> good thing mom gave me a deep seated moral superiority 18:50 < kanzure> genemods: it's like telling someone they shouldn't learn to read/write, it's basic literacy. 18:50 < genemods> I like Laurie; disagree with her mostly but she's fun to talk/listen to 18:50 < kanzure> why is everyone a backwards savage? literacy is just basic and required for everyone. 18:52 < kanzure> those guys weren't really fond of my transcripts http://www.vocativ.com/428192/scientists-human-genome-struggle-transparency/ 18:52 < kanzure> anyway, enough ethics 18:53 < genemods> Yeah didn't someone yell at you on twitter about it? Lame 18:53 < genemods> Indeed, engineering is more fun 18:53 < delinquentme> nicceee! 18:53 < kanzure> are you a student and if so what are you focusing on? 18:54 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 260 seconds] 18:55 < nmz787> .title 18:55 < yoleaux> Scientists Working To Build A Human Genome Struggle With Transparency - Vocativ 18:55 < genemods> Student, currently focused on solving delivery problem for CRISPR (and 3 other projects) 18:55 < genemods> I'm in the 3rd year pit of despair with my PhD 18:56 < genemods> Thing I really like to work on is growing synbio community at Northwestern/in Chicago 18:56 < kanzure> viral delivery of crispr? 18:56 < genemods> Hence the blog/twitter account 18:56 < genemods> Nanoparticle 18:57 < genemods> Lab I work in specializes in a construct that gets actively endocytosed by mammalian cells 18:57 < kanzure> more like ligandal's approach? ceramic nanoparticle gumdrop candy thing, http://www.ligandal.com/ 18:57 < kanzure> wait no not ligandal. one sec. 18:57 < genemods> Think hairy ball, where ball is a liposome and hair is DNA oligos 18:57 < kanzure> no i got the wrong company oh noooo 18:58 < kanzure> honkala's thing 18:58 < delinquentme> genemods, do you know andre watson? 18:58 < delinquentme> is it ligandal. 18:59 < delinquentme> kanzure, honkala isnt there anymore though. 18:59 < delinquentme> Andre watson is spearheading it though. Specifically to work on crispr delivery stuffs. 18:59 < kanzure> ah okay. so it was ligandal. some sort of ceramic/fat nanoparticle delivery system to cells. 19:01 < genemods> delinquentme not by name; is he in Chicago? 19:02 < genemods> Ah, just clicked the Ligandal link 19:02 < kanzure> so, why not viruses? 19:03 < delinquentme> balls. I had a video of andre's phd thesis. I believe its an extension of that. 19:03 < delinquentme> genemods, nah hes here in SF 19:03 < genemods> immunogenicity 19:04 < delinquentme> definitely a smart dude. 19:05 < delinquentme> genemods, you should be steering mirkin towards anti-aging 19:05 < genemods> Although apparently there are ways to tolerize body to foreign proteins with a different set of nanoparticles, so repeated viral delivery might get more viable in the future 19:05 < delinquentme> id bet hes a hard guy to get a hold of though. 19:05 < delinquentme> https://www.google.com/patents/WO2015042585A1?cl=en 19:05 < genemods> hah. I'll be sure to bring that up on my Skype call with him tomorrow. 19:05 < kanzure> on the topic of immunogenicity, one of my project proposals involves intentionally infecting brains with toxo 19:06 < delinquentme> Nanoparticle-mediated gene delivery, genomic editing and ligand-targeted modification in various cell populations 19:06 < kanzure> page 15 shows the toxo-related project http://diyhpl.us/~bryan/irc/2017-02-03-beacon.pdf 19:07 < delinquentme> a core polyplex and a silica coating thereon; with a multitude of additional treatments 19:07 -!- duper [~super@ca4.blackcatz.org] has quit [Read error: Connection reset by peer] 19:07 -!- duper [~super@ca4.blackcatz.org] has joined ##hplusroadmap 19:09 < genemods> How are you planning to neutralize toxo so it's a neutral carrier? 19:09 < kanzure> it's actually not deadly-- it's other brain parasites that you need to worry about 19:10 < kanzure> usually the ones that eat your whole brain. those are the bad ones. 19:10 < kanzure> i mean, none of them are particularly good at the moment, but some are mostly benign 19:10 < genemods> So you're definitely planning on never ever becoming immunocompromised then (or spending time with immunocomped person)? 19:10 < kanzure> heh 19:10 < kanzure> yeah i'll admit there are holes. 19:11 < kanzure> toxo infects like 80% of the human population 19:11 < genemods> 84% of France according to pedia 19:11 < kanzure> er, *has* infected 19:11 < kanzure> sure. 19:12 < genemods> So what would you deliver? 19:12 < kanzure> in the slide, i propose an artificial selection method of picking out microbes from mice brain after running the mice through mazes and scoring maze solving performance 19:13 < kanzure> and then reintroducing the microbes into the experiment for strong scores 19:13 < kanzure> oh if you mean what plasmids to include in the microbe, i think you could get some interesting results by just randomly picking human brain protein genes to randomly express-- let the microbes tweak the details on their own through selection. 19:14 < kanzure> s/human/mouse 19:16 < kanzure> PMed you the link to the transcript for that hgp-write thing. 19:18 -!- jcluck [~cluckj@static-98-114-202-142.phlapa.ftas.verizon.net] has joined ##hplusroadmap 19:19 < kanzure> jcluck: you found a needle in time? 19:19 -!- cluckj [~cluckj@static-98-114-202-142.phlapa.ftas.verizon.net] has quit [Ping timeout: 258 seconds] 19:20 < kanzure> oh. 19:21 < delinquentme> genemods, i loved the one talk he gave to the USAF here: https://www.youtube.com/watch?v=lV3Yhi9ib3Y 19:22 < delinquentme> first time I heard of the guy but I was cheering during the vid at the beautiful simplicity of the solutions they came up w 19:22 < delinquentme> I think the pressure-alignment for the nanoink is my fav. 19:22 < delinquentme> nano-ink-die ** 19:24 < genemods> My personal favorite thing the lab has done is actually more recent, and macro 19:24 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Read error: Connection reset by peer] 19:25 -!- ebowden [~ebowden@2001:8003:1074:bc00:4576:4329:d320:b5ea] has joined ##hplusroadmap 19:26 -!- ebowden [~ebowden@2001:8003:1074:bc00:4576:4329:d320:b5ea] has quit [Changing host] 19:26 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 19:27 < genemods> ...and still totally under wraps? Can't find public news about it anywhere 19:31 < genemods> Welp, when it gets released someone (nudge nudge) should make an open-source version of it 19:33 < kanzure> i'll put it on the list. 19:34 < kanzure> .in 200d make an open-source somethig something (genemods) 19:34 < yoleaux> kanzure: I'll remind you on 6 Jan 2018 02:34Z 19:36 < delinquentme> just found out about this lil fuckball: 19:36 < delinquentme> https://en.wikipedia.org/wiki/SilverPush 19:36 < kanzure> genemods: so anyway, with hgp-write, i'm hoping it's not a repeat of Sc2.0--- basically a payday for IDT/Twist. i think they should focus on attempting to fund advancements in oligonucleotide synthesis chemistry. 19:36 < delinquentme> "SilverPush's tracking software can be embedded into mobile apps and is designed to operate without the knowledge of end users." 19:37 < delinquentme> "SilverPush does not have an opt-out mechanism, and users are often unaware that they are being tracked with SilverPush." 19:38 < delinquentme> "In July 2014, TechCrunch reported that SilverPush was using "ultrasonic inaudible sounds" called "audio beacons" along with cookies to reliably track users across multiple devices and that devices with an app containing the SilverPush SDK are constantly listening for audio beacons." 19:38 < kanzure> delinquentme: learn you about some sidechannels yo http://diyhpl.us/~bryan/papers2/security/ 19:39 < genemods> Totally agreed on oligo synthesis 19:40 < genemods> Was disappointed Molecular Assemblies didn't have more to show for themselves at SB7.0 19:40 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 19:40 < kanzure> there's a patent somewhere for molecular assemblies. but it's just tdt stuff. 19:40 < kanzure> there were igem groups that did as much 19:40 < kanzure> http://2014.igem.org/Team:Cooper_Union/TdT_project 19:40 < kanzure> from 19:40 < kanzure> http://diyhpl.us/wiki/dna/projects/#igem-2014 19:41 < kanzure> and http://2015.igem.org/Team:Cooper_Union/DeNovoSynthesis 19:41 < kanzure> various emails about TdT synthesis strategies https://groups.google.com/group/enzymaticsynthesis 19:43 < yashgaroth> molecular assemblies is doing a little more with their blocked nucleotides to prevent secondary structure formation, but only they know how well it actually works 19:44 < genemods> Curious: how does a phosphoramidite inkjet printer solve the hydrolysis issue? My impression with older machines is they try really hard to keep everything from being exposed to air because humidity destroys the reagents. 19:44 < kanzure> gas chamber 19:44 < genemods> Ah 19:44 < genemods> Simple enough 19:44 < kanzure> so that's one of my major concerns about that project actually 19:44 < kanzure> there's a bunch of parameters like that 19:45 < kanzure> and frankly i'm not a chemist 19:45 < kanzure> so once the machine gets built, i want to hire a chemist to take the machine and tweak it until it works 19:45 < kanzure> i also want to hire the chemist before building the machine-- so that the chemist can tell me how much of an idiot i am 19:46 < kanzure> btw the place i have in mind to build that monster is actually in chicago, he runs his own inkjet business 19:47 < genemods> YESYESYES 19:47 < genemods> come to Chicago 19:47 < genemods> I've been scheming to grow the biohacking community here 19:47 < genemods> And one of the things I've concluded is 19:47 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 19:47 < kanzure> ah there he is now. 19:47 < delinquentme> is there any really successful biohacking community? 19:48 < delinquentme> its really a "startup" isnt it? 19:48 < yashgaroth> I'd say "define successful", but no 19:48 < genemods> If we want to attract decent numbers of people we need a strong biohacking/DIYbio/open hardware component 19:48 < CaptHindsight> outside of Monsanto? :) 19:48 < delinquentme> ha 19:48 < delinquentme> sure yashgaroth 19:49 < delinquentme> genemods, why do it in chicago instead of where the bio ppl are already at? 19:49 < kanzure> genemods: i think small mission-focused projects will go better than random biohacking gyms. the trick is, where does the money come from? 19:49 < delinquentme> fecal biome transplant sales? 19:49 < kanzure> other than fecal biome transplant sales, yes. 19:49 < genemods> two reasons in no order of importance: I like the idea of growing something from the ground up, and my wife really likes Chicago 19:50 -!- delinquentme [~delinquen@2602:306:ceb7:990:b9be:f7b7:ce09:869b] has quit [Quit: Leaving] 19:50 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 19:52 < genemods> Agreed on the mission-focused (and small) projects 19:52 < genemods> I'm a fan of Sebastian Cocioba's idea of small, curiosity/local need-driven science (and tech) 19:52 < kanzure> while you're around, i should also mention that we've been drafting a paper on an electronically-controlled physically-tethered polymerase for DNA synthesis 19:53 < kanzure> https://docs.google.com/document/d/1GL_bB_eHDOEkzmayfUjTtVK6cPbSeI5HyLN4qHV25qQ/edit 19:54 < kanzure> inkjet is more near-term practical. 20:00 < genemods> reading now 20:02 -!- cevi_ [~zeb@128.12.245.10] has joined ##hplusroadmap 20:07 < kanzure> cevi_: sup. 20:08 < cevi_> I just got back from a conference in serbia 20:08 < kanzure> mission report plz 20:09 < cevi_> two of the proposed solutions to the constraint satisfaction dichotomy conjecture seem to be legit 20:10 < cevi_> also, the authors are very friendly 20:10 < cevi_> we might have gone drinking for about six hours the night before my plane flight back 20:12 < cevi_> very few of the people there seemed to think that the algorithms would be practically useful in the near future, though 20:16 < cevi_> the conference at least made it to Serbian national news 20:17 < cevi_> we had a "round table" discussion about the proposed solutions where people grilled the authors to see if they were legit 20:19 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 260 seconds] 20:21 < kanzure> ouch? 20:22 < cevi_> I think Zhuk's approach has some potential for use beyond this particular problem 20:23 < cevi_> he has a very clever way of discovering hidden linear constraints which are implied by the original constraints 20:24 < kanzure> cevi_: did i show you the error correction dna synthesis email? 20:24 < cevi_> several weeks ago? 20:24 < kanzure> yeah ok. 20:27 < cevi_> also, I might end up being the first person (other than the authors) who actually finishes reading one of these proofs and checking all the details 20:29 < kanzure> what was the proof size, can you link me again 20:29 < cevi_> 40 pages 20:29 < cevi_> https://arxiv.org/pdf/1704.01914.pdf 20:29 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 20:29 < cevi_> I've carefully checked the first 20, and I got the high-level explanation from the author 20:30 < cevi_> the whole argument is totally out of left field 20:32 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 240 seconds] 20:32 < cevi_> (we did a one-on-one discussion the day after the round table, and he explained where the idea came from) 20:33 < cevi_> it's funny because both me and him only do this stuff as a hobby 20:34 < cevi_> if you just try to read his paper straight through, you will probably have some trouble though 20:34 < cevi_> it has some prerequisites 20:34 < cevi_> I put together a reading guide 20:34 < cevi_> http://math.stanford.edu/~notzeb/csp.html 20:35 < kanzure> the last mathy thing i was doing at stanford was hanging out with this guy http://diyhpl.us/wiki/transcripts/2016-july-bitcoin-developers-miners-meeting/dan-boneh/ 20:35 < kanzure> ( http://diyhpl.us/wiki/transcripts/simons-institute/pairing-cryptography/ ) 20:47 < kanzure> cevi_: most of the math i run into is very simple finite field stuff. elliptic curves over finite fields, and such. 20:48 < cevi_> the fact that a gaussian distribution is spherically symmetric seems to come up in computer science occasionally 20:49 < kanzure> andytosh1: are you around 20:49 < cevi_> it's why a lot of semidefinite programming things work, at a vague hand-wavy level 20:50 < cevi_> relatedly, there is the central limit theorem 20:50 < cevi_> oh, it also seems to come up a lot in machine learning 20:52 < kanzure> are you familiar with cryptography basics? 20:52 < cevi_> a bit - I was very interested in it in high school 20:53 < cevi_> and theoretical computer science is very nearly cryptography stuff 20:54 < kanzure> bilinear maps are really useful for a bunch of "zero-knowledge proofs" that will be important for bitcoin in the future. 20:55 < cevi_> "bilinear maps" is not very specific 20:55 < kanzure> erm.. one sec. 20:56 < cevi_> oh, is this the pairing cryptography transcript you sent a few minutes ago? 20:56 < kanzure> http://diyhpl.us/~bryan/papers2/bitcoin/snarks/Quadratic%20span%20programs%20and%20succinct%20NIZKs%20without%20PCPs%20-%20GGPR.pdf 20:57 < kanzure> not really a good intro. hrm. 20:58 < cevi_> oh, I haven't seen this before 20:59 < kanzure> ah maybe this one, 20:59 < kanzure> https://people.xiph.org/~greg/simple_verifyable_execution.txt 21:02 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 21:05 < kanzure> cevi_: Madars (a user in here) wrote this one about linear constraint satisfaction problems for zero-knowledge proofs http://diyhpl.us/~bryan/papers2/bitcoin/snarks/Quasilinear-size%20zero%20knowledge%20from%20linear-algebraic%20PCPs%20-%202016.pdf 21:06 < cevi_> you seem to be really into PCPs - is this for cryptocurrency applications? 21:07 < kanzure> snarks and PCP theorem stuff is useful for bitcoin because you can transmit the proof instead of a tremendous amount of data 21:07 < kanzure> ((or instead of checking the data again) 21:07 < cevi_> I thought in practice that PCPs end up being an even more tremendous amount of data 21:08 < kanzure> bottleneck is prover is slow 21:08 < cevi_> oh, but I guess you are only looking at three bits of it or whatever 21:09 < kanzure> https://github.com/scipr-lab/libsnark is used in some bitcoin forks 21:10 < kanzure> although i should warn that one of the big problems with this approach is that it requires trusted setup (basically this is a really uncomfortable requirement that users are not okay with; usually the vulnerability is somtehing like: if one of the setup participants keeps the data instead of deleting their setup data, then they have an infinitely powerful backdoor into the prover/system) 21:11 < kanzure> in fact someone who did a trusted setup ritual for libsnark wrote a blog post about it, https://petertodd.org/2016/cypherpunk-desert-bus-zcash-trusted-setup-ceremony 21:17 < kanzure> genemods: wait are you still reading that :) 21:17 < genemods> Among many other things, you link monster :P 21:18 < kanzure> yea it's a bit of a problem.. i have many tens of thousands of bookmarks. 21:19 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 260 seconds] 21:48 -!- maaku [~mark@173.234.25.100] has quit [Quit: Lost terminal] 22:01 -!- maaku [~mark@173.234.25.100] has joined ##hplusroadmap 22:04 -!- Solgriffin [~Sol@c-69-141-24-242.hsd1.nj.comcast.net] has quit [Ping timeout: 240 seconds] 22:15 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Killed (kornbluth.freenode.net (Nickname regained by services))] 22:15 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 22:23 -!- rancyd_ [stryfe@2604:a880:800:10::539:100f] has joined ##hplusroadmap 22:38 -!- Gurkenglas_ [~Gurkengla@dslb-178-000-211-218.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 22:41 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 258 seconds] 22:46 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Remote host closed the connection] 22:46 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 22:48 -!- ebowden_ [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 22:51 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 22:52 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 276 seconds] 22:53 -!- Gurkenglas_ [~Gurkengla@dslb-178-000-211-218.178.000.pools.vodafone-ip.de] has quit [Ping timeout: 255 seconds] 22:54 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:02 -!- ebowden [~ebowden@2001:8003:1054:a100:95e1:23b3:c37e:563a] has joined ##hplusroadmap 23:02 -!- ebowden [~ebowden@2001:8003:1054:a100:95e1:23b3:c37e:563a] has quit [Changing host] 23:02 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 23:06 -!- ebowden_ [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 255 seconds] 23:09 -!- emeraldgreen [~user@188.227.115.178] has joined ##hplusroadmap 23:14 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 276 seconds] 23:29 -!- MrHindsight [~2020@pacific1614.dedicatedpanel.com] has joined ##hplusroadmap 23:29 -!- MrHindsight [~2020@pacific1614.dedicatedpanel.com] has quit [Changing host] 23:29 -!- MrHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 23:30 -!- emeraldgreen [~user@188.227.115.178] has quit [Quit: Leaving.] 23:33 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has quit [Ping timeout: 260 seconds] --- Log closed Tue Jun 20 00:00:27 2017