--- Log opened Wed Jul 08 00:00:04 2015 00:29 -!- zadock [~outsider@81.180.210.87] has quit [Quit: Leaving] 00:31 -!- nmz787_i [~ntmccork@134.134.139.77] has joined ##hplusroadmap 00:37 -!- nmz787_i [~ntmccork@134.134.139.77] has quit [Ping timeout: 252 seconds] 00:52 -!- ebowden [~ebowden@147.69.32.113] has quit [Remote host closed the connection] 00:53 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 00:57 -!- knobuddy [~Coax@unaffiliated/knobuddy] has quit [Remote host closed the connection] 00:58 -!- ebowden [~ebowden@147.69.32.113] has quit [Remote host closed the connection] 01:06 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 01:51 -!- Porb [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has joined ##hplusroadmap 02:41 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] 02:47 < archels> .tell alu re your trans vs. posthuman question, if you want a thorough answer you should read Stefan Sorgner's latest book 02:47 < yoleaux> archels: I'll pass your message to alu. 02:47 < archels> but I side with the rest of the channel on this one: it's a very non-universal and somewhat pointless distinction 02:47 < archels> everyone has their own ideas of what these terms "mean" 02:48 -!- Beatzebub [~beatzebub@d108-180-217-85.bchsia.telus.net] has quit [Quit: Beatzebub] 02:49 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 02:58 -!- drewbot [~cinch@ec2-54-159-67-61.compute-1.amazonaws.com] has quit [Remote host closed the connection] 02:58 -!- drewbot [~cinch@ec2-54-159-145-94.compute-1.amazonaws.com] has joined ##hplusroadmap 03:02 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 03:17 -!- proofoflogic [uid65184@gateway/web/irccloud.com/x-aygrydngbuywmrlx] has quit [Quit: Connection closed for inactivity] 03:17 -!- wrldpc1 [~ben@215.131.169.216.client.dyn.strong-sf94.as22781.net] has quit [Quit: wrldpc1] 03:25 -!- Quashie_ [~boingredd@50.14.92.17] has joined ##hplusroadmap 03:26 -!- Quashie [~boingredd@50.14.92.17] has quit [Ping timeout: 256 seconds] 03:27 -!- Porb [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has quit [Ping timeout: 265 seconds] 03:28 -!- ebowden [~ebowden@147.69.32.113] has quit [Remote host closed the connection] 04:07 -!- Porb [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has joined ##hplusroadmap 04:14 -!- Porb_ [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has joined ##hplusroadmap 04:15 -!- Porb [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has quit [Ping timeout: 276 seconds] 04:19 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 04:36 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 05:14 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Read error: Connection reset by peer] 05:16 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-ttqcdbzpugecowvz] has quit [Quit: Connection closed for inactivity] 05:49 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 244 seconds] 05:49 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 05:59 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has joined ##hplusroadmap 05:59 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - george church 05:59 -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Wed May 20 12:46:25 2015] 05:59 [Users ##hplusroadmap] 05:59 [ Acty ] [ CaptHindsight] [ EnabrinTain ] [ kanzure ] [ Porb_ ] [ Stskeeps ] 05:59 [ Adlai ] [ catern ] [ EnLilaSko ] [ kindoflike ] [ Qfwfq ] [ superkuh ] 05:59 [ altersid ] [ chris_99 ] [ eudoxia ] [ kish ] [ Quashie_ ] [ Taek ] 05:59 [ alu ] [ crescendo ] [ fenn ] [ mf1008 ] [ redlegion ] [ the8thbit] 05:59 [ andytoshi] [ Daeken ] [ gnusha ] [ midnightmagic ] [ rigel ] [ ThomasEgi] 05:59 [ archels ] [ diginet ] [ Guest27737 ] [ nickjohnson ] [ ryankarason ] [ thundara ] 05:59 [ augur ] [ dingo_ ] [ Guest82433 ] [ nmz787 ] [ saurik ] [ TMA ] 05:59 [ Bakkot ] [ Douhet ] [ heath ] [ nsh ] [ sh ] [ Urchin ] 05:59 [ balrog ] [ dpk ] [ HEx1 ] [ p4nd4 ] [ sheena ] [ Viper168 ] 05:59 [ berndj ] [ drethelin ] [ JayDugger ] [ padz ] [ sivoais ] [ vivi ] 05:59 [ Betawolf ] [ drewbot ] [ jrayhawk ] [ ParahSailin_ ] [ smeaaagle ] [ xrr ] 05:59 [ bkero ] [ dustinm ] [ juri_ ] [ pasky ] [ strages ] [ yoleaux ] 05:59 [ BobaMa ] [ ebowden ] [ justanotheruser] [ PatrickRobotham] [ strangewarp_] [ yorick ] 05:59 [ Burnin8 ] [ eleitl ] [ juul ] [ poohbear ] [ streety ] 05:59 -!- Irssi: ##hplusroadmap: Total of 83 nicks [0 ops, 0 halfops, 0 voices, 83 normal] 05:59 !asimov.freenode.net [freenode-info] if you're at a conference and other people are having trouble connecting, please mention it to staff: http://freenode.net/faq.shtml#gettinghelp 05:59 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 06:00 -!- Irssi: Join to ##hplusroadmap was synced in 13 secs 06:26 < kanzure> yes i'm not sure there's any benefit conferred by one versus the other term 06:34 -!- ebowden [~ebowden@147.69.32.113] has quit [Remote host closed the connection] 06:40 < JayDugger> Good morning, everyone. 06:43 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 06:43 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 06:55 -!- dao [bc1ad134@gateway/web/freenode/ip.188.26.209.52] has joined ##hplusroadmap 06:55 < dao> hi 06:56 -!- wrldpc1 [~ben@154.131.169.216.client.dyn.strong-sf94.as22781.net] has joined ##hplusroadmap 07:08 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 07:09 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 07:15 < kanzure> hello dao 07:34 -!- dao [bc1ad134@gateway/web/freenode/ip.188.26.209.52] has quit [Quit: Page closed] 07:44 -!- nmz787_i [ntmccork@nat/intel/x-mtqiyluhfssvgndy] has joined ##hplusroadmap 07:52 < wrldpc1> dao .. as in 道? 07:53 < archels> the dao that can be spoken is not the eternal dao 07:55 < fenn> if you meet the dao on the road, kill him 07:55 < kanzure> do i have to 07:56 < fenn> .wik dao vallis 07:56 < yoleaux> "Dao Vallis is a valley on Mars that appears to have been carved by water. It runs southwestward into Hellas Planitia from the southern slopes of the volcano Hadriacus Mons, and has been identified as an outflow channel. It and its tributary, Niger Vallis, extend for about 1,200 km (750 mi)." — https://en.wikipedia.org/wiki/Dao_vallis 07:57 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has quit [Ping timeout: 256 seconds] 07:57 < fenn> it's also a number in hexadecimal, and a color i use a lot 07:59 < archels> hey, that's not a bad looking colour 08:06 -!- ebowden [~ebowden@147.69.32.113] has quit [Remote host closed the connection] 08:06 < fenn> .wik decentralized autonomous organization 08:06 < yoleaux> "A decentralized autonomous organization (DAO), fully automated business entity (FAB), or distributed autonomous corporation/company (DAC) is a decentralized network of narrow-AI autonomous agents which perform an output-maximizing production function and which divides its labor into computationally intractable tasks (which it incentivizes …" — https://en.wikipedia.org/wiki/Decentralized_autonomous_organization 08:08 < fenn> please don't actually bother with any of those links 08:11 < kanzure> as far as i can tell the primary interest that people have in "decentralized autonomous organizations" is using the concept as a method to skirt business registration and regulation 08:26 < kanzure> in the posam operations document there's a lot of steps that involve non-synthesizer equipment, like a rotary mixer apparatus. ugh. 08:27 < kanzure> i'm also a little confused why they had only one humidity sensor. wouldn't you want one on each far corner of the gas-enclosure chamber? 08:32 -!- nmz787_i [ntmccork@nat/intel/x-mtqiyluhfssvgndy] has quit [Quit: Leaving.] 08:36 < kanzure> pre-synthesis script http://diyhpl.us/~bryan/papers2/DNA/posam/pogo/pogo-vb/Basic.pp1 08:37 < kanzure> stepwise synthesis script http://diyhpl.us/~bryan/papers2/DNA/posam/pogo/pogo-vb/Basic.pp2 08:37 < kanzure> post-synthesis script (just flushing) http://diyhpl.us/~bryan/papers2/DNA/posam/pogo/pogo-vb/Basic.pp3 08:37 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 08:45 < kanzure> huh i don't think they were doing a specific oligo sequence 08:48 < kanzure> ah nevermind 08:48 < kanzure> "Dim iBank(6) As Integer 'E.g. 1:X/88 2:Y/89 3:A/65 4:C/67 5:G/71 6:T/84." 08:58 -!- nmz787_i [~ntmccork@192.55.55.39] has joined ##hplusroadmap 09:02 -!- nmz787_i1 [~ntmccork@192.55.54.42] has joined ##hplusroadmap 09:03 -!- nmz787_i [~ntmccork@192.55.55.39] has quit [Ping timeout: 256 seconds] 09:03 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 09:10 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 09:14 < CaptHindsight> the POSaM has the sample tray mounted and moving on a X-axis positioner and the printhead on a ZY combo 09:15 < CaptHindsight> what is our target accuracy and repeatability of each axis? 09:16 < kanzure> well we need to do up to 80 or 100 layers per drop 09:16 < CaptHindsight> yesterdays discussion mentioned that variances in drop placement will have an effect on synthesis 09:16 < kanzure> and probably the head has to be moved long-distance during purge steps, so whatever it takes to get it back to the correct location 09:18 < CaptHindsight> Epson doesn't have a public spec on drop variation for volume or straightness 09:18 < kanzure> i think this is just an optimization issue 09:19 < CaptHindsight> most piezo heads hold +/- 10% drop size variation and straightness is <1.5 deg from centerline 09:20 < CaptHindsight> since the sample trays are non-porous the actual drop size will vary based on the fluids surface tension and the surface tension of the surface it lands on 09:21 < CaptHindsight> drop size = landed drop diameter/size of splotch 09:23 < CaptHindsight> so the fluids and reactions near the outer edge of the drops will have the most variance 09:23 < CaptHindsight> bbl 09:26 -!- alu is now known as woahbot 09:27 -!- woahbot [~alu@unaffiliated/alu] has quit [Changing host] 09:27 -!- woahbot [~alu@unaffiliated/alusion] has joined ##hplusroadmap 09:27 -!- woahbot is now known as alu 09:49 -!- sheena [~home@d154-5-201-222.bchsia.telus.net] has quit [Ping timeout: 265 seconds] 09:52 -!- alu [~alu@unaffiliated/alusion] has left ##hplusroadmap ["WeeChat 0.3.8"] 10:04 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 10:04 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 10:09 -!- Porb_ [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has quit [Ping timeout: 256 seconds] 10:18 < eudoxia> who wants five bucks in starbucks credit 10:18 < eudoxia> a client gave it to me and we don't have starbucks in pooruguay 10:23 < kanzure> you let someone pay you $5? 10:24 < eudoxia> they asked me for feedback on a tiny app and i gave them a five minute email to ~spread the good vibes~, technically it was work-related so i got paid 10:35 < CaptHindsight> the POSaM papers don't mention anything about tweaking drive waveforms since they can't modify the fluids to adjust for viscosity, surface tension etc 10:35 < CaptHindsight> it looks like they just got lucky 10:36 < nmz787_i1> most biologists probably wouldn't know about drive waveforms 10:36 < nmz787_i1> unless the off-the-shelf controller supported it 10:36 < CaptHindsight> it's impressive that they did as much as they did 10:36 < nmz787_i1> (for stepper controllers the most I've seen is mixed decay mode) 10:46 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Read error: Connection reset by peer] 10:47 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 10:48 -!- soylentbomb [~k@unaffiliated/soylentbomb] has joined ##hplusroadmap 10:48 < kanzure> .title http://arxiv.org/abs/1504.07065 10:48 < yoleaux> [1504.07065] The doubly eclipsing quintuple low-mass star system 1SWASP J093010.78+533859.5 10:50 -!- HEx1 [~HEx@hexwab.plus.com] has quit [Ping timeout: 246 seconds] 10:58 -!- nmz787_i [~ntmccork@134.134.139.78] has joined ##hplusroadmap 10:58 -!- nmz787_i1 [~ntmccork@192.55.54.42] has quit [Read error: Connection reset by peer] 11:00 -!- nmz787_i [~ntmccork@134.134.139.78] has left ##hplusroadmap [] 11:14 -!- proofoflogic [uid65184@gateway/web/irccloud.com/x-qiqbtzskxdutwwwb] has joined ##hplusroadmap 11:17 -!- HEx1 [~HEx@hexwab.plus.com] has joined ##hplusroadmap 11:20 -!- nmz787_i [~ntmccork@192.55.54.42] has joined ##hplusroadmap 11:40 < kanzure> .wik glymphatic system 11:40 < yoleaux> "The glymphatic system (or glymphatic clearance pathway) is a functional waste clearance pathway for the mammalian central nervous system (CNS)." — https://en.wikipedia.org/wiki/Glymphatic_system 11:41 < kanzure> .title http://www.sciencemag.org/content/290/5490/350 11:41 < yoleaux> Replaying the Game: Hypnagogic Images in Normals and Amnesics 11:41 < kanzure> .title http://www.sciencemag.org/content/342/6156/373 11:41 < yoleaux> Sleep Drives Metabolite Clearance from the Adult Brain 11:43 < kanzure> "Impairment of paravascular clearance pathways in the aging brain" http://www.researchgate.net/profile/Benjamin_Kress/publication/236601893_Evaluating_glymphatic_pathway_function_utilizing_clinically_relevant_intrathecal_infusion_of_CSF_tracer/links/54e265980cf2edaea092e8f2.pdf 11:56 < kanzure> hmph 11:56 < kanzure> "There is some supporting evidence of the restorative function of sleep. The sleeping brain has been shown to remove metabolic waste products at a faster rate than during an awake state.[88] While awake, metabolism generates reactive oxygen species, which are damaging to cells. In sleep, metabolic rates decrease and reactive oxygen species generation is reduced allowing restorative processes to take over. It is theorized that sleep helps ... 11:56 < kanzure> ... facilitate the synthesis of molecules that help repair and protect the brain from these harmful elements generated during waking.[89] The metabolic phase during sleep is anabolic; anabolic hormones such as growth hormones (as mentioned above) are secreted preferentially during sleep. The duration of sleep among species is, broadly speaking, inversely related to animal size[citation needed] and directly related to basal metabolic rate ... 11:56 < kanzure> ... (BMR). Rats, which have a high BMR, sleep for up to 14 hours a day, whereas elephants and giraffes, which have lower BMRs, sleep only 3–4 hours per day." 11:57 -!- nmz787_i [~ntmccork@192.55.54.42] has quit [Quit: Leaving.] 12:01 < drethelin> wasn't there a study recently about a specific chemical in the brain that was removed during sleep 12:01 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 250 seconds] 12:09 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 12:19 < kanzure> another crispr overview http://andrew.gibiansky.com/blog/genetics/crispr/ 12:43 -!- crescendo [~mozart@unaffiliated/crescendo] has quit [Ping timeout: 248 seconds] 12:46 -!- crescendo [~mozart@unaffiliated/crescendo] has joined ##hplusroadmap 13:01 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-wzmaratwrclasbey] has joined ##hplusroadmap 13:10 -!- hiko [59d98902@gateway/web/freenode/ip.89.217.137.2] has joined ##hplusroadmap 13:10 -!- nmz787_i [~ntmccork@134.134.137.75] has joined ##hplusroadmap 13:10 -!- hiko [59d98902@gateway/web/freenode/ip.89.217.137.2] has quit [Client Quit] 13:17 -!- Beatzebub [~beatzebub@d108-180-217-85.bchsia.telus.net] has joined ##hplusroadmap 13:26 < CaptHindsight> kanzure: http://www.fujifilmusa.com/products/industrial_inkjet_printheads/deposition-products/dmp-2800/ $30k off the shelf 13:27 < kanzure> friend of mine says she was working with this one http://www.fujifilmusa.com/shared/bin/PDS00085-DMP2831.pdf 13:27 < CaptHindsight> thats it 13:27 < kanzure> but she was cheating, she says she just went to their offices to use it (computer had a driver installed on it) 13:27 < kanzure> oh well 13:28 < CaptHindsight> i think they charge 1.5K/day for lab use 13:28 < kanzure> yea she's part of some research group 13:28 < kanzure> so either paid or research collaboration project thingy 13:30 < CaptHindsight> should we stay at 25um repeatability or tighter? 13:31 < kanzure> let's aim for maybe a milion spots ish? so i think the repeatability and spacing have some relationship that i forget. 13:31 < kanzure> actually i don't know how many spots to aim for 13:32 < kanzure> at least a million. but if we can manage way more, then why not.. 13:33 < CaptHindsight> POSam had ~150um dia spots 13:33 -!- delinquentme [~delinquen@74.61.157.78] has joined ##hplusroadmap 13:33 < delinquentme> kanzure, do you have access to JOVE? 13:34 < delinquentme> nmz787, fenn 13:34 < kanzure> not at the moment 13:34 < kanzure> delinquentme: http://diyhpl.us/~bryan/jove.urls.txt 13:34 < kanzure> they have since moved their files though :-( 13:35 < CaptHindsight> run the numbers, how many spots, what spot dia and what spacing? 13:35 < delinquentme> http://www.jove.com/video/50262/design-and-use-of-multiplexed-chemostat-arrays 13:35 < delinquentme> derp. 13:35 < delinquentme> http://www.jove.com/video/50168/the-use-of-chemostats-in-microbial-systems-biology 13:35 < delinquentme> that one 13:35 < kanzure> CaptHindsight: spot diameter should be based on giving a "good margin for error" or something- e.g., something not at the max performance of the poor inkjet head 13:35 < kanzure> CaptHindsight: additionally, it needs to be based on the micropipetting that will be necessary for combining different spots 13:36 < CaptHindsight> it looks like the surface tension of their tray limited their drop density 13:36 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-gcdwrcpoleiuwndk] has joined ##hplusroadmap 13:36 < kanzure> oh 13:37 < CaptHindsight> how many layer max are we shooting for? 13:37 < kanzure> well, because of chemistry yield errors, i think it's <100 bp, probably <80 bp 13:38 < CaptHindsight> maybe we should SLA print sample trays with wells 13:38 < kanzure> 50 would be nice... it would give us 20 bp on both sides for dna hybridization, and then 10 bp of unique content 13:39 < CaptHindsight> maybe 1mm deep wells 13:39 < kanzure> the wells could be wider than the drops- which might be favorable for splash reasons, or surface tension issues, etc.. 13:39 < CaptHindsight> they counted on surface tension to keep the drops from spreading 13:40 < kanzure> oh ok 13:40 < CaptHindsight> we could use a photopolymer 13:40 < kanzure> there have been some photopolymer methods of dna synthesis 13:41 < CaptHindsight> print the walls of the wells 13:41 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/Light-directed%20synthesis%20of%20high-density%20oligonucleotide%20arrays%20using%20semiconductor%20photoresists%20-%201996.pdf 13:41 < CaptHindsight> yeah, V2 13:41 < kanzure> hehe they had dna densities of 10^6 strands per cm^2 13:41 < CaptHindsight> their limit was 90 dpi 13:45 < ParahSailin_> i got a bunch of azure bizspark capacity to waste 13:46 < ParahSailin_> maybe i should stuff it full of video 13:46 < kanzure> get the 1000genomes data set 13:46 < kanzure> make some indexes etc 13:46 < ParahSailin_> oh thats not a bad idea 13:47 < ParahSailin_> sra is such a bizarre file format 13:47 -!- _0bitcount [~Big_Byte@81.61.208.88.dyn.user.ono.com] has joined ##hplusroadmap 13:47 < ParahSailin_> but ncbi tools work on them about 75% of the time 13:47 < ParahSailin_> the 25% is really awful 13:47 < kanzure> is that their format for 1000potatoes? 13:47 < ParahSailin_> doesnt azco use electrochemical control for their array synth? 13:48 < ParahSailin_> yeah, short read archive 13:48 < ParahSailin_> admittedly sra uses some pretty clever compression 13:48 < CaptHindsight> will WASH WITH ACETONITRILE be able to properly dry if we have shallow wells? 13:48 < ParahSailin_> but it is completely inpenetrable with any sort of third party tool 13:48 < kanzure> ParahSailin_: captain is going to be making an oligo assembler, make lots of advice comments or else 13:49 < ParahSailin_> if someone gives me $20k i will make a usable third party library in python and c for dealing with sra files 13:50 < ParahSailin_> theoretically, ncbi has an sdk for sratoolkit, but it is totally abstruse 13:50 < ParahSailin_> maybe its intrinsic to the sra file format, similar to pdf, that makes it impossible to write good tools for 13:59 < delinquentme> directed evolution kanzure ... surely weve got someone in here whos totally bad ass at this right? 14:00 < nmz787_i> i'm badass at this, but not that 14:01 < nmz787_i> CaptHindsight: won't shallow wells help evap? 14:01 < nmz787_i> isn't evap same as dry? 14:05 < kanzure> delinquentme: i know various things about the subject. state your request. 14:07 < delinquentme> site directed mutagenesis ... this can be reduced to a liquid handling operation right? 14:07 < delinquentme> plus heating / cooling 14:09 < delinquentme> seems to be the case http://kirschner.med.harvard.edu/files/protocols/Stratagene_quickchangepdf.pdf 14:09 < delinquentme> possibly bad assumption: all site directed mutagenesis protocols are like the above 14:12 -!- eudoxia [~eudoxia@r167-57-79-198.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 14:12 < nmz787_i> delinquentme: crispr could probably be considered part of a newer strategy 14:14 < nmz787_i> # flux ╨ 14:14 < nmz787_i> # ╥ 14:14 < nmz787_i> ah, damn, the extended ASCII doesn't show up well in the logs 14:18 < kanzure> delinquentme: there's also things like http://arep.med.harvard.edu/pdf/Bonde_2014.pdf 14:19 < delinquentme> kanzure, what would you guess is the time utilization on churches MAGE ? 14:22 < kanzure> no idea 14:26 -!- balrog [~balrog@unaffiliated/balrog] has quit [Ping timeout: 245 seconds] 14:27 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 14:57 -!- proofoflogic [uid65184@gateway/web/irccloud.com/x-qiqbtzskxdutwwwb] has quit [Quit: Connection closed for inactivity] 15:07 -!- _0bitcount [~Big_Byte@81.61.208.88.dyn.user.ono.com] has quit [Quit: Leaving] 15:22 < kanzure> ParahSailin_: what's the ideal output of the dna synthesis machine? at first we're shipping the output to someone to do dna sequencing. but it's technically not dna yet. and also the physical format... they are not going to like 100 microscope slides with 10 million spots... 15:23 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 15:34 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Quit: good_luck] 15:43 < kanzure> "he destruction of extracellular matrix by enzymes such as serine proteases, threonine proteases, and matrix metalloproteinases.[3][7]" 15:45 < nmz787_i> kanzure: why would it not technically be DNA as output? 15:46 < kanzure> it's just an oligo 15:46 < kanzure> i don't even think it qualifies as ssDNA 15:47 < ParahSailin_> is it a nucleic acid? 15:48 < kanzure> oh maybe it does qualify as ssDNA, weird 15:48 < kanzure> well anyway, don't these places have requirements like you gotta pellet it, you have to deliver it on a specific tray? 15:49 < ParahSailin_> sequencers are used to getting whatever 15:50 < kanzure> but surely not 1 million spots with 20 micron spacing? 15:50 < ParahSailin_> that would be pretty unusual 15:50 < kanzure> :-) 15:50 < kanzure> right, so we have to pick something that is normal and expected 15:50 < ParahSailin_> you wanna pool it all together and attach illumina tags? 15:51 < ParahSailin_> and dump it on a lane? 15:51 < ParahSailin_> that would work 15:51 < kanzure> well... it would be nice to do microarray sequencing? 15:51 < ParahSailin_> you could even synthesize with illumina tags on both ends 15:52 < nmz787_i> microarray is tag/affinity-binding based 15:52 < kanzure> wait no, surely someone is doing microarray sequencing-by-synthesis with polymerase? 15:52 < nmz787_i> yeah, that one company 15:52 < ParahSailin_> illumina is kinda 15:52 < nmz787_i> not pacbio 15:52 < nmz787_i> helix---something? 15:52 < nmz787_i> helicos? 15:53 < kanzure> blah 15:53 < kanzure> ok, so maybe gibson assembly first, then ship a pellet to someone 15:53 < ParahSailin_> the new illumina flow cells look more like arrays with metered wells 15:53 < ParahSailin_> do what i said 15:53 < kanzure> if you put it all in one lane, how would you know which sequence was wrong? 15:53 < ParahSailin_> attach illumina tags and send it in as a library 15:54 < ParahSailin_> approximate string matching 15:54 < kanzure> illumina tags seem to be limited to 96 unique molecules at a time 15:54 < ParahSailin_> nah 15:54 < kanzure> http://www.illumina.com/documents/products/datasheets/datasheet_sequencing_multiplex.pdf 15:55 < ParahSailin_> ideally when you do library prep you want ever cluster to be a unique molecule 15:55 < kanzure> i am going to have 1 million unique molecules (or more) 15:55 < kanzure> er.. 1 million different sequences. 15:55 < ParahSailin_> if you have a million unique sequences, thats what you will read out 15:56 < kanzure> so i'll have a million unique illumina tags too? 15:56 < kanzure> "each index is six bases in length" 15:56 < ParahSailin_> youd put a common illumina tag, and you could put a million random sequences along with your business biology if you wanted 15:56 < ParahSailin_> but i would think the biological sequence you want would be enough 15:57 < ParahSailin_> eh, we use 15mer indexes here at affy 15:57 < kanzure> the point is to verify that the right thing was sequenced in each location/spot. it's the mapping between spot and unique dna molecule that is important. i suppose you could say "well just make sure none of your sequences are anywhere close to similar"... 15:58 < kanzure> i was thinking of situations like "500 of the unique molecules are only unique by one nucleotide" 15:58 < ParahSailin_> make some unique tag for each then 15:58 < kanzure> hm 15:58 < kanzure> yeah i see what you mean now 15:59 < kanzure> and this is the typical <$1000/run sequencing? 15:59 < ParahSailin_> i see what you're saying that it would be good to have a known mapping to location... but what are the odds that at well A1, you tell the machine to make ACGT and it makes GGGG instead 15:59 < kanzure> well... who knows. myabe the machine sucks? 15:59 -!- poohbear is now known as StuffedBear 15:59 < ParahSailin_> so that it swaps it with some other location 15:59 < nmz787_i> in that case the tag wont even be right 16:00 < ParahSailin_> yeah more likely you will have no discernable read at all 16:00 < kanzure> i wonder if we could do sequencing-by-polymerase on this machine. that might help. hmm. 16:01 < ParahSailin_> if you just synthesize your million spots so that they have Nmers with sufficient edit distance to each other, then you have a pretty reliable way to test the machine 16:01 < kanzure> so what's the format that illumina shops would expect? just pipette everything into a tube and call it quits? 16:01 < kanzure> yes, i agree 16:01 < ParahSailin_> stick it in a tube 16:01 < kanzure> i wasn't assuming the edit distance thing earlier, but yes it makes sense to do it that way :-) 16:02 < ParahSailin_> how do you think they came up with the 6 base or 15 base index barcodes 16:02 < kanzure> no idea 16:03 < ParahSailin_> illumina's 6 base ones were geared towards hamming distance 16:03 < ParahSailin_> which kinda sucks when you consider like index 3 and index 26 or something ended up being one indel apart, oops 16:04 < kanzure> and their 15 bp index was not based on hamming distance? 16:05 < ParahSailin_> illumina doesnt have a 15bp index 16:06 < ParahSailin_> but basically anyone who uses their machines can make oligos that will read the same way as illumina's so they can make whatever indexes they like 16:07 < kanzure> how do people normally do microarray to single tube? 16:07 < kanzure> i can possibly arrange for there to be beads in each well/pore on the surface, and then just dump all the beads out at the end into a tube, then cut the dna off? 16:07 < ParahSailin_> add a drop of water and suck it back up 16:07 < kanzure> or does everyone just do lots of micropipetting? 16:09 < kanzure> maybe i can use a piece of tissue paper to absorb all the liquid, then dissolve the tissue paper and keep the dna 16:10 < ParahSailin_> what i said above is how we dealt with microarray synthesized oligos that we just needed to pool 16:10 < kanzure> used a pipette to suck up each well? 16:10 < ParahSailin_> its not a well, its a glass slide 16:10 < kanzure> that's a lot of pipetting if it's 1 million pores 16:10 < kanzure> well whatever- i haven't decided whether to use glass slides or pores yet 16:10 < ParahSailin_> you add like one big drop of water and suck it up 16:11 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 16:11 < kanzure> oh, all of it at once. cool. 16:12 < kanzure> does gibson work with pooling arbitrarily large sets? 16:13 < ParahSailin_> oh if you put any enzyme in that pot, it would make a whole bunch of junk 16:13 < ParahSailin_> much less three enzymes together 16:14 < kanzure> why don't we have one-pot ligation techniques yet? bleh 16:15 < kanzure> what would be a good assembly approach for 1 to 10 million unique strands? 16:15 < ParahSailin_> ligase is one enzyme, i think you could try that 16:15 < ParahSailin_> ive seen papers where they use one ligase and lots of ssdna 16:16 < kanzure> also assume i can do 20 bp wings on both ends if necessary 16:18 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-huqxxpethiamnedl] has quit [Quit: Connection closed for inactivity] 16:20 < kanzure> .title http://www.nature.com/articles/nmeth.1318 16:20 < yoleaux> Access : Enzymatic assembly of DNA molecules up to several hundred kilobases : Nature Methods 16:20 < kanzure> ah right, yeast assembly too 16:23 < kanzure> gibson assembly, yeast assembly, golden gate, dna ligase, ligase cycling reaction, what's the one with dna hybridization and polymerase (just pcr assembly?), paperclip, golden braid, ... 16:23 < kanzure> .title http://www.nature.com/articles/srep11302 16:23 < yoleaux> RapGene: a fast and accurate strategy for synthetic gene assembly in Escherichia coli : Scientific Reports : Nature Publishing Group 16:32 -!- marchtemp [~bitnami@ec2-54-69-125-142.us-west-2.compute.amazonaws.com] has joined ##hplusroadmap 16:35 -!- nmz787_i [~ntmccork@134.134.137.75] has quit [Quit: Leaving.] 16:46 -!- nmz787_i [ntmccork@nat/intel/x-krbemuktwqutpfcq] has joined ##hplusroadmap 16:49 < nmz787_i> kanzure: see, on-chip sequencing makes everything easier 16:49 < nmz787_i> and if it's on-chip, you don't even need sequencing as much as length-assertion 16:51 < CaptHindsight> the POSaM papers leave out lots of little details 16:52 < CaptHindsight> they mention the 90dpi but not the spot diameters they were getting 16:55 < CaptHindsight> the 700 series heads were specified by Epson at 6pL but they were getting closer to 10pL drops... 16:55 -!- nmz787_i [ntmccork@nat/intel/x-krbemuktwqutpfcq] has quit [Ping timeout: 264 seconds] 16:55 < CaptHindsight> I don't know if that is because of the fluids that they were using or the waveform they chose 16:56 < CaptHindsight> I don't know why they said that they were getting close to 10pL either, they don't say how they determined that 16:57 < CaptHindsight> 1.000 drops into a microbalance or just a hunch 16:59 -!- Porb [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has joined ##hplusroadmap 17:16 < kanzure> they may not have been measuring their spot diameter 17:18 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Read error: Connection reset by peer] 17:20 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 17:39 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 18:04 -!- Madplatypus is now known as MadUrsine 18:07 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-kcnlwjdoaryrqkbk] has joined ##hplusroadmap 18:08 -!- delinquentme [~delinquen@74.61.157.78] has quit [Ping timeout: 256 seconds] 18:10 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-wzmaratwrclasbey] has quit [Quit: Connection closed for inactivity] 18:11 -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 18:12 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 256 seconds] 18:12 < ParahSailin_> you guys should have bought the GA2x if you wanted to reverse engineer chip sequencing 18:13 -!- proofoflogic [uid65184@gateway/web/irccloud.com/x-ryseqhfriigcpdmh] has joined ##hplusroadmap 18:13 < ParahSailin_> actually, my friend may have just stashed it in his warehouse 18:13 -!- MadUrsine is now known as Madplatypus 18:17 < CaptHindsight> since the Epson heads are specifically made for deposition but as low cost aqueous ink printers we'll just make the best of them 18:17 -!- Viper168_ is now known as Viper168 18:17 < CaptHindsight> sorry are not made for deposition 18:18 < ParahSailin_> kanzure: an azco array synthesis run is like a few k 18:18 < ParahSailin_> kanzure: i'd say start from there 18:19 < ParahSailin_> do an illumina library to see what the error rate is like 18:22 < ParahSailin_> then if its good enough look at whatever patents they have a rip them off 18:42 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 276 seconds] 18:46 -!- StuffedBear is now known as poohbear 18:48 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 18:56 -!- ebowden [~ebowden@147.69.32.113] has quit [Remote host closed the connection] 19:05 -!- night [~Adifex@unaffiliated/adifex] has joined ##hplusroadmap 19:41 < kanzure> http://www.customarrayinc.com/oligos_main.htm 19:41 < kanzure> 79 bp * 12472 for $1600 19:42 < kanzure> and 170 bp * 12472 for $2400 19:42 < kanzure> or 79 bp * 92918 for $4000 or 170 bp * 92918 for $6000 19:43 < kanzure> so 15 million bp for $6000. hmm. 19:43 < kanzure> "CustomArray uses advanced CMOS semiconductor technology to enable it to synthesize thousands of oligonucleotides simultaneously. Each array contains thousands of individually addressable electrodes, which electrochemically synthesize a unique oligonucleotide at each electrode. The oligonucleotides are cleaved from the surface to create custom oligo pools." 19:43 < kanzure> "Extremely competitive pricing -- as low as 0.04 cents per base." 19:44 < kanzure> "On-board quality control systems" hmm looks like they put sensors on their microarrays 19:45 < kanzure> "CustomArray's chips use electrochemical detritylation to control DNA synthesis. Electrochemical detritylation can be a much-more-efficient method to synthesize oligonucleotides than light-based synthesis processes. This means the oligonucleotides are of highest quality, and the sensitivity of the microarray is maximized. Since physical photolithographic masks or pre-built collections of oligos are NOT involved in the process, all probes ... 19:45 < kanzure> ... can be easily changed without extra time or costs." 19:45 < kanzure> pfft physical photolithography masks 19:51 -!- Acty [uid89656@gateway/web/irccloud.com/x-zawktfdxtmgzcllv] has quit [Quit: Connection closed for inactivity] 19:58 < CaptHindsight> http://customarrayinc.com/faq_main.htm 19:58 < kanzure> .wik tetrazole 19:58 < yoleaux> "Tetrazoles are a class of synthetic organic heterocyclic compound, consisting of a 5-member ring of four nitrogen and one carbon atom (plus hydrogens). The simplest is tetrazole itself, CH2N4. They are unknown in nature." — https://en.wikipedia.org/wiki/Tetrazole 20:02 < CaptHindsight> http://www.pnas.org/content/106/36/15219.full Photoelectrochemical synthesis of DNA microarrays 20:04 < kanzure> also see http://diyhpl.us/~bryan/papers2/DNA/Photoelectromechanical%20synthesis%20of%20low-cost%20DNA%20microarrays%20-%20thesis%20-%202008.pdf 20:04 < kanzure> filename is wrong heh 20:04 < kanzure> more generally for photoremovable protecting groups, see http://diyhpl.us/~bryan/papers2/DNA/Photoremovable%20protecting%20groups%20in%20chemistry%20and%20biology%20-%20reaction%20mechanisms%20and%20efficiency.pdf 20:08 -!- delinquentme [~delinquen@74.61.157.78] has joined ##hplusroadmap 20:16 < CaptHindsight> kanzure: what are the costs of the chems used in photo deprotection vs the ones for inkjet? 20:24 < ParahSailin_> i wonder if you could cleave oligos from surface with electrochemistry too 20:26 < ParahSailin_> not clear here if all of the oligos need to be same length 20:34 -!- ant4t [~s3an@50.141.76.136] has joined ##hplusroadmap 20:37 < kanzure> CaptHindsight: it's probably on the azco biotech website 20:37 < kanzure> ParahSailin_: for my purposes? nah different length is fine 20:37 -!- delinquentme [~delinquen@74.61.157.78] has quit [Ping timeout: 256 seconds] 20:37 < kanzure> ParahSailin_: also, if you're unable to cleave (chemically/electronically/whatever) then one option is just dropping in dna polymerase i think 20:38 < ParahSailin_> pretty much anyone wants different length-- certain array processes dictate that all oligos be the same length 20:39 < ParahSailin_> so if this one supports mixed lengths, thats just one more plus 20:39 < kanzure> oh, why do the others require same length? .. no skips? 20:40 < ParahSailin_> affy's im pretty sure does, so does mycroarray 20:40 < kanzure> i think one of the inkjet-related cleaning steps might be unskippable- like when blowing argon at everything. 20:40 < kanzure> actually maybe the argon cleaning can be more specifically targeted 20:41 < CaptHindsight> how long does each base take using Photoelectrochemical synthesis? 20:41 < ParahSailin_> does inkjet ever atomize liquid? 20:41 < CaptHindsight> define atomize 20:41 < CaptHindsight> what size drop? 20:42 < ParahSailin_> does it make a droplet that only hits where you want it without contaminating every cell in N radius 20:42 -!- ant4t [~s3an@50.141.76.136] has quit [Remote host closed the connection] 20:42 < kanzure> only hits where you want it 20:42 < ParahSailin_> that is a big concern with the lithography, be it mask or scanning laser 20:42 < CaptHindsight> drop volume from the current Epson heads are 1.5pL 20:42 < ParahSailin_> so no molecules hit the wrong place? 20:42 < kanzure> correct 20:43 < ParahSailin_> that seems unlikely that it doesnt aerosol at all 20:43 < kanzure> it's pressurized 20:43 < CaptHindsight> surface tension 20:43 < ParahSailin_> we've done some interesting experiments with aerosoling in liquid handling 20:43 < ParahSailin_> easily see 3% contamination in adjacent wells of a 384 well plate 20:43 < ParahSailin_> and thats at macro scale 20:44 < kanzure> yeah but i bet you had humidity and stuff 20:44 < ParahSailin_> who knows 20:44 < ParahSailin_> maybe not a concern at all 20:44 < ParahSailin_> seems the electrochemistry is pretty battle tested 20:45 < CaptHindsight> 20-28 seconds 20:49 < CaptHindsight> Complete deprotection or detritylation was achieved without noticeable acid diffusion halos typically between 20–28 s 20:50 < CaptHindsight> http://www.pnas.org/content/106/36/15219.full#F3 20:51 < CaptHindsight> this is a lot faster than inkjet 20:51 < CaptHindsight> have to see the price of the chems 20:51 < kanzure> inkjet can do more spots 20:52 < kanzure> .title 20:52 < yoleaux> Photoelectrochemical synthesis of DNA microarrays 20:52 < kanzure> this is going to be limited by the size of the LCD 20:52 < kanzure> inkjets can trivially do >100 million spots 20:52 < CaptHindsight> apples and oranges 20:53 < ParahSailin_> optimize for number of spots before you can even do anything with 100 spot? 20:53 < kanzure> 100 spots is useless 20:53 < ParahSailin_> 96k spots? 20:54 < kanzure> significantly more useful 20:55 < ParahSailin_> 100 spots would not be useless if you had a good method of assembly 20:55 < ParahSailin_> id say that would be a viable product 20:56 < ParahSailin_> being able to make a plasmid in the 10-20kb range in one machine step 20:57 < kanzure> each spot would be <100 bp, how are you getting 20 kb from 100 spots? 20:57 < ParahSailin_> azco will do up to 200bp in a spot 20:58 < kanzure> i wouldn't trust yield to be that good yet- but if we can push it that high then sure... 20:58 < ParahSailin_> i dont know what the error rate is like, you might need to keep it below 100 for that reason, but 5-10kb is nothing to scoff at 20:58 < kanzure> right 21:01 < CaptHindsight> how many seconds per base using inkjet? 21:05 < kanzure> don't know; hard to find. 21:06 < CaptHindsight> looks like a few minutes from the sample program 21:10 < CaptHindsight> http://customarrayinc.com/images/Array_Manufacture_Features.gif 21:13 < CaptHindsight> not difficult to fab 21:14 < CaptHindsight> this is the chemistry to look at 21:17 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 21:27 -!- proofoflogic [uid65184@gateway/web/irccloud.com/x-ryseqhfriigcpdmh] has quit [Quit: Connection closed for inactivity] 21:29 -!- superobserver [~superobse@unaffiliated/superobserver] has joined ##hplusroadmap 21:38 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 244 seconds] 21:44 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 21:58 -!- Guest27737 [~quassel@50-0-37-37.dsl.static.fusionbroadband.com] has quit [Remote host closed the connection] 22:01 -!- maaku [~quassel@50-0-37-37.dsl.static.fusionbroadband.com] has joined ##hplusroadmap 22:02 -!- maaku is now known as Guest72554 22:19 -!- proofoflogic [uid65184@gateway/web/irccloud.com/x-mooxyevrgsnbkbjc] has joined ##hplusroadmap 22:21 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Quit: Namaste ] 22:27 -!- Guest72554 [~quassel@50-0-37-37.dsl.static.fusionbroadband.com] has quit [Remote host closed the connection] 22:27 -!- maaku_ [~quassel@50-0-37-37.dsl.static.fusionbroadband.com] has joined ##hplusroadmap 22:27 -!- Acty [uid89656@gateway/web/irccloud.com/x-bodckjomqpcxeqat] has joined ##hplusroadmap 22:36 -!- Quashie_ [~boingredd@50.14.92.17] has quit [Ping timeout: 256 seconds] 22:47 -!- Porb [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has quit [Quit: Leaving] 22:48 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-kcnlwjdoaryrqkbk] has quit [Quit: Connection closed for inactivity] 22:51 -!- Quashie [~boingredd@50.14.92.17] has joined ##hplusroadmap 23:53 -!- augur [~augur@c-73-46-94-9.hsd1.fl.comcast.net] has quit [Ping timeout: 246 seconds] 23:54 -!- augur [~augur@c-73-46-94-9.hsd1.fl.comcast.net] has joined ##hplusroadmap --- Log closed Thu Jul 09 00:00:05 2015