--- Log opened Mon Jul 06 00:00:02 2015 00:13 -!- wrldpc1 [~ben@206.104.133.27.ap.yournet.ne.jp] has quit [Quit: wrldpc1] 00:37 -!- justinzero [~justinzer@71.3.249.91] has joined ##hplusroadmap 00:41 -!- justinzero [~justinzer@71.3.249.91] has quit [Ping timeout: 246 seconds] 01:20 -!- wrldpc1 [~ben@204.131.169.216.client.dyn.strong-sf94.as22781.net] has joined ##hplusroadmap 01:59 -!- superkuh [~superkuh@unaffiliated/superkuh] has quit [Ping timeout: 248 seconds] 02:00 -!- drewbot_ [~cinch@ec2-54-227-103-23.compute-1.amazonaws.com] has quit [Remote host closed the connection] 02:01 -!- drewbot [~cinch@ec2-23-22-249-87.compute-1.amazonaws.com] has joined ##hplusroadmap 02:16 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 02:38 -!- justinzero [~justinzer@71.3.249.91] has joined ##hplusroadmap 02:42 -!- justinzero [~justinzer@71.3.249.91] has quit [Ping timeout: 248 seconds] 02:46 < jrayhawk> https://www.flickr.com/photos/kylemcdonald/19266856649/sizes/o/ 03:19 -!- DarmokAndJalad [~Porbus@58.164.109.57] has quit [Quit: Leaving] 03:27 < kanzure> .title https://news.ycombinator.com/item?id=9836336 03:27 < yoleaux> Hacking Team hacked, attackers claim 400GB in dumped data | Hacker News 03:44 < kanzure> "Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces" http://www.bakerlab.org/system/files/Gonen_2DArrays_Baker2015.pdf 03:44 < kanzure> "We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We used the method to design ... 03:45 < kanzure> ... proteins that self-assemble into layer groups P 3 2 1, P 4 2(1) 2, and P 6. Projection maps of micrometer-scale arrays, assembled both in vitro and in vivo, are consistent with the design models and display the target layer group symmetry. Such programmable 2D protein lattices should enable new approaches to structure determination, sensing, and nanomaterial engineering." 03:47 < kanzure> "Accurate design of co-assembling multi-component protein nanomaterials" http://www.bakerlab.org/system/files/King_Nature2014A.pdf 03:47 < kanzure> figure 4 "Electron micrographs of designed two-component protein 03:47 < kanzure> nanomaterials." 03:47 < kanzure> no wait, figure 5 is better 03:51 < kanzure> "Automating human intuition for protein design" http://www.bakerlab.org/system/files/Niv%C3%B3n_prot24463_13M.pdf 03:51 -!- streety [streety@2a01:7e00::f03c:91ff:feae:ded6] has quit [Ping timeout: 252 seconds] 03:54 < kanzure> a more general review of de novo protein design (open access) http://www.sciencedirect.com/science/article/pii/S0959440X1500069X 03:55 < kanzure> a grammar for protein backbone structure using "protein blocks" http://onlinelibrary.wiley.com/doi/10.1002/pro.2581/pdf 03:56 -!- streety [streety@2a01:7e00::f03c:91ff:feae:ded6] has joined ##hplusroadmap 04:39 -!- justinzero [~justinzer@71.3.249.91] has joined ##hplusroadmap 04:40 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 256 seconds] 04:43 -!- justinzero [~justinzer@71.3.249.91] has quit [Ping timeout: 256 seconds] 04:48 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 04:54 -!- wrldpc1_ [~ben@195.131.169.216.client.dyn.strong-sf94.as22781.net] has joined ##hplusroadmap 04:55 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 04:55 -!- wrldpc1 [~ben@204.131.169.216.client.dyn.strong-sf94.as22781.net] has quit [Ping timeout: 255 seconds] 04:55 -!- wrldpc1_ is now known as wrldpc1 05:01 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 05:32 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-kqxvaefjzgrtubva] has quit [Quit: Connection closed for inactivity] 05:48 -!- eudoxia [~eudoxia@r167-57-107-194.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 05:52 -!- FourFire [~FourFire@84.48.234.116] has joined ##hplusroadmap 05:52 < kanzure> eudoxia: same request goes for you (regarding listmaking of useful molecular machines) 05:54 < eudoxia> hmm 05:54 < eudoxia> MNT style machines or just anything useful? 05:59 < kanzure> anything useful 05:59 < kanzure> not necessarily molecular nanoprobe stuff 06:00 < eudoxia> right, also proteins and shit 06:02 < kanzure> well, protein-equivalent machines could count, but let's skip proteins themselves here 06:02 < kanzure> having a molecular differential gear is nice, but only if you have other components to make use of it. meanwhile there are probably simple molecular machines that are useful in isolation. 06:04 < eudoxia> sort of like what the parts library of NE was meant to become 06:05 < kanzure> huh? 06:06 < kanzure> the parts library was full of differential gears 06:06 < eudoxia> .title http://crnano.org/interview.freitas.htm 06:06 < yoleaux> Nanotechnology: Robert Freitas Interview 06:06 < eudoxia> >We’d expect the library of designed machine systems to rapidly expand from the current 1-2 dozen items (including mostly just a few bearings, gears, and joints) into the hundreds or thousands in just a few years. 06:06 < eudoxia> oh bobbie 06:07 < kanzure> so you're saying the only simple molecular machines you are aware of are the ones listed here? https://github.com/kanzure/nanoengineer/tree/874e4c9f8a9190f093625b267f9767e19f82e6c4/cad/partlib 06:08 < eudoxia> not really, there's also a nanotube linear motor and this rack and pinion system that's not there 06:09 < eudoxia> then there's all sorts of bespoke binding sites people have designed over the years 06:09 < eudoxia> wait a sec who did this https://github.com/kanzure/nanoengineer/tree/874e4c9f8a9190f093625b267f9767e19f82e6c4/cad/partlib/schafmeister 06:10 < justanotheruser> kanzure: do you have a list started? 06:10 < justanotheruser> All I know of are drexlers designs 06:11 < kanzure> well the files in nanoengineer.git are a list beyond just drexler's designs 06:11 < kanzure> here are some protein things that are interesting, if that's what you're asking about http://diyhpl.us/wiki/dna/projects/#proteins 06:12 < justanotheruser> yes, that is interesting 06:12 < justanotheruser> wasn't aware of all the designs that come with nanoengineer 06:13 * justanotheruser bookmarks 06:15 -!- balrog [~balrog@discferret/developer/balrog] has quit [Changing host] 06:15 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 06:16 -!- balrog [~balrog@unaffiliated/balrog] has quit [Quit: Bye] 06:16 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-scxpsufxxqxmxgmj] has joined ##hplusroadmap 06:17 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 06:26 < kanzure> i'm surprised at the lack of responses- i was expecting obvious things like antennae arrays, rod arrays (for sensors or even dna separation), polymerase clamps, springs, spheres or beads, machine tools... 06:27 < eudoxia> regarding springs 06:27 < eudoxia> drexler mentioned in the design of rod logic that you'd need springs to bring the rods back into place 06:27 < eudoxia> not knowing if there were small spring molecules like that, i imagined the way it would work would be something like 06:27 < eudoxia> a rotor with a cam would push the rods back into place, and travel perpendicular to a stack of identical rod-logical circuits 06:28 < eudoxia> but there are probably small linear spring molecules, no? 06:28 < kanzure> here is a more chemistry-oriented review of molecular machines http://www.researchgate.net/profile/Alberto_Credi/publication/12237218_Artificial_Molecular_Machines/links/0a85e531aec5618f45000000.pdf 06:30 < kanzure> i don't think that small-scale rod logic is likely to work for a while-- you need lots of other machinery to make use of it 06:30 < eudoxia> certainly, just asking cause it came to mind 06:32 < justanotheruser> http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002086 06:32 < justanotheruser> .title 06:33 < yoleaux> PLOS Biology: Open Labware: 3-D Printing Your Own Lab Equipment 06:40 -!- justinzero [~justinzer@71.3.249.91] has joined ##hplusroadmap 06:44 -!- justinzero [~justinzer@71.3.249.91] has quit [Ping timeout: 248 seconds] 06:47 -!- crescendo [~mozart@unaffiliated/crescendo] has quit [Ping timeout: 250 seconds] 06:48 -!- ebowden [~ebowden@147.69.32.113] has quit [Remote host closed the connection] 06:48 -!- crescendo [~mozart@unaffiliated/crescendo] has joined ##hplusroadmap 06:53 -!- andytoshi [~andytoshi@wpsoftware.net] has quit [Ping timeout: 248 seconds] 07:05 -!- DarmokAndJalad [~Porbus@58.164.109.57] has joined ##hplusroadmap 07:08 -!- eudoxia [~eudoxia@r167-57-107-194.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 07:09 -!- andytoshi [~andytoshi@wpsoftware.net] has joined ##hplusroadmap 07:14 -!- Porb_ [~Porbus@58.164.109.57] has joined ##hplusroadmap 07:16 -!- superkuh [~superkuh@c-24-245-50-222.hsd1.wi.comcast.net] has joined ##hplusroadmap 07:16 -!- superkuh [~superkuh@c-24-245-50-222.hsd1.wi.comcast.net] has quit [Changing host] 07:16 -!- superkuh [~superkuh@unaffiliated/superkuh] has joined ##hplusroadmap 07:18 -!- DarmokAndJalad [~Porbus@58.164.109.57] has quit [Ping timeout: 264 seconds] 07:19 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 07:20 < kanzure> steganography framework https://github.com/bramcohen/DissidentX 07:24 -!- ebowden [~ebowden@147.69.32.113] has quit [Ping timeout: 276 seconds] 07:31 < CaptHindsight> kanzure: the Agilent inkjet may be used for more than oligo probe hybridization, they are just focusing on that with their NextGen 07:32 < CaptHindsight> HP makes lots of printheads that they don't resell 07:33 < kanzure> it's not the inkjet which limits it; it's the lack of sample recovery 07:33 < CaptHindsight> it looks like they have made some just for printing oligos 07:34 < CaptHindsight> what's stopping/preventing the sample recovery? 07:34 < CaptHindsight> it's a stack of oligos in wells 07:34 < kanzure> see pm 07:35 < kanzure> wells are problematic because the only way to recover dna from wells (in this scenario) is pipetting, and if you have 2 million pores/wells then uh.. well.. pipetting will take forever. 07:36 < CaptHindsight> drop the bottom out 07:36 < kanzure> to where? you need to keep the samples separated. 07:37 < CaptHindsight> you have to start connecting them somewhere 07:37 < kanzure> now would be an okay time for a phone call if you're up for it 07:44 < archels> hmm, these guys coded their spiking neural network in Julia. I wonder why 07:44 < archels> 447 SLOC, pretty tight 07:44 < archels> no parallelism though 07:46 < archels> if spiked[cc] #spike occurred 07:46 < archels> spiked[cc] = true; 07:46 < archels> # make **REALLY REALLY** sure that this variable is set to true 08:24 < kanzure> CaptHindsight: good talking with you capt'n 08:26 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-scxpsufxxqxmxgmj] has quit [Quit: Connection closed for inactivity] 08:39 < kanzure> win 5 08:39 < kanzure> eijroeqjrqi whoops 08:40 -!- justinzero [~justinzer@71.3.249.91] has joined ##hplusroadmap 08:45 -!- justinzero [~justinzer@71.3.249.91] has quit [Ping timeout: 255 seconds] 08:51 -!- eudoxia [~eudoxia@r167-57-107-194.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 08:57 -!- FourFire [~FourFire@84.48.234.116] has quit [Quit: Leaving] 09:05 -!- nmz787_i [~ntmccork@134.134.139.77] has joined ##hplusroadmap 09:06 < kanzure> https://np.reddit.com/r/IAmA/comments/38jawf/im_the_president_of_the_liberland_settlement/crw1d0f?context=10 09:20 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Ping timeout: 252 seconds] 09:28 -!- nmz787_i [~ntmccork@134.134.139.77] has quit [Quit: Leaving.] 09:32 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 09:44 -!- Porb_ [~Porbus@58.164.109.57] has quit [Quit: Leaving] 09:48 -!- Netsplit *.net <-> *.split quits: vivi, Guest39888 09:49 -!- blueskin [~blueskin@2001:41d0:1:9185::1] has joined ##hplusroadmap 09:49 -!- blueskin is now known as Guest82433 09:52 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-ucszjmwhdgugzhil] has joined ##hplusroadmap 09:52 -!- Netsplit over, joins: vivi 09:53 -!- vivi is now known as Guest41761 09:54 -!- Guest41761 is now known as vivi 09:56 -!- strangewarp_ [~strangewa@c-76-25-206-3.hsd1.co.comcast.net] has quit [Read error: Connection reset by peer] 09:56 -!- strangewarp_ [~strangewa@c-76-25-206-3.hsd1.co.comcast.net] has joined ##hplusroadmap 10:28 -!- nmz787_i [~ntmccork@192.55.54.40] has joined ##hplusroadmap 10:33 -!- nmz787_i1 [~ntmccork@134.134.137.75] has joined ##hplusroadmap 10:33 -!- nmz787_i [~ntmccork@192.55.54.40] has quit [Ping timeout: 255 seconds] 10:36 < nmz787_i1> kanzure: so what does CaptHindsight want to improve on specifically, just cost to manufacture a POSAM clone? 10:37 < nmz787_i1> if that's the case, then I think replicating the POSAM chemicals list would be the best idea 10:38 < nmz787_i1> and send me an email for the items that are no longer available with direct replacements... and we can search for a substitute 10:38 < nmz787_i1> kanzure: a more interesting question to me is, who here would want to help with a micro/nano device? 10:39 < kanzure> why bother with micro or nano if you can get enough scale without it? inkjet printing can do picoliter droplets. 10:39 < nmz787_i1> yeah but eww 10:39 < nmz787_i1> you want to do offsite sequencing 10:39 < kanzure> elaborate? 10:39 < nmz787_i1> how gross 10:39 < kanzure> yes, i want to do offsite sequencing for now 10:39 < kanzure> v2 can include other components 10:39 < nmz787_i1> you need sequencing after every 1 to 10 or 50 additions 10:40 < kanzure> putting all work upfront is not good.... likewise, putting everything off until later is also bad. 10:40 < nmz787_i1> tdt plus nanopore would be more interesting 10:40 < kanzure> i thought that required a mutated/not-yet-existing version of tdt 10:40 < nmz787_i1> na 10:41 < nmz787_i1> just some wires to sense the nanopore for when a nucleotide passes through 10:41 < nmz787_i1> impedanceometry or whatever 10:41 < kanzure> i'm not sure why you think that is easier than working with off-the-shelf inkjet heads? 10:42 < nmz787_i1> because I have access to a FIB and silicon and gas-injection... I don't have inkjets, know their interfaces aren't stable for offlabel use 10:45 < kanzure> fib is not the hard part when confining an enzyme in a nanopore 10:47 < nmz787_i1> you don't want the enzyme in the nanopore though 10:47 < nmz787_i1> the nanopore is just to limit diffusion and tunnel molecules past your molecule-counter electrodes 10:47 < nmz787_i1> so you can know when to turn off the nucleotide pump 10:48 < nmz787_i1> but anyway, yeah I'd say just replicate the POSAM chem list, and shoot me an email if there are items with questions or supply problems 10:49 < kanzure> one thing you might be able to convince me about is single-molecule emulsions 10:50 < nmz787_i1> the HO on water looks like the HO on the 2' site on the nucleotide rings, that's why it lowers efficiency... so anything with a similar HO can have that effect 10:50 < nmz787_i1> (just FYI) 10:50 < nmz787_i1> https://en.wikipedia.org/wiki/Directionality_(molecular_biology) 10:50 < nmz787_i1> err 10:50 < nmz787_i1> the 3' 10:51 < nmz787_i1> https://en.wikipedia.org/wiki/Nucleotide 10:51 < nmz787_i1> (the first link shows the hidden polymer form) 10:51 -!- drethelin [~drethelin@71-87-115-157.dhcp.mdsn.wi.charter.com] has joined ##hplusroadmap 10:51 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 250 seconds] 10:55 < kanzure> .title http://www.sciencemag.org/content/333/6042/613.short 10:56 < kanzure> "A Single Molecule of Water Encapsulated in Fullerene C60" 10:56 < yoleaux> A Single Molecule of Water Encapsulated in Fullerene C60 10:57 < kanzure> https://scholar.google.com/scholar?hl=en&q=%22organic+cage%22+&btnG=&as_sdt=1%2C44&as_sdtp= 11:00 < kanzure> or nanopipette stuff.. hm. 11:07 < kanzure> huh i'm surprised that single-molecule emulsions are not a thing 11:08 < archels> superkuh: the website is down :( 11:17 < archels> this should be fun https://www.youtube.com/watch?v=7u8mheM2Hrg 11:17 < archels> .title 11:17 < yoleaux> RESPONSE TO ROBOT DUEL CHALLENGE. - YouTube 11:17 < nmz787_i1> I think I'd basically just need some help with CAD models and idea putting-together... then I could convert them to FIB files or mask files, do the micro/nano work... then maybe send that off to someone with a machine shop to make the macro to micro manifold, hookup the pumps and chemicals. Before that the sensing board would need to be built or a good analog frontend (amplifier) would need purchased 11:18 < kanzure> which cad models? 11:19 < CaptHindsight> nmz787: what do you want to fabricate? the manifold? 11:20 < nmz787_i1> I'd do the actual micro and nano device (on-chip peristaltic pumps, some mixing areas, a nanopore for each nucleotide, a chamber for tdt, a nano-lattice/pore-matrix to retain tdt so waste can flow, some purification areas) 11:21 < superkuh> Uh oh. Something didn't come back up from the lightning strike. 11:21 < nmz787_i1> the manifold I'm guessing will look something like this http://www.ifitjams.com/images/f4-11.jpg 11:21 < superkuh> Oh, no, just another IP change. 11:22 < CaptHindsight> a zero insertion force socket 11:22 < nmz787_i1> the microchip just compresses onto the steel manifold, with some rubber or teflon between 11:22 < nmz787_i1> I think that is LGA 11:22 < nmz787_i1> so not quite ZIF 11:22 < CaptHindsight> nmz787: LGA PGA 11:22 < nmz787_i1> since there's no insertion 11:22 < CaptHindsight> yeah just the pores 11:23 < CaptHindsight> inlets 11:26 < CaptHindsight> CAD models are no problem 11:27 < CaptHindsight> kanzure: you have to decide which way you want to go 11:27 -!- FourFire [~FourFire@26-110-11.connect.netcom.no] has joined ##hplusroadmap 11:28 < nmz787_i1> I would prefer BRL-CAD personally 11:28 < CaptHindsight> nmz787: heh, well you can spend the time converting from Step or Iges 11:29 < nmz787_i1> that seems like the only approach that is reliable 11:29 < nmz787_i1> nah i'd just use my python interface ;) 11:30 < nmz787_i1> To make the CAD automated for the FIB, I ultimated neem a .BMP type file 11:30 < nmz787_i1> need* 11:30 < nmz787_i1> but if the device is a one-off, I can do it by hand 11:31 < nmz787_i1> but we still need to layout the components, break/fan them out to the macro manifold, and design the manifold 11:33 < CaptHindsight> I have all the design tools. I just don't bother with all the open source almost CAD tools 11:34 -!- FourFire [~FourFire@26-110-11.connect.netcom.no] has quit [Ping timeout: 248 seconds] 11:39 < CaptHindsight> heh, how does a single molecule qualify as in emulsion? 11:39 < CaptHindsight> in/an 11:39 < nmz787_i1> the cage would be the emulsifier 11:39 < CaptHindsight> kidding 11:39 < archels> superkuh: excellent 11:40 < CaptHindsight> low cost DIY FIB 11:41 < CaptHindsight> a handy tool of the nano machine shop 11:41 < nmz787_i1> yeah it would work as a mass-spec too, if reversed 11:42 < nmz787_i1> err, maybe the DIY SEM would be a better candidate 11:42 < CaptHindsight> what tools to build first? that was the discussion 11:42 < nmz787_i1> but the DIY DUAL-BEAM would definitely be reversible for mass-spec 11:42 < CaptHindsight> well both, but where do we start 11:42 < CaptHindsight> build tools to build tools 11:43 < CaptHindsight> 3-axis inkjet is pretty simple 11:44 < CaptHindsight> also DLP micro printer 11:44 < CaptHindsight> there are lots of old SEM's around 11:45 < CaptHindsight> the electronics could all be modular, motion control, imaging etc can all be done on a PC 11:45 < kanzure> there really is no substitute at the moment for solidworks, really 11:45 < kanzure> brlcad has iges/step support, so just do it in solidworks then export to step/iges 11:46 < CaptHindsight> there are not really any open analog boards for drivers and sensors 11:46 -!- Beatzebub [~beatzebub@d108-180-217-85.bchsia.telus.net] has quit [Quit: Beatzebub] 11:46 < CaptHindsight> NX, Catia, Creo, SW we run em all 11:47 < CaptHindsight> brl is coming along 11:47 < nmz787_i1> BRL seemed to have better support for wide dynamic range in CAD models (they claim molecular to planetary scales) 11:48 < CaptHindsight> it's all the automated plug-ins and tools in the CAD package that save you so much time 11:49 < CaptHindsight> most on the surface act about the same 11:49 < nmz787_i1> BRL doesn't have great support for harder to define curves, at least in terms of defining them with math/equations 11:49 < CaptHindsight> extrude, cut, rotate, chamfer etc 11:50 < CaptHindsight> it's when you need to blend from one surface to another or hold some inner diameter on a contorted tube or similar is when the extra features come in handy 11:50 < CaptHindsight> or generate a pattern of holes etc 11:51 < CaptHindsight> but that's not holding us back 11:51 < CaptHindsight> that's just a preference for tools 11:52 < CaptHindsight> and how much time you have 11:52 < nmz787_i1> I just need a BMP file 11:52 < nmz787_i1> :P 11:52 < CaptHindsight> yeah 11:53 < nmz787_i1> 256-bit greyscale and single-layer per BMP 11:55 < kanzure> CaptHindsight: i'm a big fan of keeping it simple. nanopore stuff is fun, worth doing, but i still think keeping things simple can lead to good results. 11:55 < CaptHindsight> kanzure: we have to start somewhere 11:55 -!- eudoxia [~eudoxia@r167-57-107-194.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 11:56 < CaptHindsight> build a tool at a time, in a few years there will be a whole sub-micron CNC shop 11:58 < kanzure> oh regarding the emulsion question earlier: the idea was to use an emulsion where the contents of the emulsion is a single molecule 11:58 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-eiwfohxuxlpebkmq] has quit [Quit: Connection closed for inactivity] 11:58 < kanzure> the actual emulsifier could be many multiple molecules 12:00 < CaptHindsight> kanzure: whats the solvent or vehicle it's suspended in? 12:01 < nmz787_i1> CaptHindsight: IMO the nanopore stuff is immensely less complicated from a success standpoint... no one is going to care if you make POSAM cheaper, because the reagents are so relatively unavailable, short shelf life, low value output (it creates stuff that was available mail-order 30 years ago) 12:01 < kanzure> no idea, i was just looking around for papers to see if the emulsion idea exists elsewhere, doesn't matter 12:01 < CaptHindsight> I'm translating from Bio to coating, ink, paint chemistry terminology 12:01 -!- streety [streety@2a01:7e00::f03c:91ff:feae:ded6] has quit [Ping timeout: 252 seconds] 12:02 < kanzure> nmz787_i1: whether "no one is going to care if you make POSAM cheaper" does not modulate whether "the nanopore stuff is immensely less complicated from a success standpoint"... 12:02 < kanzure> short shelf life is probably because of contamination 12:02 < kanzure> being available by mail-order is irrelevant 12:02 < nmz787_i1> nope, that's why I included the chemistry point(s) 12:03 -!- streety [streety@2a01:7e00::f03c:91ff:feae:ded6] has joined ##hplusroadmap 12:03 < nmz787_i1> tdt is all water-based, can be achieved with a few home-brew enzymes and purified molecules 12:11 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 12:12 < CaptHindsight> nmz787: https://en.wikipedia.org/wiki/Terminal_deoxynucleotidyl_transferase making sure we are talking about this 12:12 < kanzure> yes 12:13 < kanzure> terrible diagram of tdt, it's essentially a donut 12:14 < kanzure> but the diagram fails to express this 12:17 < CaptHindsight> squished donut 12:18 < kanzure> a less delicious donut 12:25 < CaptHindsight> http://www.ebay.com/itm/Cambridge-Stereoscan-250-MK2-Scanning-Electron-Microscope-SEM-/400758845514 $800 as-is 12:25 < kanzure> working? 12:25 < CaptHindsight> looks like "untested" we have no clue how to either 12:28 < CaptHindsight> I usually spot one or two for a few $K that are in working condition 12:31 < nmz787_i1> e-ink remote control on Sony's home-grown crowdfunding site https://first-flight.sony.com/pj/2/HUIS%20REMOTE%20CONTROLLER 12:32 < CaptHindsight> http://www.ebay.com/itm/Zeiss-Electron-Microscope-EM-109-/181783812468 $3500 was working 12:32 < drethelin> nice 12:33 < CaptHindsight> and another: This instrument was pulled from service many years ago and its operational status is not known, thus we are listing it as "for parts or not working" because we cannot guarantee its proper operation. http://www.ebay.com/itm/JEOL-JSM-35C-Scanning-Electron-Microscope-with-Spectrum-Analysis-/331482051373 12:33 < CaptHindsight> $2500 12:33 < CaptHindsight> with Spectrum Analysis 12:35 < CaptHindsight> http://www.ebay.com/itm/JEOL-T330A-Electron-Microscope-working/331599003517 $2500 working 12:35 < CaptHindsight> with video of it working https://www.youtube.com/watch?v=FVpqDrAeKLU 12:36 < CaptHindsight> https://www.youtube.com/watch?v=gejSPGIcWPo 12:37 < nmz787_i1> the T330A looks pretty much like the scope I have (T200)... I think I might even have some schematics for the T330A too 12:40 < CaptHindsight> I should try to find surplus gun, chamber, detector assemblies 12:40 < nmz787_i1> https://www.tedpella.com/calibration_html/SEM_Calibration.htm 12:41 < nmz787_i1> I think that JSM-35C was on craigslist for a while 12:42 < nmz787_i1> oh, maybe not 12:42 -!- justinzero [~justinzer@71.3.249.91] has joined ##hplusroadmap 12:47 -!- justinzero [~justinzer@71.3.249.91] has quit [Ping timeout: 248 seconds] 12:58 < kanzure> .tell eleitl http://www.metzdowd.com/pipermail/cryptography/2015-July/025971.html 12:58 < yoleaux> kanzure: I'll pass your message to eleitl. 13:31 -!- Acty [uid89656@gateway/web/irccloud.com/x-izdwldopwoywsyfi] has quit [Quit: Connection closed for inactivity] 13:32 -!- nmz787_i1 [~ntmccork@134.134.137.75] has quit [Quit: Leaving.] 13:42 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 256 seconds] 13:46 -!- Acty [uid89656@gateway/web/irccloud.com/x-skhzrhoiiabcmpdh] has joined ##hplusroadmap 13:48 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 13:49 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 13:52 < kanzure> apparently firefly synchronization is a thing http://www.eecs.harvard.edu/ssr/projects/sync/ 13:53 -!- namespace [~user@50-35-177-83.evrt.wa.frontiernet.net] has quit [Quit: leaving] 13:59 < kanzure> "Some viruses that infect Archaea have complex structures that are unrelated to any other form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped structures, to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures.[80]" 13:59 < kanzure> [80] Prangishvili D, Forterre P, Garrett RA. Viruses of the Archaea: a unifying view. Nature Reviews Microbiology. 2006;4(11):837–48. doi:10.1038/nrmicro1527. PMID 17041631. 13:59 < kanzure> http://www.nature.com/nrmicro/journal/v4/n11/full/nrmicro1527.html 13:59 -!- nmz787_i [~ntmccork@192.55.54.36] has joined ##hplusroadmap 13:59 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Read error: Connection reset by peer] 13:59 < kanzure> http://www.researchgate.net/profile/Patrick_Forterre/publication/6753226_Viruses_of_the_Archaea_a_unifying_view/links/53f5c8700cf2888a7491e75e.pdf 14:02 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 14:11 -!- ant4t [~s3an@50.141.77.4] has joined ##hplusroadmap 14:38 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-rhzdqkplzptkmzpx] has joined ##hplusroadmap 14:42 -!- ant4t [~s3an@50.141.77.4] has quit [Ping timeout: 244 seconds] 14:55 -!- nmz787_i [~ntmccork@192.55.54.36] has left ##hplusroadmap [] 15:16 -!- sheena [~home@S0106c8be196316d1.ok.shawcable.net] has quit [Ping timeout: 244 seconds] 15:20 -!- nmz787_i [ntmccork@nat/intel/x-bzlsvcgcumceqkxx] has joined ##hplusroadmap 15:20 < nmz787_i> .title http://hplusmagazine.com/2015/02/15/biology-technology-darpa-back-game-big-vision-h/ 15:20 < yoleaux> Biology is Technology - DARPA is Back in the Game With A Big Vision and It Is H+ - h+ Mediah+ Media 15:26 < nmz787_i> 'Most lenses are, by definition, curved. After all, they are named for their resemblance to lentils, and a glass lens made flat is just a window with no special powers.' 15:26 < nmz787_i> /me had no idea of the relation to lentils 15:26 < nmz787_i> =-O 15:27 < kanzure> "Well known Silicon Valley venture capitalist, rocketeer, transhumanist, and super guy Steve Jurvetson was spotted “high fiving” a DARPA funded telepresence robot developed at Johns Hopkins APL at the reception." 15:27 < kanzure> (jurvetson is the J and draper is the D in DFJ) 15:28 < kanzure> (draper is the one with the kid that is desperate to fund someone building an iron man exoskeleton) 15:28 < kanzure> didn't know that these were the organ-on-a-chip people http://emulatebio.com/ 15:36 < nmz787_i> .title http://keyssa.com/technology/ 15:36 < yoleaux> Our Technology - Keyssa 15:40 -!- ant4t [~s3an@50.141.77.149] has joined ##hplusroadmap 15:45 < nmz787_i> .title http://www.voxel8.co/ 15:45 < yoleaux> Voxel8: 3D Electronics Printing 15:58 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 255 seconds] 16:05 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 16:17 -!- bobs [040f4b25@gateway/web/freenode/ip.4.15.75.37] has joined ##hplusroadmap 16:18 -!- bobs [040f4b25@gateway/web/freenode/ip.4.15.75.37] has quit [Client Quit] 16:24 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Read error: Connection reset by peer] 16:44 -!- justinzero [~justinzer@71.3.249.91] has joined ##hplusroadmap 16:48 -!- justinzero [~justinzer@71.3.249.91] has quit [Ping timeout: 248 seconds] 16:54 -!- ant4t [~s3an@50.141.77.149] has quit [Ping timeout: 240 seconds] 16:56 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 17:01 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has quit [Quit: gone] 17:03 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 264 seconds] 17:05 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 17:06 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has quit [Client Quit] 17:06 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 17:07 -!- CaptHindsight [~2020@adsl-75-57-146-56.dsl.emhril.sbcglobal.net] has joined ##hplusroadmap 17:07 -!- CaptHindsight [~2020@adsl-75-57-146-56.dsl.emhril.sbcglobal.net] has quit [Changing host] 17:07 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 17:07 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has quit [Client Quit] 17:07 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 17:14 -!- nmz787_i [ntmccork@nat/intel/x-bzlsvcgcumceqkxx] has quit [Ping timeout: 248 seconds] 17:36 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 17:37 -!- DarmokAndJalad [~Porbus@58.164.109.57] has joined ##hplusroadmap 17:44 -!- justinzero [~justinzer@71.3.249.91] has joined ##hplusroadmap 17:51 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 18:06 -!- ebowden [~ebowden@147.69.32.113] has quit [Ping timeout: 265 seconds] 18:08 < kanzure> .title https://news.ycombinator.com/item?id=9841209 18:08 < yoleaux> Antibody wipeout relieves symptoms of chronic fatigue syndrome | Hacker News 18:10 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 18:10 -!- justinzero [~justinzer@71.3.249.91] has quit [Quit: Leaving...] 18:12 -!- ebowden_ [~ebowden@147.69.32.113] has joined ##hplusroadmap 18:12 -!- ebowden [~ebowden@147.69.32.113] has quit [Read error: Connection reset by peer] 18:17 -!- noobuddy [~kvirc@unaffiliated/knobuddy] has joined ##hplusroadmap 18:22 < kanzure> .wik treponema pallidum 18:22 < yoleaux> "Treponema pallidum is a spirochaete bacterium with subspecies that cause treponemal diseases such as syphilis, bejel, pinta, and yaws. The treponemes have a cytoplasmic and an outer membrane. Using light microscopy, treponemes are only visible using dark field illumination. They are gram negative, but some regard them too thin to be gram stained." — https://en.wikipedia.org/wiki/Treponema_pallidum 18:23 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 18:23 < kanzure> oh cool we have the genome of neurosyphilis 18:24 -!- ebowden_ [~ebowden@147.69.32.113] has quit [Ping timeout: 256 seconds] 18:25 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-yfznjngdojccfdlj] has joined ##hplusroadmap 18:25 -!- sheena [~home@24.244.32.10] has joined ##hplusroadmap 18:29 < drethelin> great, now we can synthesize it! 18:30 < kanzure> there are easier ways to get neurosyphilis 18:32 -!- ebowden [~ebowden@147.69.32.113] has quit [Read error: Connection reset by peer] 18:33 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 18:40 < kanzure> "The metalloprotease Mpr1 has been demonstrated to be critical in blood-brain barrier penetration.[16]" 18:52 -!- sheena [~home@24.244.32.10] has quit [Ping timeout: 264 seconds] 19:04 -!- noobuddy [~kvirc@unaffiliated/knobuddy] has left ##hplusroadmap [] 19:13 -!- ebowden [~ebowden@147.69.32.113] has quit [Remote host closed the connection] 19:24 -!- ebowden [~ebowden@147.69.32.113] has joined ##hplusroadmap 19:25 < ryankarason> nmz787: ha! @ lentils.. nor did i.. 19:28 -!- ebowden [~ebowden@147.69.32.113] has quit [Ping timeout: 248 seconds] 19:46 -!- nmz787_i [ntmccork@nat/intel/x-hxsmucrwqqgpphmi] has joined ##hplusroadmap 20:09 < kanzure> hm 20:10 < kanzure> whatever happened to the brain preservation prize results. did that happen? or was it just a hit-and-run thing. 20:10 -!- DarmokAndJalad [~Porbus@58.164.109.57] has quit [Read error: Connection reset by peer] 20:10 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-rhzdqkplzptkmzpx] has quit [Quit: Connection closed for inactivity] 20:38 -!- nmz787_i [ntmccork@nat/intel/x-hxsmucrwqqgpphmi] has quit [Quit: Leaving.] 20:42 -!- wrldpc1 [~ben@195.131.169.216.client.dyn.strong-sf94.as22781.net] has quit [Quit: wrldpc1] 20:43 -!- wrldpc1 [~ben@195.131.169.216.client.dyn.strong-sf94.as22781.net] has joined ##hplusroadmap 20:51 -!- Beatzebub [~beatzebub@d108-180-217-85.bchsia.telus.net] has joined ##hplusroadmap 21:06 < kanzure> hrm. 21:08 -!- nmz787_i [ntmccork@nat/intel/x-rzaforkgcltygxbe] has joined ##hplusroadmap 21:11 -!- DarmokAndJalad [~Porbus@58.164.109.57] has joined ##hplusroadmap 21:15 -!- DarmokAndJalad [~Porbus@58.164.109.57] has quit [Ping timeout: 264 seconds] 21:56 -!- crescendo [~mozart@unaffiliated/crescendo] has quit [Ping timeout: 248 seconds] 21:56 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-ucszjmwhdgugzhil] has quit [Quit: Connection closed for inactivity] 21:56 -!- crescendo [~mozart@unaffiliated/crescendo] has joined ##hplusroadmap 22:21 -!- Acty [uid89656@gateway/web/irccloud.com/x-skhzrhoiiabcmpdh] has quit [Quit: Connection closed for inactivity] 22:38 -!- sheena [~home@S0106c8be196316d1.ok.shawcable.net] has joined ##hplusroadmap 22:47 -!- DarmokAndJalad [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has joined ##hplusroadmap 23:05 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-iczldqileyoomlwx] has joined ##hplusroadmap 23:08 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 240 seconds] 23:13 -!- crescendo [~mozart@unaffiliated/crescendo] has quit [Ping timeout: 248 seconds] 23:14 -!- crescendo [~mozart@unaffiliated/crescendo] has joined ##hplusroadmap 23:28 -!- DarmokAndJalad [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has quit [Read error: Connection reset by peer] 23:29 -!- night [~Adifex@unaffiliated/adifex] has quit [Remote host closed the connection] 23:29 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Quit: Namaste ] 23:32 -!- Acty [uid89656@gateway/web/irccloud.com/x-mbpzakrkusyjdsga] has joined ##hplusroadmap 23:32 -!- Adlai [~Adlai@unaffiliated/adlai] has joined ##hplusroadmap 23:34 -!- DarmokAndJalad [~Porbus@CPE-120-144-165-200.lnse5.lon.bigpond.net.au] has joined ##hplusroadmap --- Log closed Tue Jul 07 00:00:03 2015