--- Log opened Sat Feb 02 00:00:48 2013
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00:35 <@fenn> no objection, but it would have been better a year ago
00:36 <@fenn> huh seems like it was longer than that
00:37 <@kanzure> not true, it's better now because nmz787 has a home and things
00:37 <@kanzure> <--- unit tests passing, i'm a very happy person.
00:38 < nmz787> what?
00:38 < nmz787> ahh
00:40 < nmz787> if we built laser anything, i think it would still have micro XY, but that it would expose resist rather than ablate
00:40 < nmz787> well
00:40 < nmz787> i guess it would use the same optics actually
00:40 < nmz787> so we could just try both
00:41 < nmz787> fenn: what's your situation these days?
00:41 < nmz787> fenn: i drove past indiana in december and thought of you, i think you had been there back then maybe
00:42 < nmz787> fenn: i last remember you asking me to find 3D schematics for some part of that laser cutter
00:42 <@fenn> i'm in DC doing nothing interesting
00:42 < nmz787> fenn this is what I'm looking at now
00:43 < nmz787> paperbot: http://pubs.acs.org/doi/abs/10.1021/ed800170t
00:43 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Three-Dimensional%20Printing%20Using%20a%20Photoinitiated%20Polymer.pdf
00:44 < brownies> well that doesn't sound very interesting.
00:44 <@fenn> looks identical to lemoncurry
00:44 < nmz787> fenn https://nano-cemms.illinois.edu/materials/3d_printing_full
00:45 <@fenn> except it goes down into a vat instead of being exposed on the bottom and drawing out
00:45 < nmz787> this way makes more sense than that
00:45 <@fenn> why do they call it "nano"
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00:46 < nmz787> where?
00:46 <@fenn> nevermind, that's just the institution they're at
00:47 <@fenn> " incredibly thin polymer layers (on the order of 400 nm)" so by this definition reprap is "nanotechnology"
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00:47 < nmz787> so basically i was thinking I'd hook up a projector to my microscope, add a webcam for feedback, and make casting masters
00:48 <@fenn> make it so, number one
00:49 < nmz787> but you could just as easily put a laser in place of the projector and scan the exposure
00:50 < nmz787> that's what azonenberg wants to do
00:50 <@fenn> you could even do two photon for sooper dooper resolution
00:51 <@fenn> but i imagine you want the negative of what a laser would scan
00:51 < nmz787> i don't know if this gel is compatible with the reactions I want to do though, so I might be limited to one layer anyway, just to stamp into PDMS
00:51 <@fenn> probably better that way
00:51 < nmz787> but if it was able to be coerced into compatibility, that would be cool
00:51 <@fenn> "embossed"
00:51 < nmz787> it's basically polyacrylamide
00:52 < nmz787> with some http://www.sigmaaldrich.com/catalog/product/aldrich/246816?lang=en&region=US
00:53 <@fenn> there are other chemistries available, see http://code.google.com/p/lemoncurry/wiki/main
00:53 <@fenn> jeez they haven't made any progress on that at all
00:55 <@fenn> see "customers also viewed" on that sigma page :)
00:55 <@fenn> anyway, bucktownpolymers might do what you want without the hassle of sigma aldrich
00:56 <@kanzure> there, i've added http response saving for unit tests
00:56 <@kanzure> https://github.com/kanzure/python-requestions#readme
00:59 <@fenn> now it's just a SMOP to get it to actually do something
00:59 <@kanzure> ?
01:00 <@fenn> httpickle or whatever you're calling it
01:01 <@kanzure> httpretty is just some unit testing wrapper thing for mocking the requests library
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01:01 < nmz787> fenn: bucktown looks like it might be a lot more expensive than sigma
01:01 <@kanzure> but why would i want to manually write HTTPretty.register_uri in each unit test.. why not just load the actual result i received from the real request, and just test against that.
01:02 <@fenn> nmz787: really? i thought they were quoting something like $40/kg
01:02 <@fenn> anyway the problem with sigma is getting them to sell anything at all
01:03 < nmz787> i've bought from sigma before
01:03 < nmz787> they just need a commercial shipping address
01:04 < nmz787> that's with most of these companies
01:04 <@fenn> kanzure: so this whole thing is just unit tests for python-requests? doesn't it have its own unit tests?
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01:04 <@kanzure> did langton count as commercial?
01:04 <@kanzure> fenn: python-requests comes bundled with httpbin, and i think it runs an httpbin server
01:04 <@kanzure> i mean it runs an instance of httpbin for the unit testing
01:04 < nmz787> fenn: gallon of vis curable $235, gallon of UV curable $1040
01:04 <@fenn> um, langton probably could have gotten away with commercial shipping
01:05 <@kanzure> "fenn why are there 20 barrels marked 'alibaba, not illicit' in the garage?"
01:05 < nmz787> it literally depends on the property zoning record
01:05 <@kanzure> nobody would have noticed
01:06 <@fenn> is there no readily available UV cure resin for hobby stuff?
01:06 <@kanzure> what does lemoncurry use?
01:06 < nmz787> I might be able to use the sigma stuff for electrophoresis gel too
01:06 <@fenn> i mean this is basic chemistry, just need to add some uv absorbing dye to limit penetration
01:07 <@kanzure> also if there is no curable polymer we can always get treadwell to make something up, he has been begging for a relevant project.
01:07 < nmz787> hmm well i guess sigma wants $150 for kg
01:07 < nmz787> so that's prob 1/4 gallon ish
01:07 <@kanzure> . units 1 kg
01:07 <@kanzure> .units
01:07 <@kanzure> fuck the bots
01:07 < nmz787> and that's the 80%
01:08 <@fenn> 80%?
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01:08 <@fenn> i for one welcome our silent IRC overlords
01:09 < nmz787> yeah i dunno what the other 20% is!
01:09 <@kanzure> fenn: no really why don't we have a unitbot
01:10 <@fenn> so people dont use the channel as their personal command line
01:10 <@fenn> .wa kg
01:10 < yoleaux> kg (kilogram): Conversions to other units: 1 kg: 2.205 lb (pounds): 2 pounds 3.274 ounces: 1000 grams; Conversions from other units: 1 lb: 0.4536 kg; 1 oz: 0.02835 kg; 1 g: 0.001 kg; Physical quantity: mass; Unit type: SI base unit; Unit systems: Système International d'Unités (SI): decimeter-kilogram-second (DKS): meter-kilogram-second (MKS)
01:10 <@kanzure> oh, wolfram.
01:11 <@fenn> anyway we don't know the density or at least i'm too lazy to look it up
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01:13 < nmz787> yeah i'll just assume it's water
01:13 < nmz787> :p
01:14 <@fenn> always a valid assumption when dealing with unfamiliar organics
01:14 <@fenn> "hexanediol acrylamide? goes well with gin"
01:16 <@fenn> well it's past my bedtime. i believe we've discussed most of this before
01:17 < nmz787> this is pretty similar http://www.sigmaaldrich.com/catalog/product/aldrich/411744?lang=en&region=US
01:17 < nmz787> $1/mL
01:17 < nmz787> so add the activator and you're at the same price as bucktown
01:18 < nmz787> so i guess their visible stuff is OK priced
01:18 < nmz787> maybe they'll sell me less for a sample
01:18 < nmz787> hmm, but they seem to only take paypal
01:19 <@fenn> try asking info@bucktownpolymers.com
01:20 <@fenn> it's probably just one guy
01:22 < nmz787> cool
01:22 < nmz787> thanks
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08:53 < AirmanEpic> hey guys! I'm stefan, curious about biohacking but with very little actual experience
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09:03 < AirmanEpic> ohai
09:04 < yashgaroth> I'll warn you, saturday mornings aren't usually our busiest, but welcome
09:05 < AirmanEpic> thanks. I just recently found this, it was just what I was looking for so I figured I'd keep it open
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09:30 < AirmanEpic> hey, I just remembered what a plasmid is!
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09:30 < yashgaroth> well, good
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09:33 < AirmanEpic> xD this stuff is ridiculously beyond my league.
09:34 < yashgaroth> I recommend a copy of Molecular Biology of the Gene, to be paired with Molecular Biology of the Cell
09:36 < chris_99> yeah i got the latter one, seems really good
09:37 < AirmanEpic> I'm getting the former as we speak
09:37 < AirmanEpic> never really read a textbook before, meh
09:37 < yashgaroth> well you're gonna need to if you want to do anything beyond making a glowing bacterium
09:38 < yashgaroth> and you'll need to read it anyway if you want to understand how you're making said bacterium
09:38 < yashgaroth> don't worry it's easy there's no math
09:39 < AirmanEpic> Which I do, eventually xD. Thanks for the help. What's the craziest thing you've done, yash?
09:40 < yashgaroth> craziest? I try to do everything in a coherent state of mind
09:40 < AirmanEpic> oh. ... well good point
09:40 < AirmanEpic> How about "most impressive"
09:41 < yashgaroth> idk I purified like 15 grams of plasmid last week, that was impressive to me
09:41 < AirmanEpic> what was the plasmid for?
09:41 < yashgaroth> I'm afraid I can't disclose that information since it was for work, but it was part of a DNA vaccine
09:42 < yashgaroth> in my free time, I'm working on a plasmid that expresses follistatin, which I will then inject into my muscles
09:43 < yashgaroth> I hope to have that done within 6 months, depending on a lot of factors
09:44 < AirmanEpic> damn, sorry, I didn't want to pry. I googled follistatin but couldn't get any answers. What is it?
09:45 < yashgaroth> it's one of several inhibitors of myostatin, and myostatin is a muscle regulating factor, i.e. if you reduce the action of myostatin, muscles will grow
09:45 < AirmanEpic> ah so it's a bit of a steriod
09:45 < AirmanEpic> steroid?
09:45 < yashgaroth> yes, in a way, but without most of the side-effects hopefully
09:45 < yashgaroth> not that steroids have many side effects if used correctly, but still
09:46 < AirmanEpic> sweet. That is impressive indeed, good luck, can't wait to see the results
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09:49 < AirmanEpic> this may be a stupid question, but why is it that your body won't reject the plasmids?
09:50 < yashgaroth> the immune system doesn't have any problem with DNA in itself, and follistatin is a normal human protein, I just want to make more of it
09:50 < yashgaroth> most gene therapy work involves viruses and/or foreign proteins, which is when you might get rejection
09:51 < yashgaroth> err, 'foreign' in the sense that you're lacking a normal protein, which would be immunogenic since you don't have it
09:52 < AirmanEpic> I see. That makes sense. Hmmm. Is there a way to make a protein not immunogenic?
09:53 < yashgaroth> you can mess around with the sequence, but not reliably - that's one of the holy grails of biomedicine
09:53 < AirmanEpic> of course xD.
09:53 < AirmanEpic> I was getting all excited
09:54 < yashgaroth> so while those with big research dollaz investigate that, I'm sticking with non-immunogenic proteins that I already have, and having my body make more of them
09:55 < yashgaroth> that's also why I spend a lot of time telling people that getting a glowing GFP tattoo isn't useful for anything at the moment, except as a vaccine against GFP
09:55 < AirmanEpic> exactly. I came to the same conclusion. Or messing with bacteria and keeping them outside the dermis
09:56 < yashgaroth> yes, modifying gut bacteria to make useful things is another interest, and applicable to DIYbio
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09:58 < AirmanEpic> It would be incredibly handy to allow a diet expansion
10:00 < yashgaroth> or contraction - eat whatever you want, and your gut flora will make sure you have enough vitamins, essential amino acids etc
10:02 < AirmanEpic> gut flora xD that's a pretty freakin awesome thought. Could you make something that, say, detects your BMI and adjusts it?
10:04 < yashgaroth> that would be far more complex, but your brain does an okay job of it already
10:05 < AirmanEpic> ah ok.
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10:49 < cpopell> I'll be around here a lot more from now on
10:50 < AirmanEpic> sweet
10:50 < cpopell> fucking budget cuts.
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10:57 < AirmanEpic> budget cuts?
10:57 < cpopell> yeah.
10:57 < cpopell> I worked for the navy
10:58 < AirmanEpic> oh yes.
10:58 < AirmanEpic> Haven't really effected the AF yet
10:59 < cpopell> are you active duty?
10:59 < AirmanEpic> yeah.
10:59 < cpopell> I was two steps away from safety
10:59 < cpopell> I was a civilian contractor
10:59 < cpopell> not even technically a fed employee
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11:00 < AirmanEpic> sorry man
11:00 < cpopell> Shrug.
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11:00 < cpopell> Time to spread my wings.
11:02 < AirmanEpic> metaphorical pr physical?
11:02 < cpopell> metaphorical.
11:02 < AirmanEpic> damn. dreams crushed.
11:03 < cpopell> I already spread them physically :P http://www.exrx.net/WeightExercises/PectoralSternal/DBFly.html
11:03 < AirmanEpic> wasn't exactly what I had in mind ;P
11:08 < cpopell> brb with a real client
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11:13 < ThomasEgi> AirmanEpic, physical wings on humans wouldn't be enough for flying anyway.
11:13 < ThomasEgi> gliding wolud work.
11:13 < chris_99> some cats have wings ;)
11:13 < chris_99> alas they don't fly
11:13 < ThomasEgi> so you could jump down a skyscraper or a mountain wihout breaking your bones
11:14 < ThomasEgi> would still be fun to se a foldable wing for gliding in action.
11:14 < AirmanEpic> I was kidding ThomasEgi, I'm well aware of the lack of muscle structure/bone density
11:15 < chris_99> http://upload.wikimedia.org/wikipedia/commons/thumb/d/df/Wingsuit-01.jpg/300px-Wingsuit-01.jpg ThomasEgi
11:15 < ThomasEgi> chris_99, not exactly what i had in mind with foldable. those are more.. über-cool-falling-suits
11:16 < chris_99> mm, they look amazing fun
11:16 < ThomasEgi> i was more thinking about something that slows your fall down enough to be used to land yourself without breaking everybone in your body
11:16 < ThomasEgi> so maybe somewhere along the 5m wingspan or so
11:16 < chris_99> heh, supposedly iirc some people where going to try and land using one of those wingsuits
11:16 < chris_99> not sure how though
11:17 < ThomasEgi> hm.. you'd have to gain speed first.
11:17 < AirmanEpic> retro rockets, just sayin
11:17 < AirmanEpic> or a huge pile of boxes
11:17 < ThomasEgi> and once you have top speed. you pull horizontal short above the ground. using your momentum and the wings to create vertical lift.
11:17 < ThomasEgi> it': still be a very fast landing
11:18 < ThomasEgi> might work well if you land on wet grass or ice
11:18 < ThomasEgi> where friction is rather low so you don't immedially stumble and roll all over the place
11:18 < ThomasEgi> would be a bit like.. jumping off a speeding car
11:19 < AirmanEpic> why not just use a parachute during the last bit?
11:19 < ThomasEgi> that's standard^
11:19 < AirmanEpic> exactly.
11:19 < ThomasEgi> everyone does that. almost no risk, no thrill, no chance to die or ripp of half your skin on the ground
11:19 < chris_99> haha
11:20 < AirmanEpic> sounds good to me ;D
11:20 < AirmanEpic> http://en.wikipedia.org/wiki/Flying_squirrel
11:20 < ThomasEgi> one idea that i totaly liked.. taking a parachute and be slingshot in the air
11:20 < ThomasEgi> that name is missleading. it's actually gliding
11:20 < AirmanEpic> "This changes the tautness of the patagium, a furry parachute-like membrane that stretches from wrist to ankle.[4] It has a fluffy tail that stabilizes in flight. The tail acts as an adjunct airfoil, working as an air brake before landing on a tree trunk.[5]
11:21 < chris_99> http://www.youtube.com/watch?v=dRB-woVjlFY
11:21 < chris_99> it's been done
11:21 < AirmanEpic> fluffy tails, people, why didn't I think of that
11:22 < ThomasEgi> AirmanEpic, cause if you stuck a fluffy tail to your behind you'd no longer do anything else but be obsessed with your own fluffyness
11:22 < AirmanEpic> I didn't think of that bit.
11:23 < AirmanEpic> you can make it selectively fluffy, only made fluffy instinctively
11:23 < ThomasEgi> those cardboard boxes..
11:23 < ThomasEgi> that'd make the most awesome cardboardboxfortress ever!!
11:25 < ThomasEgi> ok how bout wingsuits and rocketboots?
11:25 < AirmanEpic> been done
11:25 < chris_99> haha
11:25 < AirmanEpic> the trick is coming up with a rocket boot that doesn't kill you with fumes or require huge ammounts of reaction mass
11:26 < AirmanEpic> the only thing they've really come up with is a hydrogen peroxide engine
11:27 < ThomasEgi> hm.. how bout good ol RC turbines?
11:28 < AirmanEpic> highly explosive fuel, fumes, heat, etc.
11:29 < AirmanEpic> http://en.wikipedia.org/wiki/Wingsuit_flying#Jet-powered_wingsuits
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11:31 < cpopell_> hey look a real client
11:31 < cpopell_> lol
11:32 < AirmanEpic> I'm just using the plain old web client xD
11:33 < ThomasEgi> still better than flipping microswitches like  madness
11:34 < AirmanEpic> how so?
11:34 < ThomasEgi> ever typed with microswitches as input?
11:34 < AirmanEpic> ......... no
11:35 < ThomasEgi> aint too much fun
11:35 < AirmanEpic> I beleive you
11:36 < AirmanEpic> I'm making a doorbell for my room.
11:37 < AirmanEpic> dorm* room
11:39 < AirmanEpic> I love how closely related biohacking is to normal hacking
11:40 < AirmanEpic> need a micro xy control for your camera? No worries, plug your arduino board in.
11:40 < AirmanEpic> need a quick centerfuge? 3D print one!
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12:42 < AirmanEpic> I'll be back eventually
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13:05 <@kanzure> "Regaring parseInt(), the story is even more complex though :) You should never use it without the radix because that behavior is not reliable when it comes to implying octal representation. Calling parseInt("016") yields 16 in Chrome (ES5 compliant [1]), while 14 in Firefox, Opera and IE8."
13:05 <@kanzure> https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/parseInt
13:05 <@kanzure> argh javascript
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13:55 <@kanzure> bwahahaha dub of the north star http://www.youtube.com/watch?v=twH93a4JYgI
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15:20 < nmz787> interesting use of microfluidics http://www.tactustechnology.com/documents/Tactus_Technology_White_Paper.pdf
15:20 < nmz787> i want one already
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15:42 <@fenn> tactus technology: bringing new dimensions to sexting
15:43 <@fenn> it's not very many buttons
15:46 <@fenn> it seems like they're not addressable, just inanimate plastic blobs that you can push
15:46 <@fenn> "A class-action lawsuit
15:46 <@fenn> was filed by LightHouse for the Blind and Visually Impaired against videodisc rental service
15:46 <@fenn> Redbox
15:47 <@fenn> why do blind people need access to video disc rental?
15:47 <@kanzure> because maybe they watch movies
15:47 <@kanzure> legally blind is not no visual input whatsoever
15:47 <@kanzure> s/no visual input/no audio-visual input whatsoever
15:48 <@kanzure> blergh broken regex.
15:48 < juri_> i support a blind user, who enjoys all kinds of series'. he just listens to them.
15:48 <@kanzure> but, realistically, they should use torrents and not be subjected to the horrors of redbox
15:49 <@kanzure> braille computer interfaces are terrible and evil, people think that crippling a device for a cripple is a good idea
15:50 <@kanzure> "let's put windows ce on it! yeah!"
15:50 < juri_> my blind user uses windows XP.
15:51 <@fenn> i'm really wondering why there aren't any good or popular audio operating systems in common use
15:51 <@fenn> at least some kind of standard interface that could be implemented anywhere
15:51 <@kanzure> 口笛が聴こえるiu ios has good tty support i hearos
15:51 <@kanzure> wtf happened in that message
15:52 < juri_> something something something speaking?
15:52 <@fenn> "whistle can be heard"
15:53 < juri_> i still have basically no kanji.
15:53 <@fenn> i cheated :)
15:53 < juri_> :P
15:53 <@kanzure> ah i blame hiei http://www.youtube.com/watch?v=0XHa2HMBxiU
15:53 < juri_> me and my partner are both teaching ourselves japanese.
15:54 < juri_> we're to the point where we watch as much anime without subs, as with subs.
15:54 <@fenn> ... and you can understand anything?
15:54 < juri_> oh yes.
15:55 <@fenn> kanzure: you listen to jpop?
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15:55 <@kanzure> juri_: then you can join us for the hplusroadmap re-enactment of 北斗の拳
15:56 <@kanzure> fenn: sorta.. http://www.youtube.com/playlist?list=PL85F050BEFA28E044
15:56 < juri_> kanzure: again, i don't do much kanji. ;)
15:57 <@fenn> fist of the north star
15:57 <@kanzure> dub of the north star was hilarious. "last time on mad max..."
15:57 < juri_> mm. not one of my series.
15:57 <@fenn> it's what will happen when yashgaroth's myostatin inhibitors interact with the ultrasonic transcranial stimulation
15:58 <@kanzure> or when we revive bruce lee through skeleton dna sampling
15:58 <@fenn> how does he expect plasmids injected into the muscle to be expressed anyway?
15:59 < yashgaroth> by strong viral promoters
15:59 <@fenn> but mammalian cells aren't competent
15:59 <@kanzure> he has spoken
15:59 <@kanzure> electroporation
15:59 < yashgaroth> you make them competent with elec yeah
15:59 <@fenn> in vivo electroporation?
15:59 <@kanzure> ex vivo
15:59 < yashgaroth> fuck yeah bro
15:59 < yashgaroth> it's in vivo
15:59 <@fenn> ex vivo, so, red blood cells?
15:59 < yashgaroth> all up in those vivos
15:59 <@kanzure> erm, i mean, stabbing yourself
16:00 <@fenn> okay so, uh, how do you keep from burning the shit out of yourself with the electricity
16:00 < yashgaroth> it's only a millisecond pulse
16:00 <@fenn> but it's a lot of energy
16:00 < yashgaroth> not necessarily
16:00 <@fenn> i mean it works by ripping holes in the membrane
16:00 < yashgaroth> small, transient holes
16:01 < yashgaroth> also there's theoretically an electrophoresis effect
16:01 <@kanzure> what's wrong with steroids again?
16:01 < yashgaroth> nothing, really
16:02 < yashgaroth> ironically, experimental genetic augmentation is easier for me
16:02 <@fenn> steroids don't do quite the same thing
16:02 <@fenn> you still have to lift weights to gain muscle with steroids
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16:03 < yashgaroth> you still gain some muscle just sitting around with 'roids
16:03 <@kanzure> no you gain just by sitting around
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16:03 <@kanzure> not as much
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16:04 <@fenn> huh so this is basically the same technology as the DNA vaccine you're doing
16:05 < yashgaroth> which DNA vaccine, the one I mentioned to that diybio fellow?
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16:06 < yashgaroth> pretty much all DNA vaccines and non-viral gene therapy trials these days use electroporation, and many of them use Ichor Medical's electroporator
16:07 <@fenn> man that's some star trek shit
16:08 < yashgaroth> yeah I don't know why they designed it like that
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16:09 < yashgaroth> anyway point is you get a solid 100-1000x increase in plasmid uptake, which is better/cheaper/less toxic than all the various chemicals that people otherwise use for transfection
16:11 < cpopell> yash, I got my 23andme results.
16:11 <@fenn> i guess it's easier than viral packaging?
16:12 < yashgaroth> cpopell: yeah you mentioned, and also my condolences - about the work stuff that is, not your genes
16:12 < cpopell> Shrug. Going to spread wings a bit.
16:12 < cpopell> anyway, I'm 47.6% ashkenazi :V
16:12 < cpopell> my dad was way, way more pure blood than he thought he was.
16:12 < yashgaroth> it's quite a lot easier than viruses, though mostly I dislike viruses because you need to be on severe immunosuppressants before/during/after
16:12 < yashgaroth> congrats
16:12 <@fenn> oh i didn't know that
16:13 <@fenn> people aren't exposed to milligrams of intravenous viral material in the wild
16:13 < yashgaroth> and most wild-type humans have pre-existing immunities to AAV, the current darling viral vector
16:14 < yashgaroth> unlike the lab monkeys and mice that they test it on
16:14 < yashgaroth> so you have an initial response that kills all cells that took up the viral particles, and then you develop a neutralizing response the next time you need said virus
16:15 < yashgaroth> I mean, you can try doing immunosuppressants for a month, but I'm sure as fuck not doing that outside of a bubble-boy bubble
16:15 <@fenn> yeah that sounds sub optimal
16:16 < yashgaroth> so if you've got [serious medical condition] viruses are fine, since you'd die otherwise
16:17 <@fenn> did my idea of ex vivo electroporation with blood cells make sense? does follistatin need to be expressed in muscle tissue?
16:17 < yashgaroth> it makes sense; it doesn't necessarily need to be in muscle cells, but it's a semi-localized effect so you'd need a lot of it circulating, which can cause off-target effects
16:17 < yashgaroth> also muscle cells persist for a long time so you get excellent duration, unlike skin/liver/immune cells
16:18 <@fenn> well that's not necessarily a good thing if you discover unexpected side effects
16:19 < yashgaroth> there's been a few studies, they haven't noticed anything weird; primary concern is effects on your nads
16:19 < AirmanEpic> hope you like your brand new fur xD
16:19 < yashgaroth> here's one in primates that's now in clinical trials http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852878/
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16:21 < AirmanEpic> well there ya go, no need to worry
16:21 <@fenn> cool. i didn't think it would be so easy to do this
16:21 < yashgaroth> oh it won't be easy, plasmids are still far less efficient than viruses
16:21 < yashgaroth> there's some optimization you can do, but still
16:22 <@fenn> how are you cloning plasmids?
16:22 < yashgaroth> the traditional way
16:22 < yashgaroth> btw our diybio lab in san diego got approved
16:23 < AirmanEpic> nice. 'gratz.
16:23 <@fenn> what's "approved" mean?
16:24 < AirmanEpic> by the way, can you get off of immunosupressants once the virus is through it's course?
16:24 < yashgaroth> the city agreed to lease us the space for $1/year and pay all utilities
16:24 < yashgaroth> you can go off immunosuppressants once all the viral particles have been digested by your cells, so maybe like a week after or something idk
16:24 <@fenn> the reason i ask about cloning is if people start injecting themselves with lysate they might not know about endotoxin and so on
16:24 < yashgaroth> well I am going to purify it
16:25 < yashgaroth> endotoxin is fairly easy to separate from plasmid with the right protocols, as it turns out
16:25 <@fenn> how do you get just plasmid dna and not genomic dna? (don't you need large quantities of DNA too?)
16:26 < yashgaroth> genomic is harder to separate but it's usually only a tiny fraction, same with RNA
16:26 < yashgaroth> current FDA regs are like 1% genomic, which is high, but the method I have access to is very good at separating that out too
16:26 < AirmanEpic> might i ask what endotoxin is?
16:27 <@fenn> AirmanEpic: bacterial cell wall material; it's inherently irritating to your immune system and can cause side effects
16:27 < yashgaroth> damn your fast fingers, yes
16:27 < AirmanEpic> how bad, and what can you do to prevent it?
16:27 < AirmanEpic> bow shicka xD
16:27 < yashgaroth> anything up to and including septic shock
16:27 < AirmanEpic> oh shyt.
16:28 < yashgaroth> I always wonder how heroin addicts get away with it since heroin ain't exactly endo-free
16:28 <@fenn> honestly i dont know that much about it
16:28 <@fenn> well heroin is a semi purified product
16:29 < yashgaroth> sure, but they're handling it with their grubby fingers and filth-infested spoons and whatnot
16:29 <@fenn> i mean it's not a bacterial culture lysate
16:29 < yashgaroth> true, but anyway my previously mentioned method is capable of <1EU/mg easy
16:30 < yashgaroth> nonetheless I'll need to hunt down some horseshoe crab blood to make sure
16:30 <@fenn> how does EU compare to CFU or ng or whatever
16:31 < yashgaroth> 1 EU is like 1ng or something, I'll check
16:31 < yashgaroth> ah 5 EU/ng
16:31 < yashgaroth> CFU is harder to compare
16:31 <@fenn> 1 EU = "about 10^5 bacteria"
16:32 < AirmanEpic> horseshoe crab blood... you put foreign cells in it and it clumps up, right?
16:32 < yashgaroth> yes, it's the classic assay for endotoxin
16:33 < yashgaroth> CFUs will be approximately 0 since the final DNA process uses ethanol, and I've purified plasmid hundreds of times from culture and not had any issue with contamination
16:33 < yashgaroth> assuming a working tissue culture hood, which I'm buying for the diybio lab
16:33 <@fenn> well sure, because most molecular protocols kill bacteria through sheer chemical harshness
16:34 <@fenn> but the dead cells are still there
16:34 < yashgaroth> sure, but you can reliably bind DNA to a resin and not endotoxins, then wash
16:35 <@fenn> so do you think this method would work for any peptide hormone?
16:35 < yashgaroth> depends on the peptide, but "probably"
16:36 <@fenn> i'm personally more interested by HGH than myostatin
16:36 <@fenn> of course you can just get HGH on the grey market
16:36 < yashgaroth> still expensive as fuck
16:36 <@fenn> yeah, so if you're taking it daily as anti-aging therapy it's not feasible with the current system
16:36 < yashgaroth> problem is, I doubt many labs will sell you either the HGH gene or the primers to get it
16:37 < yashgaroth> and even if you get the primers you still need a fresh human pituitary gland
16:37 < AirmanEpic> is there something I can use to restrict hair growth for a long time, like 2-4 years, but not permanently?
16:37 < yashgaroth> wax and lasers
16:37 <@fenn> i thought those blacklists were only for bio weapons and smallpox etc
16:37 < yashgaroth> HGH is anti-aging now? what the hell
16:37 <@fenn> has been for some time
16:37 < yashgaroth> sure but I'm not risking the DEA coming down on my ass
16:37 < AirmanEpic> thanks yash xD
16:38 < yashgaroth> the synthesis companies don't *have* to report it, but they might just for kicks
16:38 <@fenn> well anyway the genome is known and gene synthesis is coming down in price
16:38 < yashgaroth> coming down excruciatingly slowly
16:38 <@fenn> but purified HGH is going UP in price
16:38 <@fenn> same old prohibition story
16:39 < yashgaroth> because they can (tm)
16:40 <@fenn> who would they report it to anyway
16:40 < yashgaroth> DEA handles HGH
16:40 < yashgaroth> and they have a lot more guns than the FDA
16:40 <@fenn> bizarre
16:41 <@fenn> "co-sponsored by the Death Enforcement Administration"
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16:41 < AirmanEpic> just head to nebraska and do it in an underground lab. They'd never find you.
16:42 <@fenn> AirmanEpic: that's part of why we're working on a DIY DNA synthesizer
16:42 < yashgaroth> once you have the gene it's no problem, the main concern is sourcing that
16:42 < yashgaroth> I could just go to mexichina and do it there if I was that worried
16:43 < AirmanEpic> DNA synthesis. How do you do that?
16:43 <@fenn> what about site specific mutation of ... monkey pituitary or something
16:43 <@fenn> nevermind that's stupid
16:43 <@kanzure> AirmanEpic: http://diyhpl.us/wiki/dna-synthesis.html
16:43 < yashgaroth> no, I considered it; that's a whole lot of mutations and the primers you need for that would also indicate you're working with HGH
16:43 <@kanzure> AirmanEpic: http://diyhpl.us/~bryan/nucleic/fbi-diybio-dna-v1.pdf
16:43 < AirmanEpic> holy wall of text *gets reading*
16:44 < yashgaroth> even a 20 basepair primer for site mutations would pinpoint which gene you're working on
16:45 <@fenn> oh, it's genomic so you don't need pituitary tissue
16:45 <@fenn> *bonk*
16:45 < yashgaroth> I meant pituitary so you could get the cDNA
16:45 < yashgaroth> if you take it from genomic you'll just need a lot more incriminating primers
16:46 <@fenn> huh? it's not rocket science to screen for the complementary sequence as well
16:46 < yashgaroth> yeah, it's just a fuckton of sequencing and cloning and libraries
16:47 <@fenn> hold on, let me read up on cDNA
16:48 <@fenn> why can't you just clone the genomic DNA and let the target (human) cell do all the intron/exon crap after electroporation
16:49 <@fenn> is it to get good expression?
16:49 < yashgaroth> that would make the vector extremely large, which means low expression
16:49 < yashgaroth> and still requires HGH-specific primers, which we're being paranoid about ordering
16:49 < AirmanEpic> my cells can make copies of my  genome all day long for $0.00001/genome. This  shows that lower costs are at least imaginable.
16:49 < AirmanEpic> xD
16:50 < yashgaroth> copies are cheap
16:51 < yashgaroth> the only way you'd be able to do it without ordering hgh-related primers is to make a library of all RNAs in a human pituitary, clone those into bacteria, and sequence several thousand until you find HGH
16:52 < yashgaroth> maybe lower that to a few hundred with some creative size-based separation of the cDNAs
16:52 <@kanzure> for the record, i never explored the costs or mechanisms of a non-microfluidic dna synthesizer so nobody should assume i covered those bases.
16:53 <@fenn> iirc the main cost in bulk DNA synthesis was the initial five or six bottles of phosphoramidites
16:53 <@fenn> the actual mixing and stirring is relatively inexpensive
16:53 <@kanzure> no i mean the machines
16:53 <@fenn> the machines dont come with reagents do they?
16:53 <@kanzure> i haven't figured out if they are just extraordinarily expensive because of bullshit or if the components are actually really that expensive
16:54 < yashgaroth> they do need to be fairly high-purity
16:54 <@fenn> depends on how long the oligos you're making need to be
16:54 <@kanzure> 'cause it might turn out that ubilding a bigger synthesizer might make more sense, especially since those sorts of components can be found at hardware stores
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16:54 < yashgaroth> there's also the cost of sequencing each ~50bp fragment to make sure they're correct before you string them together
16:55 <@fenn> just for cloning, not gene synthesis i meant
16:55 < yashgaroth> oh, then it's much easier yeah
16:55 <@fenn> gene synthesis is currently expensive for precisely this reason, the cost of bulk synthesis reagents
16:56 <@kanzure> that doesn't explain why the machines cost a lot too
16:56 <@fenn> oh that's just the usual business to business scam paradigm
16:56 < AirmanEpic> Kanzure: how can you make channels that small?
16:56 < yashgaroth> that seems odd since you use such a tiny amount, I mean you only need microgram yields on the oligo
16:56 <@kanzure> lasers
16:56 <@fenn> "call and ask us for a quote"
16:57 <@fenn> yashgaroth: it's true, if there were a good method of accurately synthesizing micrograms of DNA it would drop the cost of gene synthesis
16:57 <@fenn> this is what cambrian genomics is trying to do
16:57 < yashgaroth> yes how is anselm these days
16:57 <@fenn> i haven't talked to him for a long time
16:58 < yashgaroth> I still have no idea exactly what technique(s) they're using so I can't really say how realistic or useful his methods will be
16:58 < yashgaroth> except the whole lasers thing
16:58 <@fenn> i kind of want to go back to the bay area, but so do 9 million new yorkers
16:58 < AirmanEpic> Does DIYbio have the equipment to make that?
16:58 <@kanzure> AirmanEpic: http://diyhpl.us/laser_etcher/laser_etcher
16:59 < eudoxia> hi AirmanEpic
16:59 < eudoxia> welcome
16:59 < AirmanEpic> oh thanks eudo.
16:59 < AirmanEpic> I'm stefan, I'm very, very new at biohacking but would like to get further into it
16:59 <@fenn> yashgaroth: they're doing UV directed synthesis on beads, then sequencing each bead (which should be a single strand that's been cloned on the surface of the bead) to verify that each oligo is correct
17:00 < eudoxia> hi cpopell, sorry about your job
17:00 < yashgaroth> single strand, as in single molecule per bead?
17:00 <@fenn> yes at first
17:00 <@fenn> you can't sequence a single molecule though so they amplify it on the bead
17:01 <@fenn> it's like having a lot of little wells on a plate, but you use beads instead of wells
17:01 <@fenn> i forget the buzzword
17:01 <@fenn> clonal amplification?
17:01 < yashgaroth> sure, but I mean they'd need to have literally a single molecule that gets amplified, otherwise you can't get an accurate read on the sequence
17:02 < AirmanEpic> still in awe of this picture. http://gyazo.com/e5c31102fbcaf21f99c27f8256ad3a60. all you'd really need to do is laser ech a whole bunch of super thin slides
17:03 < yashgaroth> I can see what they're going for, just seems like several technologies that we don't have need to come together
17:03 <@fenn> apparently everything is standard tech in sequencers already
17:03 <@fenn> except for the bead handling
17:04 < yashgaroth> well you can do single-molecule sequencing, sort of/sometimes
17:04 <@fenn> "All second-generation platforms (except Helicos) rely on some clonal amplification method. Bridge amplification (two-dimensional PCR)"
17:05 <@fenn> http://seq.molbiol.ru/sch_clon_ampl.html has some nice drawings
17:05 < yashgaroth> I've still no idea how they ensure literally a single strand is grown on each bead
17:06 < yashgaroth> how do you enforce a single atomic nucleation point
17:06 <@fenn> uh, i could be wrong about the process
17:07 < yashgaroth> this is why I wish he'd release some info, though I grudgingly accept why he doesn't
17:07 <@fenn> this say they use emulsion PCR http://www.laserfocusworld.com/blogs/spectralbytes/2012/12/how-laser-printing-builds-dna.html
17:08 <@fenn> oh i get it
17:08 <@fenn> 1) synthesize dna on a plate 2) release dna into solution 3) bind single molecule to bead
17:08 < yashgaroth> it's the " single molecule to bead" part that gets me
17:08 <@fenn> that's just statistics
17:09 <@fenn> if you have two dissimilar sequences on a single bead your sequencing comes out as garbage
17:09 <@fenn> so aim to have just enough dna in solution that you aren't wasting beads by letting them go empty, but not too much to keep from having more than one strand per bead
17:10 < yashgaroth> even cutting-edge single-molecule sequencing still has an obscenely high error rate what with the signal/noise
17:11 <@fenn> you sequence multiple points in the gene synthesis assembly process, so that should weed out any PCR errors
17:11 < yashgaroth> but you're relying on reads on the short oligos to determine which ones to use for the longer gene synthesis
17:12 <@fenn> yes, and you sequence the larger constructs too
17:12 < yashgaroth> and with the short oligos on beads you either have a crappy signal from single-molecule, or you have ambiguity about which sequence you get by using multiple templates
17:12 < yashgaroth> in that case it's just traditional gene synthesis at a smaller scale
17:13 <@fenn> hm
17:14 < yashgaroth> he's a smart guy and so is Church, so hopefully they have something
17:14 <@fenn> i assume the error rate of new polymerases is lower than the error rate of UV directed synthesis
17:14 < yashgaroth> it's not the polymerase you have to worry about, it's the signal-reading method
17:15 < yashgaroth> assuming you even have a single molecule that's bound to a trackable bead, your read won't be more accurate than your synthesis process
17:16 <@fenn> of course
17:16 <@fenn> wait, don't you mean "read wont be more accurate than your amplification process"
17:17 < yashgaroth> pcr amplification is pretty okay with new high-fidelity polymerases, like 1/30,000bp or something
17:17 < yashgaroth> the error rate, that is
17:17 <@fenn> sure but if you're amplifying 10^5 times it adds up
17:17 < yashgaroth> yes and that's another problem, but since those errors are distributed across many molecules you still get a clean read
17:18 < yashgaroth> randomly across many molecules, I should say
17:18 <@fenn> okay so what's the problem
17:18 <@fenn> that there's no single perfect gene anywhere?
17:18 < yashgaroth> well you've got your single molecules, and you bind them to single beads somehow: any sequencing method you use on them won't be accurate enough to rely on
17:19 < yashgaroth> so you shuttle in the "good" ones for gene synthesis, but that makes it no better than traditional methods
17:19 <@fenn> oh, btw you can use yeast cloning which has fantastically low error rates
17:19 < yashgaroth> even e.coli has super-low error rates
17:20 < yashgaroth> the errors come from the CCD or nanopore or whatever method you use
17:20 <@fenn> sure, so once you've got something large enough that it makes sense to clone, you clone it and then sequence it, and all the DNA in that blob of goo is the same sequence
17:21 < yashgaroth> cloning into a cell is gonna be extremely involved with that many sequences, and no one's really miniaturized it
17:21 <@fenn> the longer the sequence the more likely it has an error, so it's a tradeoff between cost of synthesis and cost of cloning
17:22 <@fenn> i'm not worried about sequencing fidelity
17:22 < yashgaroth> you should be
17:22 < yashgaroth> and that's traditional synthesis, where they get a 50bp oligo and clone+sequence it before moving it into a larger assembly anyway
17:22 <@fenn> sequencing read errors are random error, not systematic error
17:23 < yashgaroth> well, usually, but yes
17:23 <@fenn> why bother cloning a 50bp sequence? just pretend it's good and concatenate enough oligos until you start getting errors
17:24 < yashgaroth> that's what trad methods probably do these days anyway, I don't know
17:25 <@fenn> the other thing you're forgetting is this is happening massively parallel, there's no need to miniaturize the cloning step
17:25 < yashgaroth> if they can get a single molecule+bead into a well, and then amplify it, and then sequence that amplification product, then it'd work, so that's what I assume they're doing
17:25 < yashgaroth> massively parallel, *and* disruptive? my god
17:25 <@fenn> heh
17:26 < yashgaroth> all they need is some genetic algorithms and bam
17:26 <@fenn> heh
17:26 <@fenn> grr
17:26 < yashgaroth> I guess my main concern is their ability to get single molecules onto single beads
17:27 < yashgaroth> I don't know how the hell they catalyze single sites, and/or ensure that's happening reliably enough to count on
17:27 <@fenn> no that's not what's happening
17:27 < yashgaroth> then [my previous concerns]
17:27 <@fenn> you UV synthesize on a plate, then transfer individual molecules to beads
17:28 < yashgaroth> how do they get a bead with a single functional group on the whole bead
17:28 <@fenn> the bound oligos are amplified on the bead surface with "2d" surface-bound pcr
17:28 < yashgaroth> yes that part works in my mind
17:28 <@fenn> generic primers are bound to the bead surface
17:29 < yashgaroth> sure you can use vanishingly small concentrations of DNA to hope that only one binds per bead, but that sounds like a technical clusterfuck
17:30 <@fenn> 33% of the time there's nothing on the bead but primers, 50% of the time there's one molecule, the rest of the time there's more than one molecule (numbers made up for conversation's sake)
17:30 < yashgaroth> but it's more like 99.9% have nothing but primers
17:30 <@fenn> why you say that?
17:31 < yashgaroth> because otherwise you'd end up with 99.9% having 2+ molecules
17:31 < yashgaroth> this is where the money would be going, not the PCR steps
17:31 -!- lolcat is now known as Mikel
17:31 <@fenn> i'm really not sure how the statistics work out here
17:32 < yashgaroth> everything after "single molecules on single beads" is relatively simple
17:32 < yashgaroth> I don't do statistics I'm a biologist
17:32 <@fenn> in the article it says "synthesize 10^6 oligos, sequence 10^9 beads, laser eject 10^6 beads"
17:32 <@fenn> so you're right, 99.9% of the beads are wasted
17:32 <@fenn> how many nines is that
17:33 < yashgaroth> ok if they're categorizing and saving each single-molecule bead I can see it working, where they just build libraries of single sequences
17:33 < yashgaroth> and dole them out as needed for a gene, like what our project is hopefully going to do
17:34 < yashgaroth> also, 10^9 sequences per oligo seems expensive compared to traditional methods, no matter how massively parallel it is
17:34 <@fenn> yeah i don't really get that part
17:34 < yashgaroth> or 10^6 whatever it's still a lot
17:35 <@fenn> maybe they meant "stain for DNA"
17:35 < yashgaroth> nah it still needs to be sequenced, I'd think
17:36 < yashgaroth> oh right for determining which beads have DNA, then yeah maybe
17:36 <@fenn> dont you love publically funded science
17:36 < yashgaroth> haha
17:36 <@fenn> :(
17:36 < AirmanEpic> @fenn, if you have .1% of all your beads wasted, isn't it easy to copy the working ones?
17:37 < AirmanEpic> sorry 99.9% wasted
17:38 <@fenn> AirmanEpic: sort of, there's still the problem of polymerase errors in amplifying the single molecule
17:39 < AirmanEpic> What is a polymerase?
17:39 < yashgaroth> oh dear
17:39 <@fenn> an enzyme that copies DNA
17:39 <@fenn> but if you don't know that you aren't going to understand what we're talking about anyway
17:39 -!- Mikel is now known as lolcat
17:40 < AirmanEpic> =/ I'm trying but I really suck at memorizing all the terms
17:40 <@kanzure> ArmilusDajjal: http://www.youtube.com/watch?v=teV62zrm2P0
17:40 < yashgaroth> it's not about memorizing, it's about 'oh good there's a word for this thing so I don't need to use 10 words to describe it each time'
17:41 < AirmanEpic> it's always a freakin long and latinish name.
17:41 < yashgaroth> 4 years of latin did spoil me, I'll admit
17:41 < AirmanEpic> why can't we just be like coding. "oh, that's a copier"
17:41 <@fenn> huh they actually sequence the beads on the slide
17:41 < yashgaroth> kanzure I think you username-autofinished one too few/many times
17:42 < ArmilusDajjal> lol
17:42 <@kanzure> yashgaroth: ?
17:42 < yashgaroth> yes but once you get a hundred different enzymes "copier" becomes too simplistic
17:42 <@kanzure> oh right
17:42 <@kanzure> AirmanEpic.
17:42 < AirmanEpic> oh yes, I get it. I remember this from high school now
17:42 < AirmanEpic> just didn't remember the term
17:43 <@kanzure> you went to high school? get the hell out.
17:43 <@fenn> AirmanEpic: there actually is a naming system that makes a bit of sense.. usually the enzyme is named after its substrate, and ends with -ase
17:43 < AirmanEpic> Gah damng it
17:43 < AirmanEpic> dang it*
17:43 < AirmanEpic> sorry fenn, I gotta run 'cause I went through highschool.
17:43 <@fenn> it's actually called "DNA polymerase"
17:44 < AirmanEpic> and there are multiple polymerases? dear god
17:45 <@fenn> there's RNA polymerase, and about ten different versions of each
17:45 < AirmanEpic> my dreams of world domination may have to wait for a while while I wrap my head around these terms
17:45 < AirmanEpic> and the concepts
17:45 < yashgaroth> it happens
17:46 < yashgaroth> but hey I don't know the difference between the many types of RNA pol, because fuck that, I can look it up
17:46 < yashgaroth> also because I don't really work with RNA, thank fuck
17:47 <@fenn> fuck welcomes you
17:47 < yashgaroth> RNA is just an annoying intermediate between the glorious DNA and proteins, but that's a whole other thing
17:48 <@fenn> i think you've got it backwards
17:48 <@fenn> DNA is just an annoying intermediate between RNA and proteins :P
17:48 < AirmanEpic> fuck has been really active today
17:49 < yashgaroth> "ooh look at me I'm RNA I can carry information and perform enzymatic functions" well that's what DNA and proteins are for you asshole RNA
17:49 < yashgaroth> p.s. fuck
17:50 <@fenn> maybe you can invent DNA based life and shock the world
17:50 < yashgaroth> wow I am bizarrely biased against a molecule
17:50 <@fenn> straight from genome to protein in one step
17:51 < AirmanEpic> nah, I feel like DNA based life is a little too over the top
17:51 < AirmanEpic> like hipster glasses
17:52 <@fenn> you'd have to have a very wide array of promoters to make different amounts of protein
17:52 <@fenn> also there's that whole tRNA thing
17:53 < yashgaroth> 5' UTRs and RNAi are just RNA's way of trying to keep itself relevant
17:53 < yashgaroth> yeah it's not a realistic proposal, my plan of a superior DNA->protein master race will have to wait
17:53 <@fenn> you're so eukaryo-centric
17:53 < yashgaroth> nuclei4lyfe
17:54 <@fenn> how can you have a dna based life with a nuclear membrane? it's hopeless
17:54 < yashgaroth> it's an RNA conspiracy
17:54 <@kanzure> check the eukaryotic privilege
17:59 <@fenn> yashgaroth: so i guess they can sequence 10^6 beads at once because there's enough optical signal from millions of oligos on each bead
18:00 <@fenn> pacific bio had problems with optical SNR because they were doing single molecule sequencing
18:00 < yashgaroth> yeah it's probably something like pacbio's deal
18:00 < yashgaroth> I don't know about millions if they only have a single template molecule though
18:01 < yashgaroth> it just seems like the kind of thing they'd need millions for to get the whole thing working
18:01 < yashgaroth> millions of $ I mean
18:01 <@fenn> it's pyrosequencing
18:02 <@kanzure> "This weekend is Ushicon, an 18+ anime convention. By 18+, we mean *no teenagers*, not adult content. This will be held from Feb 8 to 10 in Round Rock, TX.
18:02 <@kanzure> It'll be fun."
18:02 <@kanzure> do i dare..
18:02 < yashgaroth> uguu~~
18:02 < yashgaroth> also, more like 10s-100s of million $s
18:03 <@fenn> do you have a sailor moon costume :\
18:03 <@fenn> yashgaroth: why would you need that much money for development?
18:03 < yashgaroth> because biotech
18:04 <@fenn> to pay 5 guys and their robots?
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18:04 < yashgaroth> well sure if they want to take a hundred years to develop it
18:05 <@fenn> money doesn't automatically speed things up
18:05 < yashgaroth> it don't hurt
18:06 < yashgaroth> I kind of feel like all this speculating is for naught when I don't have access to their specific methods
18:06 <@fenn> it does if you lose all your equity
18:06 < yashgaroth> I don't really know what equity is, so
18:06 <@fenn> stock in your own company
18:07 < yashgaroth> oh, yeah
18:07 < yashgaroth> well I wish them the best of luck
18:07 <@fenn> VC's don't just give you money, they buy stock. if you sell all your stock you don't get rich when the company goes big (presumably when you're done making X gizmo work)
18:08 < yashgaroth> oh right the whole rich thing
18:09 <@fenn> there's also maintaining control of your company
18:11 < yashgaroth> see this is why I'm not in business...this and many other reasons
18:12 <@fenn> this is a bit ridiculous (list of companies co founded by george church) http://arep.med.harvard.edu/gmc/tech.html
18:13 < yashgaroth> he really needs to get around to adding this channel to that list
18:13 <@kanzure> he probably doesn't remember that he handed me a penny at a conference in 2009
18:13 < yashgaroth> maybe we could work out a deal with just his beard
18:14 < yashgaroth> legally it operates independently of his body
18:14 <@fenn> aubrey de grey has a patent on autonomous beard technology
18:14 < yashgaroth> aubrey is simply a puppet for his sweet beard
18:14 <@fenn> then the beard has the patent
18:15 < yashgaroth> I'm no expert in beard law
18:15 <@kanzure>  http://diyhpl.us/~bryan/irc/aubrey.jpg
18:15 <@fenn> hey it's not any crazier than patenting genomes
18:17 <@kanzure> ah he's on the board of sigma and NEB
18:17 <@kanzure> pfft "Edge Foundation 1988 (2005-present; science communication) "
18:17 <@fenn> jealous?
18:17 <@fenn> you could be part of the "third culture"
18:17 <@kanzure> :(
18:18 <@kanzure> i
18:18 <@kanzure> i'm gestalt, i swear.
18:18 < yashgaroth> oh huh cambrian is listed under "past advisory roles", 2011-2012
18:18 <@kanzure> third culture always sounded like protoculture to me
18:19 <@kanzure> yashgaroth: interesting detail
18:19 <@kanzure> he is still listed on
18:19 <@kanzure> https://angel.co/cambrian-genomics
18:19 <@fenn> church was estimating $1500 per genome (40x coverage) in 2009, what happened there?
18:20 < yashgaroth> I've no idea what that means, but george church getting *out* of an advisory role must take something serious, considering
18:21 <@kanzure> we should track changes to this page. he seems to keep it somewhat updated.
18:21 < yashgaroth> fenn: that's black market prices, I've got a guy in hong kong who can sequence your genome for $1000 no questions asked
18:21 <@kanzure> well fuck you too
18:21 <@kanzure> i'll take one
18:21 <@kanzure> what coverage?
18:21 < yashgaroth> oh you know, enough
18:22 <@fenn> he was estimating consumable costs and with labor it's more like $4k
18:22 <@fenn> "for bulk orders of 50 or more"
18:22 < yashgaroth> also the 'no questions asked' part was on the consumer end
18:23 <@fenn> hm?
18:23 < yashgaroth> oh, nothing
18:23 <@fenn> like if you have obama's napkin or something?
18:24 < yashgaroth> guys don't worry, the government sequenced everyone's genomes back in the 2000s as part of operation Omeg
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18:24 < yashgaroth> :V
18:24 -!- kanzure changed the topic of ##hplusroadmap to: biohacking, nootropics, transhumanism, open hardware | sponsored by george church and the NRA | http://gnusha.org/logs http://diyhpl.us/wiki http://groups.google.com/group/diybio | banned by the Federal Death Administration | 3.5 kidneys for sale | no questions asked
18:25 < AirmanEpic> can I get a third of a kidney please?
18:25 < yashgaroth> 'federal death administration' sounds like an alex jones thing, I wonder if we could get him to sponsor as well
18:25 <@kanzure> yashgaroth: sadly people might take that one seriously, so no thanks
18:25 < yashgaroth> heh
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18:57 <@kanzure> gene_hacker: welcome back
19:00 < gene_hacker> kanzure is this article paywalled for you? :http://nar.oxfordjournals.org/content/32/18/5409.full
19:02 < gene_hacker> anyway, I just figured something out
19:02 <@kanzure> paperbot: http://nar.oxfordjournals.org/content/32/18/5409.full
19:02 < gene_hacker> you know that microfluidics thread in diybio where they showed you can use a diy laser cutter to make microfluidics?
19:02 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences.pdf
19:02 < gene_hacker> it should be free isn't it?
19:02 <@kanzure> hey wait i published in this journal before
19:03 < gene_hacker> what?
19:03 <@kanzure> this is nar
19:03 < gene_hacker> oh on aptamers?
19:03 <@kanzure> nah on bioinformatics things
19:03 <@kanzure> anyway that paper seems to be open access
19:03 < gene_hacker> anyway, that diy lasercutter has sufficient resolution to make a kilobase level DNA synthesizer
19:04 <@kanzure> also it's in my collection already,
19:04 <@kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf
19:04 < gene_hacker> figured as much
19:04 <@kanzure> gene_hacker: have you seen http://diyhpl.us/laser_etcher/laser_etcher
19:05 < gene_hacker> hacketeria laser cutter is simpler
19:05 <@kanzure> it had a cutting area of only 45 mm^2
19:06 <@kanzure> is this it? http://hackteria.org/wiki/index.php/DIY_Micro_Laser_Cutter
19:06 < gene_hacker> yup
19:06 < gene_hacker> it is sufficient for microfluidics
19:06 <@kanzure> nmz787: are you around?
19:07 < AirmanEpic> man, that's sweet. Do you just epoxy each layer of glass together?
19:08 < gene_hacker> nah, you use pdms and electrical tape
19:08 < gene_hacker> though I wonder if the process could be adapted to use something more solvent resistant
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19:26 <@kanzure> gene_hacker: there are other things worth reading here, http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/
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19:39 < gene_hacker> picoarray is nice because it's massively parallel
19:39 < gene_hacker> and uses up very small amounts of oligos
19:40 <@kanzure> damn it i should seriously stop writing annotations about papers in irc, it makes it hard to find my notes
19:41 <@kanzure> 16:18 < kanzure> ok i don't get it. xeotron made this microfluidic picoarray dna synthesizer in 2003ish
19:41 <@kanzure> 16:18 < kanzure> had $45mil in sales
19:41 <@kanzure> 16:18 < kanzure> got bought by invitrogen. and now no such product is on the market.
19:41 <@kanzure> 16:18 < kanzure> warning: this paper is written very poorly
19:43 <@kanzure> also you mentioned this same paper last year
19:43 <@kanzure> http://gnusha.org/logs/2012-01-25.log
19:50 <@kanzure> also here's a new compressed archive of logs,
19:50 <@kanzure> http://gnusha.org/logs/archives/hplusroadmap-2013-02-02.tar.gz
19:50 <@kanzure> http://gnusha.org/logs/archives/
19:55 <@kanzure> also here's a new dump of links from the logs,
19:55 <@kanzure> http://gnusha.org/logs/meta/hplusroadmap-2013-02-02-links.url.txt
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20:14 <@kanzure> "Reality must take precedence over public relations." - RICHARD FUCKING FEYNMAN
20:14 <@kanzure> argument from authority, but bite me
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20:32 <@kanzure> "Trust me, if dental composites took 15 minutes to cure, or had to be baked at all, no dentist would ever use them. A typical dental composite might take under a minute's exposure to high-intensity blue light. Other systems can be much, much faster."
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21:37 < heath> humor (scene from time bandits) :: http://www.youtube.com/watch?v=R6OKLgLZHFk
21:44 <@kanzure> more javascript funkery http://christmasexperiments.com/23/
21:49 <@kanzure> http://christmasexperiments.com/23/js/
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22:32 < nmz787> kanzure: back
22:33 <@kanzure> gene_hacker: are you still around?
22:33 <@kanzure> i wanted you two to meet a while ago
22:34 <@kanzure> hrm well whatever. i think he's gone.
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22:37 < nmz787> hmm
22:39 <@kanzure> i talked with my photopolymer guy
22:39 <@kanzure> (david treadwell)
22:39 <@kanzure> " can shop around, but the price seems reasonable for small-quantity purchases."
22:39 <@kanzure> "I'd be interested exploring this further. If there is sufficient need in the community, I could work on a public-domain produce. I currently lack the facilities to do such formulation, however."
22:39 <@kanzure> "I recall from some work I did ten years ago that making a decent UV/vis cure polymer is not especially involved, but the intricacies of making a polymer system which works in a rapid prototyping environment would take some experimentation."
22:40 <@kanzure> nmz787: do you have anything you would say in response? i'm at least going to tell him "YES DO IT".
22:42 < nmz787> I dunno, I found a place offering 3D printable UV polymer for ~$250 per gallon
22:43 <@kanzure> bucktown was $150/gal
22:43 < nmz787> was it?
22:43 <@kanzure> maybe i didn't check the right product
22:43 < nmz787> this is prob what i'm gonna try out first http://www.solarez.com/productsnew/fly_tie_uv_resin_thin.html
22:44 < nmz787> bucktown was : gallon of vis curable $235, gallon of UV curable $1040
22:44 <@kanzure> what.
22:44 < nmz787> and sigma was around $1100 per gallon
22:44 < nmz787> kanzure: you can add to cart on their site to see prices
22:44 <@kanzure> have we done any estimates on how much we would use per prototype?
22:45 < nmz787> very little
22:45 < nmz787> lemm calc
22:45 <@kanzure> yeah but is 1 gallon only enough for 100 prototypes? 1000?
22:45 <@kanzure> k
22:45 < nmz787> (50 microns) * (2 cm) * (2 cm) = 0.02 milliliters
22:45 <@kanzure> haha
22:46 < nmz787> 189270.5892 prototypes per gallon at that rate
22:46 <@kanzure> i'm not sure we'll be doing 50 microns, let's say we are sloppy and we pour enough for 500 microns
22:46 <@kanzure> ok, 18927 prototypes
22:46 < nmz787> 1 gallon / (200 microns * 4 cm * 4 cm) = 11829.411825
22:47 < nmz787> that's 2.2 cents each
22:47 < nmz787> so if you didn't need to prototype, like you were using a proven design, that seems pretty cheap
22:47 < nmz787> <10 cents for a multilayer design
22:48 < nmz787> plus PDMS costs of course
22:49 < nmz787> PDMS looks cheaper
22:49 < nmz787> http://www.amazon.com/Sylgard-Solar-Encapsulation-Making-Panels/dp/B004IJENBG
22:49 < nmz787> gonna assume that's 500mL worth
22:50 <@kanzure> oh right spincoating
22:50 < nmz787> so at that price it's around 3.9 cents per PDMS prototype
22:51 <@kanzure> how do you spincoat a visible curable polymer safely?
22:51 <@kanzure> keep the spincoater dark?
23:01 < nmz787> red light
23:01 < nmz787> 'dark room lighting;
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23:26 < gene_hacker> you called kanzure?
23:29 <@kanzure> gene_hacker: yo meet nmz787, he's doing microfluidics/photocurable stuff
23:29 < gene_hacker> with a DLP?
23:30 <@kanzure> well sort of, i was supposed to buy him a dlp yesterday but i flaked out
23:30 < gene_hacker> Oh, Nathan McCorkle
23:31 < gene_hacker> you really should use a DL:P, met a german guy who hooked one up to a microscope to do micron sized printing
23:32 < nmz787> hi gene_hacker
23:32 < gene_hacker> though, you might need to use some exotic stuff if you're going to run solvent resistant stuff
23:32 < gene_hacker> sup
23:32 < nmz787> no need for solvent resistance
23:32 < nmz787> since i'm just gonna use the DLP printed stuff to cast PDMS on top
23:32 < gene_hacker> so a one shot?
23:33 < gene_hacker> PDMS is far from solvent resistant from what I've read
23:33 < nmz787> nah, expose then cure photoresin, lay PDMS on top, cure, peel, attach layers, hook up to macro
23:33 < nmz787> depends what solvent
23:34 < nmz787> for most of what I am aiming for, I can use PDMS no prob
23:34 < gene_hacker> for DNA synthesis?
23:34 < nmz787> yes
23:34 < gene_hacker> what type?
23:35 < nmz787> phosphoramidite
23:36 < gene_hacker> well, if you're going to make a high resolution DLP system for curing photopolymer, you really should look into making a picoarry
23:36 < nmz787> hah
23:36 < nmz787> no way
23:37 < nmz787> i want to output >1kb DNA strands, not oligos
23:38 < gene_hacker> in one step?
23:38 < gene_hacker> without putting different strands together?
23:38 < nmz787> no
23:39 <@kanzure> army.mil vulnerabilities http://pastebin.com/Cpgp9jHE
23:39 < nmz787> no, around 30 or 50bp is what i'm targeting for onchip oligos
23:39 < gene_hacker> because otherwise, you can do the same with picoarrays can you not?
23:40 < nmz787> pico arrays are just microarrays, right?
23:40 <@kanzure> no, he's referring to a specific paper
23:40 < nmz787> photobased synthesis?
23:40 < gene_hacker> yes
23:40 <@kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf
23:40 < gene_hacker> but without fancy photolabile bases
23:40 < gene_hacker> you use photogenerated acid instead
23:41 <@kanzure> iirc this was a continuous flow device
23:42 < nmz787> nope wasn't planning on using photoacid
23:42 < nmz787> (haven't seen photolabile bases actually)
23:43 < nmz787> I think i saw something about photo-based activation being less efficient
23:43 <@kanzure> gene_hacker: we were thinking of using bubbles to store beads with library dna
23:43 < nmz787> I can't really remember why i stopped considering it
23:43 < nmz787> but the reaction is pretty simple, so adding one extra valve seems trivial to me
23:44 < gene_hacker> where you have nxn combinations of every possible DNA sequence and put them together right?
23:44 <@kanzure> yes that type of library
23:44 <@kanzure> of course, a basic oligo synthesizer would also be worth working on
23:44 < nmz787> also i am not considering continuous-flow
23:45 < gene_hacker> are you sure that's going to scale well?
23:45 < nmz787> pretty sure, i have a few specific ideas on reducing the error rate of each oligo
23:45 -!- gene_hacker_ [~chatzilla@cpe-70-113-84-191.austin.res.rr.com] has joined ##hplusroadmap
23:46 < nmz787> and there's been a lot of single-molecule work done, so each reactor can be really small, so you gain in parallelizing
23:46 < nmz787> not that i will be requiring single molecules
23:46 < nmz787> or aiming for work with thm
23:46 < nmz787> them
23:47 <@kanzure> nmz787: is there any particular reason that neither of us has checked in how much it would cost to build a more traditional synthesizer?
23:47 < nmz787> i'm probably going to try using DLP to make molds that get edited with a FIB for nano features
23:48 < gene_hacker_> what sort of nanofeatures?
23:48 < nmz787> kanzure: reagent costs will go up, we won't really gain any benefit over existing systems
23:48 < gene_hacker_> and why?
23:48 < nmz787> nanocapillaries mainl
23:48 < nmz787> you can do gel-free separations
23:49 < nmz787> or pull a growing molecule back into a nanochannel to hide it from the active chemistry
23:49 < gene_hacker_> ok now that's neat
23:49 < nmz787> a significant error contributor is damage to early-added nucleotides
23:49 < gene_hacker_> is that actually done?
23:49 -!- gene_hacker [~chatzilla@cpe-70-113-84-191.austin.res.rr.com] has quit [Ping timeout: 252 seconds]
23:49 <@kanzure> cost per bp would be closer to existing systems, but the benefit is that we'd have an open source synthesizer (and one that might be slightly more practical to build for others who don't have a dlp setup)
23:49 -!- gene_hacker_ is now known as gene_hacker
23:50 < nmz787> i think i read about someone mentioning it would help
23:50 < nmz787> kanzure: DLP is on everycraigslist
23:50 <@kanzure> why early-added in particular ?
23:50 < gene_hacker> how do you pull the DNA in and out? electrical charge?
23:50 < nmz787> well because they're gonna see more chances to interact
23:50 < nmz787> yeah electric
23:50 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving]
23:51 < nmz787> you could also use an optical trap, but i have not looked into that
23:51 < nmz787> as it requires some fancy-ish optics
23:54 < gene_hacker> now if only you could pull the DNA with varying degrees, you could make a DNA origami nanomechanism
23:55 <@kanzure> diybio-eu is trying to decide on logos
23:55 <@kanzure> http://diyhpl.us/~bryan/papers2/diybio/diybio-eu-logo01.jpg
23:55 <@kanzure> http://diyhpl.us/~bryan/papers2/diybio/diybio-eu-logo02.jpg
23:55 <@kanzure> http://diyhpl.us/~bryan/papers2/diybio/diybio-eu-logo03.jpg
23:55 <@kanzure> http://diyhpl.us/~bryan/papers2/diybio/diybio-eu-logo04.jpg
23:57 <@kanzure> paperbot: http://www.sciencedirect.com/science/article/pii/S0962892402023516
23:57 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Chromosome%20positioning%20in%20the%20interphase%20nucleus.pdf
--- Log closed Sun Feb 03 00:00:49 2013