--- Log opened Sat Jul 18 00:00:14 2015
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00:44 < JayDugger> Good morning, everyone.
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01:53 < JayDugger> Anyone remember a paper describing the effects of tDCS on the likelihood of lucid dreaming?
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06:11 < JayDugger> Don't all answer at once.
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06:53 < kanzure> JayDugger: all i gots is http://diyhpl.us/~bryan/papers2/neuro/tdcs/
06:54 < QuadIngi> kanzure, hey I might do some research/personal testing on tdcs, I'll make sure to share it when I'm done
06:55 < kanzure> i didn't know that there was video of the fox domestication work https://www.youtube.com/watch?v=0jFGNQScRNY
06:57 < QuadIngi> Hey, what's the purpose of the oxygen equipment you were talking about setting up a while back (six months?) kanzure
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06:58 < kanzure> oxygen equipment. hmm.
07:02 < FourFire> something about gluing something in a vacuum
07:06 < JayDugger> Thank you both. I haven't yet searched the archive, and it doesn't look likely to happen today.
07:09 < CaptHindsight> 1) the first base gets a silane bond to the substrate. This bond is cleaved after synthesis with a free 3'-hydroxyl
07:10 < kanzure> here is a checklist for chemistry projects http://safety.uchicago.edu/files/Lab%20Design%20Guide%20Checklist.pdf
07:11 < CaptHindsight> The starting material is the solid support derivatized with the nucleoside which will become the 3'-hydroxyl end of the oligonucleotide.
07:11 < CaptHindsight> the nucleoside is bound to the solid support through a linker attached at the 3'-hydroxyl. The 5'-hydroxyl is blocked with a dimethoxytrityl (DMT) group
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07:12 < CaptHindsight> 2) SYNTHESIS  The first step of the synthesis cycle is treatment of the derivatized solid support with acid to remove the DMT group
07:12 < CaptHindsight>  This frees the 5'-hydroxyl for the coupling reaction.
07:13 < CaptHindsight>  An
07:13 < CaptHindsight> activated intermediate is created by simultaneously adding the phosphoramidite nucleoside monomer
07:13 < CaptHindsight> and tetrazole, a weak acid, to the reaction column. The tetrazole protonates the nitrogen of the
07:13 < CaptHindsight> phosphoramidite, making it susceptible to nucleophilic attack. This intermediate is so reactive that addition is complete within 30 seconds.
07:13 < CaptHindsight> the phosphoramidite is blocked at the 5'-OH with the dimethoxytrityl group.
07:14 < CaptHindsight> The next step, capping, terminates any chains which did not undergo addition. Since the unreacted chains have a free 5'-OH, they can be terminated or capped by acetylation.
07:14 < CaptHindsight> Capping is done with acetic anhydride and 1-methylimidazole.5 Since the chains which reacted with the phosphoramidite in the previous step are still blocked with
07:14 < CaptHindsight> the dimethoxytrityl group, they are not affected by this step. Although capping is not required for
07:14 < CaptHindsight> DNA synthesis, it is highly recommended because it minimizes the length of the impurities and thus facilitates product identification and purification
07:15 < CaptHindsight> The internucleotide linkage is then converted from the phosphite to the more stable phosphotriester.
07:15 < CaptHindsight> Iodine is used as the oxidizing agent and water as the oxygen donor. This reaction is complete in less than 30 seconds
07:15 < CaptHindsight> After oxidation, the dimethoxytrityl group is removed with a protic acid, either trichloroacetic or dichloroacetic acid. The cycle is repeated until chain elongation is complete.
07:16 < kanzure> and yet no washing steps were mentioned
07:16 < kanzure> nobody finds this strange?
07:16 < CaptHindsight> The oligonucleotide is cleaved from the support by a one-hour treatment with concentrated ammonium hydroxide.
07:19 < CaptHindsight> it's mentioned later
07:19 < ebowden> What're you reading from?
07:19 < CaptHindsight> I really want to send the writers to an editing class
07:19 < kanzure> ebowden: http://diyhpl.us/wiki/dna/synthesis/notes/
07:20 < ebowden> Thanks.
07:20 < CaptHindsight> Immediately before detritylation, the CPG support is washed with acetonitrile to eliminate traces of the preceding reagent.
07:20 < CaptHindsight> Any residual TCA must be removed by an acetonitrile wash
07:20 < CaptHindsight> to prevent detritylation of the incoming phosphoramidite. If the phosphoramidite monomer becomes
07:20 < CaptHindsight> detritylated, an unwanted dimer can form in solution and then couple to the support-bound
07:20 < CaptHindsight> nucleotide chain. Continued chain propagation would result in some sequences being longer than the product, making purification difficult.
07:21 < CaptHindsight> Following both acetonitrile washes, the remaining solvent is forced out of the column by an argon
07:21 < CaptHindsight> reverse flush - argon passes through the column from top to bottom and pushes the liquid to waste.
07:22 < CaptHindsight> so they wrote the steps in order more than once going over the different details in different paragraphs vs just going through the steps one by one and including the details as they go along
07:23 < ebowden> ...Why?
07:23 < CaptHindsight> so it's all there, it just needs to be rewritten clearly and in order
07:23 < ebowden> It's as if it's written in crayon.
07:23 < CaptHindsight> yeah
07:24 < CaptHindsight> like the POSaM doc, like you're sharing the info but not making it easy to follow
07:25 < CaptHindsight> maybe they had several writers and just tried to hurriedly piece it all together at the last minute to meet someone deadline
07:25 < CaptHindsight> that's how docs end up like this without an editor
07:25 < kanzure> well they had no copyediting because they call it cyctosine a few times (instead of cytosine)
07:25 < CaptHindsight> or try to write docs over IRC  :)
07:26 < CaptHindsight> no technical editor
07:28 < CaptHindsight> How to disarm a bomb. 1) cut red wire 2) but not before cutting blue wire   :)
07:30 < chris_99> haha
07:31 < CaptHindsight> the ABI 391 uses glass beads and the inkjet uses glass slides
07:32 < CaptHindsight> both use silane bonds to the fist base
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07:34 < CaptHindsight> fist/first
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07:37 < CaptHindsight> the ABI 391 floods the oligo building volume with each chem step by step but only build one type of oligo at a time
07:38 < CaptHindsight> the inkjet can build 1M different oligos at a time but the ones built around the outer edges of each drop might have more errors
07:40 < kanzure> probably some square of the distance dropoff law
07:40 < CaptHindsight> so the washing, drying, rinsing steps don't wash away the baby oligos, they are bonded to the slide
07:41 < kanzure> yup
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07:44 < CaptHindsight> POSaM got lucky by discovering that Rain-X bonds to the glass slide, modifies the surface tension yet leaves space for the first base to be anchored to the slide
07:45 < CaptHindsight> then again Rain-X isn't rocket science, just low cost and readily available, like finding out that reagents are available from the paint on Chinese toys or similar
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07:57 < CaptHindsight> it would be nice to have photocleavable bond to the slide
07:58 < CaptHindsight> just use a laser to selectively cleave and launch the infant oligos from the slides
07:58 < CaptHindsight> in the order you want
07:58 < CaptHindsight> but since you're printing them you can have in the order you wish anyway
08:00 < CaptHindsight> I wonder if you could steer the launching electrostatically?
08:01 < CaptHindsight> have them jump from the slides to an electrostatic array for ligation
08:01 < CaptHindsight> or would you even have to
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08:02 < CaptHindsight> selectively launch in the order you want into a ligation machine
08:03 < CaptHindsight> and if ligation is done in parallel then you can have multiple launches and form longer stands more quickly
08:04 < CaptHindsight> have to decide at what stages of this to have QC
08:09 < CaptHindsight> you could also have beads on the tray and use an inkjet
08:09 < CaptHindsight> bonds the beads to the tray and then cleave them when needed
08:10 < CaptHindsight> so maybe inkjet + beads + laser launcher is as faster way to build oligos
08:10 < CaptHindsight> as/a
08:11 < CaptHindsight> between patents on inkjet and laser launched beads I can see why this has taken so long
08:13 < CaptHindsight> kanzure: so what's the next step?
08:14 < CaptHindsight> does anyone have access to one of the Cambrian bead launchers?
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08:20 < kanzure> cambrian only has one or two as far as i know
08:21 < CaptHindsight> ah I assumed that they were mass producing them
08:21 < kanzure> CaptHindsight: next steps are things like "figure out the actual requirements for these reactions, and then make sure all requirements are satisfied" and "look at all the setup and shutdown procedures for posam, and figure out how much time and resources those require, and also document them better"
08:21 < kanzure> no, they will never mass produce them-- they want to do in-house gene synthesis
08:22 < CaptHindsight> so nobody will sell them for 15-20 years
08:23 < CaptHindsight> they will all build them in house
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08:25 < CaptHindsight> kanzure: let me know when you're ready to move forward
08:29 < ParahSailin_> the cambrian stuff doesnt work though
08:30 < CaptHindsight> ParahSailin_: I thought it did
08:30 < CaptHindsight> what does it actually do and not do?
08:30 < ParahSailin_> https://reason.com/blog/2015/06/30/rip-austen-heinz
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08:45 < CaptHindsight> he could have asked for help in more ways than one
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08:52 < CaptHindsight> Cambrian is up for sale before liquidation
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08:57 < CaptHindsight> someone in linuxcnc is in charge of liquidating or finding buyers for Cambrian
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09:03 < CaptHindsight> ok, so I'm right about my steps and how to QC using PCR and then launch only the good beads for ligation
09:06 < CaptHindsight> for $4M you can have the whole Cambrian Lab
09:07 < ParahSailin_> hm, maybe ill tell affy to buy it
09:07 < ParahSailin_> is it in mtv?
09:08 < ParahSailin_> ah, sf
09:09 < CaptHindsight> yeah, let me know if they want to meet the broker
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09:09 < ParahSailin_> oh yeah, do they have any swag?
09:10 < ParahSailin_> can i view the lab?
09:10 < ParahSailin_> collecting swag from these things is kinda my hobby
09:11 < CaptHindsight> heh, they will check you bag at the door  :)
09:12 < ParahSailin_> oh hey, theyre right by dropbox
09:12 < ParahSailin_> oh, fridge magents and pens fit in my pocket
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09:20 < CaptHindsight> looks like they had one complete system and another partially assembled
09:21 < CaptHindsight> the real trick was QC and using the laser to only launch know good beads
09:22 < CaptHindsight> know/known
09:22 < CaptHindsight> bbl after hands wake up
09:26 < kanzure> 09:03 < CaptHindsight> ok, so I'm right about my steps and how to QC using PCR and then launch only the good beads for ligation
09:26 < kanzure> was this from #linuxcnc?
09:26 < kanzure> also, i wonder what anselm is going to be doing if he's not going to continue with cambrian genomics
09:27 < CaptHindsight> it's a mess, looks like people are spooked by the death
09:28 < CaptHindsight> how do people with so much $$ get so stupidstitious
09:29 < CaptHindsight> somebody will probably buy the ip and sit on it
09:29 < CaptHindsight> the lab will get sold for scrap/auction
09:30 < CaptHindsight> 20 years later the next set of makers with reprap it
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09:31 < CaptHindsight> still arguing over ramps vs 27 vs poopieboard v13
09:31 < CaptHindsight> for the controller
09:33 < kanzure> cambrian genomics lab https://www.dropbox.com/sh/chg9tw7o2rv3ub1/AAAXeKmYUz4h7ERlPvd0SYUJa?dl=1
09:33 < kanzure> https://www.dropbox.com/sh/chg9tw7o2rv3ub1/AAAXeKmYUz4h7ERlPvd0SYUJa?dl=0
09:35 < kanzure> cambrian genomics assembly rig https://www.dropbox.com/sc/f5dupaq9bxn0jad/AADqcynzb0moLhlQv3XNxoIRa
09:39 < ParahSailin_> is that an illumina?
09:40 < ParahSailin_> oh, labcyte
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09:51 < kanzure> i didn't realize that t12 was employed by cambrian genomics this whole time
09:51 < kanzure> v. annoying
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09:59 < kanzure> 09:42 < t12> honestly we just paid customarray to run their own machines to supply us with material
09:59 < kanzure> 09:42 < t12> and we had one on site as a business partnership commitment and as a show peice
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10:06 < kanzure> CaptHindsight: the main way to do gene assembly is by pipetting different dna fragments together into the same pot, then running a reaction. this needs to be done in parallel though for any reasonable scale to be reached.
10:07 < CaptHindsight> yeah, one way
10:07 < kanzure> well, tell me another way that works
10:07 < CaptHindsight> i think we need to build a ligation machine
10:07 < kanzure> you need to keep the beads separated (or tagged or visually tracked or something). you need to keep droplets separated. the ligation reactions don't yet work with >10 dna fragments in a reliable way.
10:08 < CaptHindsight> cambrian took known good beads and then combined them
10:08 < CaptHindsight> lets see what they used
10:08 < kanzure> they used thermocyclers
10:08 < kanzure> that's what the 20 machines in a line is
10:08 < CaptHindsight> yuk
10:09 < CaptHindsight> i was thinking of building small ones
10:09 < kanzure> each of those cost $5k at least (thermocyclers are notoriously expensive for no good reason- it's really a <$200 machine in parts)
10:09 < kanzure> my favorite pcr method is the one where you shoot an infrared laser beam at different droplets in an oil emulsion
10:09 < kanzure> then you heat the droplets and cycle the temperature at each drop
10:09 < CaptHindsight> yeah well, welcome to the world of scientific supply
10:12 < kanzure> so the most basic design that i can think of that would work is having an array of pipettes that transport individual samples to a line of reaction chambers inside the same machine
10:13 < CaptHindsight> ligation is done inside cells
10:13 < kanzure> no
10:13 < kanzure> i mean, let's not
10:13 < CaptHindsight> we should improve on that design
10:13 < CaptHindsight> down the road
10:13 < kanzure> ok but that's like.. research. that's not going to work immediately.
10:14 < fenn> t12> cambrian genomics
10:14 < fenn> t12> the tech works
10:14 < fenn> t12> it works well
10:14 < fenn> t12> i build most of the 2nd gen of it
10:15 < fenn> t12> but after ceo suicide everyone pretty much lost morale
10:15 < fenn> for the record
10:15 < kanzure> 08:53 < t12> including investors
10:15 < kanzure> 08:54 < t12> i have weeks to round up a buyout pruced essentially on liquidation value
10:15 < kanzure> 08:54 < t12> before it goes to asset liquidator
10:15 < kanzure> 08:57 < CaptHindsight> t12: how many "laser printers" are there?
10:15 < kanzure> 08:57 < t12> 3 depending on how you count. 1 that is reallyy rigged up
10:15 < kanzure> 08:57 < t12> if yoy want to check it out sometime let me know
10:15 < kanzure> 08:58 < t12> its a neat lab to check out
10:16 < kanzure> 08:59 < t12> thats what cambrian really did
10:16 < kanzure> 09:00 < t12> microarray purificatiin
10:16 < kanzure> 09:00 < t12> its a giant in vitro cloning system
10:16 < kanzure> 09:00 < t12> despite all the othrr statenents if what it is
10:16 < kanzure> 09:01 < t12> make dna, critical dilution emulsion pcr to isolatr strands
10:16 < kanzure> 09:02 < t12> barcode the strands
10:16 < kanzure> 09:02 < t12> sewuence them in illumina, and our custom sequencer
10:16 < kanzure> 09:02 < t12> that gives yoy map of immobalized beads to correct beads
10:16 < kanzure> 09:02 < t12> eject those
10:16 < kanzure> 09:07 < t12> competitor beat us to the core product, maybe
10:17 < kanzure> 09:08 < t12> due to better management really
10:23 < kanzure> a line of 20 thermocyclers should not be the design goal here
10:23 < kanzure> that's just... poor planning.
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11:23 < kanzure> https://patents.google.com/patent/US20140309119A1/en?assignee=Gen9
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12:19 < kanzure> 10:54 < t12> re lineup of pcr machines, pcr in bulk is suprisingly annoying
12:19 < kanzure> 10:54 < t12> https://www.dropbox.com/s/ydjowb969ak3ka0/20150601-20150601-_6010050.jpg?dl=0 that thing can do like 200 plates at a time though
12:19 < kanzure> 10:55 < t12> all the customarray r&d was in their electrode, not the chemistry
12:22 < kanzure> 11:36 < t12> the real guts for us lie in emulsion pcr techniques
12:22 < kanzure> 11:36 < t12> which are a nightmare to develop
12:22 < kanzure> 11:37 < t12> so theres all kinds of expensive/slow cleanups you can do
12:22 < kanzure> 11:37 < t12> like you can gel purify what you've made on the beads to select for some length
12:22 < kanzure> 11:38 < t12> nanopores are just finnecky as hell
12:22 < kanzure> 11:38 < t12> and very high error rates
12:24 < kanzure> 11:52 < t12> i'd say the hangups are first how to actually design the machine, second is successfully building them
12:24 < kanzure> 11:53 < t12> like in the protein world taking a structure and rationally making it be better at some thing is very hard
12:25 < kanzure> 11:53 < t12> and kinda laughed at
12:25 < kanzure> 11:53 < t12> how it seems to really be done is maybe some human guidance, and alot of shotgun expirements and screening
12:25 < kanzure> 11:53 < t12> mutagenesis expirements cover the problem space faster than human mind rationality
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12:41 < ParahSailin_> kanzure: hear that? customarray
12:43 < ParahSailin_> surprised the tech "works well"
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12:43 < CaptHindsight> he just had other issues
12:43 < ParahSailin_> if tech works well, then just do what they are doing, not this whole inkjet shit
12:43 < CaptHindsight> the tech worked
12:45 < ParahSailin_> no need to waste time when theres already proven way to do it
12:46 < CaptHindsight> it wasn't optimal, but it worked
12:46 < CaptHindsight> I mean the setup wasn't optimal
12:46 < CaptHindsight> it evolved irrationally
12:46 < ParahSailin_> works or it didnt?
12:47 < CaptHindsight> it still works
12:47 < CaptHindsight> the assembly like just evolved irrationally
12:47 < CaptHindsight> like/line
12:47 < ParahSailin_> so then build it correctly?
12:48 < CaptHindsight> so nobody quit your days jobs yet
12:48 < CaptHindsight> well that requires a plan and funding
12:49 < ParahSailin_> isnt that what you guys are doing?
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12:53 < CaptHindsight> http://www.ebay.com/itm//201388723543
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13:07 < fenn> it looked expensive
13:07 < fenn> $4 million to be precise
13:09 < fenn> that was a response to ParahSailin_
13:15 < CaptHindsight> yeah t12 said $4m
13:15 < CaptHindsight> or it goes to auction is 2 weeks
13:15 < CaptHindsight> ebay for parts in 3  :)
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13:51 < kanzure> i never said that cutomarray didn't work
13:53 < kanzure> $4M was the liquidation potential price i think, not the actual cost of building it
13:53 < kanzure> may be more or less
13:55 < CaptHindsight> should have been far less but then again who knows
13:57 < kanzure> i was talking with fenn earlier today,
13:57 < kanzure> i proposed wax printing and wax melting
13:57 < kanzure> to separate drops
13:58 < kanzure> you could use infrared or heated pin needles
13:58 < kanzure> you could also have different wax types that melt at different temperatures
13:58 < kanzure> that sounds like a thing
13:58 < kanzure> i wonder if the wax would contaminate the chemistry though
14:00 < kanzure> (er, more specifically, the wax heating would be to make the drops mix and touch somehow)
14:00 < kanzure> oh right, if you heat wax then it will just melt and mix with the other chemicals. that's not good.
14:04 < fenn> the idea here being that the well walls are made of wax and when you melt one wall with a laser the two droplets combine into one droplet
14:05 < fenn> i also suggested inkjetting a line of soap between droplets to break down the hydrophobic barrier
14:05 < fenn> the point being you combine droplets on the plate without doing a bunch of pipetting
14:06 < fenn> now that i think about it though, soap would reduce the surface tension for the whole droplet and it would go everywhere
14:08 < CaptHindsight> whats wrong with electrostatic guides?
14:08 < fenn> what is that?
14:08 < fenn> like a UV laser generating a surface charge?
14:08 < CaptHindsight> kanzure: an inert wax
14:09 < kanzure> are there inert waxes?
14:09 < fenn> most waxes are relatively inert already
14:09 < CaptHindsight> inert from the DNA perspective
14:10 < CaptHindsight> or we can make a low Tg oligomer
14:10 < CaptHindsight> reflow it by heating with a laser
14:11 < kanzure> it's not just dna inertness that matters, but also all the other chemicals in the system- unless the wax is never touched by any of them
14:11 < kanzure> not sure what a tg oligomer is
14:12 < CaptHindsight> what problem are you trying to solve?
14:12 < kanzure> genome synthesis
14:12 < CaptHindsight> kanzure: we can tailor the Tg of the oligomer
14:12 < CaptHindsight> heh, what step?
14:13 < fenn> if there are a million spots you have to combine a small number of them at a time or the oligos will not be able to find their one true love
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14:13 < CaptHindsight> you can plan the order/ their arrangement
14:14 < CaptHindsight> https://www.youtube.com/watch?v=u2MK81wWQPM  what do they call these for fluids?
14:15 < fenn> programmable droplet array
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14:15 < kanzure> "EOWD" stuff
14:15 < kanzure> .title
14:15 < yoleaux> Thermal-Biomorph/Electrostatic Organic Ciliary Array (the array manipulates parts) - YouTube
14:15 < CaptHindsight> the hurdle seems to be QC like t12 mentioned
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14:16 < kanzure> er, he only said that because he was using a pre-made dna synthesis system
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14:16 < CaptHindsight> the rest is academic
14:17 < kanzure> CaptHindsight: new plan is that we'll move forward, but we're shipping everything to fenn instead
14:17 < CaptHindsight> I'll look into ligation on the nanoscale
14:18 < CaptHindsight> a small machine that does QC and makes and or repairs connections
14:18 < fenn> aka ligase
14:18 < CaptHindsight> that would appear to be ideal
14:18 < CaptHindsight> a nano-ligator
14:18 < fenn> .wik ligase
14:18 < yoleaux> "In biochemistry, ligase (from the Latin verb ligāre — "to bind" or "to glue together") is an enzyme that can catalyze the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small pendant chemical group on one of the larger molecules or the enzyme catalyzing the linking together of two  …" — https://en.wikipedia.org/wiki/Ligase
14:19 < kanzure> wax printing would be inconvenient on this system, because you need to print wax at a different size (in between all the other spots)
14:19 < kanzure> and it needs to be continuous
14:19 < kanzure> or something
14:19 < CaptHindsight> yeah, just didn't use the term
14:19 < CaptHindsight> kanzure: you make a template and mass produce them
14:19 < kanzure> perhaps, but only if you can keep them clean
14:19 < CaptHindsight> wax coated slides
14:20 < kanzure> you could also mill a multi-layer wax surface
14:20 < CaptHindsight> with the proper space and channels
14:20 < kanzure> (or laser heat it anyway)
14:20 < kanzure> if you heat it, where does the wax go.. it will just pool and block everything once it cools.
14:21 < fenn> polyimides (kapton) have the convenient property of sublimating instead of melting
14:21 < kanzure> perhaps if you can .
14:21 < kanzure> ah
14:21 < juri_> um.
14:22 < fenn> probably not very inert tho
14:23 < kanzure> what about just giant wax walls that don't change. the wax wall surrounds 10 spots. then you add liquid into that container to mix them.
14:23 < juri_> call me stupid, but, why not use a wax containing magnetic particles? heat the wax with a laser, and let a magnet under the slide pull the half melted wax to the bottom, allowing your droplets to mingle at the surface?
14:23 < kanzure> so it is an elevated surface, that you can flood at your convenience
14:23 < CaptHindsight> if you inkjet onto a programmable droplet array you can move things around, but how about QC?
14:24 < kanzure> droplet arrays have their own host of problems... electrowetting etc. is something that jonathan cline experimented with, but his results- while interesting- do not seem practical for this sort of project.
14:24 < fenn> a wax with higher density than water would accomplish the same thing
14:24 < fenn> actually, are these droplets even made of water?
14:24 < kanzure> i think that an elevated wax surface (not requiring melting or sublimation) would work.
14:24 < kanzure> i don't know what the droplets are made of
14:25 < CaptHindsight> at what point are you speaking?
14:25 < kanzure> at any step
14:25 < juri_> fenn: fair point.
14:25 < kanzure> at all steps
14:25 < kanzure> for pcr and ligation it's water but that's all i know
14:26 < kanzure> elevated wall approach (for different "flood groups") allows for any material, not just wax- could be metal, teflon, whatever.
14:27 < CaptHindsight> what is in the wells?
14:27 < kanzure> same thing as always
14:27 < CaptHindsight> beads, free floating oligos?
14:27 < kanzure> "flood groups" are for mixing things together
14:27 < kanzure> "mix groups"
14:28 < kanzure> the point is that if you flood it with a liquid that you know which spots are going to be covered in the liquid, and it's some subset of the total set of spots
14:29 < kanzure> (inverted pyramid)
14:29 < kanzure> whoops i mean flipped pyramid. i'm not sure what an inverted pyramid would be.
14:30 < CaptHindsight> potato potato
14:30 < CaptHindsight> storms are over bbl
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14:49 < kanzure> man i hate gimp
14:50 < kanzure> here is an illustration of the "flood group" concept http://diyhpl.us/~bryan/papers2/DNA/flood-groups.png
14:50 < kanzure> however, the larger "flood groups" have more volume and thus require more fluid- and the concentration of the oligos is going to be lower....
14:52 < kanzure> also i think there would be 10 members of each group
14:53 < kanzure> so there would be 9 height-depths if the plan is to have 1 million spots
14:53 < kanzure> oh, i guess 10. it depends on whether height=0 counts as a height.
14:56 < kanzure> if there is an inert sublimating compatible wax, then that might be preferable because you would presumably have some way of using much less liquid by volume for your later reactions (and thus higher oligo concentrations)
14:58 < kanzure> also perhaps it's possible to use gas to push droplets around and merge with other droplets. if that's the case then a lot of this is pointless.
14:59 < kanzure> (you could use a syringe pump plus needle to blow nitrogen or argon at droplets)
15:04 < kanzure> .title https://www.youtube.com/watch?v=YphnDXf4Vm4
15:04 < yoleaux> Single cell membrane poration by bubble-induced microjets in a microfluidic chip - YouTube
15:04 < kanzure> hmm that's not what i wanted
15:07 < kanzure> .title https://www.youtube.com/watch?v=Mw_MaFA9mhc
15:07 < yoleaux> Droplets falling from a pipette - YouTube
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15:10 < streety> the idea being the oligos in group 1 and 2 combine in the first flood fill, then the pool from groups 1 and 2 combine in the second flood fill, and so on?
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15:13 < kanzure> streety: correct
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15:16 < streety> would there be any issues in spreading of the dot/spots with the increased separation between substrate and print head?
15:17 < fenn> probably not
15:17 < kanzure> printhead would be done, or just depositing enzymes and extra reagents anywhere- and lots of 'em
15:20 < kanzure> perhaps you could use a syringe pump + needle to blast nitrogen into each flooded area to mix it (but not enough to blow all the junk out)
15:20 < streety> I came across http://pubs.acs.org/doi/abs/10.1021/acssynbio.5b00062 recently, at least somewhat relevant
15:20 < kanzure> .title
15:20 < yoleaux> An Error Occurred Setting Your User Cookie
15:21 < kanzure> "A Versatile Microfluidic Device for Automating Synthetic Biology" (keasling)
15:21 < kanzure> or maybe this is a different keasling
15:22 < kanzure> this looks like it's doing assembly only (which is fine, but just a caveat)
15:22 < kanzure> also claims on-chip electroporation and incubation
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16:22 < kanzure> .g russian pet foxes
16:22 < yoleaux> http://www.youtube.com/watch?v=d1G2yZMUNUQ
16:22 < kanzure> .title
16:22 < yoleaux> Russian Domesticated Foxes - YouTube
16:22 < kanzure> .g russian pet foxes -site:youtube.com
16:22 < yoleaux> http://www.fastcompany.com/3037451/pet-week/meet-your-new-pet-a-domesticated-fox
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17:47 < kanzure> you could also use hydrophobic blunt ends to push around droplets i think
17:48 < kanzure> .title https://www.youtube.com/watch?v=MkLbVLGcn-A
17:48 < yoleaux> Superhydrophobic Water - Part II - YouTube
17:49 < kanzure> .title https://www.youtube.com/watch?v=qHrBhgwq__Q
17:49 < yoleaux> Science off the Sphere: Knitting Needle Experiment - YouTube
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17:51 < kanzure> .title https://www.youtube.com/watch?v=RM6m7GcSKx8
17:51 < yoleaux> Cutting a water droplet using a superhydrophobic knife - YouTube
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17:53 < kanzure> ah here we go, this is what i want:
17:53 < kanzure> .title https://www.youtube.com/watch?v=UhwU2VDyrH4
17:53 < yoleaux> Drag water droplet - YouTube
17:58 < kanzure> i guess sometimes it doesn't work...? https://www.youtube.com/watch?v=EWnx1-iChbA
18:05 < kanzure> there's also the marangoni flow method but i don't know how to hook it up to a non-microfluidic dna synthesizer
18:06 < kanzure> .title https://www.youtube.com/watch?v=DRR6-qgHB-I
18:06 < yoleaux> Superhydrophobic teflon surface - YouTube
18:07 < kanzure> "I took teflon/PTFE and roughened it with 240 grit wet and dry paper. It is very cool to watch but the surface is delicate, rub it with your finger and you bruise the structure (I assume) and it stops working."
18:09 < kanzure> dat one.
18:09 < kanzure> he has a bunch of machine shop videos
18:11 < kanzure> also he did a printer https://www.youtube.com/watch?v=a14zELKPw8M
18:12 < kanzure> .wik fluorinert
18:12 < yoleaux> "Fluorinert is the trademarked brand name for the line of electronics coolant liquids sold commercially by 3M. It is an electrically insulating, stable fluorocarbon-based fluid which is used in various cooling applications. It is mainly used for cooling electronics." — https://en.wikipedia.org/wiki/Fluorinert
18:14 < CaptHindsight> HP gen1 tij looks like
18:17 < CaptHindsight> https://www.youtube.com/watch?v=iSZc5I90ddA  Epson head shown here
18:18 < CaptHindsight> https://www.youtube.com/watch?v=pLbHvBvChSk  another Epson, turn down the reggae mon
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19:39 < kanzure> so flooding vs. pushing drops around?
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20:26 < ParahSailin_> cant believe that instead of going to jvm, erlang etc to make concurrency work, dropbox hired guido instead to make their python go
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22:10 < drethelin> http://lesswrong.com/r/discussion/lw/mht/i_have_just_donated_10000_to_the_immortality_bus/#comments
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23:01 < kanzure> "... ... this is a bad reality show for personal promotion, nothing more and nothing less. It's not even a good one. I just showed the indiegogo page to a friend who literally called it 'facepunch worthy'."
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23:08 < delinquentme> kanzure, i didnt pay attention in #linuxcnc
23:09 < delinquentme> what was the TLDR?
23:12 < kanzure> ctrl-f t12 http://gnusha.org/logs/2015-07-18.log
23:14 < kanzure> emulsion pcr stuff https://gtc.soe.ucsc.edu/content/emulsion-pcr-and-bead-enrichment
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23:15 < kanzure> "single-molecule emulsion pcr in microfluidic droplets" http://link.springer.com/article/10.1007%2Fs00216-012-5914-x
23:15 < kanzure> emulsion pcr infographic.. thing.. http://users.ugent.be/~avierstr/nextgen/emulsionpcr.jpg
23:16 < kanzure> hmm that seems oddly specific. i would have guessed many beads per drop.
23:17 < kanzure> oh they probably mean one-library-member-specific bead, not one bead..
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--- Log closed Sun Jul 19 00:00:15 2015