--- Log opened Fri Aug 02 00:00:43 2013
--- Day changed Fri Aug 02 2013
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00:59 <@nmz787> superkuh: what comment got removed from http://travisgoodspeed.blogspot.com/2013/07/hillbilly-tracking-of-low-earth-orbit.html
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03:05 < superkuh> I made a mistake. I misread and thought he was using a DVB-S card to send Diseqc commands. So I asked which it was. On a second read through I realized that he was talking about someone else, and he did not use Diseqc motors.
03:05 < superkuh> So I removed my comments.
03:05 < superkuh> -s
03:06 < superkuh> Doesn't matter anymore. I have bought a DVB-S card (skystar 2 HD) and it seems to work for sending positioning commands to my Diseqc motors.
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07:35 <@kanzure> fredox: august 8 is http://www.meetup.com/emergence-24/events/120263392/ (yes the topic might seem boring, but the people aren't)
07:37 < fredox> very vague that group
07:37 <@kanzure> they are a bunch of old perl hackers turned scifi authors
07:38 < gradstudentbot> Yeah, there's a clear trend.
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07:50 < klafka> what?
07:50 <@kanzure> huh?
07:50 < klafka> like who?
07:50 < klafka> old perl hackers turned scifi authors
07:51 <@kanzure> what do you mean who? check the page.
07:51 <@kanzure> it's nobody you know
07:58 < klafka> oh
07:58 < klafka> well i mean they could be well known scifi authors!
07:58 <@kanzure> they could be.. but they aren't. hah.
07:59 < klafka> yeah they aren't
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10:32 < klafka> btw 'in our dna' is a new techy term i hate
10:33 <@kanzure> why? we have sequenced your dna and now we know things about it.
10:34 < fredox> the 'our' part bothers especially bothers me
10:35 <@kanzure> "we have sequenced 1000 people and we're pretty sure that we all have dna polymerase variants in our dna".. sounds right to me.
10:36 < fredox> its time to revive phrenology
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10:40 < klafka> um
10:40 < klafka> my problem is like
10:40 < klafka> 'oh we have sales in our dna'
10:40 < klafka> 'ad networks are really in our dna'
10:40 < klafka> 'big data is in our dna'
10:40 < klafka> 'in our dna' is the new 'wheelhouse'
10:41 <@kanzure> ah i see. yeah, that's dumb.
10:44 < klafka> btw it seems like more and more poeple are using golang
10:45 <@kanzure> sure. it seems fun.
10:46 < klafka> wow i did not know trulia ipo'd
10:47 < klafka> and has a market cap of 1.4b
10:47 < klafka> damn
10:47 < ParahSailin> golang is probably a step forward from using c for things and probably a step backward from high level languages
10:48 < klafka> but it's not the 10 steps backward c++ is
10:49 < klafka> also it seems to be really good at concurrency
10:49 < cpopell_> kanzure: new emotiv revealed today on kickstarter-know if it can follow anything more than 4 'thoughts' at a time?
10:49 < cpopell_> I haven't been staying up to date on what they do and their market releases are always cagey
10:49 <@kanzure> emotiv has been spamming me for weeks about it. let me know if you want their firmware to double check their claims.
10:49 <@kanzure> imho it's not worth your attention
10:50 < cpopell_> figured as much.
10:50 < cpopell_> Alas
10:52 <@kanzure> i wonder if emokit works for it though
10:52 <@kanzure> i should probably go crack their keys
10:52 <@kanzure> blah why does it have to be me
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11:09 < klafka> what is the cheapest single sensor eeg ?
11:10 < klafka> i've been thinking about just using cheap eegs to interject random 'crowd noise' into reactive art
11:11 <@kanzure> openeeg, neurosky, things like that
11:11 <@kanzure> they probably have links to cheap sens0rs
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11:26 < cpopell_> god the patent office is some stupid shit
11:26 < cpopell_> some chinese firm patent DLP/DMD projection. in 2008 >_>
11:27 < cpopell_> (you know, the thing TI had had patented since ~94 or so)
11:29 <@kanzure> only the claims matter, so maybe their specific combination of claims is different
11:30 <@kanzure> nmz787: we can probably just take a dna synthesizer patent. surely there might be one that is expired by now. i wonder if patents from the 80s had anything useful in them.
11:31 < cpopell_> I have a friend that recycles patents from the 80s that were never followed through on due to lack of processing power (espec. declass cold war stuff) to be 'innovative' at work
11:32 <@kanzure> makes sense to me
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11:38  * heath waves hello to everyone
11:47 <@heath> cpopell_: it takes patent examinars ~30 minutes for one query
11:48 < cpopell_> am aware. was working on figuring out tools to help with that, but it's backburnered atm
11:48 <@heath> and it isn't going to be fixed, we (open source connections and isotope11) were subcontracted out to fix this and then the budget cuts came in
11:48 <@heath> the project had ~2 years of work
11:48 <@heath> was coming to a close... aaaand scratched
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12:05 <@nmz787> kanzure: maybe, but the academic articles seem to cover things pretty well, I'm not one to ignore info though if some folks in here dig up some
12:05 <@kanzure> i bet there's even some expired patents that had some crazy designs that nobody commercialized
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12:05 <@kanzure> for synthesizers.
12:05 <@kanzure> "Nobody would want to make that much DNA"
12:16 <@nmz787> lol
12:19 <@kanzure> "Nobody needs more than 128 kb bp"
12:19 <@kanzure> erm, i mean 128 kbp
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12:20 < gradstudentbot> Yeah, I don't know.
12:23 <@nmz787> i worked on cleaning code with jslint yesterday, kinda need a break
12:23 <@nmz787> so working on synthesis a bit
12:23 <@nmz787> also backing up files
12:24 <@kanzure> also try pyflake or pylint or flake8 sometime for python things.
12:25 <@nmz787> for some reason my js code seems to break the jQuery uploader template stuff (which it uses to add new uploads to the displayed queue)
13:02 <@nmz787> fenn: so what do you know about beta agonists (since you mentioned blockers yesterday)? https://en.wikipedia.org/wiki/Ractopamine
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13:11 <@nmz787> kanzure: so macro or meso synthesizers need mixers or shakers or something, otherwise diffusion will take a long long time
13:11 <@nmz787> paperbot: http://nar.oxfordjournals.org/content/23/6/982.full.pdf
13:11 < paperbot> http://libgen.org/scimag/get.php?doi=10.1093%2Fnar%2F23.6.982
13:12 <@heath> nmz787: what's your js project?
13:13 <@nmz787> just an uploader page right now
13:16 <@nmz787> something in my code is broken though
13:17 <@nmz787> heath: this is the demo page, if you add a file an entry is created in the queue http://blueimp.github.io/jQuery-File-Upload/
13:17 <@nmz787> for me though, it doesn't happen http://dev.takeitapart.com:8002/media/jQuery-File-Upload/index_TIA.html
13:20 <@heath> nmz787: are you receiving any error in your console?
13:21 <@nmz787> no :(
13:22 <@heath> what about in the network tab, are there some requests not returning 200?
13:24 <@nmz787> there's one, but it seems unrelated and happens before i add the file
13:24 <@nmz787> i see the file show up in the add callback for the uploader
13:24 <@nmz787> i'm logging the name
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13:46 < ParahSailin> is there a more concise python way to manipulate DOM than etree?
13:47 < ParahSailin> this is quite a bit more verbose than im used to in jquery
13:49 < tomkinsc> xml.dom.minidom may be a bit more concise, but etree is arguably a better solution
13:49 < tomkinsc> google also pointed to this: https://pypi.python.org/pypi/pyquery
13:50 < ParahSailin> this makes me smile
13:54 < tomkinsc> if you are concerned at all about memory use, you might take a look at xml.dom.pulldom as well
13:58 < ParahSailin> i just dont want to type very much generating simple reports
13:58 < ParahSailin> thanks, pyquery is nice
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14:12 <@kanzure> ParahSail1n: from gi.repository import webkit... the bulldozer of dom manipulation.
14:12 <@kanzure> nmz787: can we just use a laser to heat it
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14:18 <@nmz787> kanzure: heat cycling isn't really a part of this AFAIK
14:18 <@nmz787> for PCR sure!
14:18 <@kanzure> shrug, okay
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15:18 <@nmz787> paperbot: http://pubs.rsc.org/en/Content/ArticleLanding/2012/LC/C2LC40098G
15:18 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Cell-free%20protein%20synthesis%20from%20a%20single%20copy%20of%20DNA%20in%20a%20glass%20microchamber.pdf
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16:43 <@kanzure> "Glowing Plant Project is safe but Kickstarter bans future project creators from giving away genetically-modified organisms:"
16:43 <@kanzure> http://www.theverge.com/2013/8/2/4583562/kickstarter-bans-project-creators-from-giving-GMO-rewards
16:43 <@kanzure> guess we need another crowd funding site for genetic engineering (ugh)
16:43 <@kanzure> and not microryza, they haven't really been that successful
16:47 < ParahSail1n> lol, man that deloitte scumbag made out with all the loot
16:47 < cpopell> hm?
16:47 < ParahSail1n> .title
16:47 < yoleaux> Kickstarter bans project creators from giving away genetically-modified organisms | The Verge
16:48 < cpopell> no, I mean the deloitte part
16:48 <@kanzure> just read the logs
16:48 < ParahSail1n> oh the guy who pulled off that scam was from bain or mckinsey, some such
16:49 < cpopell> oh the whole thing was a scam?
16:49 <@kanzure> i'm p. sure it was just a genome compiler marketing stunt.. i mean.. they're the ones that keep scratching each other's backs.
16:51 < ParahSail1n> i used genome compiler on the grc build 37 with -O2 and it built a lisp interpreter
16:51 <@kanzure> what?
16:56 <@kanzure> nmz787: so, i don't think we need $2000 for a 4-channel oscilloscope. that seems like a ripoff.
16:57 <@kanzure> nmz787: i also think $600/syringe pump seems a little steep..
16:57 <@kanzure> and if an hplc really costs $20k then we should work on building a cheaper one
16:57 <@kanzure> instead of this other stuff
16:58 <@kanzure> and why are we paying $350/hour x 50 hours to a random FIB shop
16:58 <@kanzure> the balance is a sane thing to want, but why on earth would anyone want it to be RS232?
16:59 < ParahSail1n> god, hplc... our lab's one broke down so much
16:59 <@kanzure> i think "enzmyes, $500" is disingenous. it seems a little random. what enzymes are we playing with?
17:00 <@kanzure> taq? and we'd only need $500 of taq for.. how many runs?
17:00 <@kanzure> https://docs.google.com/spreadsheet/ccc?key=0AkTsdtdxo56DdDFCUmNqMzVyYi04eGw4cUJ6bG1KMlE#gid=0
17:01 < ParahSail1n> depending on what you're doing, the enzymes can really add up
17:01 <@kanzure> sure
17:01 <@kanzure> i'd expect more than $500
17:02 < ParahSail1n> damn 50 hours of fib?
17:02 <@kanzure> yeah i have no idea where that's coming from
17:03 < ParahSail1n> if you have to use fib, you're probably not coming up with a very scalable fabrication protocol
17:04 < ParahSail1n> amidites: itemized; enzymes: not itemized
17:04 < ParahSail1n> heh
17:04 <@kanzure> right. there's probably some metalwork that has to be considered. or maybe we can just 3d print some junk to hold everything together. i'm not sure.
17:04 <@kanzure> also tubing..
17:06 < ParahSail1n> save on the balance cost; put that into better thermocycler
17:06 <@kanzure> i really like the oligomaker's design. 192 channels is a good intermediate between "a pippetor on an arm moving around" and "no moving parts" and "a microarray with a bajillion wells that you can't easily clean or sequence".
17:07 <@kanzure> i mean, the way the oligomaker lays out the different channels in a circular design
17:07 < ParahSail1n> thermocycler block temperature consistency avoids frustration
17:08 <@kanzure> yes, it is less frustrating when your shit works :)
17:08 <@kanzure> that's a universal truth
17:08 < ParahSail1n> decent gradient thermocycler will really save you time
17:10 <@kanzure> if you can't get a decent hplc for less than 20k then i think we should solve that problem too
17:16 <@nmz787> $2k is cheap for a 4 channel scope
17:16 <@nmz787> chinese cheap
17:16 <@nmz787> new usa models are easily $4k-5k
17:17 <@kanzure> what about just getting a bunch of sound cards
17:17 <@nmz787> ha ha ha
17:17 <@nmz787> funny
17:17 <@nmz787> (not)
17:17 <@nmz787> you want an oscope to be 'the right answer' 'the truth'
17:17 <@nmz787> not some hobbled together thing
17:19 <@nmz787> 50 hours of fib is cheaper than buying a fib
17:20 <@kanzure> what are we using a FIB for again?
17:20 <@nmz787> honestly though it seems like from their milling rate spec, it'd be quite cheap to fab things with them in production
17:21 <@nmz787> microfluidics
17:21 <@nmz787> or meso fluidics
17:21 < ParahSail1n> fib is for making nano holes in things
17:21 <@nmz787> nah these dudes use plasma ion source
17:21 < ParahSail1n> for micro and meso, you do photolithography
17:21 <@nmz787> not like most
17:21 < ParahSail1n> because fib is 300/hr
17:22 <@nmz787> http://www.oregon-physics.com/lab_services/fib_micromachining_milling.html
17:23 <@nmz787> so at 1 micron spot, they do 100 microns^3 per second
17:23 < ParahSail1n> or you can do photolithography and wet/dry etch
17:23 <@nmz787> sure
17:24 <@nmz787> i have those capabilities at a local lab for my time plus $20.hr
17:24 <@kanzure> what do you estimate making an hplc would be like
17:24 <@kanzure> because 20k is sutpid and it's an important thing
17:24 < gradstudentbot> Hey, I got 100% yield! Oh wait, no.
17:24 <@kanzure> at 20k it might be cheaper to just ship out samples to some other guy
17:25 <@kanzure> we could use science exchange hah
17:25 < ParahSail1n> that might be better than "amigad, a salt bubble in the hplc and it sploded'
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17:26 <@kanzure> ParahSail1n: maybe i should make you do the BOM
17:27 < ParahSail1n> well i think you should just stack up a whole bunch of chairs
17:27 < ParahSail1n> this is for a space program, right?
17:28 <@kanzure> sort of
17:29 < ParahSail1n> oligo synthesis?
17:30 < ParahSail1n> oligomaker clone?
17:30 <@kanzure> oligo synthesis
17:30 <@kanzure> design not determined yet. "not micron".
17:31 < ParahSail1n> is this intended to be part of a long sequence synthesis system?
17:32 <@kanzure> undecided. possibly no. my original thought was that we just need something to prove that it can be done for less than 50k or 100k or whatever in parts.
17:33 <@kanzure> ideally the answer is yes.. hell yeah i want oligos as long as fucking possible. but you can't just start at a bajillion megabases.
17:34 <@kanzure> and plus, you don't need a thousand megabases to prove that your bill of materials (well, parts) was less than $50k for a single unit.
17:35 <@kanzure> i figure that if a single unit is cheap enough you can just iterate on the design to possibly get longer oligos, or refactor the design later to try for something a little more expensive but synthesizes longer stuff.
17:35 <@kanzure> it's entirely possible that i'm wrong, though
17:35 < ParahSail1n> cambrian was doing synthesis on microbeads or something?
17:36 <@kanzure> indeterminable. they are hush hush plus i don't have a copy of their slide where they showed a picture of their setup. i think they are probably using beads somewhere, and then lasers to sample the beads either for fluorescence or for popping the beads out of wells (maybe) or something else..
17:37 <@kanzure> i don't want to start with something extremely complex that wont work
17:39 <@kanzure> i don't entirely care about what their design is. i don't think it should influence what choices i make.
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17:42 < ParahSail1n> should probably have in mind where you want to go with it eventually, as that will inform initial design considerations
17:47 <@kanzure> in the past that has overly constrained the problem space
17:47 <@kanzure> "a system that will be infinitely scalable to all future desirable amounts of DNA".. yeah right.
17:55 <@nmz787> yeah they are doing some emulsion bead shit
17:55 <@nmz787> the reagent savings and ease of separation at the microscale is so appealing though
17:56 < gradstudentbot> I think I have ebola.
17:57 <@nmz787> as for enzymes that is probably a low estimate, since my goal is to get the oligos generated into long-mers and shoved into a cell
17:57 <@nmz787> well it's reasonable estimate for that
17:57 <@nmz787> low for directed evolution (which is the next reasonable step after micro synthesis and transformation)
17:58 <@nmz787> synthego said they're doing the same thing basically, and they just got 8.3 mil, so this BOM seems totally reasonable
17:58 <@nmz787> also enzymes like tdt
17:58 < ParahSail1n> well, the fib shit is totally insane
17:58 <@nmz787> for doing 'green chem'
17:59 <@nmz787> why?
17:59 <@nmz787> it's easy
17:59 <@nmz787> and i need wires
17:59 <@nmz787> so they can mill then lay traces
17:59 < ParahSail1n> you're choosing like the most expensive possible way to do microfabrication
18:00 <@kanzure> i'm not convinced you can build longmers using this sort of system design (in general) without giant arrays or lots of parallel strands.
18:00 <@nmz787> they said they'd do a lot of the work up for free, if i wrote up a short white paper on the process
18:00 <@kanzure> from now on they shall henceforth be called longmers
18:00 <@nmz787> (of fabbing microlfuidics with fib in general)
18:00 <@nmz787> kanzure: of course there will be parallelization
18:00 <@nmz787> that's another point after low diffusion time
18:01 <@kanzure> we haven't really decided on parallelization though
18:01 <@kanzure> are we doing an array-based system
18:01 <@nmz787> i've been thinking a fluid phase synthesis
18:01 <@kanzure> or one of the more traditional n-channel systems (n=32,64,192,392,etc.)
18:01 <@nmz787> balloon-like chamber that just gets bigger
18:01 <@nmz787> silicon bottom and pdms or teflon top
18:02 <@nmz787> add stoichiometric amounts of reagents
18:02 <@nmz787> or just under
18:02 <@nmz787> then filter
18:03 <@nmz787> and start again with the filtrate
18:03 <@nmz787> like every 10 additions, skim off the 10*nRound size fragment
18:03 <@kanzure> filter through an hplc column?
18:04 <@nmz787> that or gel or some micro are media free
18:04 <@nmz787> the walls do all the work
18:04 <@nmz787> that might have been much smaller, but that's the beauty of using a fib, it can do the dynamic range
18:04 < gradstudentbot> Where did you put the revisions to the paper?
18:05 <@kanzure> how is a balloon-chamber the same as parallelization?
18:06 <@nmz787> not, just you asked are we doing array
18:09 <@kanzure> are we? i am still confused.
18:11 <@nmz787> array means?
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18:19 <@kanzure> it means either microarray or an array of mesoscopic wells or an array of containers laid out in a grid
18:19 <@kanzure> array always implies grid
18:20 <@kanzure> (in this context)
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19:02 < fredox> do you have any strand lengths in mind for particular things you want to be able to synth? say X kbp
19:12 <@kanzure> well, the minimum is a primer at least 16 bp.
19:13 <@kanzure> i am trying to keep expectations low
19:13 <@kanzure> because it's not reasonable to assume you can build a machine that can make 100mers flawlessly every time
19:14 < fredox> my limited research indicates 50mers is about as long as you'd practically go for a single well
19:15 <@kanzure> there are some machines that are claimed to do 100-250, but i've never heard of more than 250.
19:17 < fredox> time factors i've seen are around 10mins per cycle
19:19 < gradstudentbot> What do you mean this isn't going to work?
19:22 <@kanzure> i've seen 2 minutes per cycle
19:24 <@kanzure> if you make a machine that has a moving pipettor and a 100x100 array of wells then you have to wait around forever while it performs the reaction in each step. even if you have n pipettors it's still worse than dmd-based synthesis. but the advantage is that it's easier to debug than using a DMD and squinting really hard.
19:24 <@kanzure> erm by n pippetors i mean size-of-your-row number of tips acting at once
19:24 <@kanzure> i don't know what those setups are called
19:25 <@kanzure> multipipettor claw things
19:25 < gradstudentbot> Did you see that hack?
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19:30 <@nmz787> no i was planning all silicon(e) parallelization
19:30 <@nmz787> they would be an array of sorts
19:30 <@nmz787> more like a binary tree
19:31 -!- augur_ is now known as augur
19:32 < fredox> another thing i'm pondering is what would be the cheapest simplest way to verify your machine was producing the intended sequence
19:32 <@heath> """ Short oligonucleotides 15–25-nt in length can be synthesized without any capping step. Oligonucleotides >40 nt in length required a capping step to achieve high yield of full-length product. Each synthesis cycle contained seven reaction steps and four washing steps. The step-sequence was:"""
19:32 <@heath> nmz787: source?
19:33 <@nmz787> just and old sequencing will verify
19:33 <@nmz787> any old
19:33 <@nmz787> *
19:33 <@nmz787> that was a direct copy past
19:33 <@heath> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860119/
19:33 <@heath> kk
19:33  * heath decides to try google before scholar.google.com next time
19:33 <@nmz787> heath google gave this http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860119/
19:34 <@nmz787> which is probably in bryans repo
19:34 <@heath> you don't have to protect thymine
19:34 <@heath> you have dT in there
19:34 <@kanzure> fredox: the cheapest way would be to send it off for sequencing because sequencing is extremely cheap.
19:35 < fredox> no open sequencer in the works?
19:36 <@heath> maybe it's needed using the protocol from that paper though..
19:36 <@nmz787> d just emeans deoxy
19:36 < ParahSail1n> http://www.dezeen.com/2013/07/25/farm-432-insect-breeding-kitchen-appliance-by-katharina-unger/
19:37 <@nmz787> fredox: there is an open source synthesizer
19:37 <@kanzure> pogam..
19:37 <@nmz787> fredox: http://genomebiology.com/content/5/8/R58
19:37 <@nmz787> posam
19:38 <@kanzure> oh look, tito posted a teardown from biocurious of a sequencer
19:38 <@kanzure> http://titojankowski.com/the-500000-dna-sequencer-tear-down/
19:38 <@kanzure> this is literally the only thing he has ever done right
19:38 <@kanzure> now where's the firmware dump
19:38 <@nmz787> yeah
19:39 <@heath> nmz787: i was wrong for thinking d meant "protected", but i thought d stood for "dimethoxytrityl"
19:39 <@nmz787> ahh i only saw the flickr page
19:39 <@nmz787> a few days ago
19:39 <@nmz787> they didn't seem to get good closeups of the boards
19:39 <@nmz787> to see what chips were going on
19:39 <@kanzure> nope
19:39 <@heath> kkkkkkk
19:39 <@kanzure> what's really fucking annoying is that i specifically asked for that
19:39 <@nmz787> nah that's dmt heath
19:39 <@kanzure> i sent them emails and even told them in here that i wanted that shit
19:39 <@kanzure> plus firmware dumps
19:39 < gradstudentbot> Yeah, that's a reasonable explanation.
19:39 <@kanzure> but nooo they had to go piss the opportunity away
19:39 <@kanzure> the fuckers. :(
19:40  * heath hasn't fully read the paper on manual oligy synth, i became distracted with d3's source
19:40 <@kanzure> i guess they just think circuits are magical or something. "details? why would anyone want those?"
19:40 <@nmz787> kanzure: and on aliexpres the cheapest syringe pumps are $300
19:40 <@nmz787> which is kinda weird
19:41 <@kanzure> syringe pumps vary dramatically in performance
19:41 <@kanzure> but the upside is that they are usually very explicit about what they are capable of
19:41 <@nmz787> the pneumatic valves are cheaper, but aliexpress search sucks and i couldn't search "high pressure"
19:41 <@nmz787> so i was finding things that maxed at 115 psi
19:41 <@nmz787> which i think is right around or under the quake style valve psi
19:42 <@kanzure> where was that church paper about doing a micropipettor plus microarray
19:44 <@kanzure> "Owing to its open-top architecture, accessibility of the beads and the bead size, this platform is well suited for a pick-and-place approach using micropipettes to retrieve specific beads from the 454-Picotiterplate (PTP) and transfer them into conventional multi-well plates for further processing."
19:45 <@kanzure> http://arep.med.harvard.edu/pdf/Matzas_10.pdf
19:46 < fredox> nmz787: that design was essentially what i had in mind
19:47 <@kanzure> supplementary files for that last paper, http://www.nature.com/nbt/journal/v28/n12/extref/nbt.1710-S1.pdf
19:48 <@kanzure> oh look they have a pic of their setup
19:48 <@kanzure> that array is way larger than i imagined
19:49 <@kanzure> wtf "This configuration allowed semi-automated bead extraction, but requiring verification of bead locations and fine adjustments for pipette placement by a skilled operator."
19:50 <@nmz787> fredox: which?
19:51 <@kanzure> ParahSail1n: how much would a picotiter plate cost
19:52 < fredox> the inkjet
19:53 -!- randallagordon [~randall@71-34-73-76.ptld.qwest.net] has quit [Ping timeout: 264 seconds]
19:53 <@heath> ah, "A synthesis starts with an appropriately base-protected [N^6-benzoyl adine, N^2-isobutryl guanine, N^4-benzoyl cytosine(thymine is usually not protected)]"
19:53 < ParahSail1n> picotiter?
19:53  * heath was mistaking that line for what i was reading in the google doc
20:00 <@kanzure> hah their 454 GS FLX run was $15k in reagents
20:00 <@kanzure> crazy
20:00 <@kanzure> i think the church lab is like a flaming oil well
20:02 < gradstudentbot> Hey, let's write a paper about that.
20:08 <@kanzure> rofl
20:18 <@kanzure> so anyway, that might be a good way to store a library of beads. 4096x4096 means an entire 24mer library.
20:37 < ParahSail1n> 454 is a pretty expensive way to get data
20:37 <@kanzure> i just mean their plates
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21:33 <@kanzure>  /win 4
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21:44 -!- Topic for ##hplusroadmap: 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 | official paperbot fan club
21:44 -!- Topic set by kanzure [~kanzure@131.252.130.248] [Sat Mar 23 20:40:45 2013]
21:44 [Users ##hplusroadmap]
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21:44 [@kanzure ] [ cogitokat     ] [ juri_        ] [ ParahSail1n   ] [ smeaaagle  ] [ Urchin    ] 
21:44 [@nmz787  ] [ Coornail      ] [ juul         ] [ ParahSailin   ] [ spresser   ] [ valyap    ] 
21:44 [ _sol_   ] [ devrandom     ] [ klafka       ] [ pasky         ] [ strangewarp] [ yashgaroth] 
21:44 [ abetusk ] [ fenn          ] [ lichen       ] [ phryk         ] [ streety    ] [ yoleaux   ] 
21:44 [ AlonzoTG] [ fredox        ] [ lupfantomo   ] [ poppingtonic  ] [ superkuh   ] [ Zhwazi    ] 
21:44 [ archels ] [ gnusha        ] [ monkeynipples] [ randallagordon] [ Thomas42_  ] [ zubaz     ] 
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21:44 -!- Irssi: ##hplusroadmap: Total of 62 nicks [3 ops, 0 halfops, 0 voices, 59 normal]
21:44 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010
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21:58 <@kanzure> https://www.lookout.com/resources/reports/dragon-lady "Mobile security company Lookout released a report today at DefCon that reveals the amazing size, scope, and complexity of Android malware operations in Russia. The report found the bulk of this Russian malware wasn't coming from lone individuals in basements, but well-oiled malware producing machines."
22:06 < fredox> well-oiled malware producing machines ...like google
22:06 <@kanzure> "Mobile Ad Networks: Lookout recently reported on a new malware, BadNews, which was found to be a new technique to drive mobile traffic to SMS fraud campaigns. BadNews was designed to look like an advertising library in legitimate Android applications, but the advertisements that it displayed linked directly to SMS fraud malware hosted by top HQs."
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23:01 <@nmz787> kanzure: ok added tubing and assorted connectors as a cost
23:01 <@kanzure> i don't think fib is a good idea
23:01 <@kanzure> and if hplc is really 20k then we should just work on that first
23:01 <@nmz787> if you remove the hplc the total is 23k
23:02 < ParahSail1n> why is there hplc in this?
23:02 <@kanzure> and 18k fib?
23:03 <@nmz787> the fib is a good idea i think, it makes nano and micro fluidics very simple to prototype rapidly. yes it's costly, but this company /is/ willing to work with me and I'd like to take advantage of that. They were using COMSOL for their ion optics modelling so I might be able to learn some of that through them too, or get them to crunch my designs
23:03 < ParahSail1n> i only used desalted oligos
23:03 <@nmz787> how long though?
23:04 <@nmz787> i think they do hplc on all bathces
23:04 <@nmz787> batches
23:05 <@nmz787> hplc would allow moving into directed evolution work once synthesis was acquired, and could serve useful as a crude sequencer during development
23:05 < ParahSail1n> hplc is an option which i've never used with idt
23:05 <@nmz787> it sounds like i should check sci exchange
23:05 <@nmz787> but kanzure this is something the eugene lab ppl said they could help with
23:05 <@kanzure> doesn't matter to me. that's an hour away from you. fuck that.
23:05 <@nmz787> equip that is
23:06 <@nmz787> well maybe they could get it cheaper?
23:06 < yashgaroth> how are you doing sequencing via hplc?
23:06 <@nmz787> or some indefinite loan
23:06 <@kanzure> oh yeah, indefinite loan payments, that's totally what i want
23:06 <@nmz787> no
23:06 <@nmz787> like $1/year
23:07 < ParahSail1n> i think you're writing this BOM as if the the NSF is gonna foot the bill
23:07 < gradstudentbot> I am completely satisfied with the size of my bench space.
23:08 <@nmz787> i kinda just assumed it was a standard thing in any decent lab
23:08 <@nmz787> http://www.invitrogen.com/site/us/en/home/Products-and-Services/Product-Types/Primers-Oligos-Nucleotides/invitrogen-custom-dna-oligos/Oligo-Ordering-Details/Oligo-Purity-Selection-Guide.html
23:09 <@nmz787> HPLC
23:09 <@nmz787> (50 nm+, 10-55 bp)
23:09 < ParahSail1n> not just the hplc, but using FIB instead of normal microfabrication protocols
23:09 <@nmz787> thats nanomolar i believe
23:09 <@nmz787> but FIB is pretty normal around here
23:09 <@nmz787> they make them in the shop i referred to earlier
23:09 <@nmz787> and the company that makes a shitload more is local too
23:09 <@nmz787> FEI
23:10 <@nmz787> I've toured their place
23:10 <@kanzure> ParahSail1n: would you be willing to do a BOM too?
23:10 <@nmz787> it seems like a solid clean direct way to do things
23:10 <@nmz787> mill and add circuitry
23:10 < ParahSail1n> im not clear what exactly is do be done
23:11 <@kanzure> that's still being explored
23:11 <@nmz787> ParahSail1n: do you do wafer fab?
23:11 < ParahSail1n> i have in the past
23:11 <@nmz787> would you like to do it for these designs?
23:11 <@nmz787> for less than the quoted $375/hr
23:11 < ParahSail1n> i have a former boss who'd probably do it for money
23:12 < gradstudentbot> That's not really surprising since they did it ex vivo.
23:12 <@nmz787> (not including their free overhead shit that they've already done some of)
23:12 <@kanzure> i don't get it. what FIB things are involved?
23:12 <@nmz787> mill and add circuitry
23:12 <@kanzure> why would he have to waferr fab this?
23:12 <@nmz787> mill and add circuitry
23:12 <@kanzure> circuitry can be done extremely cheap, even if we need custom pcbs (which we don't. use a fucking breadboard.)
23:12 <@nmz787> not pcbs
23:12 < ParahSail1n> im unclear what is to be fabricated, but if you want a wafer etched with some sort of profile to use as a template for pdms soft lithography
23:13 <@nmz787> i could give you cad files or something
23:13 <@kanzure> i think nmz787 is talking about doing microfluidic things
23:13 <@nmz787> gerbers
23:13 <@nmz787> i dunno what you'd want
23:13 < ParahSail1n> that would be about an order of a magnitude cheaper than 50 hours of fib
23:13 <@kanzure> and he's being intentionally unclear about it
23:13 <@kanzure> because i have no other reasonable explanation of this
23:13 <@nmz787> some square channels, roughly square crosssection, some parabolic bottom channels
23:14 <@kanzure> nmz787: so hey, i'm still the same person. i'm always going to be a truly pedantic asshole, even when you're sending me potential BOMs.
23:14 <@nmz787> some traces to the ends and sides of some of the channels
23:14 <@kanzure> what channels
23:15 <@nmz787> the fluidics channels for a microfluidic synthesizer
23:15 <@kanzure> but we weren't going to do a microfluidic synthesizer
23:15 <@kanzure> it was going to be a cheap copy of some other junk
23:15 <@nmz787> you said you wouldn't mind if I did it in parallel
23:15 <@nmz787> i don't have any ideas for copies, you mentioned browsing patents
23:16 <@nmz787> i looked a bit earlier but didn't find anything
23:16 <@nmz787> that's really not interesting or promising though
23:16 <@kanzure> you don't have any ideas about how conventional synthesizers work? that sounds really bad yo.
23:16 <@kanzure> it's interesting because they work
23:16 <@nmz787> once a design is found, some wafer people could definitely come up with cheaper world available processes
23:16 <@kanzure> found?
23:16 <@nmz787> but for now it makes things easy
23:17 <@nmz787> no it's not interesting because they take long as hell and eat costly reagents
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23:17 < ParahSail1n> maybe a cheap open hplc would be a better project
23:17 <@kanzure> the costly reagents aren't the point
23:17 <@nmz787> they are to me
23:18 <@nmz787> that's a huge point
23:18 <@kanzure> you don't have any machine whatsoever, why would you care
23:18 < ParahSail1n> i dont have an idea on how cheap it could be, or how many people would benefit from such a thing
23:18 <@nmz787> because i don't want a crappy copy
23:18 <@kanzure> you don't have anything at all, though
23:18 <@nmz787> exactly
23:18 <@kanzure> ...?
23:18 <@nmz787> i need to build it
23:18 <@kanzure> yeah, a standard synthesizer
23:19 <@nmz787> no man
23:19 <@nmz787> they're different physics to make them spin
23:19 <@kanzure> the reason you don't have a synthesizer isn't because the reagents are expensive
23:19 <@nmz787> less is more
23:19 < ParahSail1n> fundamentally all you are doing is pumping fluid from a reservoir through a column that you buy at high pressure
23:19 < ParahSail1n> the detectors on the other side of the column are an independent unit
23:20 <@nmz787> the hplc would be useful if you want me to do pipettor synthesis
23:21 <@nmz787> since it can detect 10-55 bp
23:22 <@nmz787> ParahSail1n: Desalt: Oligos are processed through normal phase chromatography column which removes salts but not failure sequences
23:23 < ParahSail1n> works plenty fine unless you are doing supercool stuff like mlpa reactions with the oligos
23:24 <@nmz787> yeah but not for writing clonal genes
23:25 < ParahSail1n> well you're not really writing genes, you're writing oligos to stitch together
23:25 < ParahSail1n> and you can go over the sequence later and correct introduced snps with the usual techniques
23:26 <@nmz787> and the higher the purity between stiching operations, the higher the yield overall
23:26 < ParahSail1n> you can always improve yield after you have a working prototype
23:26 <@kanzure> and oligo length
23:26 <@kanzure> and reagent volumes
23:27 < ParahSail1n> i suspect page purification would be easier to hack together than hplc
23:27 < ParahSail1n> casting page in capillaries is pretty easy
23:28 < ParahSail1n> and you only need electric potential and buffer to push stuff through that
23:28 <@kanzure> ParahSail1n: also we don't have to do just one thing at a time. if you think we need to tackle a column then we can do that.
23:28 < ParahSail1n> the massive fluid handling and air compressor of an hplc
23:29 < ParahSail1n> kanzure, column is not essential
23:29 <@kanzure> well it would be nice for protein purification reasons
23:29 <@kanzure> dunno
23:29 < ParahSail1n> ah, well page will only do oligos
23:29 <@nmz787> yeah thats the plan for the fib, page
23:30 <@nmz787> there are some examples of just using the microchannel to do gel free separation
23:30 <@kanzure> each of those were separate research projects that took a lot of time to build up
23:30 <@kanzure> ParahSail1n: can't you chime in with your experience in microfluidics here
23:31 < ParahSail1n> ive been
23:31 <@kanzure> ParahSail1n: because nmz787 doesn't know about that
23:31 <@nmz787> page is anyways done in microchannels
23:31 <@kanzure> no i mean.. you have actual physical hands-on experience with it
23:31 <@nmz787> all the ABI sequencers use 50 micron tubes
23:31 < ParahSail1n> fib is insane for this, in microfabrication you avoid beams wherever possible
23:31 <@nmz787> why?
23:31 <@nmz787> that sounds stupid
23:32 <@nmz787> it's a sweet instrument
23:32 <@nmz787> it makes sense
23:32 < ParahSail1n> because you are drawing nano features with one tiny head
23:32 <@nmz787> and realistically if you use it, it's not that expensive to run
23:32 <@nmz787> electricity wise
23:32 < ParahSail1n> the only thing you use beams in production for is e-beam lithography of masks for normal lithography
23:32 <@nmz787> huh?
23:32 <@nmz787> you can make the beam micron sized to nano size
23:32 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving]
23:32 < ParahSail1n> because it takes you days to print a billion features in a die with an e-beam
23:33 < ParahSail1n> and you're not even talking about features that require such an expensive proces
23:33 <@nmz787> why do ebeam on a chrome plate then do lithography
23:33 <@nmz787> just beam on the silicon to mill in the first place
23:33 <@nmz787> it's just like CNC
23:33 <@nmz787> this isn't e tho
23:33 < ParahSail1n> this is simple stuff you could pattern with a photolithography mask that you printed with an inkjet printer
23:33 <@nmz787> its gallium
23:34 <@nmz787> no way, printers are at least an order of magnitude too coarse
23:34 < ParahSail1n> ok then send the cad drawing to one of the shops and theyll make it high res
23:35 <@nmz787> that's what i'm saying to do
23:35 <@nmz787> i mentioned the milling rate eariler
23:35 <@nmz787> earlier
23:35 < ParahSail1n> the "shops" dont do fib shit to make those original masks
23:35 <@nmz787> and kanzure we long ago calculated some sequencer math length
23:35 <@nmz787> it was 60 cm i believe
23:36 <@nmz787> ParahSail1n: right
23:36 <@nmz787> round here they do
23:36 < ParahSail1n> do you need <3 um features?
23:36 <@nmz787> http://www.norsam.com/
23:36 <@nmz787> yes
23:37 <@nmz787> all my reagent volumes have been based on 1 micron cube
23:37 < gradstudentbot> What do you mean this isn't going to work?
23:37 < ParahSail1n> so it would break if you made it 9x bigger volume?
23:38 <@nmz787> no
23:38 <@nmz787> but i don't want to do silicon etching
23:38 <@nmz787> this thing is CNC
23:38 <@nmz787> it's easy
23:40 <@nmz787> ok so it says 60 cm path would take 100 minutes to mill
23:41 < valyap> this is one of the busiest channels on freenode
23:41 <@nmz787> that's a column that gets 300-500 bp read length
23:41 < valyap> has their been a breakthrought?
23:41 <@kanzure> valyap: no, go away
23:41 < valyap> hi kanzure
23:42 <@nmz787> the other option is getting some folks together to seriously hack this bluray writer as a polar stereolithography writer
23:42 < ParahSail1n> so you want to use a vector scanning fabrication technique in a mass produced device?
23:42 <@nmz787> but that isn't a sure thing
23:43 <@nmz787> and wouldn't get electric traces
23:43 <@kanzure> ParahSail1n: not necessarily mass produced, not sure
23:43 <@nmz787> raster
23:43 < ParahSail1n> this thing is valuable enough that people will pay 18k for each one?
23:43 <@kanzure> ParahSail1n: also, there's nothing wrong with vector-based designs. vector writing *shrug* i'd like to try it sometime.
23:43 <@kanzure> ParahSail1n: 18k for what?
23:43 < ParahSail1n> no, its just low throughput
23:44 <@kanzure> oh, the time on the fib
23:44 <@kanzure> yeah, probably not
23:44 < ParahSail1n> 50 hours of fib time, tracing a single print head across every single feature
23:44 <@nmz787> since bluray track spacing is 300nm
23:44 <@kanzure> also, i think it's going to take more than 50 hours/100 minutes =~ 30 iterations
23:44 <@kanzure> ParahSail1n: how many iterations on a design of this magnitude/complexity do you think it would take to get a synthesizer to work?
23:44 <@kanzure> microfluidic synthesizer.
23:44 <@nmz787> i just said 100 mins
23:45 <@nmz787> not 18k?
23:45 <@kanzure> you said 100 min per 60cm (per run)
23:45 <@nmz787> and i said fib was just for prototyping
23:45 <@kanzure> so 50 hours divided by 100 minute runs
23:45 <@kanzure> is 30 iterations
23:45 <@nmz787> 50 hours?
23:45 <@kanzure> you said 50 hours
23:45 <@kanzure> sigh
23:45 < ParahSail1n> photolithography smaller than 3um feature is a thing
23:45 <@nmz787> not for a device in production
23:45 <@kanzure> no you said design time
23:45 < ParahSail1n> tell that to intel
23:45 <@nmz787> (to kanzure )
23:45 <@kanzure> please try to follow
23:45 <@nmz787> not you
23:46 < ParahSail1n> or tell that to stm micro
23:46 <@nmz787> no i def know smaller than 3 um lith
23:46 <@nmz787> i'm saying per device wont be $18k in fib
23:47 <@nmz787> that is for research and dev
23:47 <@nmz787> and worst case
23:47 <@kanzure> 30 iterations is not worst case -_-
23:47 < gradstudentbot> I don't know whether I am Turing dreaming that I am a machine, or a machine dreaming that I am Turing!
23:47 < ParahSail1n> maybe you want to do your iterations on cheap 3um photomasks
23:48 < ParahSail1n> and then you can buy a fancy ebeam mask later after you've gotten it working on easy mode
23:48 <@kanzure> "easy"
23:49 <@nmz787> i was saying that FIBing silicon to mill and add circuitry was easier and cleaner than wafer fab IMO and IME
23:50 <@nmz787> i've only made few hundred micron sized transistors once
23:50 <@nmz787> and seen some stuff FIBbed a few times
23:50 <@nmz787> like 3 or 4
23:50 <@nmz787> :/
23:50 < ParahSail1n> 100 minutes of fib time is not terrible
23:50 <@nmz787> FIB was pretty much like a laser cutter and welder in one
23:52 <@nmz787> I'm totally open to how to make the thing
23:52 <@nmz787> but i've been looking at techniques for a while, and FIB is damn attractive as someone who wants it to just work
23:53 <@nmz787> plus with nano capabilities we can start to think about using enzyme traps
23:53 <@nmz787> !!!
23:55 <@nmz787> tDt!?
23:56 <@nmz787> the circuit laying would be considerably less than 100 minutes of FIB time
23:57 <@nmz787> so even if there was no better way to do that later
23:57 <@nmz787> but I'm pretty sure there are automated fabs that could easily make at least the silcon part
23:57 <@nmz787> or glass
23:59 <@nmz787> for the $500 a pop in R&D, i'd rather spend it locally than send to that stanford foundry
--- Log closed Sat Aug 03 00:00:44 2013