| --- Log opened Fri Aug 02 00:00:43 2013 | ||
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| @nmz787 | superkuh: what comment got removed from http://travisgoodspeed.blogspot.com/2013/07/hillbilly-tracking-of-low-earth-orbit.html | 00:59 |
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| 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 | 03:05 |
| 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. | 03:06 |
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| @kanzure | fredox: august 8 is http://www.meetup.com/emergence-24/events/120263392/ (yes the topic might seem boring, but the people aren't) | 07:35 |
| fredox | very vague that group | 07:37 |
| @kanzure | they are a bunch of old perl hackers turned scifi authors | 07:37 |
| gradstudentbot | Yeah, there's a clear trend. | 07:38 |
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| klafka | what? | 07:50 |
| @kanzure | huh? | 07:50 |
| klafka | like who? | 07:50 |
| klafka | old perl hackers turned scifi authors | 07:50 |
| @kanzure | what do you mean who? check the page. | 07:51 |
| @kanzure | it's nobody you know | 07:51 |
| 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. | 07:58 |
| klafka | yeah they aren't | 07:59 |
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| klafka | btw 'in our dna' is a new techy term i hate | 10:32 |
| @kanzure | why? we have sequenced your dna and now we know things about it. | 10:33 |
| fredox | the 'our' part bothers especially bothers me | 10:34 |
| @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. | 10:35 |
| fredox | its time to revive phrenology | 10:36 |
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| 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' | 10:40 |
| @kanzure | ah i see. yeah, that's dumb. | 10:41 |
| klafka | btw it seems like more and more poeple are using golang | 10:44 |
| @kanzure | sure. it seems fun. | 10:45 |
| klafka | wow i did not know trulia ipo'd | 10:46 |
| 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 | 10:47 |
| klafka | but it's not the 10 steps backward c++ is | 10:48 |
| 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 | 10:49 |
| cpopell_ | figured as much. | 10:50 |
| cpopell_ | Alas | 10:50 |
| @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 | 10:52 |
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| klafka | what is the cheapest single sensor eeg ? | 11:09 |
| klafka | i've been thinking about just using cheap eegs to interject random 'crowd noise' into reactive art | 11:10 |
| @kanzure | openeeg, neurosky, things like that | 11:11 |
| @kanzure | they probably have links to cheap sens0rs | 11:11 |
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| cpopell_ | god the patent office is some stupid shit | 11:26 |
| cpopell_ | some chinese firm patent DLP/DMD projection. in 2008 >_> | 11:26 |
| cpopell_ | (you know, the thing TI had had patented since ~94 or so) | 11:27 |
| @kanzure | only the claims matter, so maybe their specific combination of claims is different | 11:29 |
| @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. | 11:30 |
| 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 | 11:31 |
| @kanzure | makes sense to me | 11:32 |
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| * heath waves hello to everyone | 11:38 | |
| @heath | cpopell_: it takes patent examinars ~30 minutes for one query | 11:47 |
| 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 | 11:48 |
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| @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 | 12:05 |
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| @kanzure | for synthesizers. | 12:05 |
| @kanzure | "Nobody would want to make that much DNA" | 12:05 |
| @nmz787 | lol | 12:16 |
| @kanzure | "Nobody needs more than 128 kb bp" | 12:19 |
| @kanzure | erm, i mean 128 kbp | 12:19 |
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| gradstudentbot | Yeah, I don't know. | 12:20 |
| @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 | 12:23 |
| @kanzure | also try pyflake or pylint or flake8 sometime for python things. | 12:24 |
| @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) | 12:25 |
| @nmz787 | fenn: so what do you know about beta agonists (since you mentioned blockers yesterday)? https://en.wikipedia.org/wiki/Ractopamine | 13:02 |
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| @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 | 13:11 |
| @heath | nmz787: what's your js project? | 13:12 |
| @nmz787 | just an uploader page right now | 13:13 |
| @nmz787 | something in my code is broken though | 13:16 |
| @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 | 13:17 |
| @heath | nmz787: are you receiving any error in your console? | 13:20 |
| @nmz787 | no :( | 13:21 |
| @heath | what about in the network tab, are there some requests not returning 200? | 13:22 |
| @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 | 13:24 |
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| ParahSailin | is there a more concise python way to manipulate DOM than etree? | 13:46 |
| ParahSailin | this is quite a bit more verbose than im used to in jquery | 13:47 |
| 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 | 13:49 |
| ParahSailin | this makes me smile | 13:50 |
| tomkinsc | if you are concerned at all about memory use, you might take a look at xml.dom.pulldom as well | 13:54 |
| ParahSailin | i just dont want to type very much generating simple reports | 13:58 |
| ParahSailin | thanks, pyquery is nice | 13:58 |
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| @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 | 14:12 |
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| @nmz787 | kanzure: heat cycling isn't really a part of this AFAIK | 14:18 |
| @nmz787 | for PCR sure! | 14:18 |
| @kanzure | shrug, okay | 14:18 |
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| @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 | 15:18 |
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| @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 | 16:43 |
| 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 | 16:47 |
| 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 | 16:48 |
| 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. | 16:49 |
| ParahSail1n | i used genome compiler on the grc build 37 with -O2 and it built a lisp interpreter | 16:51 |
| @kanzure | what? | 16:51 |
| @kanzure | nmz787: so, i don't think we need $2000 for a 4-channel oscilloscope. that seems like a ripoff. | 16:56 |
| @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 | 16:57 |
| @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? | 16:58 |
| 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? | 16:59 |
| @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 | 17:00 |
| 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 | 17:01 |
| ParahSail1n | damn 50 hours of fib? | 17:02 |
| @kanzure | yeah i have no idea where that's coming from | 17:02 |
| ParahSail1n | if you have to use fib, you're probably not coming up with a very scalable fabrication protocol | 17:03 |
| 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.. | 17:04 |
| 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". | 17:06 |
| @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 | 17:07 |
| @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 | 17:08 |
| @kanzure | if you can't get a decent hplc for less than 20k then i think we should solve that problem too | 17:10 |
| @nmz787 | $2k is cheap for a 4 channel scope | 17:16 |
| @nmz787 | chinese cheap | 17:16 |
| @nmz787 | new usa models are easily $4k-5k | 17:16 |
| @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 | 17:17 |
| @nmz787 | 50 hours of fib is cheaper than buying a fib | 17:19 |
| @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 | 17:20 |
| @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 | 17:21 |
| @nmz787 | http://www.oregon-physics.com/lab_services/fib_micromachining_milling.html | 17:22 |
| @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 | 17:23 |
| @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 | 17:24 |
| @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' | 17:25 |
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| @kanzure | ParahSail1n: maybe i should make you do the BOM | 17:26 |
| ParahSail1n | well i think you should just stack up a whole bunch of chairs | 17:27 |
| ParahSail1n | this is for a space program, right? | 17:27 |
| @kanzure | sort of | 17:28 |
| ParahSail1n | oligo synthesis? | 17:29 |
| ParahSail1n | oligomaker clone? | 17:30 |
| @kanzure | oligo synthesis | 17:30 |
| @kanzure | design not determined yet. "not micron". | 17:30 |
| ParahSail1n | is this intended to be part of a long sequence synthesis system? | 17:31 |
| @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. | 17:32 |
| @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. | 17:33 |
| @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. | 17:34 |
| @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? | 17:35 |
| @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.. | 17:36 |
| @kanzure | i don't want to start with something extremely complex that wont work | 17:37 |
| @kanzure | i don't entirely care about what their design is. i don't think it should influence what choices i make. | 17:39 |
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| ParahSail1n | should probably have in mind where you want to go with it eventually, as that will inform initial design considerations | 17:42 |
| @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. | 17:47 |
| @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 | 17:55 |
| gradstudentbot | I think I have ebola. | 17:56 |
| @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) | 17:57 |
| @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' | 17:58 |
| @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 | 17:59 |
| @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 | 18:00 |
| @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 | 18:01 |
| @nmz787 | add stoichiometric amounts of reagents | 18:02 |
| @nmz787 | or just under | 18:02 |
| @nmz787 | then filter | 18:02 |
| @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? | 18:03 |
| @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? | 18:04 |
| @kanzure | how is a balloon-chamber the same as parallelization? | 18:05 |
| @nmz787 | not, just you asked are we doing array | 18:06 |
| @kanzure | are we? i am still confused. | 18:09 |
| @nmz787 | array means? | 18:11 |
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| @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 | 18:19 |
| @kanzure | (in this context) | 18:20 |
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| fredox | do you have any strand lengths in mind for particular things you want to be able to synth? say X kbp | 19:02 |
| @kanzure | well, the minimum is a primer at least 16 bp. | 19:12 |
| @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 | 19:13 |
| fredox | my limited research indicates 50mers is about as long as you'd practically go for a single well | 19:14 |
| @kanzure | there are some machines that are claimed to do 100-250, but i've never heard of more than 250. | 19:15 |
| fredox | time factors i've seen are around 10mins per cycle | 19:17 |
| gradstudentbot | What do you mean this isn't going to work? | 19:19 |
| @kanzure | i've seen 2 minutes per cycle | 19:22 |
| @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 | 19:24 |
| @kanzure | multipipettor claw things | 19:25 |
| gradstudentbot | Did you see that hack? | 19:25 |
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| @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 | 19:30 |
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| 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? | 19:32 |
| @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/ | 19:33 |
| @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. | 19:34 |
| fredox | no open sequencer in the works? | 19:35 |
| @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/ | 19:36 |
| @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 | 19:37 |
| @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 | 19:38 |
| @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. :( | 19:39 |
| * 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 | 19:40 |
| @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 | 19:41 |
| @kanzure | where was that church paper about doing a micropipettor plus microarray | 19:42 |
| @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." | 19:44 |
| @kanzure | http://arep.med.harvard.edu/pdf/Matzas_10.pdf | 19:45 |
| fredox | nmz787: that design was essentially what i had in mind | 19:46 |
| @kanzure | supplementary files for that last paper, http://www.nature.com/nbt/journal/v28/n12/extref/nbt.1710-S1.pdf | 19:47 |
| @kanzure | oh look they have a pic of their setup | 19:48 |
| @kanzure | that array is way larger than i imagined | 19:48 |
| @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." | 19:49 |
| @nmz787 | fredox: which? | 19:50 |
| @kanzure | ParahSail1n: how much would a picotiter plate cost | 19:51 |
| fredox | the inkjet | 19:52 |
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| @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 | 19:53 | |
| @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 | 20:00 |
| gradstudentbot | Hey, let's write a paper about that. | 20:02 |
| @kanzure | rofl | 20:08 |
| @kanzure | so anyway, that might be a good way to store a library of beads. 4096x4096 means an entire 24mer library. | 20:18 |
| ParahSail1n | 454 is a pretty expensive way to get data | 20:37 |
| @kanzure | i just mean their plates | 20:37 |
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| @kanzure | /win 4 | 21:33 |
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| -!- 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] | 21:44 | |
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| [ AlonzoTG] [ fredox ] [ lupfantomo ] [ poppingtonic ] [ superkuh ] [ Zhwazi ] | 21:44 | |
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| -!- 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 | 21:44 | |
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| @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." | 21:58 |
| 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." | 22:06 |
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| @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 | 23:01 |
| ParahSail1n | why is there hplc in this? | 23:02 |
| @kanzure | and 18k fib? | 23:02 |
| @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? | 23:03 |
| @nmz787 | i think they do hplc on all bathces | 23:04 |
| @nmz787 | batches | 23:04 |
| @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 | 23:05 |
| @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 | 23:06 |
| 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. | 23:07 |
| @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 | 23:08 |
| @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 | 23:09 |
| @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 | 23:10 |
| @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 | 23:11 |
| 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 | 23:12 |
| @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 | 23:13 |
| @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 | 23:14 |
| @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 | 23:15 |
| @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 | 23:16 |
| @nmz787 | no it's not interesting because they take long as hell and eat costly reagents | 23:17 |
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| 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 | 23:17 |
| @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 | 23:18 |
| @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 | 23:19 |
| @nmz787 | the hplc would be useful if you want me to do pipettor synthesis | 23:20 |
| @nmz787 | since it can detect 10-55 bp | 23:21 |
| @nmz787 | ParahSail1n: Desalt: Oligos are processed through normal phase chromatography column which removes salts but not failure sequences | 23:22 |
| ParahSail1n | works plenty fine unless you are doing supercool stuff like mlpa reactions with the oligos | 23:23 |
| @nmz787 | yeah but not for writing clonal genes | 23:24 |
| 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 | 23:25 |
| @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 | 23:26 |
| ParahSail1n | i suspect page purification would be easier to hack together than hplc | 23:27 |
| ParahSail1n | casting page in capillaries is pretty easy | 23:27 |
| 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 | 23:28 |
| 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 | 23:29 |
| @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 | 23:30 |
| 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 | 23:31 |
| @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 |
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| ParahSail1n | because it takes you days to print a billion features in a die with an e-beam | 23:32 |
| 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 | 23:33 |
| @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 | 23:34 |
| @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 | 23:35 |
| @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 | 23:36 |
| @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? | 23:37 |
| @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 | 23:38 |
| @nmz787 | ok so it says 60 cm path would take 100 minutes to mill | 23:40 |
| 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 | 23:41 |
| @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 | 23:42 |
| @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 | 23:43 |
| @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 | 23:44 |
| @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 | 23:45 |
| 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 | 23:46 |
| @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 | 23:47 |
| ParahSail1n | and then you can buy a fancy ebeam mask later after you've gotten it working on easy mode | 23:48 |
| @kanzure | "easy" | 23:48 |
| @nmz787 | i was saying that FIBing silicon to mill and add circuitry was easier and cleaner than wafer fab IMO and IME | 23:49 |
| @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 | 23:50 |
| @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 | 23:52 |
| @nmz787 | plus with nano capabilities we can start to think about using enzyme traps | 23:53 |
| @nmz787 | !!! | 23:53 |
| @nmz787 | tDt!? | 23:55 |
| @nmz787 | the circuit laying would be considerably less than 100 minutes of FIB time | 23:56 |
| @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 | 23:57 |
| @nmz787 | for the $500 a pop in R&D, i'd rather spend it locally than send to that stanford foundry | 23:59 |
| --- Log closed Sat Aug 03 00:00:44 2013 | ||
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