--- Log opened Wed Jan 25 00:00:31 2012
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08:14 < jrayhawk> http://mirror.linux.org.au/pub/linux.conf.au/2012/Keynote_Bruce_Perens.ogv
08:20 < kanzure> what is it about
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09:13 < archels> http://vimeo.com/8569187
09:15 < jrayhawk> Some combination of open hardware or ideological warfare
09:15 < jrayhawk> s/or/and
09:20 < jrayhawk> and lots of other stuff in there is interesting
09:20 < jrayhawk> http://mirror.linux.org.au/pub/linux.conf.au/2012/ that is
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10:46 < kanzure> http://joostn.github.com/OpenJsCad/
10:46 < kanzure> although it's just boolean ops on meshes still (csg.js)
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10:50 < kanzure> gah
10:50 < kanzure> some guy is trying to argue that OpenJsCad is boolean operations on NURBS
10:51 < kanzure> so not only do i have to continue to explain that blender is not the same sort of engine as solidworks or catia,
10:51 < kanzure> but the developers don't even know the difference
10:55 < kanzure> this probably is insufficient
10:55 < kanzure> http://diyhpl.us/wiki/cadfaq
10:56 < kanzure> i suppose most people don't care if their models are 100s of thousands of tessellated triangles, as long as it prints on the printer.. (yawn)
10:57 < kanzure> csg.js is nice if you never, ever share the output of the file, but only the source file; also, it's nice if you never, ever actually render large models with it
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11:08 < kanzure> hah
11:08 < kanzure> http://pubs.rsc.org/en/Content/ArticleLanding/2011/LC/c0lc00577k
11:08 < kanzure> so this seems to use an optical method to guide beads into different areas for dna synthesis
11:09 < kanzure> i'm not sure how it prevents the different reservoires from mixing into the main channel
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11:18 < delinquentme> so is it a difficult thing to come up with novel math applications in bio?
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11:19 < kanzure> delinquentme: yes, it's very difficult to know whether or not someone has previously thought about a certain math concept
11:21 < delinquentme> kanzure, SO i guess its correct to say that in order to apply mathematical models effectively to these problems you've got to have a solid basis in math processes
11:21 < delinquentme> IE knows lots about the applications
11:21 < kanzure> what?
11:22 < delinquentme> you've got to know lots of math
11:22 < delinquentme> in order to pickout which model / technique
11:22 < delinquentme> would best help a problem
11:23 < kanzure> sure. or you can just make up the math on your own (this has the downside of making it hard to search for what other people call the problem, or how they approached similar problems)
11:23 < kanzure> wow wow, what
11:23 < kanzure> why is elsevier displaying ads on sciencedirect ow
11:23 < kanzure> *now
11:23 < kanzure> scroll down to the bottom on http://www.sciencedirect.com/science/article/pii/S0003269710004045
11:24 < delinquentme> ya thats quite the hefty popup
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11:27 < kanzure> hrm. it occurs to me that it should be possible to spam google scholar's index,
11:27 < kanzure> for every paper that sciencedirect hosts, generate a pdf with the same citation information
11:28 < kanzure> then allow google scholar to crawl these pdfs
11:28 < kanzure> instead of content, the pdfs will be something else
11:28 < kanzure> i'm fairly confident that nobody in their right mind goes to sciencedirect except from google scholar
11:30 < delinquentme> ok here we go:
11:31 < delinquentme> a program to check whether particular beneficial proteins are expressed in microarray data
11:32 < kanzure> can i convince you to just work on a dna synthesis instrument instead :P
11:37 < delinquentme> kanzure, what are you doing with it :D
11:38 < delinquentme> I agree that DNA synthesis will be huge soon
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11:43 < kanzure> delinquentme: well, my ideal scenario is a polymerase that i can control
11:43 < kanzure> deliquentme: but i'd settle with a microfluidic or desktop-sized device that would build oligos of any length
11:43 < kanzure> possibly from a library, or possibly from de novo synthesis
11:44 < delinquentme> well how do you get the polymerase to work
11:44 < kanzure> it would probably require on-board sequencing for verification
11:44 < kanzure> nobody knows that yet, so a more traditional dna synthesis approach is needed
11:44 < delinquentme> kanzure, sounds like you should just build a system which consistently sequences the right bases
11:45 < kanzure> what? i'm talking about synthesis
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11:46 < delinquentme> kanzure, yeah I mean skip the expensive machine
11:46 < Lucas_> good afternnon
11:46 < delinquentme> so how to isolate the polymerase?
11:46 < kanzure> isolating polymerase isn't an issue
11:46 < delinquentme> but doesnt the polymerase use a single strand to create sequences?
11:46 < Lucas_> ohh, biology
11:46 < delinquentme> ergo you'd already have a particular sequence synthesized in order for it to work?
11:47 < Lucas_> what's the issue, I am curious
11:47 < delinquentme> :P
11:47 < kanzure> delinquentme: are you talking about traditional dna synthesis, or yesterday's crazy polymerase hacking work?
11:47 < delinquentme> Lucas_, kanz is interested in DNA synthesis using really fast tools
11:47 < delinquentme> kanzure, im just asking questions as to how the polymerase would synthesize DNA
11:47 < kanzure> once you synthesize a 6nt strand, you still need to combine it with the next strand, thus polymerase.. pretty standard
11:48 < delinquentme> ( because im 95% clueless )
11:48 < kanzure> ok, are you asking how pcr works?
11:48 < Mariu> you reminded me of 'The Architect' from 'The Matrix', when you said "ergo" xD
11:48 < delinquentme> nah im fairly comfortable w themocycling
11:48 < kanzure> thermocycling is just a process...
11:48 < delinquentme> Mariu, :D
11:48 < Mariu> =p
11:48 < kanzure> pcr is polymerase chain reaction. it uses polymerase.
11:49 < delinquentme> kanzure, true but you're talking "from scratch" synthesis
11:49 < kanzure> so anyway, let's say you do de novo oligo synthesis of 6 nt, you still need to sequence and confirm that it's valid, then you do ligation+pcr
11:49 < delinquentme> PCR is simply amplification of an existing sequence
11:49 < delinquentme> 6 nt
11:49 < delinquentme> nucleotides
11:49 < delinquentme> kk
11:49 < kanzure> bp
11:50 < kanzure> usually you do single-strand synthesis.. so bp isn't accurate, but people know what you're talking about
11:50 < delinquentme> kanzure, you dont need ligation
11:50 < delinquentme> you're doing denovo synthesis ... there are no cells to rupture
11:50 < delinquentme> right?
11:51 < kanzure> ligation is the joining of two dna strands together using something like dna ligase
11:51 < delinquentme> you're talking like a machine which legos this shit together and viola you've got 6 nucleotides
11:51 < delinquentme> LIGATION not lysing ok
11:51 < kanzure> um, yeah- de ovo oligo synthesis is very standard
11:51 < delinquentme> ok
11:51 < delinquentme> im with you .. continue
11:51 < kanzure> you can run the phosphoramidite method for as long as you want, making 1000s of bp of dna
11:52 < kanzure> but there is a natural error rate due to problems
11:52 < kanzure> sometimes that's 1 in 250 or worse
11:52 < kanzure> polymerase does 1 error in 10,000 or better
11:53 < kanzure> so if yuo want to be sure that your output is correct in the process of synthesis, you sequence it along the way
11:53 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/microfluidics_Quake_DNA_synthesizer-20mers-PFPE.png
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11:54 < kanzure> then you do onboard sanger sequencing of anything you synthesize http://diyhpl.us/~bryan/papers2/microfluidics_Sanger_sequencer.png
11:56 < delinquentme> so then your polymerase hangs out in the reaction chambers
11:57 < kanzure> sure
11:57 < delinquentme> and you pump in the nucleotides through the channels
11:57 < delinquentme> Is that sanger sequencing microfluidics technique not patented?
11:57 < kanzure> i'm sure someone has patented sanger sequencing
11:58 < kanzure> and i'm sure someone has patented a form of sanger sequencing on microfluidic chips
12:03 < delinquentme> so how do current companies run their synthesis process?
12:03 < delinquentme> like mrgene
12:05 < kanzure> i think they outsource to dit :P
12:05 < kanzure> *IDT
12:06 < kanzure> but no, there's "dna synthesis machines" that use phosphoramidite synthesis or some other bead-based method
12:06 < delinquentme> so then if you've got polymerase and you've got a source for the fabrication of the chips .. what else do you need?
12:07 < kanzure> no, i'd have to build the chips
12:07 < kanzure> and build the oligo library, and some way to let people restock their oligo library.. hrm
12:09 < delinquentme> you' build the chips?
12:09 < delinquentme> that sounds nuts IMO
12:09 < delinquentme> why?
12:10 < delinquentme> chemical etching?
12:10 < kanzure> first of all, the chips don't exist
12:10 < strages_work> or if you have a laser....
12:10 < kanzure> it'd probably be pdms photolithography stuff
12:10 < kanzure> or laser cut
12:11 < kanzure> not a big deal
12:11 < delinquentme> strages_work, true but I dont think kanz has this laying around?
12:11 < kanzure> um, i do have a laser cutter
12:11 < strages_work> a local hackerspace might....
12:11 < kanzure> i'm the one who bought the laser cutter for the austin hackerspace (at least, the first laser cutter)
12:12 < kanzure> (not the one they are currently using at their new location)
12:12 < delinquentme> IMO it shoulds like shit you should just outsource
12:12 < delinquentme> and its not like you need to customize these
12:12 < kanzure> outsource the design of this device?
12:13 < delinquentme> you just need a number of them bc what you're doing it __NOT__ designing novel experiments but instead synthesizing
12:13 < kanzure> you mean the fabrication? no, i think for prototyping i should do fabrication
12:13 < delinquentme> kanzure, dont you have the design?
12:13 < kanzure> nope, i thought this is what we were talking about
12:15 < delinquentme> ah ok so you're at the design point here
12:15 < delinquentme> so you need to come up with some mechanism which would allow the polymerase to build the DNA
12:15 < delinquentme> but im still missing the key aspect
12:16 < delinquentme> polymerase is synthesis by sequenceing
12:16 < delinquentme> is it not?
12:16 < delinquentme> how does that help you with de novo snyth?
12:17 < kanzure> what?
12:17 < kanzure> are you confusing two different goals of polymerase protein engineering vs. dna synthesis?
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12:19 < delinquentme> kanzure, what you're trying to do is dna snythesis right?
12:19 < kanzure> de novo synth can happen without polymerase, but you still need to copy the resulting output so that it is usable
12:20 < delinquentme> you want insilico >> ACCACATAGAGTA>> machineX >> chemical ACCACATAGAGTA
12:20 < kanzure> (pcr)
12:21 < kanzure> yes, there's already many well known mechanism of de novo dna synthesis and strategies for dna assembly (without de novo synthesis)
12:21 < delinquentme> if what you're trying to do is take in sequences and then have a machine assemble a chemical bonded corresponding molecule based off of that sequence we're on the same page
12:21 < kanzure> the trick is picking which one, designing a microfluidic device to actually do it properly, etc.
12:21 < delinquentme> on cool
12:21 < delinquentme> but then I dont get how polymerase helps you?
12:21 < delinquentme> polymerase reads an existing chunk of DNA right?
12:22 < kanzure> are you asking "how does yesterday's chat about polymerase engineering help you?"
12:22 < delinquentme> ohhhhh
12:22 < kanzure> or "why do you need pcr after dna synthesis?"
12:22 < delinquentme> the polymerase is not part of this synthesis operation?
12:22 < delinquentme> im trying to figure out the mechanism you're wanting to use for todays chat about synthesis
12:23 < kanzure> well, you can use polymerase if you're doing bead-based synthesis (like your strand is attached to the bead); this is also the same bead strategy in phosphoramidite synthesis heh
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12:53 < delinquentme>  can i convince you to just work on a dna synthesis instrument instead :P << kanzure
12:54 < delinquentme> is this instrument using polymerase
12:55 < kanzure> depends on the design that we choose
12:56 < delinquentme> ah! ok
12:56 < delinquentme> now i comprendo
12:56 < delinquentme> arent microfluidic chips lined with some kind of fluid?
12:57 < delinquentme> like the fluids runing through the chips .. do they actually come in contact with the plastic
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12:58 < kanzure> delinquentme: yes. the plastic has channels. the fluid runs through the channels.
12:59 < delinquentme> kanzure, yeah i thought I read somewhere that those fluids are suspended w something else
12:59 < kanzure> they can be
12:59 < kanzure> like water-in-oil
12:59 < delinquentme> yeah!
12:59 < delinquentme> ok not nuts
12:59 < kanzure> which makes it "digital" microfluidics (droplets)
13:01 < delinquentme> Ohhh ok ok
13:01 < delinquentme> yeah i've seen that before
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13:03 < delinquentme> howdy bio_boris =]
13:03 < kanzure> hi bio_boris
13:03 < delinquentme> kanzure, i just posted in r/bioinformatics about a bunch of channels
13:03 < delinquentme> boris found it :D and checked us out
13:04 < bio_boris> hello
13:04 < delinquentme> bio_boris, are you a programmer?
13:04 < bio_boris> yea guess so
13:04 < bio_boris> perl
13:05 < bio_boris> im a masters student studying bioinformatics
13:05 < kanzure> have a thesis?
13:06 < bio_boris> nope
13:06 < delinquentme> oh bad ass
13:06 < bio_boris> elected the non thesis option lol
13:06 < delinquentme> theres a non thesis option??
13:06 < bio_boris> Yea its a 'professional masters'
13:06 < bio_boris> rather
13:06 < bio_boris> from a 'Professional School'
13:07 < delinquentme> oh thats cool
13:07 < delinquentme> germany?
13:07 < bio_boris> http://www.lis.illinois.edu/academics/programs/ms-bioinformatics
13:07 < delinquentme> is perl their chosen language?
13:07 < bio_boris> its what ive used the most so far
13:08 < delinquentme> bio_boris, what tetbook are you using? hows the homework?
13:08 < bio_boris> i have a few textbooks, class just started last week so not too much homework yet
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13:09 < bio_boris> im actually working on research now, tryin to remove UTRs from a FASTA file from a GFF file
13:09 < bio_boris> (using a gff3 file)
13:10 < delinquentme> bio_boris, ooooo!!!
13:10 < delinquentme> talk to me about this i've been working w GFF3 files
13:10 < delinquentme> and wouldn't that be just checking the 9th column for a Keyword?
13:11 < bio_boris> I have a list like this now
13:11 < delinquentme> bio_boris, are you working w a lab?
13:11 < bio_boris> MRNA start stop seqid | 3prime utr start stop seqid |   3prime utr start stop seqid  |  5prime utr start stop seqid
13:11 < bio_boris> so i need to do a little tiny bit of math and grab out some substrings from the fasta files
13:12 < bio_boris> of MRNA
13:12 < delinquentme> so wait are you calculating which region is the UTR?
13:12 < bio_boris> the gff says so , like
13:13 < bio_boris> MRNA 7000 to 7030   | 5 prime UTR 7000 to 7005  | 5 prime UTR 7010 to 7015
13:14 < bio_boris> so i want 7006-7009+7016-7030
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13:15 < bio_boris> i want the MRNA sequence from positions 7006 to 7009 and 7016 to 7030
13:15 < bio_boris> about to write something now to try to do that
13:15 < delinquentme>  hmmm thats a legit gff3 format?
13:15 < delinquentme> where did you pick those up?
13:15 < bio_boris> i took the GFF3 data and converted it
13:15 < bio_boris> to something easier to work with
13:15 < delinquentme> Ahhh ok
13:15 < bio_boris> cuz the GFF file was too big
13:15 < bio_boris> i only needed the start, stop, feature and description
13:15 < delinquentme> where did you get the original GFF3 from?
13:16 < bio_boris> utah.edu
13:16 < delinquentme> do they have a repo of gff3 files?
13:16 < bio_boris> im not sure, its from a particular lab
13:16 < bio_boris> working on a particular project
13:16 < delinquentme> ive been bug testing biopythons GFF parser
13:17 < bio_boris> Gff3 == Gff ?
13:18 < bio_boris> guess not
13:20 < delinquentme> so they're slightly different
13:20 < delinquentme> whats really weird is one place maintains the standards for gff2
13:20 < delinquentme> and another gf3
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15:12 < ybit> jrayhawk: oi
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17:02 < gene_hacker> you there kanzure?
17:03 < kanzure> gene_hacker: hi
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17:16 < delinquentme> gene_hacker, kanzure no sleep
17:20 < kanzure> no who?
17:20 < kanzure> he's pming me :(
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17:27 < delinquentme> kanzure, you looking for a good time?
17:27 < delinquentme> gene_hacker, share the luv
17:28 < kanzure> hi aristarchus
17:28 < gene_hacker> you'd have a huge tangle of rope attached to the ground, blowing in the wind
17:28 < aristarchus> kanzure: hello
17:28 < kanzure> gene_hacker: nah, not an issue
17:29 < kanzure> that's how it currently works
17:29 < gene_hacker> when your strand get's up to size HUGE! wouldn't it get washed out too?
17:29 < kanzure> no, it's attached to the bead
17:29 < kanzure> (or to the wall)
17:29 < gene_hacker> so in some sort of gel?
17:30 < kanzure> nope.. one sec
17:30 < gene_hacker> so are you combining oligo in parallel? or in one large chamber?
17:30 < kanzure> well, i'm not sure, i think parallel would be smart, but probably hard to manage
17:31 < kanzure> so let's say you combine A+B
17:31 < kanzure> you need to verify that A+B worked, and then store the result until you know the results
17:31 < kanzure> like if you do on chip sequencing
17:31 < kanzure> now, you might not want to sequence after every operation so maybe it's A+B+C+D+E that you want to test
17:31 < kanzure> and then you combine (A+B+C+D+E) with (F+G)
17:32 < gene_hacker> so one central bead where you apply oligo one at a time?
17:32 < kanzure> so you'd have maybe 100 different addressable "banks" to temporarily store stuff in
17:32 < kanzure> gene_hacker: where you apply the +5 bp, yes..
17:32 < kanzure> multiple chambers/reactions is possible but it complicates the circuit design
17:33 < kanzure> gene_hacker: http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Integrated%20two-step%20gene%20synthesis%20in%20a%20microfluidic%20device%20(1k%20bp,%201%20error%20per%20250%20bp).pdf
17:33 < kanzure> this is an ok example i think
17:34 < gene_hacker> are you put the dna together 5 bp at a time?
17:35 < kanzure> yes
17:36 < kanzure> but you can imagine storing the "result" of 5+5 somewhere, and later using it
17:36 < kanzure> or even "1000+5", and using that later
17:36 < gene_hacker> in the paper you mention, they put together 40 mer  oligos with 20 mer overlap
17:36 < kanzure> yeh, this paper is slightly different
17:36 < gene_hacker> how'd they get those oligos?
17:37 < kanzure> i haven't read this one in a while; it sorta depends
17:37 < kanzure> they might have synthesized those on a dna microarray with photochemistry
17:37 < gene_hacker> so it is difficult to parallelize your method?
17:37 < gene_hacker> so how long would one step take?
17:38 < kanzure> that depends on channel geometry
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17:38 < gene_hacker> what's the most reasonable estimate for how long adding one oligo would take
17:38 < kanzure> i'm looking this up, i don't want to bs oyu
17:38 < gene_hacker> 1 second, ten seconds, 30 seconds?
17:38 < kanzure> *you
17:39 < kanzure> i'd say 10-30 seconds is a good target to reach
17:39 < kanzure> but currently there's no commercial synthesizer that does anything near 1 bp/sec
17:39 < delinquentme> i learned about sample std dev and population std dev
17:40 < gene_hacker> about an hour for a kilobase
17:40 < kanzure> hmm
17:40 < gene_hacker> well I need to go
17:40 < gene_hacker> that's not bad
17:41 < kanzure> i'm pretty sure it's worse than that
17:41 < kanzure> but
17:41 < kanzure> small reaction sample sizes might allow you to increase reaction rates
17:41 < kanzure> like with pcr (nanoliter droplet + laser => orders-of-magnitude-faster pcr)
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17:41 < gene_hacker> the other problem is the rate of consumption of your oligos
17:42 < kanzure> this is why they need to be pcr tubes (or something else),
17:42 < kanzure> so that you can replace your stock
17:42 < gene_hacker> your stock could be expensie
17:42 < kanzure> yep probably
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17:42 < kanzure> hi shipwreck__
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18:03 < aristarchus> what are some good diy h+ sites?
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18:12 < kanzure> aristarchus: depends on what you want..
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18:16 < aristarchus> this might be a chicken/egg problem
18:17 < kanzure> well, then i have no trouble saying this is the best diyh+ site on the web :)
18:18 < kanzure> with the best people.
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18:21 < aristarchus> haha
18:21 < aristarchus> indeed
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18:26 < aristarchus> right now i'm looking for hi-tech home improvement  type stuff
18:26 < aristarchus> like controlling your thermostat from your phone
18:26 < minu> biohacking <- I like this term
18:29 < sylph_mako> Every house needs more of that.
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18:34 < kanzure> hi yashgaroth
18:35 < yashgaroth> whatup kanzure
18:35 < kanzure> software errors
18:35 < kanzure> this assembler i'm working with,
18:35 < kanzure> doesn't let code in for loops, access the global variables
18:35 < kanzure> i.e. all variables are reset.. hrm
18:37 < yashgaroth> I know just enough programming to know what that problem entails
18:37 < eudoxia> don't some languages have special syntax for global variables?
18:37 < kanzure> not this one
18:37 < kanzure> eudoxia: http://otakunozoku.com/RGBDSdocs/
18:38 < kanzure> oops, http://otakunozoku.com/RGBDSdocs/asm.htm
18:38 < eudoxia> oh, for that pokemon project=
18:38 < eudoxia> ?
18:39 < kanzure> heh
18:39 < kanzure> don't judge me
18:40 < eudoxia> you got my undying respect with that copy of Nanosystems
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18:40 < aristarchus> oooh rom hacking?
18:40 < kanzure> aristarchus: i'm writing source code to pokemon red
18:41 < kanzure> https://bitbucket.org/kanzure/pokered/changesets
18:43 < aristarchus> cool
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19:57 < gene_hacker> whoa you have nanosystems?
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19:58 < kanzure> gene_hacker: sure
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19:58 < eudoxia> I can't access  /stuff_to_deal_with/nanosystems.tar.gz though
19:59 < gene_hacker> where?
19:59 < kanzure> why not
19:59 < kanzure> http://gnusha.org/stuff_to_deal_with/nanosystems.tar.gz
20:00 < kanzure> try now..
20:00 < gene_hacker> forbiden
20:00 < eudoxia> 403 forbidden
20:01 < kanzure> try one more time.
20:01 < kanzure> but this time wish reallllly hard
20:01 < eudoxia> it works now
20:01 < eudoxia> hahahahahah
20:02 < gene_hacker> so is it possible to buy short 5 bp oligo nucleotides like you mentioned?
20:02 < kanzure> yes you can buy sequences of any length you want
20:02 < kanzure> http://mrgene.com/
20:03 < kanzure> huh invitrogen bought mrgene?
20:03 < kanzure> $0.35/bp .. why is it increasing in price
20:03 < kanzure> that's all wrong
20:05 < gene_hacker> but is it possible to make very pure 5 pb segments?
20:06 < gene_hacker> http://www.lightlabsusa.com/Rota-Rack-Duo-Tube-Rack.html
20:06 < kanzure> yes they will give you a high quality sample.. i mean, that's their job :p
20:06 < gene_hacker> now this is a tube rack
20:06 < gene_hacker> how much would 1024 different samples cost though?
20:06 < kanzure> a lot. you would not order 1024 samples from them
20:07 < kanzure> you'd probably setup a custom business outfit to make oligo librarise- or get better pricing from somewhere else
20:07 < gene_hacker> from the dimensions on the tube rack, 32x32 eppie tubes would take  up 2'x2'
20:07 < gene_hacker> that's pretty big
20:07 < kanzure> once you have the initial library it's really easy to just copy as much as you need
20:07 < kanzure> 2 feet? bah
20:07 < kanzure> not bad
20:07 < gene_hacker> that's pretty big
20:08 < kanzure> you could keep it under your bed :P
20:08 < gene_hacker> Now how would you dispense nanoliters of droplets from the epie tube?
20:08 < kanzure> not sure, haven't thought about that yet
20:08 < gene_hacker> 1 valve per tube?
20:08 < kanzure> probably
20:08 < gene_hacker> so you have 1024 valves
20:08 < kanzure> minimum
20:09 < kanzure> there also has to be either (1) dedicated channels for each tube or (2) a way to wash the whole thing after each withdrawal
20:09 < kanzure> s/wash/flush
20:09 < gene_hacker> that sounds complex
20:09 < kanzure> yes.. so #1 is preferable ;)
20:10 < gene_hacker> how would one replace a valve when it fails
20:10 < gene_hacker> still you're going to need moving parts
20:10 < kanzure> i haven't come up with an optimal solution yet, i'm open to ideas
20:10 < gene_hacker> plus your nanoliter droplets need to travel over 2 feet to get to where they need to go
20:11 < yashgaroth> oh ffs you can at least use multiwell plates
20:11 < kanzure> not if you want a person to replace each well
20:11 < kanzure> replenish each well
20:11 < gene_hacker> I don't think you can do that with pipes over that distance, at least not without using a bunch of expensive fluid
20:12 < yashgaroth> replenishment is no harder with a well if all you're doing is adding more
20:12 < kanzure> you can't expose the liquid to atmosphere
20:12 < kanzure> ever..
20:12 < gene_hacker> not even helium?
20:12 < yashgaroth> what why not?
20:12 < kanzure> i'd prefer not to work with helium or gases
20:12 < kanzure> yashgaroth: contamination
20:12 < yashgaroth> run the whole thing in a TC hood, those things are great
20:12 < kanzure> it's much easier if you just don't use atmosphere
20:13 < yashgaroth> I literally don't even need to use gloves, never had contamination in a thousand flasks
20:13 < kanzure> anyway, i don't really trust users to refill a 32x32 microarray with the right oligos
20:14 < gene_hacker> Could you breed oligos on the spot?
20:14 < yashgaroth> oh, me either, but that's not a case for using ep tubes
20:14 < gene_hacker> from common compounds
20:14 < kanzure> gene_hacker: yes, this is called "oligonucleotide synthesis"
20:15 < kanzure> it's a five or six step process per bp
20:15 < gene_hacker> then what benefit does the 1024 library have over conventional oligonucleotide synthesis?
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20:15 < kanzure> you don't have to synthesize any of the 1024 :P
20:15 < gene_hacker> then how do you get more?
20:16 < kanzure> 1) mail order
20:16 < kanzure> 2) pcr
20:16 < kanzure> either option.
20:16 < gene_hacker> so you're just using someone else's error prone oligonucleotide synthesis?
20:16 < kanzure> no, you'd get someone who does verification of their sequences
20:17 < kanzure> i.e. someone who synthesizes then sequences to verify
20:17 < gene_hacker> isn't oligonucleotide synthesis inherently error prone?
20:17 < yashgaroth> you can't really sequence an oligo that short, and even then it's always the 0.1% that's gonna be wrong
20:17 < kanzure> but yes, oligo synthesis does have a high error rate
20:17 < kanzure> that's why you want to get that step out of the way
20:17 < kanzure> and just use a library of known good strands
20:18 < gene_hacker> a library of 1024 unique parts that each have to be inspected before use?
20:18 < gene_hacker> that sounds expensive
20:19 < yashgaroth> couldn't you just mix a load of 6-mers together and ligate into strands? like 3 & 3 overlapping
20:19 < kanzure> yes, but you just inspect it once,
20:19 < kanzure> so let's say that you don't want to pcr your library contents when they get low,
20:19 < kanzure> you'd just ask me to send over some more, and i'd do the pcr from my stock :p
20:19 < kanzure> yashgaroth: yes but you want to keep them as 6mers really
20:20 < yashgaroth> well yes
20:20 < kanzure> so you need to keep them separated
20:20 < yashgaroth> I
20:20 < yashgaroth> 'm not saying mix everything at once
20:20 < kanzure> now, if you have a mixed library,
20:20 < kanzure> you'd need some way to address individual items in the library (like with dna)
20:20 < kanzure> so you'd synthesize your "caller".. etc.
20:20 < kanzure> anyway.. i think a separated library is a better idea
20:20 < yashgaroth> but if you make a ~30bp strand where none of the wrong 6mers would overlap each other
20:21 < kanzure> i could be convinced of doing on-chip oligo synthesis, and not having a library, but this just seems really error prone.. you'd definitely need on-chip sequencing,
20:21 < kanzure> and you'd have to sequence every 20bp chunk you make
20:21 < yashgaroth> nah, if all your 6mers are good and don't overlap the wrong way they should be fine
20:22 < kanzure> presumably you'd select a good 6mer based on the current bases near your extending end
20:22 < yashgaroth> you can extend from both ends
20:22 < gene_hacker> well I guess you're using only 200 nanoliters per kb, it might be doable
20:22 < kanzure> yashgaroth: not if one end is attached to a bead ;)
20:22 < yashgaroth> man screw beads
20:22 < gene_hacker> now how much DNA would one get from a process like this?
20:22 < kanzure> it doesn't matter,
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20:22 < kanzure> you would use pcr to copy the dna
20:23 < gene_hacker> it does
20:23 < kanzure> so let's say you end up with 1 picogram
20:23 < kanzure> you can pcr that up to a few thousand nanograms or whatever you need
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20:23 < gene_hacker> when you want to copy a big sequence of DNA from small amounts you have to go through a whole bunch of special steps
20:23 < yashgaroth> a nanogram is enough for transformation if you know what you're doing btw
20:24 < gene_hacker> I read that the PCR for that is the most difficult step
20:24 < kanzure> pcr is very well known at this point.. i wouldn't worry about it
20:24 < yashgaroth> define 'difficult'
20:24 < kanzure> yashgaroth: http://diyhpl.us/~bryan/papers2/microfluidics/PCR%20-%20Nanodroplet%20real-time%20PCR%20system%20with%20laser%20assisted%20heating.pdf
20:25 < kanzure> 40 cycles in 370 seconds = win
20:25 < yashgaroth> plus, lasers
20:25 < kanzure> and not the "have a big giant co2 tube" kind
20:26 < yashgaroth> pcr really isn't the hard part in this sort of thing anyway
20:27 < kanzure> getting 1 bp error per 100-200 is the hard part
20:27 < kanzure> the problem with on-chip sequencing is that it's a completely different process to debug
20:27 < gene_hacker> well then what's the problem craig venter is having with chromosome construction?
20:27 < kanzure> so not only do you have synthesis (or oligo library stuff), but also sequencing.. yikes
20:28 < yashgaroth> it cost millions upon millions for venter to pull that stunt
20:30 < gene_hacker> are you sequencing the strands as they are made?
20:30 < kanzure> well, if you have on-chip synthesis then yes, you should sequence as soon as you synthesize anything more than.. 10 bp
20:31 < yashgaroth> are you sequencing with PCR? because you'll need a lot more DNA than we'd be working with to get a good signal
20:32 < gene_hacker> is it possible to build an on chip synthesizer?
20:34 < yashgaroth> sure, with photolithography
20:34 < gene_hacker> oops meant sequencer
20:35 < gene_hacker> and would it be possible to move the DNA strand being synthesized around the chip on say a bead or something?
20:35 < yashgaroth> that would be extremely hard to control
20:36 < kanzure> gene_hacker: yes, people have done on-chip synthesis with various methods, though i haven't seen on-chip photo-based synthesis
20:36 < kanzure> the sequencing method would be a very simple sanger sequencing approach, i think
20:36 < gene_hacker> what about picoarray?
20:36 < gene_hacker> that's onchip photo-based synthesis
20:36 < kanzure> yes, it would be possible to move synthesized dna around, like in droplet microfluidics
20:36 < yashgaroth> sanger sequencing won't work on reads that short
20:37 < kanzure> gene_hacker: picoarray? this? http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf
20:37 < gene_hacker> yeah
20:37 < gene_hacker> the photogenerated acid one
20:37 < kanzure> been a while since i've read this one..
20:37 < gene_hacker> doesn't use any exotic photo-capped oligos
20:40 < gene_hacker> now if you have to wait 30 seconds for PCR to go through, I guess you could move the whole PCR chip to the required eppie tube while PCR is taking place
20:41 < gene_hacker> and use a 1 nanoliter sucker
20:41 < gene_hacker> instead 1024 valves
20:42 < yashgaroth> how the shit are you guys sequencing a 10bp fragment
20:42 < kanzure> i don't know, i haven't come up with that yet
20:43 < gene_hacker> Well you could use some probes to read the ends?
20:43 < kanzure> what?
20:43 < yashgaroth> even primers for sequencing are longer than 10bp
20:43 < yashgaroth> and as a rule of thumb the first 50 bases of sanger sequencing are a write-off
20:44 < gene_hacker> so kanzure are you sure that PCR has a lower error rate than oligosynthesis?
20:44 < yashgaroth> pcr amplification does, yes
20:44 < kanzure> oh man, yeah
20:44 < kanzure> just completely blan out "PCR" as a problem right now
20:44 < kanzure> *blank out
20:44 < kanzure> dna comes in -> more dna comes out
20:45 < kanzure> (plus other crap)
20:45 < gene_hacker> but when you're doing 200 or more amplification steps and your errors accumulate, is the error rate still lower?
20:45 < kanzure> the errors happen in the synthesis stage
20:45 < yashgaroth> that's why you sequence the final product, isolated from a single transformed bacterium
20:46 < kanzure> huh? let's not bring in cell cultures
20:46 < gene_hacker> why is it put into a bacteria? to amplify it I presume?
20:46 < kanzure> gene_hacker: it's just one of the things you might want to do with the dna
20:46 < yashgaroth> yes, and also bacterial amplification is a million times more accurate than PCR
20:46 < yashgaroth> due to a functioning proofreading complex
20:46 < gene_hacker> but it's slow, correct?
20:47 < kanzure> 12 hour incubation period, is my guess
20:47 < yashgaroth> within a day you have unlimited amplification
20:47 < yashgaroth> but yes, it takes a day
20:47 < gene_hacker> and isolation?
20:47 < yashgaroth> trivial
20:47 < gene_hacker> though does it involve manual labor?
20:48 < kanzure> "trivial".. on a chip? you're just making this more work for me :p
20:48 < gene_hacker> like picking glowing colonies?
20:48 < yashgaroth> liter-scale bac culture is trivial
20:48 < yashgaroth> haha if picking colonies is manual labor, then yes
20:48 < yashgaroth> also centrifuging and resuspending and all that
20:48 < gene_hacker> is it time consuming?
20:49 < kanzure> there's been some people that have done cell culture on a chip.. but meh
20:49 < gene_hacker> or expensive?
20:49 < kanzure> one microbe per droplet, etc.
20:49 < yashgaroth> it's less expensive than PCR
20:49 < yashgaroth> if you want to do anything significant with a plasmid, it'll need to go into bacteria at some point anyway
20:49 < yashgaroth> you can get nanograms from PCR and grams from bacteria
20:49 < kanzure> well your dna that you make doesn't have to be for a plasmid
20:50 < yashgaroth> true
20:50 < kanzure> i think this is definitely down-stream of the dna synthesizer
20:50 < yashgaroth> ok yes fair enough
20:51 < gene_hacker> though the process of joining strands together is PCR correct?
20:51 < yashgaroth> but the sequencing is moot; 99% of anything you read will be normal and block out anything else
20:51 < yashgaroth> no that's ligation
20:51 < gene_hacker> it requires enzymes right?
20:51 < yashgaroth> ligase
20:51 < yashgaroth> you just ligate all your fragments (of whatever size) together, transform into bacteria, and isolate a single clone
20:52 < yashgaroth> otherwise you can't ever be sure all your sequences are correct anyway
20:52 < gene_hacker> so for each synthesis step ligase enzyme would be required
20:52 < yashgaroth> not oligo synthesis
20:53 < yashgaroth> but for assembling oligos together, yes
20:53 < gene_hacker> though I guess if we're working with nanoliters, cost should be minimal
20:53 < yashgaroth> the volume is irrelevant, hell more volume/reagents might cost less than tiny valves and shit
20:54 < yashgaroth> BRB 10 mins, potatoes
20:59 < gene_hacker> so at the very least it does appear somewhat feasible
21:02 < gene_hacker> though it might be good to runs some numbers on error rate and reagent consumption
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21:03 < gene_hacker> though I wonder if nanoliter reactions like this are even feasible?
21:06 < gene_hacker> also looking for a good way to scan a book?
21:07 < kanzure> yes, nanoliters are doable
21:07 < kanzure> good way to scan a book- odesk.
21:08 < kanzure> or elancer
21:08 < kanzure> hire someone in india. mail them the book. give them $30.
21:08 < gene_hacker> can't ship the book to india
21:10 < gene_hacker> well if nanoliters are doable
21:11 < kanzure> nanoliters are definitely doable; and in many cases, biochem is faster on this level
21:11 < kanzure> you don't have to heat a whole whopping mL of liquid
21:12 < gene_hacker> and sufficiently accurate, sufficiently sized robots exist for extracting nanoliters from well plates
21:12 < kanzure> are there well plates that have microfluidic channels built in?
21:12 < gene_hacker> then this shouldn't be too hard to do
21:12 < gene_hacker> no
21:13 < gene_hacker> as long as 1024 different building blocks can be obtained
21:13 < gene_hacker> there are not
21:14 < gene_hacker> plus in order to do something like that you'd need 1024 valves over a very large area
21:14 < gene_hacker> if you move the valve to the well plate then you only need one
21:14 < kanzure> gene_hacker: could i recruit you into this?
21:14 < gene_hacker> possibly
21:15 < gene_hacker> I'd like to see that we can get 1024 different building blocks first or at least a demonstration with a couple
21:16 < gene_hacker> I don't really have that much experience in microfluidics
21:17 < kanzure> btw, did you see delinquentme's liquid handling robot?
21:17 < kanzure> instrument
21:17 < yashgaroth> link please
21:17 < kanzure> http://www.youtube.com/watch?v=ZY5IY5CZ1es
21:17 < kanzure> https://github.com/delinquentme/LH001
21:17 < kanzure> https://github.com/delinquentme/LH002
21:17 < delinquentme> ^_^ https://github.com/delinquentme/LH002/raw/master/images/LH002_full_01.png
21:17 < delinquentme> 02 03 04 05 etc
21:18 < delinquentme> kanzure, who do we have who are life extension computational biologists?
21:18 < delinquentme> im about to hit up michael rae to see who he knows
21:18 < yashgaroth> I thought michael rae starved to death
21:19 < delinquentme> O_o;;;
21:19 < yashgaroth> I saw him...3? years ago, he was more emaciated than most cancer patients I've seen
21:19 < yashgaroth> caloric restriction
21:20 < kanzure> computational biologists in life extension.. hrmmm
21:20 < gene_hacker> any work on how long that robot last until needing maintenance?
21:20 < kanzure> ask steve coles
21:20 < kanzure> about the computational biology thing
21:20 < kanzure> ask delinquentme about the maintenance thing
21:21 < gene_hacker> delinquentme any idea how long that thing will last until needing maintenance?
21:22 < gene_hacker> and any metrics of positional accuracy, repeatibility, etc?
21:23 < gene_hacker> also in the early stages of something like this we just need to get a few key parts working
21:23 < delinquentme> gene_hacker, i havnt prototyped it
21:23 < gene_hacker> like high speed ligation and what not
21:24 < delinquentme> steve coles? got an email?
21:24 < gene_hacker> any estimates?
21:24 < kanzure> gene_hacker: sure.
21:24 < kanzure> i think working on this one-part-at-a-time is important
21:24 < kanzure> otherwise it will all break simultaneously
21:25 < gene_hacker> I mean the important thing is the ligation and washing chip, and the well extraction to chip device
21:25 < delinquentme> gene_hacker, So really it should have started out as a smaller project ... could have monetized quicker
21:25 < kanzure> a macroworld well-to-chip would be too slow, i think
21:25 < gene_hacker> and the 1024 different blocks
21:25 < kanzure> maybe ot
21:25 < kanzure> *maybe not
21:26 < gene_hacker> well ligation takes about 30 seconds right?
21:26 < yashgaroth> haha no
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21:26 < kanzure> it depends on reaction volume
21:26 < kanzure> and many other variables
21:26 < kanzure> but i think you can get it down to a few seconds if you are very careful
21:27 < yashgaroth> I'd leave that as long as possible really
21:27 < yashgaroth> at least like 5 minutes
21:27 < delinquentme> kanzure,  <3 http://en.wikipedia.org/wiki/L._Stephen_Coles
21:27 < delinquentme> gene_hacker, apologies im not sure if i answered all your questions .. theres a lot going on here
21:28 < gene_hacker> real world to chip is slow, but a lot easier to do than 1024 individually addressable microvalves
21:28 < gene_hacker> I get the hang of it
21:29 < gene_hacker> and after all, you're going for accuracy not speed
21:29 < kanzure> yes
21:29 < yashgaroth> speed is the first thing you'll be sacrificing if you don't have accuracy and money to spare, which I doubt we do
21:30 < kanzure> ehh there's some money to spare
21:30 < yashgaroth> if it's all computerized just run it overnight
21:30 < kanzure> yep
21:30 < gene_hacker> also making a 2 wide microfluidic chip with 1024 vlaves at the LEAST, is insane
21:32 < gene_hacker> in reality, we'd probably need much more than that to do multiplexing and what not.
21:32 < gene_hacker> even with droplet based microfluidics it's insane
21:40 < delinquentme> i like the part where Ghost in the shell
21:43 < kanzure> delinquentme: ?
21:43 < delinquentme> its a solid anime :D
21:44 < kanzure> are you new to anime
21:45  * SDr mumbles incomprehensible about Serial Experiments Lain
21:46 < delinquentme> haha not really but i wouldnt say im well versed
21:46 < delinquentme> like Neon Genesis Evangelion is hot shit :D
21:46 < kanzure> this moment brought to you by japan
21:46 < kanzure> http://www.youtube.com/watch?v=6AYaFL6SWmk#t=1m40s
21:46 < delinquentme> OMG ROBOT WANT
21:46 < kanzure> SDr: that one was nice..
21:48 < delinquentme> lolol watching a thing on nat geo about hallucinogens
21:48 < delinquentme> total straight up white middle texas guy taking shrooms
21:48 < delinquentme> " Eets Lyke the WHitest WHHite"
21:49 < delinquentme> donloading lain :D
21:49 < delinquentme> lololol
21:49 < delinquentme> nice vid kanzure
21:50 < delinquentme> kanzure, have you ever tried to contact ben langmead of crossbow fame?
21:51 < kanzure> nope haven't talked with him
21:52 < delinquentme> hadoop or disco
21:52 < delinquentme> aka java or erlang
21:52 < delinquentme> well java erlang python
21:52 < delinquentme> i might start programming deh java
21:53 < kanzure> java isn't hard to figure out
21:56 < delinquentme> I've programmed in it in HS
21:56 < delinquentme> looking for something just FAST :D
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22:24 < delinquentme> is there a term for timing your large processing jobs in an API as to not flood them w requests?
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22:27 < kanzure> delinquentme: queuing?
22:27 < kanzure> look up aws sqs
22:28 < kanzure> or rabbitmq and shit
22:28 < delinquentme> throttling is what I was aftar
22:29 < kanzure> just spend more money throwing up new instances :P
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--- Log closed Thu Jan 26 00:00:32 2012