--- Log opened Wed Mar 07 00:00:40 2012
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00:09 < kanzure> no to make measurements in the first place...
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00:09 < kanzure> win 6
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00:10 < kanzure> hi Cyndre_
00:10 < Cyndre_> hi
00:10 < kanzure> write out the plan and we'll take a look at it
00:10 < kanzure> also, detail which parts you need help on or which parts you know
00:11  * kanzure sleeps
00:11 < Cyndre_> lmao
00:11 < kanzure> wha? i'm serious
00:12 < Cyndre_> its actually just an idea right now - say a 20x20 pin pad that gets implanted into the forearm - you then send electrical signals the same strength as neurons send into the arm in patterns matching certain charaters on the screen.  Hoping that over time I will be able to repeat in reverse and not have to worry about my carpal tunnel surgery tomorrow
00:13 < Cyndre_> like smiling works in reverse this will eventually allow you to repeat the electrical patterns back into the system to type through training
00:14 < kanzure> Cyndre_: don't worry i will probably join you for carpal surgery eventually http://www.seanwrona.com/typeracer/profile.php?username=kanzure
00:14 < Cyndre_> very nice, I am only about 100 - 110
00:15 < Cyndre_> but massive tight scars on my right hand probably limit that
00:15 < kanzure> naaah
00:16 < Cyndre_> lmao, the last knuckle on my middle finger is currently split wide open 1/8 of an inch or so from bending it
00:16 < kanzure> i think your typing technique might be flawed
00:17 < Cyndre_> using a qwerty keyboard?
00:17 < kanzure> yes
00:17 < kanzure> ok but seriously i need sleep
00:17 < Cyndre_> night man
00:17 < kanzure> you can bug Steel or something, dunno who else is up
00:17 < Cyndre_> nee3d sleep to surgery in 9 hours
00:17 < Cyndre_> and trying to finish a few things on my site before my hands gimped
00:18 < kanzure> just remember... you can always use a direct neural interface at a whopping 10 bits per minute
00:18 < kanzure> http://diyhpl.us/~bryan/papers/neuro/implants/
00:18 < kanzure> oops i mean http://diyhpl.us/~bryan/papers2/neuro/implants/
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02:10 < archels> kanzure: NL, yes
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06:55 < thesnark> hi kanzure
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08:36 < delinquentme> http://web.mit.edu/newsoffice/2012/profile-azoulay-0229.html  << some dude anzlyzing what makes scientists productive
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09:10 < kanzure> i like this billionaire:
09:10 < kanzure> https://www.nytimes.com/2011/03/06/magazine/06murdock-t.html?_r=4&ref=magazine&pagewanted=print
09:25 < jrayhawk> I think he may be the one who gave Alessio Fasano's department 40 million dollars for research.
09:33 < delinquentme> not loading for meeee
09:41 < cluckj> paywalled :(
09:42 < kanzure> cluckj: welcome back
09:43 < cluckj> howdy
09:45 < archels> kanzure: Do you need any cheese or tulips?
09:46 < kanzure> what? no i don't think so
09:46 < delinquentme> cluckj, http://www.nytimes.com/2011/03/06/magazine/06murdock-t.html?_r=1
09:46 < delinquentme> dah u go
09:46 < delinquentme> DAR*****
09:47 < cluckj> thanks
09:50 < delinquentme> jar!
09:50 < delinquentme> SO @ what level of automation can lab equipment start to benefit ?
09:51 < delinquentme> im going b ack and forth on which would be more beneficial a programmable orbital shaker or syring pump
09:51 < kanzure> syringe pump please
09:51 < delinquentme> syringe pumps can be used in microfluidics .. so that could be really helpful
09:51 < delinquentme> kanzure, im putting off the LH for a bit ... i dont feel *CURRENTLY* equipped to make it what it should be
09:52 < delinquentme> so start w something smaller and more monitizeable
09:55 < cluckj> kanzure what have you been up to lately?
09:58 < kanzure> cluckj: dna synthesizer, pokemon source code, other things i'm forgetting, scraping
09:58 < cluckj> diy dna synthesizer?
10:02 < kanzure> yes
10:02 < cluckj> sweet :)
10:05 < Vicarious> 'morning
10:05 < kanzure> Vicarious: i reject your sense of time and substitute my own
10:05 < kanzure> it is definitely not morning, good sir :)
10:06 < Vicarious> but the internet doesn't have timezones
10:06 < Vicarious> hence it's always morning on the internet :P
10:06 < kanzure> no no
10:06 < archels> kanzure: because you were asking whether I was in NL.
10:06 < kanzure> the internet is timeless
10:07 < kanzure> archels: i don't see what that has to do with cheese
10:07 < kanzure> does NL have lots of tulips?
10:07 < archels> yes, and cheese!
10:07 < Vicarious> kanzure: not true, you don't remember internet time ?
10:08 < kanzure> Vicarious: unix epoch?
10:08 < archels> @123
10:08 < kanzure> o.o
10:08 < Vicarious> http://en.wikipedia.org/wiki/Swatch_Internet_Time
10:08 < Vicarious> :P
10:08 < cluckj> lol
10:08 < archels> k, pizzatime
10:09 < kanzure> pizzatime, morning time.. i'm really confused
10:09 < cluckj> pizza for breakfast?
10:09 < cluckj> the truth is that it's always pizzatime
10:10 < cluckj> so it would not be a good measure of time....
10:10 < Vicarious> brb
10:11 < delinquentme> that makes me want pancakes
10:19 < kanzure> delinquentme: el cheapo ways to make very repeatable syringe pumps would be nice
10:19 < kanzure> especially programmable syringe pumps that i can leave running for 20-50 hours at a time
10:19 < kanzure> also, especially if i can cram a lot of them together in a small space
10:19 < kanzure> also! if they don't cost a fuckton. i think i mentioned that.
10:23 < ThomasEgi> kanzure, stepper motor + thread ?
10:23 < kanzure> probably
10:23 < ThomasEgi> easy to controll, and very precise if you need it to be
10:23 < kanzure> ThomasEgi: http://staff.bath.ac.uk/ensab/replicator/Pix/syringe-pump-h.jpg
10:23 < kanzure> that's the one that adrian bowyer (of reprap fame) made
10:25 < kanzure> here's a commercial one:
10:25 < kanzure> http://www.syringepump.com/Micro.php
10:25 < kanzure> $1500 hah
10:25 < kanzure> "Infusion rates from 8 pl/hr (.5 µl cc syringe) to 2545 µl/min (140 cc syringe)"
10:25 < ThomasEgi> hehe. lol.i could recommend the commeercial-like setup.
10:25 < kanzure> i don't understand why it costs so much
10:26 < kanzure> does the stepper cost a lot?
10:26 < ThomasEgi> with the clamp for the syringe, the linear bearing. and a fine threaded thread. and stepper motors.
10:26 < ThomasEgi> no
10:26 < ThomasEgi> they are bargain
10:26 < kanzure> ok.. maybe they charge a lot for the red paint
10:26 < ThomasEgi> they charge for the medical-grade quality
10:26 < ThomasEgi> that means , medical certification for each end every part in it.
10:26 < cluckj> cause it's so smoooooth
10:26 < kanzure> "Advance Per Step: 4.252232 Nanometers"
10:27 < ThomasEgi> your syringe wont be able to put that into actual volumentric change
10:27 < ThomasEgi> due to friction and the mechanical properties of the syringe itself
10:28 < kanzure> in an ideal world i could have any number of syringe pumps in a system
10:28 < kanzure> it looks like these take up a lot of space
10:28 < kanzure> and $1500/syringe-pump is obnoxiously high
10:29 < kanzure> diy syringe pump http://www.youtube.com/watch?v=pNdARr_t1dQ
10:29 < ThomasEgi> if you get an M5x0.25 thread. and a stepper with 200 steps per revolution, you can get 1.25μm stepping. that is probably already finer than your syringe mechanics can forward
10:30 < kanzure> his setup looks a little large but w/e http://www.youtube.com/watch?v=oIxWe7G7giY
10:31 < chris_99> could you use an inkjet printer to dispense liquid like that
10:31 < ThomasEgi> note: for stepper motors there are ready-2-use driver ic's, that allow even microstepping.
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10:32 < ThomasEgi> so.. with microstepping, you may get even better resolution, altho it would be futile unless the rest of the mechanics is superb. basic setup as seen in the vid
10:33 < ThomasEgi> you could get nanometer stepping with piezo-linear motors. not cheap and diy tho.
10:33 < kanzure> ah didn't know he had a site http://aonomus.wordpress.com/tag/microfluidics/
10:34 < kanzure> ThomasEgi: i think ultimately the form factor should be pcb board + syringe pump + maybe some chasis over it + the syringe
10:34 < kanzure> but maybe i'm misunderstanding the necessary shape
10:34 < ThomasEgi> hm.. that's not impossible. but conciderably trickier to build
10:35 < kanzure> what's the least tricky way
10:35 < ThomasEgi> that would be more like the first link you send, with the small motor unit attached to the syringe. but i would recommend a stepper motor instead of a DC one
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10:35 < kanzure> yeah i haven't used many microsteppers, i'm unaware
10:35 < kanzure> s/many/any
10:36 < ThomasEgi> what's easy usualy depends on your tools and skills. something like the big plexi-glass models are easiest for most people around
10:36 < ThomasEgi> you dont need microsteppres. just a regular stepper motor. the stepping/microstepping is done by the electronics
10:36 < kanzure> but don't i need optical encoding to track microsteps?
10:37 < ThomasEgi> no
10:37 < ThomasEgi> steppers have fixed step-sizes
10:37 < ThomasEgi> so if you make 200 steps on a 200steps per round motor. you'll get exactly one revelation.
10:37 < ThomasEgi> you can go forth and back as often as you want. as long as you stay within the parameters, the motor wont lose any steps
10:48 < chris_99> what are you making kanzure?
10:50 < kanzure> chris_99: microfluidic dna synthesizer
10:50 < chris_99> ooh neat
10:51 < chris_99> how do you create the actual microfluidic paths as it were?
10:51 < kanzure> many ways
10:51 < kanzure> my favorite is a laser cutter
10:52 < kanzure> but most people do photomasks with lithography
10:52 < kanzure> or digital photolithography with a micromirror array
10:52 < chris_99> aha, does lithography give the finest paths?
10:52 < kanzure> or laser printer masks
10:52 < kanzure> uh i don't know, it probably depends on their optical setup
10:52 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/
10:53 < chris_99> so do you etch one piece of plastic, then place another on top i guess
10:53 < chris_99> and glue together somehow
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10:54 < kanzure> chris_99: yep that's one way..
10:54 < kanzure> chris_99: here's a bootcamp doc
10:54 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/training-bootcamp.pdf
10:54 < kanzure> there's a few sections about fabrication
10:54 < kanzure> but it's not exhaustive
10:55 < chris_99> cool, thanks
10:58 < chris_99> what kind of fluidic stuff have you made before?
10:58 < kanzure> nothing worth reporting
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11:01 < lucaserickson> Hi. I'm interested in mindfulness meditation.
11:02 < lucaserickson> I've been doing yoga early in the morning for the past couple weeks, and meditating three times a day for 15 minutes each.
11:02 < kanzure> hi lucaserickson
11:02 < kanzure> sorry nobody in here is mindful
11:03 < lucaserickson> Hey kanzure, lol.
11:03 < lucaserickson> How are you?
11:03 < kanzure> great
11:05 < lucaserickson> Would you happen to know if there is a correlation between the frequency of meditation and mindfulness? I've noticed some effects, but I'd like to benefit more if possible.
11:05 < ThomasEgi> kanzure, for laser printer masks i can barely get 200μm structures clean enough (on pcb's)
11:06 < kanzure> ThomasEgi: yeh it's not the best for sure
11:06 < kanzure> lucaserickson: how the heck are you measuring "mindfulness"
11:07 < ThomasEgi> ah about micro-pumps. how about scanner mechanics?, they sometimes have very fine stepping resolutions
11:07 < cluckj> e-meter?
11:08 < kanzure> ThomasEgi: most of the scanners i've owned have been belt driven
11:08 < kanzure> is that what you're talking about?
11:08 < ThomasEgi> belt driven or not, the stepping itself is very fine.
11:09 < ThomasEgi> if you pre-apply some force, so the mechanics wont have backlash
11:09 < ThomasEgi> it might be a pretty easy way.
11:10 < lucaserickson> Kanzure: I've noticed more awareness of my own thoughts, measuring mindfulness objectively probably isn't possible. I'm wondering if there is an upper-limit of meditation time vs "possible" benefit each day.
11:10 < ThomasEgi> they usualy have good stepers, well-fit gears. if you preload them, it may work
11:15 < delinquentme> lol
11:15 < delinquentme> man i love it when i jump away for 2 seconds and the channel blows up :D
11:15 < archels> http://www.futurehi.net/archives/000117.html
11:15 < delinquentme> there are syringe pumps here for upwards of 4 grand
11:15 < delinquentme> http://www.coleparmer.com/Product/Cole_Parmer_small_sup_reg_sup_small_programmable_ten_syringe_infusion_withdrawal_pump_115_VAC/WU-74901-10
11:16 < delinquentme> whats brilliant is i can tell you right now that that does *NOT* pump those individually
11:16 < delinquentme> make a single modular pump? destroy that market
11:17 < delinquentme> Built-in program lets you enter up to eight commands to perform a variety of functions
11:17 < delinquentme> !
11:17 < delinquentme> up to EIGHT
11:17 < delinquentme> EIGHT functions ! i mean human memory can only hold 7 ! WOW!
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11:18 < kanzure> aww why did he leave
11:19 < kanzure> delinquentme: HOLY SHIT EIGHT???
11:19 < kanzure> but seriously.. that's pathetic
11:19 < kanzure> and the fact that they would even use that marketing.. is sad
11:19 < kanzure> who would buy something that advertises itself as handling N functions?
11:19 < ThomasEgi> yeah. even a 1970 daten microprocessor had a bigger command stack
11:19 < delinquentme> kanzure, its the state of the market hahah
11:20 < delinquentme> yeah man.
11:20 < delinquentme> and whats even funnier is sales people have had this convo.
11:20 < delinquentme> scientist: " It can handle EIGHT? " salesman: " E_I_G_H_T"
11:20 < ThomasEgi> hm.. that'd be agreat opportunity to laught at some pathetic arguments
11:20 < kanzure> when you say it has N functions the first thing that i think is that you're a moron
11:21 < delinquentme> and we're talking bleeding edge of the market here
11:21 < kanzure> and/or trying to peddle proprietary software on me
11:21 < delinquentme> this is on a $4000 dollar syring pump
11:21 < delinquentme> srsly i wonder what their base costs are on that
11:21 < delinquentme> $100? surely no more than $500
11:21 < ThomasEgi> as i said. medical/lab grade equipment. getting it certified is a pita
11:22 < delinquentme> doing rails tutorial again
11:22 < delinquentme> their autotests were lame
11:22 < kanzure> delinquentme: i thought you knew rails
11:22 < delinquentme> no_name_user = User.new(@attr.merge(:name => "bob_the_architect_of_the_future_mac_mc_hammerstein_bacon_III"))
11:22 < delinquentme> redux on rspec
11:22 < kanzure> wtf? no man
11:22 < kanzure> User.new(:name => ...)
11:22 < delinquentme> this is in a spec
11:23 < delinquentme> they *were* creating a new object when they didn't need to
11:23 < kanzure> ok
11:24 < delinquentme> back to the stringe pump
11:24 < delinquentme> i think the whole click hardware interface is totally unnecessary
11:24 < kanzure> it's just designed to aggitate you
11:25 < delinquentme> ^
11:25 < kanzure> it's so that you have something to punch
11:25 < kanzure> when you get angry
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11:33 < delinquentme> lololol gilette is advertising how long their shit lasts
11:34 < delinquentme> shaveclub?
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11:38 < ThomasEgi> delinquentme, if they wanted their crap to last, they would diamond-coat the surface. but to tell you the truth, they arent interested in it at all.
11:38 < ThomasEgi> because blades is what they make big money with.
11:39 < delinquentme> ^^
11:39 < ThomasEgi> srsly. i have seen polished polycristaline diamond plates. visitors were allowed to try and scratch the surface
11:40 < ThomasEgi> they had everything available you could wish for, grinding paper. steel-brushes...
11:40 < ThomasEgi> the brass block where the plate was embedded looked terrible. but the diamond surface looked brand new.
11:40 < ThomasEgi> so everyone in my class tried to scratch that thing with all their might.
11:41 < ThomasEgi> and it looked scratched. at least we thought it would. then the guy just whiped the dust off the plate. and. not a trace.
11:41 < ThomasEgi> they had that block there for full 5 years when we visited
11:44 < ThomasEgi> admitting, it aint a cheap process to diamond-coat and get polish polycristaline diamonds. pretty much the worst thing you can try to do in your life. but it lasts^
11:46 < archels> ThomasEgi, someone should bring in a diamond.
11:47 < ThomasEgi> oh about that photo-masking. anyone tried to mount a slr-camera optics over the surface-to-expose. and trace-paint the light with a reprap? (having the board and optics mounted fix, and only a laser source moved ) ?
11:48 < archels> I've heard that being done for making PCBs, but apparently it's not very productive.
11:49 < ThomasEgi> i only know about directly laser-expose with a reprap. i never heared about it by using optics to scale it down
11:50 < archels> This is for PCBs, specifically?
11:50 < ThomasEgi> DSLR optics are pretty good, after all, the image sensor pixels are only 5μm wide.
11:51 < ThomasEgi> nah. i was more thinking about maybe using it for building smaller stuff
11:51 < ThomasEgi> for pcb's you wouldnt need 2mil precision.
11:51 < archels> exactly
11:51 < ThomasEgi> or even signle-digit micrometer
11:51 < ThomasEgi> i was thinking about it for semi-conductor-masking
11:52 < ThomasEgi> it may work with micro-fluids,too.
11:52 < ThomasEgi> because it pretty much projects the mechanical resolution of a reprap onto a ways smaller area.
11:53 < ThomasEgi> with monochromatic light from a laser source, that may allow pretty good accuracy.
11:53 < archels> A reprap seems like a shitty device to start out with; why not use two electromechanically actuated, orthogonally positioned mirrors?
11:54 < ThomasEgi> cause macro-obtics are expensive
11:55 < archels> two loudspeakers, tiny mirrors and some superglue
11:55 < archels> Perhaps you could also mod the optics of a CD player (tracking/focus).
11:55 < ThomasEgi> still a very in-precise system. hard to controll, nonlinear,...
11:56 < archels> Hard to control? Just take some old computer speakers, control via soundcard. :P
11:56 < ThomasEgi> your soundcard is DC free
11:56 < ThomasEgi> so.. no positioning at all.
11:57 < archels> mh and you need a Z axis (on/off).
11:57 < ThomasEgi> turning off a laser/led really aint the problem
11:58 < ThomasEgi> the good thing about projecting the lithographic mask/trace would be, you can check your design and handle it easily.
11:59 < ThomasEgi> and in worst case, you can even hand-paint your masks on some transparent foil. (or use tape)
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12:02 < ThomasEgi> bbl. laundry
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12:40  * delinquentme cracks up
12:40 < delinquentme> RS-232 interface lets you easily control pumps from your computer
12:40 < kanzure> "... if you can find a computer with rs-232"
12:40 < delinquentme> <del> computer </del> TI-83
12:40 < delinquentme> ^
12:40 < delinquentme> what are these guys thinking
12:40 < delinquentme> i guess they need to develop w the internal talent that they've got huh
12:44 < archels> uh, RS232 is still very much alive, and contrary to crap like USB, it invariably *just works*.
12:45 < archels> It's the ultimate interchangable data connection.
12:46 < archels> Also, a lot of USB devices just use RS232 comms with a USB-to-serial converter thrown in.
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13:26 < ThomasEgi> archels, true words of wisdom. altho the converters usualy sux
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15:30 < kanzure> "For NOVA’s upcoming program “Cracking Your Genetic Code,” PBS has made a short promotional video demonstrating how you can draw your DNA out from a sample of cheek cells"
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17:52 < cluckj> kanzure I do that demo with kids, it's pretty fun
17:53 < cluckj> we make lockets for their parents with the DNA in it
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18:10 < delinquentme> cluckj, and the smart ass ones give them only gametes?
18:10 < delinquentme> lulz innaprope
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18:19 < cluckj> ...
18:20 < cluckj> they don't make those yet
18:20 < kanzure> hi yashgaroth
18:20 < yashgaroth> yo
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20:21 < kanzure> "Thankfully, Lord Nightmare from the MAME/MESS project was in contact with a savant named Dr. Decapitator, with the necessary knowledge and hardware to make this possible. Even better, he was willing to do it just for the cost of the donor cartridges and supplies. This worked out to $250 per coprocessor."
20:21 < kanzure> http://news.ycombinator.com/item?id=3675123
20:21 < kanzure> http://byuu.org/articles/emulation/snes-coprocessors
20:24 < Etherael> You're a strange guy.
20:24 < kanzure> http://byuu.org/articles/emulation/decap
20:25 < Etherael> not as strange as this chick http://www.youtube.com/watch?v=j7_lSP8Vc3o but pretty strange nonetheless.
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20:52 < strangewarp> I'm strange, lol
20:52 < strangewarp> (I tried to resist the urge to respond with something corny but I could not resist)
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21:10 < kanzure> yashgaroth: come back :(
21:10 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/Gene%20synthesis%20by%20assembly%20of%20short%20oligonucleotides%20-%20Horspool%20thesis%20-%202009.pdf
21:25 < Stieru_Ridir> is there a seenbot?
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21:30 < delinquentme> do we have electricians in here?
21:30 < delinquentme> like programmer / embedded / robotics people
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21:31 < Steel2> delinquentme, when they're on, ThomasEgi and rdb
21:32 < Steel2> and when I brush up on stuff, I've done embedded work but it's been years
21:32 < kanzure> Steel2: yes i am just a sophisticated seenbot
21:32 < kanzure> everything else about me is superfluous
21:32 < Steel2> !seen ianmathwiz7
21:32 < Steel2> :P
21:33 < delinquentme> Steel2, kanzure what microcontroller to use if i need like 10 of them .. need to be cheap .. and they've only really got to handle a stepper motor and a linear encoder
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21:34 < delinquentme> and like how do you pick these things out??
21:35 < Steel2> dunno, I worked with the stuff the school handed me :P
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22:28 < yashgaroth> a hundred and fifty pages? damn you
22:29 < kanzure> yashgaroth: you will read them and you will like them
22:29 < kanzure> also, you will probably find lots of errors
22:29 < yashgaroth> I will skim like the wind
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23:01 < yashgaroth> whew the second half went a lot faster than the first
23:02 < yashgaroth> I do agree with his points on the hour+ ligations, though the necessity of octamers is worrying
23:03 < kanzure> i'm not sure what his volumes were
23:03 < yashgaroth> still, with high enough concentrations of reactants, a string of unligated hexamers might help the ligase along
23:03 < kanzure> an hour per ligation reaction is stupid
23:03 < kanzure> Effects of basepair mismatches on joining of short oligodeoxynucleotides by DNA ligases http://www.ncbi.nlm.nih.gov/pmc/articles/PMC146903/pdf/253403.pdf
23:03 < yashgaroth> it's common for most plasmid ligation, but if you can get superconcentrated ligase in a nano-drop, then that should drop
23:03 < kanzure> plus thermal cycling
23:05 < yashgaroth> also, the expense of waiting for an inefficient 6mer based reaction vs. the extra expense and hassle of an 8mer library
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23:07 < yashgaroth> looks like he kept working at it though http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994885/
23:08 < kanzure> Efficient assembly of very short oligonucleotides using T4 DNA Ligase
23:13 < yashgaroth> but yeah doesn't seem like nmz's template strand addition will work by itself, though the coding strand addition., with the 3 hexamers, should
23:14 < yashgaroth> I'd like to think a mutant ligase with more useful short-strand binding could be made, but only very painfully
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23:19 < Steel3> wellllp
23:20 < kanzure> yashgaroth: coding strand synthesis thing in the diagram was just an unwanted side reaction
23:21 < kanzure> wait. i am corrupting things i think
23:22 < rdb> *yawn* morning
23:23 < Steel3> watson goes to wall street
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23:25 < yashgaroth> surely I'm misunderstanding that kerfuffle about the $300million transatlantic cable to shave milliseconds off of trading transaction lag
23:25 < Steel3> yashgaroth: that actually is a thing :P
23:25 < yashgaroth> arghh fuck
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23:26 < nmz787> yashagaroth, you here?
23:26 < yashgaroth> indeed
23:27 < nmz787> kanzure said you think the red bracketed step in that diagram would work
23:27 < nmz787>  but the red brackets just indicate unwanted side-reactions
23:27 < yashgaroth> it seems that the efficiency of attaching a 6mer to a 3nt overhang is very low
23:28 < nmz787> reports are that 5mer overhangs work well
23:28 < yashgaroth> sure, but then a 6mer library is right out
23:28 < nmz787> but 5mer vs 3mer is an issue of ligase optimization
23:29 < nmz787> why you say template vs coding addition would be different is interesting
23:29 < nmz787> as it does bring up the point of where ligase 'rests' relative to the 'nick'
23:29 < yashgaroth> the ligase seems to like a guiding strand on the free end
23:29 < nmz787> if it can even 'rest' on a 6 or 10mer, half of which is ssDNA
23:30 < yashgaroth> it's 'accustomed' to working with a dsDNA strand the stretches off far beyond its reach
23:30 < nmz787> well sure but it seems from this paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994885/
23:30 < yashgaroth> eventually it'll work, but when a 2 hour reaction is considered fast...
23:31 < nmz787> though the diagrams are unlabeled with respect to 5; and 3;
23:31 < nmz787> i think they set it up such that they're ligating an oligo to the coding strand
23:31 < yashgaroth> the implication is the fluorescent attaches to the 3'
23:32 < nmz787> ahh it does say that
23:33 < yashgaroth> either way, the efficiency of a 4nt overhang there is no better than a 3nt one
23:33 < yashgaroth> unless you have a helper strand, that is
23:34 < yashgaroth> but it shouldn't be a problem to add the upcoming 6mer as a helper, even if you have to wash it off and reapply it for the next step
23:36 < nmz787> i don't think even numbered sticky ends is a good idea
23:36 < nmz787> with odd numbered sticky ends, the middle nt can never be complementary
23:36 < nmz787> decreasing its melting temp
23:38 < yashgaroth> wait why can't it be compementary? you mean the middle nt in a 3bp sticky end?
23:39 < nmz787> the middle bp in any odd numbered sticky end
23:40 < nmz787> AAATAA ligates to produce a sticky end of TAA.... excess oligo is in solution, leaving AATAAA to hybridize... but the middle nt doesnt match
23:41 < yashgaroth> ohhh right okay
23:41 < yashgaroth> wasn't sure if you meant hairpinning or what, but I gotcha now
23:56 < nmz787> ttyl
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