| --- Log opened Wed Mar 07 00:00:40 2012 | ||
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| kanzure | no to make measurements in the first place... | 00:09 |
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| kanzure | win 6 | 00:09 |
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| 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 | 00:10 |
| * kanzure sleeps | 00:11 | |
| Cyndre_ | lmao | 00:11 |
| kanzure | wha? i'm serious | 00:11 |
| 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 | 00:12 |
| Cyndre_ | like smiling works in reverse this will eventually allow you to repeat the electrical patterns back into the system to type through training | 00:13 |
| 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 | 00:14 |
| Cyndre_ | but massive tight scars on my right hand probably limit that | 00:15 |
| kanzure | naaah | 00:15 |
| 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 | 00:16 |
| 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 | 00:17 |
| 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/ | 00:18 |
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| archels | kanzure: NL, yes | 02:10 |
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| thesnark | hi kanzure | 06:55 |
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| delinquentme | http://web.mit.edu/newsoffice/2012/profile-azoulay-0229.html << some dude anzlyzing what makes scientists productive | 08:36 |
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| 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 | 09:10 |
| jrayhawk | I think he may be the one who gave Alessio Fasano's department 40 million dollars for research. | 09:25 |
| delinquentme | not loading for meeee | 09:33 |
| cluckj | paywalled :( | 09:41 |
| kanzure | cluckj: welcome back | 09:42 |
| cluckj | howdy | 09:43 |
| archels | kanzure: Do you need any cheese or tulips? | 09:45 |
| 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***** | 09:46 |
| cluckj | thanks | 09:47 |
| delinquentme | jar! | 09:50 |
| delinquentme | SO @ what level of automation can lab equipment start to benefit ? | 09:50 |
| 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 | 09:51 |
| delinquentme | so start w something smaller and more monitizeable | 09:52 |
| cluckj | kanzure what have you been up to lately? | 09:55 |
| kanzure | cluckj: dna synthesizer, pokemon source code, other things i'm forgetting, scraping | 09:58 |
| cluckj | diy dna synthesizer? | 09:58 |
| kanzure | yes | 10:02 |
| cluckj | sweet :) | 10:02 |
| 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 :) | 10:05 |
| 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 | 10:06 |
| 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 ? | 10:07 |
| 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 | 10:08 |
| 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 | 10:09 |
| cluckj | so it would not be a good measure of time.... | 10:10 |
| Vicarious | brb | 10:10 |
| delinquentme | that makes me want pancakes | 10:11 |
| 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. | 10:19 |
| 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 | 10:23 |
| 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 | 10:25 |
| 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" | 10:26 |
| 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 | 10:27 |
| 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 | 10:28 |
| 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 | 10:29 |
| kanzure | his setup looks a little large but w/e http://www.youtube.com/watch?v=oIxWe7G7giY | 10:30 |
| 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. | 10:31 |
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| 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 | 10:32 |
| 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/ | 10:33 |
| 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 | 10:34 |
| 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 | 10:35 |
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| kanzure | yeah i haven't used many microsteppers, i'm unaware | 10:35 |
| kanzure | s/many/any | 10:35 |
| 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? | 10:36 |
| 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 | 10:37 |
| chris_99 | what are you making kanzure? | 10:48 |
| kanzure | chris_99: microfluidic dna synthesizer | 10:50 |
| chris_99 | ooh neat | 10:50 |
| 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 | 10:51 |
| 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/ | 10:52 |
| 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 | 10:53 |
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| 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 | 10:54 |
| chris_99 | cool, thanks | 10:55 |
| chris_99 | what kind of fluidic stuff have you made before? | 10:58 |
| kanzure | nothing worth reporting | 10:58 |
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| lucaserickson | Hi. I'm interested in mindfulness meditation. | 11:01 |
| 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 | 11:02 |
| lucaserickson | Hey kanzure, lol. | 11:03 |
| lucaserickson | How are you? | 11:03 |
| kanzure | great | 11:03 |
| 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) | 11:05 |
| kanzure | ThomasEgi: yeh it's not the best for sure | 11:06 |
| kanzure | lucaserickson: how the heck are you measuring "mindfulness" | 11:06 |
| ThomasEgi | ah about micro-pumps. how about scanner mechanics?, they sometimes have very fine stepping resolutions | 11:07 |
| cluckj | e-meter? | 11:07 |
| 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. | 11:08 |
| ThomasEgi | if you pre-apply some force, so the mechanics wont have backlash | 11:09 |
| ThomasEgi | it might be a pretty easy way. | 11:09 |
| 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 | 11:10 |
| 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 | 11:15 |
| 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 | 11:16 |
| 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! | 11:17 |
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| kanzure | aww why did he leave | 11:18 |
| 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 | 11:19 |
| 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 | 11:20 |
| 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 | 11:21 |
| 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 | 11:22 |
| delinquentme | they *were* creating a new object when they didn't need to | 11:23 |
| kanzure | ok | 11:23 |
| 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 | 11:24 |
| delinquentme | ^ | 11:25 |
| kanzure | it's so that you have something to punch | 11:25 |
| kanzure | when you get angry | 11:25 |
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| delinquentme | lololol gilette is advertising how long their shit lasts | 11:33 |
| delinquentme | shaveclub? | 11:34 |
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| 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. | 11:38 |
| delinquentme | ^^ | 11:39 |
| ThomasEgi | srsly. i have seen polished polycristaline diamond plates. visitors were allowed to try and scratch the surface | 11:39 |
| 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. | 11:40 |
| 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 | 11:41 |
| 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^ | 11:44 |
| archels | ThomasEgi, someone should bring in a diamond. | 11:46 |
| 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 ) ? | 11:47 |
| archels | I've heard that being done for making PCBs, but apparently it's not very productive. | 11:48 |
| ThomasEgi | i only know about directly laser-expose with a reprap. i never heared about it by using optics to scale it down | 11:49 |
| archels | This is for PCBs, specifically? | 11:50 |
| ThomasEgi | DSLR optics are pretty good, after all, the image sensor pixels are only 5μm wide. | 11:50 |
| 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 | 11:51 |
| 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. | 11:52 |
| 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? | 11:53 |
| ThomasEgi | cause macro-obtics are expensive | 11:54 |
| 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,... | 11:55 |
| 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. | 11:56 |
| archels | mh and you need a Z axis (on/off). | 11:57 |
| ThomasEgi | turning off a laser/led really aint the problem | 11:57 |
| ThomasEgi | the good thing about projecting the lithographic mask/trace would be, you can check your design and handle it easily. | 11:58 |
| ThomasEgi | and in worst case, you can even hand-paint your masks on some transparent foil. (or use tape) | 11:59 |
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| ThomasEgi | bbl. laundry | 12:02 |
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| * 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 | 12:40 |
| archels | uh, RS232 is still very much alive, and contrary to crap like USB, it invariably *just works*. | 12:44 |
| archels | It's the ultimate interchangable data connection. | 12:45 |
| archels | Also, a lot of USB devices just use RS232 comms with a USB-to-serial converter thrown in. | 12:46 |
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| ThomasEgi | archels, true words of wisdom. altho the converters usualy sux | 13:26 |
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| 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" | 15:30 |
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| cluckj | kanzure I do that demo with kids, it's pretty fun | 17:52 |
| cluckj | we make lockets for their parents with the DNA in it | 17:53 |
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| delinquentme | cluckj, and the smart ass ones give them only gametes? | 18:10 |
| delinquentme | lulz innaprope | 18:10 |
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| cluckj | ... | 18:19 |
| cluckj | they don't make those yet | 18:20 |
| kanzure | hi yashgaroth | 18:20 |
| yashgaroth | yo | 18:20 |
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| 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 | 20:21 |
| Etherael | You're a strange guy. | 20:24 |
| kanzure | http://byuu.org/articles/emulation/decap | 20:24 |
| Etherael | not as strange as this chick http://www.youtube.com/watch?v=j7_lSP8Vc3o but pretty strange nonetheless. | 20:25 |
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| strangewarp | I'm strange, lol | 20:52 |
| strangewarp | (I tried to resist the urge to respond with something corny but I could not resist) | 20:52 |
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| 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 | 21:10 |
| Stieru_Ridir | is there a seenbot? | 21:25 |
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| delinquentme | do we have electricians in here? | 21:30 |
| delinquentme | like programmer / embedded / robotics people | 21:30 |
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| Steel2 | delinquentme, when they're on, ThomasEgi and rdb | 21:31 |
| 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 | 21:32 |
| 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 | 21:33 |
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| delinquentme | and like how do you pick these things out?? | 21:34 |
| Steel2 | dunno, I worked with the stuff the school handed me :P | 21:35 |
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| yashgaroth | a hundred and fifty pages? damn you | 22:28 |
| 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 | 22:29 |
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| yashgaroth | whew the second half went a lot faster than the first | 23:01 |
| yashgaroth | I do agree with his points on the hour+ ligations, though the necessity of octamers is worrying | 23:02 |
| 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 | 23:03 |
| yashgaroth | also, the expense of waiting for an inefficient 6mer based reaction vs. the extra expense and hassle of an 8mer library | 23:05 |
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| yashgaroth | looks like he kept working at it though http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994885/ | 23:07 |
| kanzure | Efficient assembly of very short oligonucleotides using T4 DNA Ligase | 23:08 |
| 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 | 23:13 |
| yashgaroth | I'd like to think a mutant ligase with more useful short-strand binding could be made, but only very painfully | 23:14 |
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| Steel3 | wellllp | 23:19 |
| kanzure | yashgaroth: coding strand synthesis thing in the diagram was just an unwanted side reaction | 23:20 |
| kanzure | wait. i am corrupting things i think | 23:21 |
| rdb | *yawn* morning | 23:22 |
| Steel3 | watson goes to wall street | 23:23 |
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| 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 | 23:25 |
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| nmz787 | yashagaroth, you here? | 23:26 |
| yashgaroth | indeed | 23:26 |
| 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 | 23:27 |
| 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 | 23:28 |
| 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 | 23:29 |
| 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... | 23:30 |
| 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' | 23:31 |
| nmz787 | ahh it does say that | 23:32 |
| 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 | 23:33 |
| 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 | 23:34 |
| 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 | 23:36 |
| yashgaroth | wait why can't it be compementary? you mean the middle nt in a 3bp sticky end? | 23:38 |
| nmz787 | the middle bp in any odd numbered sticky end | 23:39 |
| 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 | 23:40 |
| yashgaroth | ohhh right okay | 23:41 |
| yashgaroth | wasn't sure if you meant hairpinning or what, but I gotcha now | 23:41 |
| nmz787 | ttyl | 23:56 |
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| * yashgaroth sleeps | 23:58 | |
| -!- yashgaroth [~f@cpe-24-94-5-223.san.res.rr.com] has quit [Quit: Leaving] | 23:58 | |
| -!- Etherael [~Eric@r49-2-8-56.cpe.vividwireless.net.au] has left ##hplusroadmap [] | 23:58 | |
| --- Log closed Thu Mar 08 00:00:42 2012 | ||
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