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| nmz787 | ||0_-_0||: :( | 00:48 |
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| gene_hacker | ( ＞◡❛) | 01:09 |
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| kanzure | i think you can do spatial light modulation of cookie dough | 04:26 |
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| mstevens | I heard something about .wa? | 08:45 |
| mosasaur | .wa speed of light | 08:46 |
| yoleaux | c (speed of light in vacuum): Value: 299.8 km/ms (kilometers per millisecond); 299792 km/s (kilometers per second); 2.998×10⁸ m/s (meters per second); 186282 mi/s (miles per second); 6.706×10⁸ mph (miles per hour); 1 Planck speed; Comparison: ~2.4 × speed of light in diamond (~1.24×10⁸ m/s); Interpretation: speed; Basic unit dimensions: [length] [time]⁽⁻¹⁾; Corresponding quantities: Time to travel 1 meter from t … | 08:46 |
| yoleaux | = d/v:: 3.3 ns (nanoseconds) | 08:46 |
| mstevens | .wa 36835442688 | 08:46 |
| yoleaux | 36835442688: Scientific notation: 3.6835442688 × 10¹⁰; Number name: 36 billion 835 million 442 thousand 688; Number line: http://is.gd/G0QtIW; Number length: 11 decimal digits; Binary form: 100010010011100100000100000000000000₂; Prime factorization: 2¹⁴×3×11×193×353; Residues modulo small integers: m: 2: 3: 4: 5: 6: 7: 8: 9; 36835442688 mod m: 0: 0: 0: 3: 0: 2: 0: 3; Property: 36835442688 is an even number. | 08:46 |
| eudoxia | .wa 10000 years in gigaseconds | 08:47 |
| yoleaux | convert 10000 years to gigaseconds: 315.4 Gs (gigaseconds); Additional conversions: 3.154×10¹¹ seconds; 9993 average Gregorian years; 99.93 average Gregorian centuries; 9.993 average Gregorian millennia; Comparisons as time: ~0.5 × time since the last glacial maximum (~20000 yr); ~360 × generation (~28 yr); Comparison as period: ~0.39 × equinox precession period (25770 yr) | 08:47 |
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| kanzure | .title http://browserg.nom.es/ | 09:02 |
| yoleaux | One year of Blink and WebKit | 09:02 |
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| kanzure | "In the end, they closed him down based on a single reading of slightly elevated mercury levels in his yard." | 09:07 |
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| kanzure | .title http://www.thingiverse.com/thing:64977 | 09:15 |
| yoleaux | Adjustable Volume Straw Pipette by kwalus | 09:15 |
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| kanzure | thta 100 kilometer-wide telescope could be used to do whole earth optical imaging and OCR | 09:20 |
| kanzure | *that | 09:20 |
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| mosasaur | tell me about fenn kanzure | 09:33 |
| kanzure | i refuse | 09:33 |
| kanzure | what would you like to know? | 09:33 |
| mosasaur | why are they silent, what happened to perovskite? | 09:34 |
| kanzure | what do you mean silent...? | 09:34 |
| mosasaur | So you want to not tell, but you still you want to know what I want to know? | 09:36 |
| kanzure | i reserve the right to judge you poorly | 09:36 |
| chris_99 | anyone know why bioreactors are so dear | 09:37 |
| kanzure | because growing stuff is useful | 09:37 |
| chris_99 | mm this is true | 09:38 |
| mosasaur | http://www.eetimes.com/document.asp?doc_id=1321746 | 09:46 |
| mosasaur | .title | 09:46 |
| yoleaux | mosasaur: Sorry, that command (.title) took too long to process. | 09:46 |
| gene_hacker | zymurgy is also fun | 09:47 |
| mosasaur | "Perovskite, a New Meta Material, Turns Light Into Power, Lasers" | 09:47 |
| chris_99 | gene_hacker, do you brew beer? | 09:47 |
| gene_hacker | well I am most certainly attempting to turn sugars into ethanol | 09:48 |
| chris_99 | what for, drinking? | 09:49 |
| gradstudentbot | Yeah, but his project was so easy. | 09:49 |
| gene_hacker | primarily yes | 09:49 |
| chris_99 | something that i'm workin' on - http://hackaday.io/project/1231-Zymeter | 09:50 |
| gene_hacker | in short beer no | 09:53 |
| gene_hacker | mead yes | 09:53 |
| chris_99 | ah, never made mead, i make beer though | 09:53 |
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| chris_99 | do you keep the bees? or buy the honey? | 09:54 |
| gradstudentbot | Do I use a one or two sided t-test for that? | 09:54 |
| chris_99 | sure gradstudentbot both | 09:54 |
| gradstudentbot | What the hell is up with these indecisive transcription factors? | 09:54 |
| chris_99 | heh on wikipedia it says "The research efforts undertaken by the Danish Carlsberg scientists greatly accelerated the increase in knowledge about yeast and brewing. The Carlsberg scientists are generally acknowledged[by whom?] as jump-starting the entire field of molecular biology." | 09:57 |
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| mosasaur | Wouldn't a mass spectrometer be more conclusive? http://www.eetimes.com/document.asp?doc_id=1319727 | 10:10 |
| chris_99 | sure | 10:10 |
| chris_99 | but they're more expensive | 10:10 |
| gene_hacker_ | http://www.sens.org/sites/srf.org/files/images/Sample_Grant_Proposal.pdf | 10:20 |
| kanzure | gene_hacker_: a few ex-sens people are in here | 10:20 |
| kanzure | before they fired their whole lab | 10:20 |
| gene_hacker_ | the sens sample grant proposal is great | 10:20 |
| gene_hacker_ | it's about making GFP beer | 10:20 |
| kanzure | i bet john wrote it | 10:21 |
| chris_99 | haha i thought about doing something like that using electroporation for the yeasties | 10:21 |
| gene_hacker_ | I wonder why no one has done it yet... | 10:21 |
| chris_99 | with a hefeweizen it could work quite well, as that's full of a tonne of yeast in the bottle | 10:22 |
| gene_hacker_ | well back to making machine phase systems! | 10:23 |
| kanzure | gene_hacker_: would you be interested in building and having a micro/photolithography setup/device thing? | 10:23 |
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| gene_hacker_ | need to make machinephase systems now | 10:23 |
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| chris_99 | machine phase? | 10:23 |
| kanzure | yeah like http://www.chemistryviews.org/details/news/2051985/Metal-Organic_Framework_for_Rotaxanes.html | 10:24 |
| kanzure | 23:51 < gene_hacker> it's a metal organic framework that's supposed to change shape | 10:24 |
| kanzure | http://gnusha.org/logs/2014-05-03.log | 10:25 |
| chris_99 | intriguing | 10:25 |
| gradstudentbot | This laproscopic camera is so easy to use. | 10:26 |
| gradstudentbot | Where are the thermometers? | 10:26 |
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| kanzure | sup Angle | 10:35 |
| Angle | sup | 10:35 |
| kanzure | i would say this channel is very broad interest | 10:35 |
| kanzure | hardware is pretty broad in general | 10:35 |
| Angle | true | 10:36 |
| seba- | yes, for example i'm doing an open thermonuclear bomb | 10:36 |
| Angle | O-O | 10:37 |
| seba- | 3d printed | 10:37 |
| Angle | I see | 10:37 |
| kanzure | i don't think that 3d printing will give you all the necessary components for a thermonuclear warhead | 10:37 |
| kanzure | but nice try | 10:37 |
| Angle | well, I'm not so big on bombs | 10:37 |
| chris_99 | thermonuclear is so last year seba- | 10:37 |
| kanzure | pssh that's just propaganda | 10:37 |
| kanzure | "making bombs is bad" | 10:37 |
| seba- | kanzure, i'll use now my incubator to cook sous-vide meat | 10:37 |
| Angle | I was more hinking counter culture type stuff | 10:37 |
| kanzure | i wonder if counter culture is internally inconsistent (how can you be counter your own culture?) | 10:38 |
| Angle | though DIY projects in general are interesting | 10:38 |
| Angle | Well, you'r counter our societies dominant culture | 10:38 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=78addeb1 Bryan Bishop: dna-specific folder >> http://diyhpl.us/diyhpluswiki/dna/journals/ | 10:50 |
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| kanzure | .wik nuclear magnetic resonance spectroscopy of nucleic acids | 11:03 |
| yoleaux | "Nucleic acid NMR is the use of nuclear magnetic resonance spectroscopy to obtain information about the structure and dynamics of nucleic acid molecules, such as DNA or RNA. It is useful for molecules of up to 100 nucleotides, and as of 2003, nearly half of all known RNA structures had been determined by NMR spectroscopy." — http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy_of_nucleic_acids | 11:03 |
| kanzure | "In the early 1960s, Eschenmoser began work on what was the most complex natural product synthesized at the time—vitamin B12. In a remarkable collaboration with his colleague Robert Burns Woodward in Harvard, a team of almost one hundred students and postdoctoral workers worked for many years on the synthesis of this molecule. The work was finally published in 1973, and it marked a landmark in the history of organic chemistry." | 11:22 |
| kanzure | http://en.wikipedia.org/wiki/Albert_Eschenmoser | 11:22 |
| kanzure | http://en.wikipedia.org/wiki/Vitamin_B12_total_synthesis | 11:23 |
| Angle | well, thank you for your time. Have a good day everyone! | 11:24 |
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| chris_99 | nmz787, you about, i'm curious what sensor your spectrometer use | 11:24 |
| chris_99 | s | 11:24 |
| kanzure | i am pretty sure that synthesis would have been completed much faster if they had a database of organic reactions to run against it | 11:26 |
| kanzure | take the final molecule, then proceed to work backwards using known reactions from the database, rather than slavedriving 100 researchers for "many years" | 11:26 |
| kanzure | full synthesis: http://www.synarchive.com/syn/71 | 11:27 |
| kanzure | .title | 11:27 |
| yoleaux | kanzure: Sorry, that command (.title) took too long to process. | 11:27 |
| kanzure | "This famous synthesis was achieved through a collaboration between the research groups of Rober B. Woodward and of Albert Eschemoser. It took a team of about a hundred co-workers working for over a decade to perform the complete synthesis." | 11:29 |
| kanzure | "over a decade" | 11:29 |
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| Daeken | this may be a weird question ... anyone know of a commercial personal genome sequencing firm that's under $10k and reputable? i'm having a hard time finding much that's concrete. | 12:05 |
| Daeken | https://www.scienceexchange.com/labs/kinghorn-centre-for-clinical-genomics looks way too cheap -- $1500 for a whole human genome sequence. | 12:06 |
| chris_99 | i thought that popular one did it for <10k | 12:08 |
| chris_99 | the one that tells you the diseases you'll get | 12:08 |
| kanzure | ithink a lot of them are under $10k these days | 12:14 |
| kanzure | $1500 is on target | 12:14 |
| kanzure | depends on how much coverage they do | 12:15 |
| kanzure | if they are claiming 200x coverage for $1500 probably a scam | 12:15 |
| gradstudentbot | This laproscopic camera is so easy to use. | 12:15 |
| chris_99 | what's 200x coverage mean | 12:15 |
| kanzure | they do it 200 times | 12:16 |
| kanzure | well, sort of | 12:16 |
| chris_99 | ah cool | 12:16 |
| kanzure | "Sequence coverage is the average number of times a base is read (as described above)." | 12:16 |
| chris_99 | ok | 12:17 |
| kanzure | Daeken: ask ParahSailin for a reference.. | 12:17 |
| kanzure | i know someone that used knome once but at the time it was expensive (>$10k) and i'm not sure if their prices have dropped | 12:18 |
| gradstudentbot | Someone's sitting at my bench space. | 12:18 |
| kanzure | 30x coverage is fine for your purposes | 12:19 |
| kanzure | i wonder if they do the sequence alignment for you.. hehe. | 12:20 |
| kanzure | damn for $1500 i should do that huh | 12:20 |
| chris_99 | mm sounds pretty good | 12:21 |
| kanzure | note that scienceexchange or that particular provider may not respond well to a non-academic-institution request | 12:22 |
| seba- | let's form an institute | 12:25 |
| seba- | institute for everything for everyone | 12:25 |
| seba- | http://j-ever.org/ojs/ | 12:26 |
| seba- | see | 12:26 |
| seba- | JOURNAL FOR EVERYTHING | 12:26 |
| seba- | FOR EVERYONE | 12:26 |
| seba- | http://j-ever.org/scripts/rscient.php you can generate a random russian scientist here | 12:26 |
| chris_99 | kanzure, i'm just looking at the wikipedia page on sequence alignment, is it similarity between multiple sequences then? | 12:31 |
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| kanzure | what is your question? | 12:33 |
| kanzure | sequence alignment is necessary because traditional forms of dna sequencing only produce short reads | 12:34 |
| kanzure | so you have to put a giant jigsaw puzzle together | 12:34 |
| chris_99 | oh so it's aligning multiple reads, the wikipage didn't realy mention that. that makese sense now, ta | 12:35 |
| gradstudentbot | I don't know what to tell you, I thought I would have graduated by now. | 12:38 |
| Daeken | kanzure: woops, sorry, landlord came by. 30x coverage is what they're offering for $1500. it looks pretty reasonable, but i'm concerned about that price. | 12:42 |
| Daeken | i'm tempted to give it a shot though. i mean, if it's shit, i'm only out $1500. | 12:44 |
| Daeken | ohhh. i believe that that's why it's so cheap: Number of Samples - Minimum of 20 per order (volume orders may attract a discount) | 12:44 |
| chris_99 | is it easy to tell things like eye colour from that data | 12:44 |
| kanzure | Daeken: you can probably convince a "core facility" somewhere to do it for you for just $1500 without the volume order requirement | 12:45 |
| gradstudentbot | I am completely satisfied with the size of my bench space. | 12:45 |
| Daeken | chris_99: some things 'like' eye color, yes. but eye color itself, no. eye color is actually determined by a bunch of genes. | 12:45 |
| Daeken | some of which are still unknown | 12:46 |
| kanzure | also depends on what you mean by easy | 12:46 |
| Daeken | kanzure: hrm, maybe. | 12:46 |
| kanzure | after alignment you would still have to identify genes and polymorphisms in those genes | 12:46 |
| chris_99 | interesting, so we've got a long way to go | 12:46 |
| kanzure | huh? | 12:46 |
| kanzure | no, it's doable, it's just not "open up the 50 GB file and look" | 12:46 |
| Daeken | chris_99: in some regards, yes. but for many things, not so much. | 12:46 |
| kanzure | http://snpedia.com/ | 12:47 |
| kanzure | lots of open source software is available for the analysis pipeline, i'd even hazard to say it's mostly a solved problem | 12:47 |
| Daeken | i'll put it like this: for $1500, you can at least know everything that 23andme knows, and have the flexibility to find out anything else in the future without more profiling. | 12:47 |
| Daeken | yeah | 12:47 |
| chris_99 | that site looks really neat | 12:48 |
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| Daeken | honestly though, i don't want my genome for anything practical at the moment. i just want it, and maybe it'll be more useful in the future. | 12:49 |
| Daeken | and if i can do it for a couple grand? hell yes i'm going to. | 12:49 |
| Daeken | i've pissed away far more on far less :) | 12:49 |
| kanzure | prices will continue to drop | 12:49 |
| kanzure | there's intense competitive pressure between 30 different venture backed companies doing dna sequencing | 12:50 |
| Daeken | yeah, but $1500 for that is well within impulse buy range honestly. | 12:50 |
| kanzure | and they all know they have to compete on price | 12:50 |
| kanzure | sure, but it's going to get much much cheaper | 12:50 |
| Daeken | yep | 12:50 |
| kanzure | the fda's reaction to 23andme is sorta eyerolling because it's not like you can do much with the information anyway, besides general lifestyle improvement stuff, and in some cases stop eating poisons | 12:51 |
| chris_99 | could you DIY with one of the nanopore ones | 12:51 |
| kanzure | a lot of nano things are often very difficult to assemble correctly | 12:51 |
| kanzure | if you were going to do your own sequencing, it would probably be sanger sequencing | 12:51 |
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| nmz787_i | chris_99: TCD1304AP | 13:13 |
| chris_99 | how far into IR does that see out of interest | 13:14 |
| nmz787_i | chris_99: there are lots of similar TCD1304 sensors, mainly packaging differences in the last two chars | 13:14 |
| nmz787_i | umm | 13:14 |
| nmz787_i | normal silicon response | 13:14 |
| nmz787_i | prob 1100nm | 13:14 |
| nmz787_i | idk | 13:14 |
| nmz787_i | 900 maybe | 13:14 |
| chris_99 | oh it's silicon ok | 13:15 |
| nmz787_i | if you want far out, InGaAs is what you want to look for I believe | 13:15 |
| chris_99 | mm i looked into it | 13:15 |
| chris_99 | not cheap | 13:15 |
| nmz787_i | I think i reduced the board size last night to 70 or 80% | 13:15 |
| chris_99 | do you know with ramen spectroscopy | 13:15 |
| nmz787_i | I saw some InGaAs advertised on Alibaba but never got a reply from the seller | 13:15 |
| chris_99 | if you could measure ethanol with silicon | 13:15 |
| nmz787_i | likely | 13:15 |
| chris_99 | i contacted a japanese company around £90 for one | 13:16 |
| chris_99 | of the cheapeest ones | 13:16 |
| nmz787_i | ? | 13:16 |
| nmz787_i | question mark 90 | 13:16 |
| nmz787_i | is what i see | 13:16 |
| chris_99 | oh, pounds | 13:16 |
| chris_99 | i think my encoding is screwed | 13:16 |
| chris_99 | somehow | 13:16 |
| nmz787_i | oh | 13:16 |
| kanzure | nope | 13:16 |
| nmz787_i | for an ingass? | 13:16 |
| chris_99 | yup | 13:16 |
| nmz787_i | ingaas | 13:16 |
| chris_99 | InGaAs | 13:17 |
| kanzure | you typed £ which is correct | 13:17 |
| nmz787_i | array or single pixel? | 13:17 |
| chris_99 | array | 13:17 |
| nmz787_i | kanzure: i can see your pound sign | 13:17 |
| chris_99 | i forget how many pixels now | 13:17 |
| nmz787_i | oh that might be decent | 13:17 |
| chris_99 | Hammastu | 13:17 |
| chris_99 | or somthing | 13:17 |
| chris_99 | iirc | 13:17 |
| nmz787_i | I think this PCB will be like $70 or $80 for 3, plus electronics parts like $50 I think | 13:18 |
| nmz787_i | including the CCD | 13:18 |
| nmz787_i | so remove ~$15 or 20 for the CCD and add on the InGaAs sensor | 13:19 |
| nmz787_i | ($50 for 1 board) | 13:19 |
| chris_99 | i'm confused though right, as from what i've read with standard IR spectroscopy at least, the ethanol peaks/troughs i foroget which, is in the InGaAs range | 13:19 |
| nmz787_i | (just in componenets) | 13:19 |
| chris_99 | how does Raman spectrscopy differ in that respect | 13:19 |
| nmz787_i | raman uses a laser | 13:19 |
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| chris_99 | but it still needs a sensor | 13:20 |
| nmz787_i | and the electronic structure (sortof the antenna effect of a molecule) perturbs it characteristically | 13:20 |
| chris_99 | perturbs in what sesne | 13:20 |
| nmz787_i | so you assume the input freq is constant/stable, and you look at the spectra of the returning photons, minus the laser freq | 13:21 |
| nmz787_i | perturbs the freq of the photons | 13:21 |
| chris_99 | hmm interesting | 13:21 |
| chris_99 | so the colour changes effectively? | 13:21 |
| nmz787_i | the photons shoot toward the sample, interact with the electronics of the molecule(s) then if the molecule doesn't resonate destructively (absorbtion) it re-emits a photon, and the freq will be changed depending on the strength of the interaction | 13:22 |
| nmz787_i | it kinda helps to think about this in terms of radio signals and antennas | 13:23 |
| nmz787_i | yeah, the color changes very very slightly | 13:23 |
| nmz787_i | like single nm or thereabouts | 13:23 |
| chris_99 | so surely you need a _very_ | 13:23 |
| chris_99 | good sensor | 13:23 |
| nmz787_i | maybe 10s of nm | 13:23 |
| nmz787_i | well you need a very good laser filter | 13:23 |
| chris_99 | how can you pick that up with that CCD thing | 13:23 |
| nmz787_i | as the contrast/dynamic range to see them both would be crazy high | 13:23 |
| nmz787_i | then you need a good enough grating to separate the few nm range into a few cm to spread over the pixels | 13:24 |
| chris_99 | oh gotcha | 13:24 |
| nmz787_i | shoot a laser, it bounces back, pass through filter specific for the laser color, then pass through/off-of grating, then onto CCD | 13:25 |
| gradstudentbot | I don't know what to tell you, I thought I would have graduated by now. | 13:25 |
| nmz787_i | gradstudentbot: I just got off the phone with my school, they're looking into it | 13:25 |
| gradstudentbot | I don't think our fume hood is safe. | 13:25 |
| chris_99 | haha | 13:25 |
| chris_99 | sounds v. cool nmz787 | 13:26 |
| nmz787_i | yeah, g2g do work, was up late working on the PCB | 13:26 |
| nmz787_i | GUI LAND! | 13:26 |
| chris_99 | heh, good luck | 13:26 |
| gradstudentbot | Sure, I've been spending a lot of time at a pub.... well, pubmed at least. | 13:29 |
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| nmz787_i | wasn't/isn't there something called club-med? | 13:38 |
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| delinquentme | nmz787, yeaaahhh! | 14:05 |
| nmz787_i | diffraction is the new refraction | 14:11 |
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| kanzure | what was that competition for making backdoors non-obvious? | 16:00 |
| dingo | i remember a backdoor hidden in a Makefile | 16:05 |
| dingo | that was very non-obvious.... what was that for ... | 16:05 |
| dingo | gosh i forget | 16:05 |
| dingo | or rather hidden in ./configure or some such | 16:05 |
| dingo | 10 years ago now it must be | 16:05 |
| kanzure | .wgetrc is a cool trick | 16:06 |
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| eudoxia | kanzure: the underhanded c code contest? | 16:15 |
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| joepie91__ | underhanded indeed | 16:29 |
| kanzure | aha | 16:29 |
| joepie91__ | entirely unrelated | 16:29 |
| kanzure | would be fun to have one of those where you get to use existing open source software | 16:29 |
| joepie91__ | http://cryto.net/~joepie91/blog/2014/06/04/research-journalist-de-winter-followed-more-intensively-than-previously-assumed/ | 16:29 |
| joepie91__ | newsybits | 16:29 |
| joepie91__ | kanzure: and make it function as a backdoor unintentionally? | 16:29 |
| joepie91__ | :P | 16:29 |
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| kanzure | joepie91__: well yes it's a backdoor | 16:29 |
| kanzure | joepie91__: but the point of the contest is to demonstrate possible vulnerabilities | 16:30 |
| kanzure | joepie91__: and, in some cases, stumble into existing backdoors | 16:30 |
| joepie91__ | NSA would win, every time | 16:30 |
| kanzure | they would not publicly compete | 16:30 |
| kanzure | as far as i know | 16:30 |
| kanzure | just not their style | 16:30 |
| joepie91__ | didn't say they'd carry the NSA banner ;) | 16:31 |
| kanzure | well what's the difference from that and acccusing random people of being nsa | 16:31 |
| kanzure | ugh | 16:31 |
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| heath | https://github.com/heath/treemap-web | 16:54 |
| heath | k, app pretty much complete, need to build something with phonegap so people can add trees | 16:54 |
| heath | ^ what my coding style is like presently | 16:55 |
| heath | for anyone who wants to visit | 16:55 |
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| heath | todo: phonegap app -> python version -> elixir version -> haskell version -> clojure version | 16:56 |
| heath | just because | 16:57 |
| * heath spends time with his gf for the rest of the evening | 16:57 | |
| kanzure | dna synthesis idea: photocleavable nucleotides that, depending on the wavelength of light, cleave into the appropriate nucleotide still in the same chain. also, you would probably do this in a nanopore where you could guarantee that the photons are hitting only a single nucleotide. | 17:02 |
| nsh | oh. in that case i'll have to make new plans | 17:02 |
| kanzure | i think it's called cordova now, instead of phonegap :p | 17:02 |
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| kanzure | win 5 | 17:17 |
| kanzure | jdfokadsjfka | 17:17 |
| delinquentme | kanzure, just the opposite :D | 17:18 |
| delinquentme | its stewpid though. | 17:19 |
| delinquentme | TLDR: I cant wait for my 10 lbs of human gruel. | 17:19 |
| delinquentme | I got it for like $50 off. I'm pretty excited to get my protizzle. | 17:19 |
| delinquentme | ( plz dont ban me for saying that ^ ) lololo | 17:19 |
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| kanzure | oops, not a nanopore. you would have a solid wall with the exception of a small few nanometer opening and run the dna on the other side of the wall and ratchet forward/backward somehow. of course, it wouldn't be dna really. | 17:27 |
| kanzure | i dunno about coming up with a molecule that responds that specifically to four different wavelengths of light. | 17:28 |
| kanzure | .wik database of molecular motions | 17:31 |
| yoleaux | "The Database of Macromolecular Motions (molmovdb) is a bioinformatics database that attempts to categorize macromolecular motions, sometimes also known as conformational change. It was original developed by Mark B. Gerstein, Samuel Flores, Werner Krebs, and Nat Echols in the Molecular Biophysics & Biochemistry Department at Yale University." — http://en.wikipedia.org/wiki/Database_of_molecular_motions | 17:31 |
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| kanzure | maybe you could have a protein that undergoes a series of conformational changes, where once you go past the fourth one, it goes back to the first, such that each one moves an arm with the right nucleotide into position | 17:34 |
| kanzure | also, their database is down | 17:34 |
| kanzure | http://www.molmovdb.org/ | 17:34 |
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| kanzure | http://web.archive.org/web/20060213125048/http://www.molmovdb.org/ | 17:35 |
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| kanzure | http://hackaday.com/2014/04/29/a-diy-atomic-force-microscope/ | 18:16 |
| kanzure | 14:55 < nballs> SEM is the superior technology. Just throw any old thing in there and there you go. No sample preparation, no waiting, put it in, pump it down, image. | 18:16 |
| kanzure | http://www.instructables.com/id/A-Low-Cost-Atomic-Force-Microscope-%E4%BD%8E%E6%88%90%E6%9C%AC%E5%8E%9F%E5%AD%90%E5%8A%9B%E9%A1%AF%E5%BE%AE%E9%8F%A1/?ALLSTEPS | 18:17 |
| kanzure | "Here we use data tracks on DVD and Blu-ray disks (protection layer are torn out) for AFM system evaluations and calibrations." | 18:18 |
| kanzure | "The low cost AFM can easily measure the DVD data tracks which can not be observed by the optical microscope." is that true? huh | 18:18 |
| kanzure | .title http://books.google.com.tw/books/about?id=rRtyAwAAQBAJ&redir_esc=y | 18:19 |
| kanzure | author is "En-Te Hwu" | 18:19 |
| yoleaux | kanzure: Sorry, that command (.title) took too long to process. | 18:20 |
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| kanzure | http://mcise.uri.edu/park/MNEL/legoafm/index.html | 18:26 |
| kanzure | .title https://www.youtube.com/watch?v=GjVWN0YQUfM | 18:26 |
| yoleaux | kanzure: Sorry, that command (.title) took too long to process. | 18:27 |
| dpk | title command is mysterioisly broken | 18:27 |
| dpk | will inffestigate tomorrow, about to sleep now | 18:27 |
| kanzure | oh, wait, they aren't using small cantilevers? they are just scanning lego bricks? what the fuck | 18:29 |
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| kanzure | 07:55 < MJHelper> lildlper is a small dlp uv resin printer designed by goopyplastic. BOM: https://docs.google.com/spreadsheet/ccc?key=0Au5Hr99Np6jddC1kdF8zUjlHT2taYjQwN0NUV3dkSkE&usp=sharing#gid=0, or https://www.dropbox.com/sh/x5f0i1roh4cztoc/dXp8bzUbiY | 18:36 |
| kanzure | man do people seriously not use their own web servers any more | 18:36 |
| kanzure | this future sucks | 18:37 |
| kanzure | https://www.dropbox.com/s/8q7rcyibqpguamp/2014-06-03%2020.30.36.jpg | 18:38 |
| gene_hacker | yes I would be interested in have a DLP photolithography system | 18:38 |
| gene_hacker | welcome to the cloud | 18:39 |
| seba- | kanzure, what do you mean, i have my own | 18:40 |
| kanzure | context please? | 18:41 |
| seba- | kanzure, web server | 18:41 |
| kanzure | do you use it | 18:41 |
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| kanzure | gene_hacker: i'm thinking it should be something with a separate xy stage, and share optics with a dlp+microscope and uv/bluray led thing for cutting (so that it could be interchanged) | 18:42 |
| seba- | kanzure yes | 18:44 |
| kanzure | another option is to shine the uv/bluray led at the dlp/dmd directly | 18:45 |
| gene_hacker | I just want something that throws off enough UV to photopolymerize resin with ceramic particles in it | 18:47 |
| gene_hacker | I want to make some jet turbine blades | 18:47 |
| kanzure | "Lunavast XG2" "This is an open source high resolution DIY DLP 3D printer kit with RepRap technologies. A projector with native XGA (1024 x 768 pixels) resolution and a normal lamp (NOT LED) is required separately. Resolution: X-Y 0.1mm Z 0.1mm" | 18:48 |
| seba- | why don't you use a UV laser | 18:48 |
| kanzure | hmm 0.1mm.. hmm. | 18:48 |
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| kanzure | that is maybe acceptable | 18:50 |
| kanzure | it would be nice to have 1 micron-ish resolution | 18:50 |
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| gradstudentbot | Anyone else think pol II looks like a butt? | 18:51 |
| nsh | .t http://www.bioopticsworld.com/articles/2014/06/optogenetics-confirms-that-strengthened-connections-between-neurons-fuel-memories.html | 18:52 |
| yoleaux | nsh: Sorry, I don't know a timezone by that name. | 18:52 |
| nsh | shup | 18:53 |
| nsh | .title http://www.bioopticsworld.com/articles/2014/06/optogenetics-confirms-that-strengthened-connections-between-neurons-fuel-memories.html | 18:53 |
| yoleaux | nsh: Sorry, that command (.title) took too long to process. | 18:53 |
| nsh | i haet you; you're not my real dad | 18:54 |
| kanzure | also, the title is in the url | 18:54 |
| gene_hacker | because there's a lot more you can do if you have grayscale | 18:56 |
| kanzure | for the sake of simplicity, i think sticking with only (uv) LEDs and regular old lamps for light sources is best | 18:56 |
| kanzure | maintaining a laser tube is annoying | 18:56 |
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| kanzure | huh they used a food blender as a spin coater (with a custom attacher/gripper thing instead of a blade) | 19:01 |
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| kanzure | i forgot about azonenberg's paper, http://diyhpl.us/~bryan/papers2/optics/photolithography/DIY%20fabrication%20of%20microstructures%20by%20projection%20photolithography.pdf | 20:21 |
| kanzure | dcary: did i show you http://diyhpl.us/laser_etcher/laser_etcher | 20:22 |
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| dcary | No, I haven't seen that laser etcher -- 10 um cutting spot is pretty amazing. | 20:29 |
| dcary | I see a couple of highly influential microprocessors were manufactured with 10 um transistors -- https://en.wikipedia.org/wiki/10_%C2%B5m_process . | 20:30 |
| kanzure | there's simply lots of propaganda against micron-scale electronics by the Big Silicon industry :) | 20:31 |
| kanzure | (how else are they going to keep shoveling coal into their multi-billion-dollar silicon furnace?) | 20:31 |
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| dcary | Yes, I'm beginning to suspect that many things aren't nearly as hard as people say they are. | 20:38 |
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| kanzure | you may be entertained by the other files in there: http://diyhpl.us/~bryan/papers2/optics/photolithography/ | 20:42 |
| dcary | Somewhere I heard that many systems trend toward unnecessary complexity: Simple systems lead to people thinking they understand them enough to change them, often to make them more complex; but people are reluctant to change a system that is obviously too complex for any one person to understand. | 20:44 |
| kanzure | so speaketh http://en.wikipedia.org/wiki/Systemantics | 20:45 |
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| dcary | Since those microprocessors were manufactured with 10 um transistors in 1971 and 1972, decades after the first transistorized computers (around 1955), I suspect that several computers used transistors with a linewidth larger than 10 um. | 20:53 |
| kanzure | the first computers using transistors were probably using the non-planarly-integrated type | 20:54 |
| kanzure | dcary: i mean surface-mount transistors | 20:56 |
| kanzure | http://en.wikipedia.org/wiki/TO-92 | 20:57 |
| dcary | Right, the first transistorized computers used individually packaged transistors (sometimes called "discrete transistors"). | 20:59 |
| kanzure | oops, yes, that's the right name | 20:59 |
| dcary | But a few highly influential computers were each designed out of a large pile of integrated circuits, with a few transistors per chip, years before those first "single-chip computers". | 21:02 |
| gradstudentbot | The freezer was too cold and fucked up my sample DNA. | 21:03 |
| dcary | I'm still looking for an excuse to build my own CPU out of a few handfuls of integrated circuits -- meanwhile, I see that many other people have built such homebrew CPUs. http://en.wikibooks.org/wiki/Microprocessor_Design/Wire_Wrap | 21:04 |
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| dcary | So how does 10 um resolution help with diybio DNA stuff? | 21:10 |
| kanzure | there's a variant of oligonucleotide synthesis that uses light to protect/deprotect growing strands | 21:10 |
| kanzure | http://diyhpl.us/~bryan/papers2/DNA/Light-directed%20synthesis%20of%20high-density%20oligonucleotide%20arrays%20using%20semiconductor%20photoresists%20-%201996.pdf | 21:11 |
| kanzure | 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 | 21:11 |
| kanzure | (using a micromirror array is the part that would help the most. also the ability to construct microfluidic circuits.) | 21:13 |
| gradstudentbot | Whatever, I'm really dating school anyway. | 21:15 |
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| kanzure | kuudes: hi | 21:19 |
| kuudes | hi kanzure | 21:27 |
| kanzure | .title http://micro.sci-toys.com/grinding | 21:31 |
| yoleaux | Grinding your own microscope lens | 21:31 |
| dcary | I hear that several people are extracting the micro-mirror array (DLP) from an off-the-shelf projector and using it for stereolithography ( http://reprap.org/wiki/Category:Stereolithography ). Can any of their ideas be applied to diybio stuff? | 21:37 |
| kanzure | definitely, although i think all of those have a spot size of ("at most") 100 microns (which might not be the end of the world) | 21:43 |
| kanzure | there's also a bunch of larger objects from thingiverse etc for pipettes, grips, holders, mounters, dremelfuges, etc. that come in handy for doing biology things | 21:43 |
| joepie91__ | oh dear | 21:52 |
| joepie91__ | I think I spotted a failed-redaction PDF | 21:52 |
| joepie91__ | https://pdf.yt/d/z8ThY1sr68YEQ-Fy | 21:53 |
| kanzure | do people really think that works | 22:01 |
| joepie91__ | kanzure: apparently | 22:02 |
| joepie91__ | it rendered a bit slowly here | 22:02 |
| joepie91__ | so I spotted the address under the rectangl | 22:02 |
| joepie91__ | rectangle * | 22:02 |
| joepie91__ | I presume the other rectangles are similarly poorly redacted | 22:02 |
| joepie91__ | I'm sure cops won't be happy - they were already complaining about the overlooked name on the second page in the original | 22:03 |
| joepie91__ | "oh, btw, the other redactions were worthless too" | 22:03 |
| kanzure | ugh the last thing i want to do is wait for pdfs to render | 22:04 |
| kanzure | what a wonderful use of my time on this planet | 22:04 |
| joepie91__ | heh | 22:05 |
| joepie91__ | well thankfully some advances are made on that | 22:05 |
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| --- Log closed Wed Jun 04 00:00:24 2014 | ||
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