| --- Log opened Sun Jun 21 00:00:28 2015 | ||
| --- Day changed Sun Jun 21 2015 | ||
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| fenn | there's no reason to flip a well over to transfer it to another plate, just glue a grid of walls/wells on top of the plate | 02:05 |
|---|---|---|
| fenn | transforming a glass slide into a 96 well plate or whatever | 02:05 |
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| CaptHindsight | whats the point of wells if the entire sample tray are all the same oligos? | 02:31 |
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| fenn | they're not all the same, each 20 micron spot would be a different oligo; each well could have up to 1.5 million of these | 02:36 |
| fenn | so there could be 144 million oligos per plate | 02:37 |
| fenn | 20 micron spot sizes is probably too optimistic though | 02:38 |
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| CaptHindsight | fenn: why are 20 dia spots optimistic? | 02:40 |
| CaptHindsight | 20um | 02:40 |
| fenn | because the droplets splash when they hit the surface | 02:40 |
| CaptHindsight | if they are hitting a flat surface then yeah it's like a cow pissing on a flat rock | 02:41 |
| fenn | do you think chemical vapor deposition could help raise the surface wetting and get more repeatable spot sizes? | 02:42 |
| fenn | er, growing a forest of pillars out of something or other | 02:43 |
| fenn | or some kind of etching process | 02:43 |
| CaptHindsight | what problem are you trying to solve? Do the drops need to be same size or are you trying to avoid contamination? | 02:44 |
| fenn | to avoid contamination | 02:45 |
| CaptHindsight | just make a better sample tray | 02:45 |
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| CaptHindsight | why isn't all this already available as low cost modular lab systems? | 02:49 |
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| CaptHindsight | now I understand why I see Cole-Parmer and Fisher and similar on everything at 10-100x the price it could be | 02:58 |
| eleitl | Why is that? | 03:04 |
| CaptHindsight | http://www.gtcr.com/ heh they purchased Cole Parmer, look at their pics | 03:09 |
| CaptHindsight | I need to rinse my eyes with IPA | 03:09 |
| eleitl | Standard coprophagate type. | 03:11 |
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| ltiele | So many virtual servers to migrate, so little motivation. | 03:55 |
| ltiele | ARIN IPv4 exhaustion estimated 27 July | 04:10 |
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| fenn | wow unbelievable this was written 13 years ago and still no solution in sight: http://cr.yp.to/djbdns/ipv6mess.html | 05:29 |
| kanzure | djb's still around, you know | 05:39 |
| fenn | i didn't realize that ipv6 was incompatible with ipv4 because why would you do that | 05:40 |
| kanzure | holy shit i guessed the libgen person | 05:40 |
| kanzure | shit | 05:40 |
| kanzure | oijreolkjdsa;lkjaas | 05:40 |
| fenn | i thought you already knew | 05:41 |
| fenn | "As with IPv4, the Department of Defense holds a larger IPv6 allocation than any other entity, a /13 block, enough to create almost 2.3 quadrillion (2.3×10^15) local area networks" | 05:42 |
| fenn | but will it be enough? | 05:43 |
| fenn | not even avogadro-scale | 05:43 |
| kanzure | i had not known | 06:04 |
| kanzure | (we're screwed by the way) | 06:04 |
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| kanzure | hmm | 06:28 |
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| ltiele | Which libgen person? | 06:37 |
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| ltiele | afk | 06:45 |
| kanzure | i don't think we should talk about their names | 06:51 |
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| kanzure | but now some other options are available for me to get data | 07:00 |
| kanzure | even if they are initially uncooperative | 07:00 |
| kanzure | CaptHindsight: i'm uncomfortable with increasing the scope of a dna synthesis machine to also include cell incubation, dna sequencing, cell transformation, thermocycling, and a whole host of other stuff. | 07:02 |
| kanzure | CaptHindsight: usually as the scope increases the probability of the project being successful goes down... http://diyhpl.us/wiki/projects/heuristics/ | 07:03 |
| kanzure | weird there's nothing about scope on this page. that should be fixed. | 07:03 |
| kanzure | http://c2.com/cgi/wiki?ScopeCreep | 07:05 |
| fenn | it's easier to add a line to a requirements doc than to start a new project entirely | 07:13 |
| kanzure | i suppose an argument could be made that "without some way to use the 100k dots or pores and the synthesized oligos, the whole machine is useless anyway" but... | 07:14 |
| kanzure | hmm. | 07:14 |
| kanzure | "gibson assembly has been used to reliably join up to 6 dna fragments into a single molecule".. oh. only 6. | 07:17 |
| kanzure | (also: oligos aren't dna molecules) | 07:18 |
| fenn | pretty sure the number is higher than that | 07:18 |
| fenn | .c 400000/80 | 07:18 |
| yoleaux | 400000/80 = 5000 | 07:18 |
| fenn | at least 5000 oligos were combined to make m. laboratorium | 07:19 |
| kanzure | probably wasn't single-pot | 07:19 |
| kanzure | grr | 07:23 |
| fenn | no it definitely was not in a single pot. it was a long hierarchical synthesis involving plasmids and yeast recombination with sequencing to verify each step | 07:24 |
| fenn | .title http://www.sciencemag.org/content/319/5867/1215.abstract | 07:26 |
| yoleaux | Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome | 07:26 |
| fenn | oh they used e. coli | 07:26 |
| ltiele | Indeed one should observe opsec in regards to lg | 07:48 |
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| heath | https://vaultproject.io | 08:44 |
| heath | "Vault is a tool for securely accessing secrets. A secret is anything that you want to tightly control access to, such as API keys, passwords, certificates, and more. Vault provides a unified interface to any secret, while providing tight access control and recording a detailed audit log." | 08:44 |
| heath | the summary in the link is better: "Vault secures, stores, and tightly controls access to tokens, passwords, certificates, API keys, and other secrets in modern computing. Vault handles leasing, key revocation, key rolling, and auditing. Vault presents a unified API to access multiple backends: HSMs, AWS IAM, SQL databases, raw key/value, and more." | 08:45 |
| kanzure | scanning tunneling microscopy stuff http://dberard.com/home-built-stm/electronics/ | 08:47 |
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| Urchin[emacs] | nice | 09:10 |
| Urchin[emacs] | I know open air STMs are not too complex, some friends built them themselves | 09:10 |
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| kanzure | you could spin-dry the oligos | 09:27 |
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| CaptHindsight | kanzure: the inkjet printer is just one step in an assembly line, you just need to decide what the next step is to best configure the print sample and also how samples are best removed from the printer | 09:33 |
| CaptHindsight | do all the samples start in the printer or will any samples be returned from later processing steps for more layers of oligos? | 09:37 |
| kanzure | but if you add too many steps then nothing's ever going to get done, too much work | 09:37 |
| kanzure | oligo molecules are not returned to the synthesizer | 09:38 |
| kanzure | er, i mean: oligo molecules do not need to be returned to the synthesizer | 09:39 |
| kanzure | it's hard to decide whether i want the output of the system to be a single (large) oligo, or thousands of (somewhat large) oligos, or a transformed (dna-inserted) cell or cell culture or many transformed cell cultures with the different constructed molecules. all of these are legitimate options that others have used in engineering/research projects before. | 09:42 |
| kanzure | (and unfortunately that sort of question is unrelated to the construction of a dna synthesizer, i think.) | 09:43 |
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| CaptHindsight | kanzure: give some thought to how the sample trays should best be handled by the next steps, that will determine their size and shape | 10:28 |
| kanzure | there's at least 100 different types of thermocyclers you could make for the polymerase chain reaction step | 10:28 |
| kanzure | (laser, thermal heat element, circulating + thermal, grid-array thermal peltier thingy, lightbulb thingy, waterbath thingy, ...) | 10:29 |
| kanzure | ((i'm sure there's even an open flame variation)) | 10:30 |
| kanzure | and some of them require different handling procedures | 10:36 |
| kanzure | or er, physical part compatibility is different.. | 10:36 |
| kanzure | shapes. | 10:36 |
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| delinquentme | https://www.youtube.com/watch?v=Ch1j_bnBtB | 11:06 |
| delinquentme | thi sis super fun. | 11:06 |
| kanzure | .title | 11:06 |
| yoleaux | YouTube | 11:06 |
| kanzure | .title https://www.youtube.com/watch?v=Ch1j_bnBtBM | 11:06 |
| yoleaux | Legolas - High-precision robots available in kit form - YouTube | 11:06 |
| kanzure | dpk: what just happened? | 11:06 |
| CaptHindsight | kanzure: so the printer should have a flexible design to allow for variations in sample tray sizes and shapes | 11:10 |
| kanzure | probably | 11:14 |
| CaptHindsight | the printer is just a 3-axis Cartesian stage, with a printhead | 11:14 |
| CaptHindsight | you just ave to decide what other options get mounted on it such as a pipette and how the enclosure works | 11:15 |
| CaptHindsight | and how the printer loads to sample trays into the print area | 11:15 |
| CaptHindsight | to/the | 11:16 |
| CaptHindsight | the sample tray is just another mechanism, such as a conveyor belt, rotary table/indexer, etc | 11:17 |
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| kanzure | probably | 11:20 |
| ltiele | You're not targetable as an individual user, only as a class of (Tor) users. | 11:26 |
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| kanzure | ltiele: i think you switched topics on me? heh | 11:28 |
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| dpk | kanzure: no idea. the .title command might have got an anti-scraping CAPTCHA or something? but that wouldn't explain why it worked the second time | 14:11 |
| sheena | http://www.newproductsplus.net/cortisol_test.html anyone seen this in a purchasable format? | 14:23 |
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| wrldpc1 | Random fact: DC-2, the first robot to be arrested, was taken into custody in Beverly Hills for distributing business cards in 1982. | 15:22 |
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| kanzure | hmph | 15:53 |
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| FourFire | kanzure, | 16:18 |
| FourFire | Hi | 16:18 |
| FourFire | I failed. | 16:18 |
| FourFire | Please tell me why | 16:18 |
| FourFire | <FourFire> I'm staying off IRC & Reddit for the next 30 days, productivity experiment | 16:18 |
| FourFire | <FourFire> cya all on the 7th, | 16:18 |
| FourFire | <dingo> kanzure: we set vova up with a new job remote, he's working on some ~1,000 graphviz node graph of something (product build related), i'm about to make one myself (salt state dependency tree), you ever play with graphviz much? any tips? | 16:18 |
| FourFire | <FourFire> (or not) | 16:18 |
| FourFire | <kanzure> FourFire: that's going to be a disaster | 16:18 |
| FourFire | <FourFire> kanzure, tell me about it once I've failed | 16:18 |
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| kanzure | FourFire: because the most productive people you know, are on irc | 16:43 |
| FourFire | hmm | 16:46 |
| FourFire | are you talking about yourself, or perhaps people in other channels? | 16:46 |
| FourFire | I've been on IRC since about mid 2010, and in the lesswrong channel since early 2011, I don't think I've gained much by osmosis in terms of productivity techniques during that time | 16:48 |
| jrayhawk_ | come to think of it, kanzure does occasionally trick me into being productive | 16:48 |
| FourFire | but perhaps I'm overlooking some things | 16:48 |
| kanzure | i would not say the lesswrong people are productive | 16:48 |
| kanzure | perhaps eliezer is sometimes vaguely productive, but he just farts out lots of fanfiction and then gloats about how much money he deserves | 16:48 |
| kanzure | blogwriting is not something you should be aspiring towards | 16:49 |
| kanzure | anyway, cutting yourself off from productive people is no way to become productive, people don't work that way | 16:49 |
| kanzure | bbl (blame andytoshi) | 16:49 |
| jrayhawk_ | thank you, andytoshi. now i am safe from the ravages of productivity. | 16:50 |
| FourFire | EY has been in that channel a grand total of once AFAIK, and I wasn't there | 16:50 |
| jrayhawk_ | that channel is dominated by gwern, who does stuff sometimes | 16:51 |
| jrayhawk_ | i would expect him to at least impart an aesthetic for what productivity looks like | 16:57 |
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| FourFire | yeah | 16:57 |
| FourFire | I sorta aspire to be more like gwern, but | 16:58 |
| FourFire | less writing about drugs and darkmarkets and statitics, and more trying to solve the aging problem | 16:58 |
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| FourFire | well I'll be back | 17:10 |
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| kanzure | yes gwern isn't a good role model | 19:21 |
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| maaku | obvious statement of the year award | 20:02 |
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| superkuh | http://www.sciencedirect.com/ - and all sciencedirect urls seem to be reporting errors. | 21:00 |
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| --- Log closed Mon Jun 22 00:00:48 2015 | ||
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