| --- Log opened Sat Apr 07 00:00:24 2012 | ||
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| diginet | is this guy literally schizophrenic, or just crazy? | 00:35 |
|---|---|---|
| @kanzure | literally schizophrenic | 00:35 |
| @kanzure | i think archels knows him in person? | 00:36 |
| diginet | wow | 00:36 |
| diginet | that's sad, I feel bad for him :( | 00:36 |
| @kanzure | he's a smart fellow. he'll figure something out. | 00:36 |
| diginet | the worst part is that schizophrenia is definitely treatable with medication | 00:36 |
| diginet | it's just, a lot of schizophrenics don't want to take it | 00:36 |
| @kanzure | he's also homeless or something | 00:37 |
| diginet | :( | 00:37 |
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| lichen | ive heard of schizos using nicotine | 00:53 |
| lichen | am i bad for finding schizo rants really amusing? | 00:57 |
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| nmz787 | kanzure: awake? | 01:02 |
| strangewarp | lichen: They show how the human brain works when it loses its reality-checking mechanism. They are definitely morbidly fascinating | 01:04 |
| nmz787 | strangewarp: what is this? | 01:05 |
| lichen | im looking at flamoot's blog | 01:06 |
| lichen | seems like a troubled dude | 01:06 |
| strangewarp | nmz787: what lichen said | 01:15 |
| lichen | this 'transalchemy' channel is odd | 01:20 |
| lichen | and the name does not really make me think of transhumanism | 01:20 |
| lichen | i also cant tell if these videos are for or against transhumanism | 01:20 |
| nmz787 | ahh, yes | 01:23 |
| yashgaroth | I think he's decided that transhumanism is backed by aliens and thus unstoppable, so he's both for and against it | 01:24 |
| lichen | uh. huh... | 01:25 |
| yashgaroth | what am I, a psychologist | 01:25 |
| yashgaroth | he does have remarkable video editing abilities for a hobo | 01:27 |
| lichen | indeed | 01:27 |
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| diginet | isn't transalchemy kind of redundant? | 08:31 |
| diginet | considering alchemy, by definition, is the study of transmutation? | 08:32 |
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| archels | I don't think anyone in this channel will have anything to do with that website. | 08:44 |
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| chris_99 | what have i missed, which website? | 08:47 |
| diginet | some nutcase who think aliens are directing our evolution or something silly like that | 08:47 |
| @kanzure | damn are you guys still talking about that? | 08:48 |
| diginet | I was just pointing out the ridiculous of the name of the channel "transalchemy," but tbh that's the least of the concerns | 08:48 |
| diginet | sorry, I brought it back up | 08:48 |
| * diginet backs away, slowly | 08:48 | |
| delinquentme | so what are practices which allow open source hardware | 08:49 |
| delinquentme | to be built | 08:49 |
| delinquentme | expanded on | 08:49 |
| delinquentme | by others | 08:49 |
| diginet | you know, we should stop calling it "open source hardware" considering something which doesn't entail source code makes no sense to be called as such | 08:49 |
| diginet | sorry, if I was too acerbic, it's just a pet peeve of mine | 08:50 |
| diginet | kanzure, how close are you/whoever else is working on it, to DIY artificial gene synthesis?? | 08:50 |
| delinquentme | Is there a precedent in this area? | 08:50 |
| diginet | didn't mean to put two question marks | 08:50 |
| chris_99 | i'd disagree with you on that one diginet | 08:50 |
| diginet | I think the standard is just open hardware | 08:50 |
| diginet | chris_99, explain | 08:50 |
| chris_99 | have you heard of licences like creative commons? | 08:50 |
| diginet | sure, it's not "open source" though | 08:51 |
| delinquentme | semantics | 08:51 |
| delinquentme | masturbation | 08:51 |
| delinquentme | jerk off elsewhere | 08:51 |
| delinquentme | seriously | 08:51 |
| diginet | well hold on | 08:51 |
| chris_99 | oh you're being picky about the source word | 08:51 |
| diginet | semantics is the study of meaning, isn't that important? | 08:51 |
| diginet | I don't like it when people say "oh don't argue semantics" since semantics is the entire point of language | 08:51 |
| diginet | It's sort of like the misappropriation of the word "science" | 08:53 |
| diginet | science is not phenomenology, it's the employment of the scientific method to obtain reliable, objective information on the natural world | 08:54 |
| delinquentme | diginet, is there nothing more productive youd rather be working on? | 08:54 |
| delinquentme | yes we're human yes we like gab | 08:54 |
| diginet | I'm not trying to be comabtive! I didn't mean it as an affront, sorry if it came across that way | 08:55 |
| delinquentme | if you want to talk about what makes a platform expandable lets talk | 08:55 |
| diginet | I just think its important that names are chosen wisely | 08:55 |
| delinquentme | noted, but its just not constructive ... which is why im raping myself over this | 08:55 |
| @kanzure | hardware is programmed just like software | 08:55 |
| delinquentme | linux is easy you can compile that shit and build out the features in code | 08:55 |
| @kanzure | both has source code | 08:55 |
| delinquentme | hardware the compile is different | 08:56 |
| chris_99 | not necessarily kanzure | 08:56 |
| diginet | if you're talking about something like FPGAs sure | 08:56 |
| diginet | VHDL, Verilog | 08:56 |
| chris_99 | it could just be discrete logic ;) | 08:56 |
| diginet | I'd even count LaTeX as "code" | 08:56 |
| diginet | but schematics are definitely not "code" unless you dilute the terms so much as to be meaningless | 08:56 |
| @kanzure | diginet: artificial gene synthesis has been around for a long time | 08:57 |
| delinquentme | damn klaf no here | 08:57 |
| @kanzure | diginet: autolisp | 08:57 |
| @kanzure | that's code. stop lying to me. | 08:57 |
| diginet | well sure, I'm not saying all hardware doesn't have associated code, but for instance, if someone calls instructions licensed under creative commons or what have you "open source" I think thats kind of a stretch | 08:58 |
| Urchin | TeX is a propper Turing complete programming language | 08:58 |
| @kanzure | creative commons is very often misused for hardware licensing | 08:59 |
| @kanzure | but the reality is that patents cover hardware | 08:59 |
| @kanzure | copyright can be used for the expression of a design, but not the design itself | 08:59 |
| diginet | well, for example, are you familiar with aerogel.org? | 08:59 |
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| diginet | that's a really cool site, but they call it "open source aerogel" or something, when it's really freely available instructions, I really think that's a stretch | 09:00 |
| @kanzure | is it licensed with some OSI-approved license? | 09:01 |
| diginet | There's no "code" to license | 09:01 |
| @kanzure | that's not what i am asking | 09:01 |
| diginet | it's a set of protocols | 09:01 |
| diginet | I think its creative commons | 09:01 |
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| diginet | if it is licensed under and OSI license, then that's a misusage of the purpose of such licenses | 09:02 |
| diginet | *an | 09:02 |
| @kanzure | ok. CC can be vaguely misconstrued as open source. but not "some restrictive license. yeah we're totally open source." | 09:02 |
| @kanzure | diginet: GFDL. | 09:02 |
| delinquentme | KANZ | 09:02 |
| delinquentme | EYE HATE YEW | 09:02 |
| @kanzure | no you don't | 09:02 |
| delinquentme | you doing that in python last night got me thinking about what to program the server in for the syringe | 09:02 |
| delinquentme | its obvs python. | 09:02 |
| @kanzure | delinquentme: http://diyhpl.us/~bryan/irc/ezproxy.py | 09:02 |
| delinquentme | <# | 09:03 |
| delinquentme | <333 | 09:03 |
| diginet | the thing is: what bothers me is the the term open source seems to be in the process of being severly watered down, what worries me is that profiteerers might latch on (as some already have) and exploit the term | 09:03 |
| delinquentme | but yeah rails isnt the software for that piece of hardware | 09:03 |
| delinquentme | django and python dont u think? | 09:03 |
| diginet | a good example would be google, calling Android "open source" is a farce | 09:03 |
| @kanzure | i think the code is distributed with an open source license bro | 09:03 |
| n_bentha | ke ke ke "delinquentme:jerk off elsewhere" | 09:03 |
| @kanzure | you should be more upset at things like openpcr which took 2 years to release any source at all | 09:04 |
| diginet | except they've postponed releasing of code for newer releases indefinitely | 09:04 |
| diginet | (last time I checked) | 09:04 |
| @kanzure | diginet: aosp 4 was released recently | 09:04 |
| diginet | and only parts of it are open sourced | 09:04 |
| delinquentme | n_bentha, Huk HuK! Me GoSU! >_<;;;;;;;;;;;; <( '.' < ) <( '.' )> ( > '.' )> | 09:04 |
| delinquentme | the ones on the ends are too fat | 09:05 |
| delinquentme | damn! | 09:05 |
| n_bentha | lol | 09:05 |
| diginet | anyway, sorry for this tangent, it's just one of my rather eccentric collections of hang-ups | 09:05 |
| diginet | anyhow, kanzure I'm aware that gene synthesis is a fairly old technology, but is it anywhere near the real of being doable on a hobbyist budget? | 09:06 |
| ParahSailin_ | openpcr is being niggardly with the soarces? | 09:06 |
| @kanzure | ParahSailin_: they finally released code/plans but it took them forever | 09:06 |
| @kanzure | diginet: btw what do you count as a hobbyist budget | 09:06 |
| diginet | a good example of flagrant abuse of the world open source would be dd-wrt | 09:06 |
| diginet | *word | 09:07 |
| diginet | kanzure, hmm, good question, maybe a few hundred dollars max? | 09:07 |
| @kanzure | really? come on at least give me a budget of $3k/year | 09:07 |
| diginet | potentially more or lesss, depending on how much one is capable/willing to diy | 09:07 |
| diginet | kanzure, that's why I asked :P | 09:07 |
| @kanzure | diginet: chemicals for dna synthesis are <$1k | 09:07 |
| diginet | ugh | 09:08 |
| diginet | I gather highly proprietary as well? | 09:08 |
| @kanzure | no | 09:08 |
| diginet | oh | 09:08 |
| diginet | any chance of diy synthesis? | 09:08 |
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| n_bentha | hey gais | 09:08 |
| @kanzure | yeah.. that's what the chip is about :P | 09:08 |
| diginet | ahhh right | 09:08 |
| diginet | cool | 09:08 |
| n_bentha | is there a way to kill someone's stero-system through a wall? | 09:08 |
| delinquentme | ParahSailin_, lolol | 09:08 |
| n_bentha | (that i can afford) | 09:08 |
| @kanzure | phosphoramidites, acetonitrile, pyridine, thf, some oxidizer, tca, etc.. | 09:09 |
| ParahSailin_ | openpcr started as a kickstarter? | 09:09 |
| @kanzure | n_bentha: sniper rifle | 09:09 |
| @kanzure | ParahSailin_: yes :/ | 09:09 |
| ParahSailin_ | i think im seeing an obvious problem with kickstarter | 09:09 |
| @kanzure | it's like begging | 09:09 |
| diginet | n_bentha, depends, if it's radio, that's easy, just get a jammer, if not, then you could try and get into the mains and get it to powersurge | 09:09 |
| ParahSailin_ | its really just a way to scam/bleg, yah | 09:09 |
| diginet | kickstarter, while fine in theory, represents a lot of what I can't stand about a lot of things | 09:09 |
| ParahSailin_ | needs to be a way to crowdfund with equity or something | 09:10 |
| diginet | one particularly egregious example was the so-called "manifold clock" | 09:10 |
| ParahSailin_ | thank you sec for making that illegal | 09:10 |
| diginet | it was just crummy timex wall clock fitted with some aluminized film, took about 10 min to make and about $10 in materials | 09:10 |
| @kanzure | here is a list of culprits who supported openpcr | 09:11 |
| diginet | except they have a damn fundraiser for that POS | 09:11 |
| @kanzure | http://diyhpl.us/~bryan/irc/openpcr.txt | 09:11 |
| diginet | kanzure, I'm guessing that you're not too fond of OpenPCR, what did they do? scam people with spurious claims of "openness?" | 09:11 |
| @kanzure | yes.. but they finally repented so i'm apparently not allowed to be angry about it anymore? | 09:12 |
| diginet | haha, well that's no fun! | 09:12 |
| diginet | I've kind of had it with these profiteerers riding the DIY wave | 09:12 |
| diginet | you look at the absurd markup on some of this "open source" stuff | 09:12 |
| diginet | ugh | 09:12 |
| diginet | the worst repeat offenders are the arduino crowd | 09:13 |
| @kanzure | i think people are moving on from the "open source" buzzword.. hopefully into "maker" | 09:13 |
| diginet | nevermind the fact that anyone who can't build something as trivial as the arduino doesn't need to be doing electronics | 09:13 |
| diginet | there's just so much pseudo-intellectualism, and attentions seekers who do stupid things but get attention because ZOMG ARDWEENOZ | 09:14 |
| @kanzure | diginet: another reason i'm not fond is the incredibly high cost | 09:14 |
| diginet | yeah, $30+ for a dev board? what a joke | 09:14 |
| @kanzure | there's really no good reason it should cost >$500 | 09:14 |
| diginet | OpenPCR you mean? | 09:14 |
| diginet | yeah | 09:14 |
| @kanzure | yes.. | 09:14 |
| diginet | if it's that expensive, it defeats the purpose | 09:14 |
| delinquentme | open DJ equipment! http://en.wikipedia.org/wiki/File:Aurora_224_-_2ch_Open_Source_DJ_Mixer_(3).jpg | 09:15 |
| @kanzure | delinquentme: so wait | 09:15 |
| @kanzure | you want to run a syringe pump with django? | 09:15 |
| @kanzure | what | 09:15 |
| delinquentme | kanzure, http://www.thingiverse.com/thing:20733 | 09:15 |
| @kanzure | yep.. this ain't gonna be hard | 09:16 |
| @kanzure | but getting precise amounts might be | 09:16 |
| @kanzure | like runnning at 1 nanoliter/hour | 09:17 |
| diginet | http://forums.hackaday.com/viewtopic.php?f=2&t=2124 if anyone is interested, there's a polemic I wrote on this very subject | 09:18 |
| delinquentme | kanzure, i mean the demographic who would use it | 09:19 |
| delinquentme | they're going to be python | 09:20 |
| @kanzure | ah. | 09:20 |
| @kanzure | delinquentme: i'll finish up the sciencedirect integration today on ezproxy.py | 09:22 |
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| @kanzure | delinquentme: are you able to run the unit tests? | 09:23 |
| n_bentha | thanks diginet, i'll see about getting into the mains | 09:24 |
| delinquentme | ive built in rigged up asserts | 09:25 |
| delinquentme | not any legit testing frameworks .. but i mean the data is bone simple and we just need to ensure those 3 structures are being fed into whatever we're saving | 09:25 |
| @kanzure | yeah but i mean | 09:25 |
| @kanzure | i have unit tests in ezproxy.py and are you able to run them? | 09:25 |
| delinquentme | didnt try | 09:26 |
| delinquentme | but I think i've got unit test | 09:26 |
| ParahSailin_ | http://www.haaretz.com/jewish-world/were-jews-ever-really-slaves-in-egypt-or-is-passover-a-myth-1.420844 heh | 09:26 |
| ParahSailin_ | interesting to see that in israeli media | 09:27 |
| diginet | n_bentha, I feel for you, stuff like that is miserable | 09:27 |
| n_bentha | it's the subwoofers that are killing me | 09:27 |
| diginet | ParahSailin_, yeah, you have to admire their honesty, considering Israeli archaeologists would be more biased towards finding evidence of the exodus than literally any other group | 09:27 |
| diginet | n_bentha, oh, dear, god | 09:27 |
| n_bentha | to hear the trebel, i have to put my head against the wall. i can hear the bass from the far end of my place | 09:28 |
| @kanzure | n_bentha: file a police report? | 09:28 |
| n_bentha | how do i do that? | 09:28 |
| @kanzure | call up the non-emergecy line | 09:28 |
| diginet | noise pollution | 09:28 |
| @kanzure | non-emergency | 09:28 |
| diginet | it's a real thing | 09:28 |
| n_bentha | sweet. will do | 09:29 |
| n_bentha | crap. there's a part-time job opening but the hours are 9am-2pm for a lab-tech. i've got the perfect skills set too... | 09:30 |
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| diginet | so my sister sent me this video: http://youtu.be/0Au_8GMUxVs | 09:39 |
| diginet | the amount of douchebaggery at wherever that is makes me gag a little | 09:39 |
| delinquentme | kanzure, reprap > makerbot? | 09:40 |
| @kanzure | i'd say so. | 09:40 |
| delinquentme | i dont like the cutesy wood crap either | 09:41 |
| ParahSailin_ | is plywood actually a useful material to build out of? | 09:42 |
| delinquentme | Gmail Tap ! http://www.youtube.com/watch?v=1KhZKNZO8mQ | 09:43 |
| delinquentme | ROFL | 09:43 |
| Urchin | http://xkcd.com/1031/ this really does make internet 100 times better | 09:54 |
| delinquentme | ParahSailin_, plywood? USB? | 09:55 |
| ParahSailin_ | what about it? | 09:55 |
| delinquentme | like if you're talking the chipped and reglued layered wood absolutely | 09:56 |
| delinquentme | all the benefits of natural fiber ... none of the weird bowing and crap | 09:56 |
| delinquentme | that stuff = human win | 09:57 |
| ParahSailin_ | are they not using plywood? | 09:57 |
| ParahSailin_ | like actual wood? | 09:57 |
| ParahSailin_ | im not that familiar, i just remember it having vaguely wood-like material | 09:58 |
| delinquentme | ParahSailin_, i dont follow what you're asking | 10:04 |
| delinquentme | are you saying if it can be replace 1:1? | 10:04 |
| delinquentme | not quite | 10:04 |
| ParahSailin_ | "i dont like the cutesy wood crap either" | 10:04 |
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| delinquentme | OHHhh lolol | 10:09 |
| delinquentme | idk what it is | 10:09 |
| delinquentme | its to make it look friendly | 10:09 |
| delinquentme | i want it to look evil | 10:09 |
| delinquentme | >=] | 10:09 |
| delinquentme | kanzure, you guys wern't planning on using the reprap as the XYZ for that laser huh | 10:10 |
| @kanzure | no | 10:10 |
| delinquentme | that'd give me a warm fuzzy feeling | 10:10 |
| delinquentme | because you know something about standing on the shoulders of chipmunks | 10:10 |
| delinquentme | and nuts | 10:10 |
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| delinquentme | kanzure, does it make sense to build everything from scratch? | 10:18 |
| @kanzure | depends on what | 10:24 |
| @kanzure | the rails are definitely buoght | 10:24 |
| @kanzure | bought | 10:24 |
| delinquentme | hehe | 10:24 |
| delinquentme | so like what if you guys designed *just* the laser | 10:25 |
| @kanzure | instead of what? | 10:25 |
| delinquentme | and contacted the reprap guys and talked w them about installing it on that gantry | 10:25 |
| @kanzure | their gantry isn't precise enough | 10:25 |
| @kanzure | fenn would be able to tell you exactly why :| | 10:26 |
| delinquentme | 1/80th of a mm? | 10:26 |
| @kanzure | that's not a micron | 10:29 |
| delinquentme | whats the budget on this gantry? | 10:30 |
| @kanzure | *shrug* | 10:30 |
| delinquentme | the most accurate price / res sensor i've found is $50 | 10:30 |
| @kanzure | well, more than $100 haha | 10:30 |
| @kanzure | probably less than $100k | 10:30 |
| delinquentme | and you see why im skeptical? | 10:31 |
| @kanzure | no | 10:32 |
| delinquentme | i find that hard to believe | 10:32 |
| @kanzure | if you're so skeptical.. why not tell me to buy a DNA synthesizer straight up? | 10:32 |
| delinquentme | isnt that what you're building? | 10:32 |
| @kanzure | yes :) but you're skeptical.. | 10:32 |
| delinquentme | are you 1) making a microfluidics chip prototyper 2) a microfluidics based synthesizer or 3) a synthesizing company | 10:33 |
| delinquentme | if its 3 .. then yes buy a synthesizer | 10:33 |
| @kanzure | #2 requires #1 in our case | 10:33 |
| delinquentme | on a gradation between fact and opinon | 10:35 |
| delinquentme | where does that statement fall | 10:35 |
| @kanzure | well we need to make prototypes | 10:36 |
| @kanzure | so let's assume that on average getting someone else to make a prototype costs $400 | 10:36 |
| @kanzure | let's also say that we will be needing at least 100 prototypes because, let's face it, we're going to make mistakes | 10:36 |
| delinquentme | $250 | 10:36 |
| @kanzure | so 100 * $40 = $40,000 | 10:37 |
| delinquentme | kanzure, that is the part where i seriously doubt | 10:37 |
| delinquentme | you want an excuse to build things | 10:37 |
| delinquentme | thats awesome | 10:37 |
| @kanzure | if the cost of a prototyper is less than $40,000 then i say go for it | 10:37 |
| delinquentme | but | 10:37 |
| delinquentme | if you're a kid building toys say it | 10:37 |
| delinquentme | you're not going to fuck up 100 times unless you're retarded about it | 10:37 |
| delinquentme | in 10 tries youll get it if you're smart about it | 10:37 |
| @kanzure | have you ever built a microfluidics device? | 10:37 |
| delinquentme | in addition its not like the microfluidics lab wont have best practices for this | 10:37 |
| delinquentme | afterall | 10:37 |
| @kanzure | it might take 10 times just to optimize the pressure valves | 10:38 |
| delinquentme | it is what they *do* | 10:38 |
| @kanzure | they don't do design.. they just fab | 10:38 |
| delinquentme | because i have a million dollar machine to make things | 10:38 |
| delinquentme | i only fab on it | 10:38 |
| @kanzure | what million dollar machine? | 10:38 |
| delinquentme | i cannot offer any thoughts on how to build those things | 10:38 |
| delinquentme | im saying if they've got the hardware to build X | 10:38 |
| delinquentme | they might know some things about building X | 10:38 |
| @kanzure | http://www.stanford.edu/group/foundry/ | 10:39 |
| @kanzure | "Fabrication of Pre-designed Microfluidic Chips" | 10:39 |
| @kanzure | "Consulting on Microfluidic Design Using the Design Rules Outlined by the Stanford Microfluidics Foundry" | 10:39 |
| @kanzure | consulting = $$$ | 10:39 |
| delinquentme | so lets assume its too expensive | 10:39 |
| archels | "pre-designed" as opposed to "randomly wired"? | 10:39 |
| delinquentme | safe assumption. | 10:39 |
| @kanzure | archels: no it means "here are some files to choose from" | 10:39 |
| @kanzure | archels: http://www.stanford.edu/group/foundry/pre-design%20chips.html | 10:39 |
| archels | oh, neat | 10:40 |
| delinquentme | kanzure, im gonna write them an email | 10:40 |
| delinquentme | could you give me a write up of what technical issues you expect to come across | 10:41 |
| delinquentme | id guess you already have it | 10:41 |
| @kanzure | there are so many bugs. it's hard to think of something that wouldn't be buggy. | 10:41 |
| @kanzure | channels collapsing, valves malfunctioning, valves not closing completely, valves not opening completely, non-smooth channels | 10:42 |
| @kanzure | unexpected fluid physics | 10:42 |
| @kanzure | corrosive chemical effects | 10:42 |
| @kanzure | unexpected droplet merging, stable/reliable droplet generation, droplet pumping, droplet popping, contamination, ... | 10:43 |
| delinquentme | well channel smoothness is solved in hardware | 10:43 |
| delinquentme | OH and about that video you've got on youtube at the t junction | 10:43 |
| delinquentme | the scale of those physics aren't nano | 10:43 |
| delinquentme | the fluids are waay less dynamic at small levels | 10:43 |
| @kanzure | haha "Crossovers of control lines and flow lines can be created without resulting in a valve at each crossover point. To achieve this, the control line should be designed narrower (15-30um) at these crossover points to ensure no membrane valve is formed." | 10:44 |
| @kanzure | yes i am familiar with laminar flow | 10:44 |
| delinquentme | ? | 10:44 |
| delinquentme | what | 10:44 |
| @kanzure | laminar flow is how you model/describe water at this scale | 10:44 |
| delinquentme | your response would indicate otherwise as laminar flow is not at all what im talking about here :D | 10:45 |
| @kanzure | http://faculty.washington.edu/yagerp/microfluidicstutorial/basicconcepts/basicconcepts.htm | 10:45 |
| @kanzure | "Due to the small dimensions of microchannels, the Re is usually much less than 100, often less than 1.0. In this Reynolds number regime, flow is completely laminar and no turbulence occurs. The transition to turbulent flow generally occurs in the range of Reynolds number 2000." | 10:45 |
| @kanzure | " Laminar flow provides a means by which molecules can be transported in a relatively predictable manner through microchannels. Note, however, that even at Reynolds numbers below 100, it is possible to have momentum-based phenomena such as as flow separation." | 10:45 |
| @kanzure | also for fenn: "One of the basic laws of fluid mechanics for pressure driven laminar flow, the so-called no-slip boundary condition, states that the fluid velocity at the walls must be zero. This produces a parabolic velocity profile within the channel (Figure 1.1)" | 10:46 |
| @kanzure | huh what is this site | 10:46 |
| delinquentme | kanzure, | 10:48 |
| delinquentme | can the synthesizer be made at macro scale cheaper? | 10:48 |
| delinquentme | ( i know fewer awesome gadgets ) | 10:48 |
| @kanzure | i'm not sure that would be useful | 10:48 |
| delinquentme | no? | 10:49 |
| delinquentme | how so? | 10:49 |
| @kanzure | let's say that the current 1980s ABI synthesizer tech can be done for <$10k | 10:49 |
| @kanzure | http://www.pegasusscientific.com/Pics/67843.jpg | 10:49 |
| @kanzure | ^ that thing | 10:49 |
| @kanzure | there are a number of disadvantages of this machine | 10:50 |
| delinquentme | kanzure, | 10:50 |
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| @kanzure | for starters: cost, form factor, reagent volume usage, max oligo length | 10:50 |
| delinquentme | would it be wise to outsource this to some company | 10:50 |
| delinquentme | http://www.precisionmicro.com/23/microfluidic-components/components-&-features/component-applications- | 10:51 |
| delinquentme | hot right? | 10:51 |
| delinquentme | fap fap? | 10:51 |
| @kanzure | i don't think it would be cheaper but it's okay to ask them | 10:51 |
| delinquentme | you might not own 100% of it | 10:51 |
| @kanzure | that's not okay. | 10:51 |
| delinquentme | but 1) you'd have a HUGE instrustry connect | 10:51 |
| @kanzure | i am fairly certain that nobody would be okay with this being open source, except me | 10:51 |
| delinquentme | why not? | 10:51 |
| @kanzure | *shrug* hopefully i am wrong and everyone wants this open source | 10:52 |
| delinquentme | well .... | 10:52 |
| delinquentme | assuming you're not a 1 trick pony | 10:52 |
| delinquentme | ( which i dont think you are ) | 10:52 |
| delinquentme | why not build something | 10:52 |
| delinquentme | make money | 10:52 |
| @kanzure | i am already making money | 10:52 |
| delinquentme | and build the next thing | 10:52 |
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| delinquentme | eh | 10:52 |
| delinquentme | i mean like | 10:52 |
| delinquentme | profitable | 10:52 |
| @kanzure | i am already profitable | 10:52 |
| delinquentme | so we've got a SV workshop | 10:52 |
| @kanzure | no i'm just cheap | 10:52 |
| delinquentme | interesting defense | 10:53 |
| delinquentme | kk | 10:53 |
| @kanzure | haha | 10:53 |
| @kanzure | well.. prove i'm not cheap :P | 10:53 |
| @kanzure | a cheapster. | 10:53 |
| @kanzure | but yeah i agree with you there's lots of money in this | 10:53 |
| @kanzure | it's worth contacting all these people and seeing what they can offer us | 10:54 |
| @kanzure | but i think we can win even if they offer nothing :) | 10:54 |
| delinquentme | true | 10:54 |
| @kanzure | delinquentme: btw.. would you CC me on those emails? | 10:54 |
| delinquentme | like dont get me wrong | 10:54 |
| delinquentme | we're here headstrong and intelligent if nothing else | 10:55 |
| delinquentme | totes! | 10:55 |
| delinquentme | but like speed is lovely is it not? | 10:55 |
| @kanzure | delinquentme: also.. it would be super super useful if you could help me find someone who i can bug about microfluidics problems, someone who has done droplet work and knows things like "max drop load". i haven't found this person yet. | 10:55 |
| @kanzure | ParahSailin_: you're close buuut you had like one gate :) | 10:55 |
| @kanzure | s/gate/valve | 10:56 |
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| @kanzure | yo AlonzoTG | 10:58 |
| delinquentme | http://www.precisionmicro.com/uploads/microfluidic2.jpg | 10:58 |
| @kanzure | delinquentme: maybe we should do a macro synthesizer | 10:58 |
| @kanzure | PoSaM was weird | 10:59 |
| @kanzure | http://www.bioinformatics.org/pogo/ | 10:59 |
| AlonzoTG | wut? | 10:59 |
| @kanzure | "The Piezoelectric Oligonucleotide Synthesizer And Microarrayer (POSAM) was developed in the Hood Laboratory to give researchers access to customizeable DNA microarrays. The result is an "open source" platform. The hardware design and protocols are being made available freely to the public and the control software is released under the GPL license." | 10:59 |
| * AlonzoTG has been playing WAAAAAY too much minecraft. | 10:59 | |
| @kanzure | oh wow i never realized they wrote their software in visual basic | 11:00 |
| @kanzure | http://bioinformatics.org/cgi-bin/cvsweb.cgi/pogo/pogo-vb/ReagentsForm.frm?rev=1.17&content-type=text/x-cvsweb-markup | 11:00 |
| @kanzure | visual basic + cvs. alright, technology! *cough* | 11:00 |
| roksprok_ | are limitations on synthesized oligonucleotide length holding back molecular biology/genetic engineering/synthetic biology? | 11:01 |
| @kanzure | http://bioinformatics.org/cgi-bin/cvsweb.cgi/pogo/pogo-vb/PogoMain.bas?rev=1.48&content-type=text/x-cvsweb-markup | 11:01 |
| @kanzure | roksprok_: YES | 11:02 |
| delinquentme | kanzure, if we've proven the chemistry and have the protocols its one more thing we can approach people with and say we;ve got this | 11:02 |
| @kanzure | roksprok_: it's also an issue of cost... >$1000 per gene | 11:02 |
| delinquentme | you do XYZ | 11:02 |
| delinquentme | profit | 11:02 |
| roksprok_ | kanzure: i am just wondering why there isn't a 'race' for synthesis like there is for sequencing | 11:02 |
| @kanzure | roksprok_: because people think synthesis companies are an OK compromise | 11:02 |
| @kanzure | actually i don't know the real answer to your question | 11:03 |
| roksprok_ | kanzure: wouldn't that indicate that they don't feel held back by it? | 11:03 |
| @kanzure | biologists are really crazy | 11:03 |
| roksprok_ | agreed, too bad biology is so interesting | 11:04 |
| @kanzure | "oh we can't synthesize this gene because it's too expensive, so let's just synthesize some primers, go to the amazon and catch a specimen, then PCR the gene out of the genome, otherwise it would cost too much to synthesize" | 11:04 |
| @kanzure | a lot of biology lab techniques are sorta because you can't just synthesize what you want | 11:05 |
| roksprok_ | maybe they just like trips to the amazon... | 11:05 |
| @kanzure | who doesn't? | 11:05 |
| @kanzure | the other weird thing is that people have said that synthesis prices are dropping | 11:05 |
| roksprok_ | that was kind of what i was looking for...just confirmation that I wasn't being completly noobish | 11:06 |
| @kanzure | but if you look at rob carlson's graphs the synthesis prices have only moved a partial order of magnitude over the past 10 years | 11:06 |
| @kanzure | http://www.synthesis.cc/assets_c/2011/06/carlson_cost%20per_base_june_2011.html | 11:06 |
| @kanzure | btw this graph is mostly "cost of ordering it from a company" | 11:06 |
| @kanzure | the per base pair costs when you own your own machine go down.. and they go down even more when you are smart about how you synthesize | 11:07 |
| roksprok_ | is it common for a bio lab to own their own machine? | 11:07 |
| @kanzure | no | 11:07 |
| @kanzure | not any more | 11:08 |
| @kanzure | now they just do mail order synthesis | 11:08 |
| @kanzure | there's usually a shared sequencing facility on a college campus but it's not uncommon to just send the dna out to some company to be sequenced | 11:08 |
| @kanzure | who wants to pay $100k+ for a synthesizer from the 80s? | 11:09 |
| roksprok_ | i guess you'd have to be really sure you'll do a lot of synthesizing | 11:09 |
| @kanzure | OligoMaker looks like a somewhat more 'modern' device in the $60k-$90k range with >90 simultaneous oligo reactions | 11:09 |
| delinquentme | brb | 11:10 |
| @kanzure | the other issue is that these machines normally do 30-200 bp and not longer because of the error rate in the chemistry | 11:11 |
| roksprok_ | what terms should i search to find more how the fragments are stiched together? | 11:12 |
| roksprok_ | is there a standard term for it? | 11:12 |
| @kanzure | http://diyhpl.us/~bryan/papers2/DNA/synthesis.html | 11:13 |
| @kanzure | there are many methods worth knowing about.. chemical oligo synthesis, ligation chemistry, extension pcr... | 11:13 |
| roksprok_ | cool....will do some reading...thanks | 11:15 |
| @kanzure | roksprok_: one of the main drivers of sequencing cost drops was the human genome project | 11:33 |
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| ParahSailin_ | close but one gate? | 11:48 |
| @kanzure | sorry i meant valve | 11:49 |
| @kanzure | anyway i was just being hard on you :) | 11:49 |
| @kanzure | ParahSailin_: any thoughts about why synthesis costs aren't falling faster | 11:49 |
| @kanzure | to me they seem stagnant.. i know the graph shows they have changed an order of magnitude over the past 8 years but.. that's nothing. | 11:49 |
| ParahSailin_ | was afk, reading scrollback | 11:49 |
| ParahSailin_ | why synthesis costs not falling, i guess its hard to develop a new technology other than solid support protect deprotect synthesis | 11:50 |
| @kanzure | i don't think so. | 11:51 |
| @kanzure | but on the other hand: have people tried? | 11:51 |
| ParahSailin_ | i think they are being quiet about it | 11:51 |
| ParahSailin_ | heres what i think | 11:52 |
| ParahSailin_ | most of the market in bio research is nih grants | 11:52 |
| ParahSailin_ | so synthesis companies can charge whatever | 11:52 |
| ParahSailin_ | and vwr, fisher, invitrogen, etc | 11:53 |
| @kanzure | if PCR didn't exist i bet synthesis costs would be dropping faster | 11:53 |
| @kanzure | ParahSailin_: ok then why have they dropped at all | 11:55 |
| ParahSailin_ | theres still some competitive pressure, but limited | 11:56 |
| @kanzure | sequencing cost drop wasn't initially due to competition was it? | 11:56 |
| ParahSailin_ | probably? | 11:56 |
| @kanzure | " The publicly funded competitor UC Santa Cruz was compelled to publish the first draft of the human genome before Celera for this reason. On July 7, 2000, the UCSC Genome Bioinformatics Group released a first working draft on the web." | 11:56 |
| @kanzure | oh. damn. | 11:56 |
| @kanzure | hahah "n March 2000, President Clinton announced that the genome sequence could not be patented, and should be made freely available to all researchers. The statement sent Celera's stock plummeting and dragged down the biotechnology-heavy Nasdaq." | 11:57 |
| @kanzure | "The biotechnology sector lost about $50 billion in market capitalization in two days." | 11:57 |
| @kanzure | bahaha "But the public release of the data ensured its fair use and availability to all mankind[citation needed]" | 11:57 |
| @kanzure | oh geeze celera doesn't dump its data into genbank?? | 11:59 |
| @kanzure | "A once-deafening debate over access to human genome sequence data ended quietly last week when Celera Genomics Corp. announced that it is closing its subscription-based database service and will release its genomic data on humans, rats, and mice to the public." (2005) | 12:04 |
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| delinquentme | kanzure, whats this? | 12:11 |
| delinquentme | subscription based database services? | 12:11 |
| @kanzure | when celera sequened the human genome they put it behind a paywall | 12:12 |
| @kanzure | *sequenced | 12:12 |
| * katsmeow-afk erases the Liberace image of the genome | 12:13 | |
| delinquentme | biofuelz : http://www.technologyreview.com/energy/40073/?p1=A1 | 12:17 |
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| delinquentme | kanzure, to say these chips will synthesize DNA is not incorrect | 12:36 |
| delinquentme | correct? | 12:36 |
| @kanzure | whaat | 12:36 |
| @kanzure | the first version will be performing phosphoramidite chemistry to create oligonucleotides | 12:37 |
| delinquentme | single stranded DNA | 12:37 |
| @kanzure | yes | 12:38 |
| delinquentme | i think we should locate engineers | 12:43 |
| delinquentme | tbh | 12:43 |
| delinquentme | contacting a whole company ... might be less receptive | 12:44 |
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| ParahSailin_ | micro scale oligo synthesis could actually be pretty nice | 12:50 |
| @kanzure | yep.. | 12:50 |
| ParahSailin_ | it is ignored by idt because it does not fit their biz model | 12:50 |
| delinquentme | idt? | 12:51 |
| @kanzure | you shouldn't have to worry about plasmids.. just print it out | 12:51 |
| @kanzure | idt is a mail order synthesis company | 12:51 |
| ParahSailin_ | but my 25 nmol or whatever vials last way too long | 12:51 |
| delinquentme | ic ic | 12:51 |
| ParahSailin_ | normally i only use a primer ideally once | 12:51 |
| ParahSailin_ | or about 5 times because dna is evil | 12:51 |
| @kanzure | right.. but you're probably using a primer to rip out a gene from a genome because you can't afford to synthesize that gene | 12:51 |
| @kanzure | well i guess i don't know what you're doing with your primers. maybe you don't have the gene sequenced anyway. | 12:52 |
| @kanzure | i bet we could get to the point where it would be cheaper to randomly synthesize strands and do hybridization.. rather than direct sequencing :P | 12:53 |
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| ParahSailin_ | dunno about that, but micro scale oligo synthesis is a very good first step towards kilobase synthesis | 12:53 |
| ParahSailin_ | because its useful in and of itself to people in the lab | 12:54 |
| ParahSailin_ | i would not optimize reaction conditions ever if i could get a picomole of oligo out in less than an hour | 12:54 |
| ParahSailin_ | i would just try again with new one | 12:55 |
| kanzure | ParahSailin_: how much have you guys spent at idt on average? | 12:57 |
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| kanzure | like average order size and number of regular orders | 12:57 |
| kanzure | mostly primers? | 12:57 |
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| ParahSailin_ | i've spent a couple hundred dollars on all the primers i've ordered in the last year or two | 12:58 |
| ParahSailin_ | only have ordered primers from them | 12:58 |
| kanzure | how much would you have ordered if it was $0.0001/bp? | 12:58 |
| kanzure | wait let's make it easier.. $1/kbp and $1/mbp | 12:59 |
| kanzure | Mbp.. units. | 12:59 |
| ParahSailin_ | our lab would have paid quite a bit to have oligos on demand | 13:00 |
| delinquentme | ^^ | 13:05 |
| delinquentme | thats the thing | 13:05 |
| delinquentme | cost = indicator of product affluence | 13:06 |
| delinquentme | http://www.newscientist.com/article/dn17688-chromosome-transplant-to-sidestep-genetic-disease.html | 13:13 |
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| delinquentme | katsmeow-afk, can I rig up a nut with this magic back lash eliminating spring? | 13:13 |
| ParahSailin_ | what do you mean product affluence | 13:14 |
| delinquentme | ParahSailin_, product A is objectively better than product B because ( cost of A > cost of B ) | 13:14 |
| delinquentme | in a consumers mind | 13:14 |
| ParahSailin_ | im not sure if thats a major driver but im sure its a part | 13:15 |
| ParahSailin_ | when a pi writes a grant proposal, the cost of the shit he actually needs is highly "elastic" (not sure if thats right economics term) | 13:16 |
| kanzure | ParahSailin_: any reason you guys don't have a $200k dna synth? | 13:16 |
| kanzure | highly "made up" :) | 13:16 |
| kanzure | usually it's an ok approximation | 13:16 |
| ParahSailin_ | whether it costs 1k or 10k to do the experiment, the nih will pay it if they deem the proposal worthy | 13:17 |
| kanzure | "oops i misestimated the project is actually $20 mil" doesn't happen | 13:17 |
| ParahSailin_ | the pi doesnt care about saving money, because he quotes his salary separately in that proposal | 13:17 |
| ParahSailin_ | his salary has no relation to the science expenses | 13:17 |
| ParahSailin_ | the only time a pi will start behaving frugally is if he is down on his luck and no governments are throwing money at him | 13:19 |
| ParahSailin_ | and those would a fortieri be the less cunning and resourceful ones | 13:20 |
| delinquentme | kanzure, what do you know about high pressue in these chips | 13:23 |
| delinquentme | sounds cool ... apparently there are experiments that can be run which have no bench top corrolary | 13:24 |
| ParahSailin_ | like what | 13:24 |
| delinquentme | thats just what the quake lab says | 13:24 |
| ParahSailin_ | thats the loc buzzphrase yeah | 13:25 |
| kanzure | delinquentme: http://diyhpl.us/~bryan/papers2/microfluidics/Pressure%20drops%20for%20droplet%20flows%20in%20microfluidic%20channels.pdf | 13:26 |
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| kanzure | neat... "the receding front of the drops suggests that the drops do not make direct contact with the walls, but instead, a thin wetting layer of oil remains in contat with the walls at all times, as also reported by others [16-18]." | 13:27 |
| kanzure | *contact | 13:27 |
| ParahSailin_ | yah we call that "plug flow" | 13:29 |
| ParahSailin_ | reynolds number and stuff | 13:29 |
| diginet | well I'm in somewhat of a predicament, because the way I see it, I have four options: 1)Find a black widow specimen, 2)get the DNA from someone, 3)pay to have the DNA synthesized, 4)wait for DIY synthesis. 1 is probably the most likely, but also rather horrifying. 4 is preferable, but I might have to wait awhile | 13:31 |
| ParahSailin_ | what is n claviceps common name | 13:32 |
| kanzure | #2 is pretty easy. just start calling around. | 13:32 |
| yashgaroth | have you decided whether to get the genomic sequence, or reverse transcribe the RNA? | 13:33 |
| diginet | ParahSailin_, I'm switching to L. hesperus (Black Widow) because the gene is already fully sequenced | 13:33 |
| ParahSailin_ | dont worry about fully sequenced | 13:34 |
| diginet | yashgaroth, see above, I'm going with the L. hesperus gene, it actually performs better than N. Clavipes anyway | 13:34 |
| ParahSailin_ | n claviceps gene have ends sequenced? | 13:34 |
| diginet | no, that's the problem, the C terminal hasn't been sequenced, otherwise it wouldnt matter | 13:34 |
| kanzure | delinquentme: also http://diyhpl.us/~bryan/papers2/microfluidics/The%20pressure%20drop%20along%20rectangular%20microchannels%20containing%20bubbles.pdf | 13:34 |
| ParahSailin_ | ah c terminal | 13:35 |
| ParahSailin_ | thats actually not a problem at all | 13:35 |
| diginet | kanzure, well, I found the woman who did the sequencing of the L. hesperus gene. It was post-doc research, and she's since moved to another university, so I doubt she still has samples | 13:35 |
| diginet | ParahSailin_, oh? | 13:35 |
| ParahSailin_ | get you a specimen and it should be easy to get that entire orf out of it | 13:35 |
| diginet | one perk of the L. hesperus gene is that there are no introns | 13:36 |
| yashgaroth | oh good | 13:36 |
| diginet | ParahSailin_, how so? | 13:36 |
| diginet | I know how to get specimen | 13:36 |
| diginet | (there are people who sell them online) | 13:36 |
| yashgaroth | lyse cells, run pcr | 13:36 |
| ParahSailin_ | you can get n claviceps specimen? | 13:36 |
| diginet | yep | 13:36 |
| diginet | but the black widow silk has better physical properties anyhow | 13:36 |
| ParahSailin_ | extract rna, use poly-t- primer with a known sequence tail for reverse transcriptase, then amplify duplex | 13:37 |
| diginet | is reverse transcriptase DIYable? | 13:37 |
| ParahSailin_ | hesperus is widow? | 13:37 |
| diginet | yes | 13:37 |
| ParahSailin_ | as diy as pcr | 13:37 |
| ParahSailin_ | shit is all just mixing enzymes in a tube and putting at temperature | 13:38 |
| diginet | yes | 13:38 |
| yashgaroth | if it doesn't have introns you don't need to bother with RT then | 13:38 |
| ParahSailin_ | id get the widow so you dont need rt | 13:38 |
| ParahSailin_ | yah | 13:38 |
| diginet | the problem is | 13:38 |
| diginet | black widows are scary :( | 13:38 |
| yashgaroth | so find a dead one | 13:38 |
| diginet | how long does DNA keep? maybe I could get a recently deceased specimen | 13:38 |
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| diginet | I bet I could go on a forum for people who keep spiders as pets (weirdos) and ask for a dead black widow | 13:39 |
| yashgaroth | it keeps well if you get them frozen, or mash them up and add some EDTA | 13:40 |
| diginet | will frozen as in, in a freezer work? or does it need like LN2 freezing? | 13:40 |
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| yashgaroth | nah just your kitchen freezer | 13:40 |
| diginet | hmm, that seems doable | 13:40 |
| diginet | so just ask for a sample of a dead black widow, frozen | 13:41 |
| diginet | they could ship it with dry ice | 13:41 |
| kanzure | you could pay them $20 or something for it | 13:41 |
| diginet | yeah | 13:41 |
| diginet | this is so weird, that this might actually come to fruition :P | 13:41 |
| yashgaroth | ehhh you'll be fine at room temp for shipping | 13:41 |
| diginet | but won't it melt? | 13:41 |
| diginet | or are you saying I need to freeze it? | 13:42 |
| diginet | (once it arrives presumabely) | 13:42 |
| yashgaroth | no I mean freezing for long term storage | 13:42 |
| diginet | ahh right | 13:42 |
| yashgaroth | depends how it died...if it got squished it'll probably get digested pretty quick | 13:42 |
| ParahSailin_ | kanzure, if you make that pdms laser id like to make a flow cyte | 13:43 |
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| diginet | yeah, I'd want one in otherwise good condition (apart from, you know, being dead) | 13:43 |
| yashgaroth | dna is stable enough to have a continuous record back to the last universal common ancestor, with the right conditions | 13:43 |
| ParahSailin_ | put an ad on zaarly for a black widow | 13:43 |
| diginet | zaarly? | 13:44 |
| diginet | nevermind | 13:45 |
| diginet | (googled it) | 13:45 |
| diginet | well, if I can get a specimen, I can definitely do it | 13:45 |
| diginet | one thing I am still wondering though, is whether sf21 cells are the ideal expression system: I mean, it seems the limiting factor would be the proprietary (and thus expensive) growth serum | 13:46 |
| kanzure | you could experiment with that.. | 13:47 |
| diginet | oh, also, what's the longest sequence you can do PCR for? | 13:48 |
| ParahSailin_ | i never explain things because i always assume the other person will google a new word when they see it | 13:48 |
| diginet | good point | 13:48 |
| ParahSailin_ | 10k is no prob with kapa hifi | 13:48 |
| diginet | because the genes are 9k and 11k respectively | 13:50 |
| ParahSailin_ | kapa will do it | 13:50 |
| ParahSailin_ | itll be like 3 minute extension, but it will do it | 13:51 |
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| ParahSailin_ | sf21s will probably grow in grace medium | 13:51 |
| diginet | excellent | 13:51 |
| diginet | well, hmm | 13:51 |
| diginet | I think it will, is grace medium expensive? | 13:52 |
| diginet | (as in, I seem to remember reading that somewhere) | 13:52 |
| ParahSailin_ | it is not proprietary | 13:52 |
| ParahSailin_ | but a bottle of media will last you a long time if you buy it | 13:53 |
| ParahSailin_ | unless you are trying to make assloads of silk, then youll need to figure out a cheaper feedstock | 13:53 |
| diginet | yeah | 13:53 |
| ParahSailin_ | pilot phase, just get expensive stuff that is known to work | 13:53 |
| diginet | yeah, that's what I think | 13:54 |
| diginet | do you know anything about high 5 cells? | 13:54 |
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| Urchin | 13:55 | |
| delinquentme | http://www.xi3.com/ | 13:55 |
| ParahSailin_ | fancy proprietary cell line i think | 13:55 |
| diginet | yeah | 13:56 |
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| ybit | diginet: if you really want a dead insect, my friend here has pet hissing cockroaches | 14:26 |
| delinquentme | lololol | 14:26 |
| delinquentme | oiy | 14:26 |
| ybit | hi | 14:26 |
| delinquentme | howy ! | 14:27 |
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| diginet | what is the largest protein P. pastoris could generally express? | 14:50 |
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| ParahSailin | http://www.economist.com/node/21552202 heh | 14:52 |
| ParahSailin | i have pichia and a vector for it | 14:52 |
| diginet | I'm wondering if pichia might be easier to deal with | 14:53 |
| diginet | I don't think the silk proteins require any sort of complex PTM | 14:53 |
| ParahSailin | i dont think it will work | 14:53 |
| diginet | oh? is pichia not so great for stuff like this? | 14:53 |
| ParahSailin | its good for normal small proteins, it might even work with this | 14:54 |
| diginet | 320 kDa? | 14:54 |
| ParahSailin | couldnt say | 14:55 |
| ParahSailin | most shit, nobody knows if it will work | 14:55 |
| diginet | well, I found an article that might have the answer | 14:55 |
| diginet | brb | 14:55 |
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| delinquentme | kanzure, did you want to release this to HN? | 15:09 |
| delinquentme | like i have 2 takes on it | 15:09 |
| delinquentme | 1) release it if we're not going to do something with it | 15:09 |
| delinquentme | 2) keep it to ourselves if we do plan on doing something with it | 15:09 |
| kanzure | yes i do want to release it but not right now | 15:09 |
| kanzure | let's get to the point of having three or four scrapers working | 15:10 |
| diginet | well according to this paper, Pichia expresses proteins as large as 4000 amino acids, which is a little bit larger than mine, so maybe it will work? | 15:10 |
| kanzure | also why aren't i using mongo? | 15:10 |
| kanzure | what was the reason behind not using mongodb? | 15:10 |
| delinquentme | i thought you said sqlite was integrated | 15:10 |
| delinquentme | yo kanzure | 15:12 |
| delinquentme | what if we monitized the peer review | 15:13 |
| delinquentme | you get paid a flat fee or according to your research klout score or something | 15:13 |
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| delinquentme | yoo this is awesome! http://www.who.int/hinari/eligibility/en/ | 15:23 |
| delinquentme | poor countries get free access | 15:23 |
| delinquentme | beautiful | 15:23 |
| ThomasEgi | kanzure, was it you who liked that micro-fluid chip that moved around bubbles so easily? | 15:29 |
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| kanzure | ThomasEgi: probably? | 15:42 |
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| diginet | I'm looking for a paper: "Microbial Production of Spider Silk Proteins" by Fahnestock, I have access to ScienceDirect, but I can't get that one, anyone here have more extensive access? | 16:09 |
| delinquentme | diginet, #biology or kanzure might | 16:09 |
| diginet | ah okay, thanks | 16:10 |
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| ParahSailin | http://www.nature.com/news/african-agriculture-dirt-poor-1.10311 is permaculture the answer? | 16:15 |
| ParahSailin | /r/scholar? | 16:15 |
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| delinquentme | holy shitbags | 16:52 |
| delinquentme | 1 publisher | 16:52 |
| delinquentme | 200 journals | 16:52 |
| delinquentme | for their "A" section | 16:52 |
| kanzure | d | 16:52 |
| kanzure | maybe i will be moving to sf after all | 16:52 |
| kanzure | http://www.padmapper.com/show.php?type=0&id=107922802&src=main | 16:52 |
| delinquentme | ^^^^^^^^^^^^^ | 16:52 |
| delinquentme | DEWWW IT | 16:52 |
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| kanzure | nmz787: http://www.padmapper.com/show.php?type=0&id=107922802&src=main | 16:56 |
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| nmz787 | what do you think about optical bench w/ vibe dampenin? | 16:57 |
| kanzure | if we design it right we shouldn't need vibrations | 16:57 |
| nmz787 | hah hah, ok, lets hope | 16:59 |
| kanzure | jbei get back with you yet? | 17:02 |
| ThomasEgi | kanzure, bout that microfluids chip. someone asked how they moved around bubbles. my guess would be , charging the fluids, have the chip surfcase oxidized and move the charged liquid by applying applying voltage under each tile and let electrostatic forces do the trick | 17:04 |
| nmz787 | ThomasEgi: bubbles, or droplets? | 17:11 |
| kanzure | ThomasEgi: that's called EWOD | 17:11 |
| ThomasEgi | droples. sry for messing up | 17:11 |
| delinquentme | quake's lab has something about PDMS dissapates air bubbles? | 17:11 |
| kanzure | http://diyhpl.us/~bryan/papers2/microfluidics/Electrowetting-based%20actuation%20of%20liquid%20droplets%20for%20microfluidic%20applications.pdf | 17:11 |
| delinquentme | gas-permiable .. not fluid though? | 17:11 |
| kanzure | ThomasEgi: the way we're thinking of using is just pumping | 17:11 |
| ThomasEgi | hm.. should work for pumping too right? | 17:12 |
| kanzure | i don't see why you would do charged fluid actuation | 17:13 |
| kanzure | if you are also pumping | 17:13 |
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| kanzure | "It's even worse in university libraries, where you can actually follow up all the references by grabbing them off the shelf. The number of books piled up around you with post-it notes marking pages is roughly like the number-of-tabs metric.." | 17:39 |
| nmz787 | i have too many tabs open, all the time... | 17:40 |
| kanzure | i never have enough tabs | 17:43 |
| ThomasEgi | tabgrouping ftw | 17:44 |
| kanzure | tab grouping doesn't work because it hides my tabs and firefox/chrome still can't handle >500 | 17:45 |
| ThomasEgi | 500 seems like a lot | 17:46 |
| ThomasEgi | maybe.. you should try something else^ | 17:46 |
| kanzure | yes especially when barely 200 works | 17:46 |
| nmz787 | bookmarking doesn't work for me either | 17:46 |
| nmz787 | i never visit bookmarks | 17:46 |
| kanzure | i just remember urls. | 17:47 |
| nmz787 | but i do visit open tabs, if they're open and my mind makes it back to the point where i mentally forked | 17:47 |
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| kanzure | http://trance.fm/ isn't too bad for coding music | 18:59 |
| Mariu | thanks kanzure | 19:02 |
| n_bentha | i like soma radio's secret agent mix | 19:03 |
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| delinquentme | kanzure, lets write a book on quantum biology with zero to no knwledge of it | 19:11 |
| delinquentme | well little | 19:11 |
| delinquentme | just to say it can be done | 19:11 |
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| delinquentme | BY YOUR POWERS COMBINED I AM CAPTAIN PLANET! | 19:11 |
| n_bentha | :) | 19:12 |
| delinquentme | I think im gonna do a little scraping project and profile the number of r/suicidewatch posts which have the word "college" in them | 19:13 |
| delinquentme | think it might make a stir? | 19:13 |
| Mariu | yup | 19:13 |
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| delinquentme | any of you guys have a good way to post up a completely anon website? | 19:18 |
| AdrianG | u mean like, 4chan? | 19:18 |
| delinquentme | well 4chan is 4 chan | 19:18 |
| delinquentme | i mean I want something that I can post up an infographic | 19:19 |
| n_bentha | LOL 4chan | 19:19 |
| n_bentha | what's r/suicidewatch | 19:19 |
| n_bentha | do ppl actually talk in there? | 19:19 |
| delinquentme | n_bentha, they do! | 19:20 |
| thylne | http://www.reddit.com/r/suicidewatch | 19:20 |
| delinquentme | infact i've helped out a number of times | 19:20 |
| delinquentme | all people need is a little positive focus | 19:20 |
| delinquentme | and novelty :D | 19:20 |
| * n_bentha goes to listen ^_^ | 19:21 | |
| thylne | That is where the an heros post | 19:23 |
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| * n_bentha lmao @ an heros | 19:25 | |
| kanzure | i wish you guys would stop using reddit | 19:25 |
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| delinquentme | does hacker news not allow reddit links to be upvoted? | 19:30 |
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| delinquentme | kanzure, what the fuck? | 19:40 |
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| kanzure | reddit has slowly been invading this channel :( | 19:40 |
| delinquentme | ... | 19:43 |
| yashgaroth | you've gotta admit reddit is pretty shit these days | 19:49 |
| sylph_mako | kanzure, someone sold you out to us =J | 19:49 |
| sylph_mako | also yes it is. | 19:49 |
| kanzure | ? | 19:49 |
| sylph_mako | Someone told reddit about the channel. | 19:50 |
| kanzure | is that why? damn. | 19:50 |
| sylph_mako | For some reason I'd always assumed you would have known =[ | 19:50 |
| kanzure | i try to ignore that site heh | 19:50 |
| sylph_mako | Like you don't just go and tell reddit about something without making sure everyone's cool with it. | 19:51 |
| sylph_mako | We need a new hivemind system that learns from reddit and steps shit up. | 19:51 |
| kanzure | hivewhatnow? | 19:51 |
| kanzure | let's not | 19:51 |
| kanzure | i don't want your mind in my mind heh | 19:51 |
| delinquentme | wth | 19:52 |
| delinquentme | no i posted that to reddit | 19:52 |
| delinquentme | nm | 19:52 |
| delinquentme | but yes i posted it to reddit | 19:52 |
| sylph_mako | OK I'm the only one who considers reddit to be a primordial hivemind system. I see a way. A glorious enlightening way. | 19:53 |
| delinquentme | what i see is we've got kids here do do shit | 19:54 |
| kanzure | so apparently this guy got into thiel's incubator: | 19:54 |
| kanzure | http://angel.co/kettner-griswold | 19:54 |
| delinquentme | *outside* of academia | 19:54 |
| kanzure | http://www.youtube.com/watch?v=x1fXAdODGvA | 19:54 |
| delinquentme | and people need more exmaples of that | 19:54 |
| kanzure | "I am the next Mark Zuckerburg, the next Craig Venter" <-- sounds like an idiot | 19:54 |
| yashgaroth | wtf are 'antibiotic resistance vaccines' | 19:55 |
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| delinquentme | thats what the kid said? | 19:55 |
| delinquentme | ugh | 19:55 |
| kanzure | it's on his angle.co profile.... | 19:55 |
| kanzure | sponsored by the us airforce :| | 19:56 |
| Mariu | :p | 19:56 |
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| delinquentme | PS theil has his own accelerator? | 19:57 |
| delinquentme | or you mean the 20 under 20 | 19:57 |
| delinquentme | is he still doing that too? | 19:58 |
| kanzure | he's still doing 20under20 yes | 19:58 |
| kanzure | but also breakout labs is via the thiel foundation | 19:58 |
| delinquentme | O_o | 19:58 |
| delinquentme | with what technology to submit? | 19:58 |
| kanzure | what ? | 19:58 |
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| delinquentme | what technology did he submit to breakout? | 19:59 |
| delinquentme | is that not part of breakout? | 19:59 |
| kanzure | 20under20 is not breakout labs | 19:59 |
| delinquentme | <kanzure> he's still doing 20under20 yes | 20:00 |
| delinquentme | <kanzure> but also breakout labs is via the thiel foundation | 20:00 |
| kanzure | "he's still doing" he=pete | 20:00 |
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| kanzure | ok so if that guy is the next "craig venter zuckerberg" then what does that make any of us | 20:03 |
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| yashgaroth | oh apparently 'antibiotic resistance vaccines' is related to the igem team he was on | 20:09 |
| yashgaroth | still looks fucking stupid | 20:09 |
| delinquentme | kanzure, so the kid is *not* doing breakout labs? | 20:14 |
| kanzure | he's doing 20under20 i think | 20:16 |
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| kanzure | hmmm so bruce perens is claiming that software freedom conservancy is ok with umbrellaing hardware projects | 20:39 |
| kanzure | for 501c3 status | 20:39 |
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| delinquentme | kanzure, i dont follow | 20:45 |
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| delinquentme | lolwut 'However, there is a certain temperature and pressure at which all three states of water can coexist. At this so-called critical transition, the distinction between gas, liquid, and solid essentially disappears.' | 21:00 |
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| kanzure | nmz787: hi | 21:02 |
| delinquentme | TRE WOMP | 21:02 |
| nmz787 | yo | 21:05 |
| nmz787 | kanzure: so did you see the line about $40 vs $150 laser goggles | 21:06 |
| kanzure | no? | 21:06 |
| nmz787 | the more expensive ones came with some certification | 21:06 |
| nmz787 | so i think i'd prefer them | 21:06 |
| nmz787 | the other ones were from a website that had spelling/english errors | 21:07 |
| nmz787 | even though it said it was based in U.S. | 21:07 |
| kanzure | haha i think goggles are an ok thing to splurge on | 21:09 |
| nmz787 | basically thats what i was thinking | 21:09 |
| nmz787 | i have to figure out the optics stuff yet, but most of it is there | 21:10 |
| nmz787 | need to add spincoater | 21:10 |
| kanzure | in the google doc? | 21:10 |
| kanzure | what step is the spincoater for? pdms layering? | 21:11 |
| nmz787 | yeah | 21:11 |
| nmz787 | or do we break that into a different spreadsheet? | 21:11 |
| kanzure | this is a good question | 21:11 |
| nmz787 | i guess thats not the next step | 21:11 |
| nmz787 | from right now | 21:12 |
| kanzure | no we should definitely plan it out | 21:12 |
| nmz787 | when the next step is to build a laser cutter that works | 21:12 |
| nmz787 | and the software | 21:12 |
| nmz787 | i guess we should start watching the market | 21:12 |
| nmz787 | i wonder if a cdrom would work to sprin coat acrylic discs | 21:12 |
| nmz787 | is fenn in here? | 21:13 |
| kanzure | fenn: ping | 21:13 |
| kanzure | nope. | 21:14 |
| kanzure | yeah i've seen a few cdrom-based spincoaters.. | 21:14 |
| nmz787 | so i was thinking that we can have the laser move in one axis, and the substrate move in the other axis | 21:15 |
| nmz787 | that way the optics could be simpler | 21:15 |
| delinquentme | ok soo my threads are running :D | 21:15 |
| delinquentme | and just dies | 21:15 |
| delinquentme | feck | 21:15 |
| delinquentme | damn dingos | 21:16 |
| charlieschwabach | diginet: why are you expressing spider silk? | 21:17 |
| kanzure | nmz787: yeah, we also need to uh think about the laser | 21:17 |
| kanzure | charlie, i think he wants to electrospin the silk into threads | 21:21 |
| charlieschwabach | ahh cool | 21:24 |
| charlieschwabach | do you know he plans on purifying it? | 21:25 |
| kanzure | i assume liquid chromatography or centrifugation | 21:25 |
| nmz787 | kanzure: have something particular in mind? | 21:29 |
| charlieschwabach | that might not be fun, although electrospinning looks very cool | 21:30 |
| delinquentme | kanzure, can / should ruby threads spawn threads? | 21:30 |
| charlieschwabach | ahh there are a bunch of papers | 21:32 |
| charlieschwabach | i did not do well in that lab in school though | 21:32 |
| charlieschwabach | and we had affinity columns :) | 21:32 |
| yashgaroth | bro protein purification is hella fun | 21:32 |
| charlieschwabach | I have only done it the once | 21:37 |
| yashgaroth | I've done it literally a thousand times | 21:37 |
| charlieschwabach | ahh, awesome | 21:38 |
| charlieschwabach | probably a lot more fun if you are purifying something real / not being graded ? | 21:38 |
| yashgaroth | I even got paid | 21:38 |
| nmz787 | i gotta do some hplc in the next week or three | 21:38 |
| nmz787 | also gcms | 21:38 |
| nmz787 | first time on both of them... though i used an ms for doing ion implant a few years ago | 21:39 |
| charlieschwabach | haha | 21:39 |
| nmz787 | that wasn't really the same, hah | 21:39 |
| charlieschwabach | yeah that probably helps too | 21:39 |
| yashgaroth | what kind of hplc column | 21:39 |
| nmz787 | dunno yet | 21:39 |
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| nmz787 | yeah actually the mass spec for ion implant had this huge plasma chamber | 21:39 |
| nmz787 | and was old as shit, with prob 4 ft x 8ft of knobs and gauges | 21:40 |
| nmz787 | pretty insane watching the lab TA tweak it | 21:40 |
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| strangewarp | So, the New Aesthetic. | 21:46 |
| strangewarp | Looks like some sort of important art movement is kicking off... and the album I've just started working on would incidentally fit right in! Motivation!! | 21:47 |
| sylph_mako | important how? | 21:54 |
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| strangewarp | Important because it engages with the aesthetics of glitch, machine vision, and general technology things in a non-sideshow manner, from what I've read | 22:07 |
| sylph_mako | interesting. | 22:19 |
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| sylph_mako | Vulpvibe is coming to mind. | 22:23 |
| sylph_mako | That wouldn't happen to be you, would it? | 22:25 |
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| strangewarp | sylph_mako: Nope. But I admire his marketing ability. X) | 22:34 |
| sylph_mako | I once saw one of his songs on a DDR machine. | 22:34 |
| strangewarp | Makes sense; pretty sure DDR machines allow for fans to make their own step patterns for their favorite songs, now | 22:35 |
| strangewarp | Impressive that he has enough saturation that you'd just stumble over something like that | 22:35 |
| sylph_mako | I was certainly stumbling. | 22:36 |
| strangewarp | heh! | 22:36 |
| sylph_mako | I'm not good at conscious control over my legs. I only know how to handle terrain. | 22:36 |
| strangewarp | 8 or 9 years ago, I was almost breaking into competitive-level DDR play, but I think I've lost all my ability by now.. | 22:37 |
| sylph_mako | sick. | 22:37 |
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| strangewarp | http://thecreatorsproject.com/blog/in-response-to-bruce-sterlings-essay-on-the-new-aesthetic - More brainfood about the New Aesthetic thingy | 23:34 |
| strangewarp | (Also contains links to the relevant material that started the discussion) | 23:38 |
| sylph_mako | What's the point. I look at myself as a survival machine but there is no surviving indefinitely. What say the gods stop computing the universe one day. What could we have done? What could we have ever done? | 23:58 |
| --- Log closed Sun Apr 08 00:00:26 2012 | ||
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