| --- Log opened Wed Apr 24 00:00:06 2013 | ||
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| rigel | any of yall used http://robotframework.org/ ? seems like it integrates with phantomjs et al | 01:17 |
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| superkuh | paperbot: http://prl.aps.org/pdf/PRL/v110/i17/e174301 | 03:50 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/83a6b2bf8e8daea69d5b92a8abb00812.txt | 03:50 |
| superkuh | paperbot: http://prl.aps.org/abstract/PRL/v110/i17/e174301 | 03:50 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/64a36b49a3af772cbb9f0cd6a3d44a80.txt | 03:50 |
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| delinquentme | paperbot, http://www.nature.com/ncomms/journal/v4/n4/full/ncomms2745.html | 05:21 |
| paperbot | HTTP 401 unauthorized http://www.nature.com/ncomms/journal/v4/n4/pdf/ncomms2745.pdf | 05:21 |
| delinquentme | phegs! | 05:21 |
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| industromatic | Is there any biodegradable film that will serve as a strong container like paper even while wet for a few days? | 06:32 |
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| chris_99 | hmm, i'm not sure how well it comes when wet, but some people made some containers out of fungi iirc | 06:34 |
| chris_99 | http://www.smartplanet.com/blog/pure-genius/ecovative-the-new-plastic-is-made-from-mushrooms/5717 | 06:35 |
| fenn | try PLA (compostable deli containers) or compostable trash bags? | 06:37 |
| fenn | need more info on what you're doing to help | 06:37 |
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| fenn | rice hulls are an interesting substance; they're inflammable because the mineral content is so high it forms a protective ash film | 06:39 |
| fenn | this property makes them nearly impossible to dispose of, so there are mountains of the stuff available for free | 06:39 |
| fenn | non-flammable* | 06:40 |
| chris_99 | intriguing | 06:42 |
| chris_99 | didn't know that | 06:42 |
| fenn | i was thinking about using it as house insulation | 06:44 |
| ParahSail1n | load newspaper with borate and it won't burn | 06:54 |
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| ParahSail1n | i think most rice hulls end up going to cows | 07:01 |
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| delinquentme | what does the current state of the art look like for sequencing assembly hardware? | 07:38 |
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| eudoxia | paperbot: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=6268161 | 09:39 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/3187ece783c7f7e64ff2605c0ff0b6a9.pdf | 09:40 |
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| kanzure | "Why not just use gpg to encrypt all the PDFs, using the hostname of the mirror of the password?" | 10:35 |
| kanzure | mirror of the password? | 10:35 |
| EnLilaSko | I assume "as the password" | 10:49 |
| EnLilaSko | idk | 10:49 |
| EnLilaSko | Can anyone help me understand "PRL-8-53 does not produce stimulation or depression of avoidance rate in rats working on a continuous avoidance schedule."? | 10:50 |
| EnLilaSko | Do they just mean that it doesn't cause any stimulatory effects nor depression? | 10:50 |
| brownies | no, not exactly | 10:51 |
| brownies | it means that it does not alter the avoidance rate in either direction in a statistically significant way | 10:51 |
| EnLilaSko | What is avoidance rate? | 10:52 |
| kanzure | that's topic-specific. an avoidance schedule has a specific definition. look up the protocol. | 10:53 |
| EnLilaSko | paperbot: http://onlinelibrary.wiley.com/doi/10.1002/cmdc.201000446/abstract;jsessionid=269962F66DEBE76849053F4302D9C7C9.d03t02 | 10:59 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/40c73dabaefed3a7b54f113f6be8b725.txt | 10:59 |
| EnLilaSko | paperbot: http://link.springer.com/article/10.1007%2FBF01934822 | 11:01 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/b964e6067d5da990a883d76175c9697e.txt | 11:01 |
| kanzure | hmm we're getting a lot of access denied | 11:01 |
| kanzure | abetusk: also there's a GET conference thing in boston happening on the 25th | 11:37 |
| kanzure | and jonathan cluck might be worth saying hi to | 11:38 |
| kanzure | i think patrik is in boston this week? | 11:38 |
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| EnLilaSko | paperbot: http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3145.html | 11:54 |
| paperbot | HTTP 401 unauthorized http://www.nature.com/nm/journal/vaop/ncurrent/pdf/nm.3145.pdf | 11:54 |
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| nmz787 | EnLilaSko:http://diyhpl.us/~nmz787/Intestinal%20microbiota%20metabolism%20of%20l-carnitine__a%20nutrient%20in%20red%20meat__promotes%20atherosclerosis.pdf | 12:10 |
| nmz787 | EnLilaSko: http://www.westonaprice.org/blogs/cmasterjohn/2013/04/10/does-carnitine-from-red-meat-contribute-to-heart-disease-through-intestinal-bacterial-metabolism-to-tmao/ | 12:10 |
| nmz787 | I'd simply read the latter | 12:10 |
| EnLilaSko | nmz787: I was guessing it was something like that, i.e. medias reporting shit about stuff they don't have a clue about | 12:13 |
| nmz787 | yeah | 12:20 |
| nmz787 | some key downfalls in the study | 12:20 |
| nmz787 | low numbers for study population for the human end | 12:20 |
| nmz787 | believing women are equivalent to men, even though there is some metabolic differences known for carnitine/assoc pathways | 12:21 |
| nmz787 | converting the amount of carnitine the mice's drinking water had (equivalent to like 1000 steaks per day for a human) | 12:21 |
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| nmz787 | delinquentme: suppp | 12:29 |
| brownies | sounds like a moonumental amount of steak | 12:29 |
| kanzure | i wish i was better at timezones | 12:32 |
| delinquentme | nmz787, derping on ICvideos | 12:32 |
| kanzure | https://mat.boum.org/ was recommended on science-liberation-front for removing metadata from .doc, .pdf, .ppt and other common file formats. | 12:32 |
| nmz787 | ICvideos? | 12:36 |
| nmz787 | klafka: so what did you learn at the psch conf? | 12:36 |
| nmz787 | psych* | 12:36 |
| klafka | hmm i didn't actually get to attend any of the sessions :( | 12:37 |
| klafka | I was at the dancesafe table the whole time | 12:37 |
| nmz787 | aww | 12:37 |
| klafka | i did get to do a lot of networking and stuff | 12:37 |
| klafka | which was cool | 12:37 |
| brownies | you're with dancesafe? | 12:37 |
| nmz787 | i heard there is unaio de vegetal or something up in oregon | 12:38 |
| klafka | oh UDV | 12:38 |
| nmz787 | or the other huasca church | 12:38 |
| klafka | it's all over | 12:38 |
| nmz787 | but i can't find any good info | 12:38 |
| klafka | brownies: yes | 12:38 |
| nmz787 | just some lady from a news article, and her facebook pages lists her as like a holistic magic person | 12:38 |
| klafka | https://mycotopia.net/forums/botanicals/51204-ayahuasxca-now-legal-church-ashland-oregon.html | 12:38 |
| nmz787 | or something weird | 12:38 |
| nmz787 | so i don't have any legit leads to find these people | 12:39 |
| klafka | idk if you want to get into that sort of thing you can probably find some 'shaman' in the area | 12:39 |
| klafka | oh i see | 12:39 |
| klafka | go to like an evolver meetup | 12:39 |
| nmz787 | i'm not sure i'd like them if they were all holistic believers | 12:39 |
| klafka | most of them are going to be like that | 12:39 |
| klafka | http://www.evolvernetwork.org/ | 12:39 |
| nmz787 | i emailed rick strassman not too long ago, he replied :P | 12:39 |
| nmz787 | but he's not in oregon | 12:40 |
| nmz787 | i don't think | 12:40 |
| klafka | he was in NM | 12:40 |
| nmz787 | at least he was in NM 20 years ago | 12:40 |
| klafka | lol | 12:40 |
| klafka | are you in pdx | 12:40 |
| klafka | or ? | 12:40 |
| nmz787 | yea | 12:40 |
| nmz787 | well burbs | 12:40 |
| klafka | let me just see | 12:40 |
| klafka | https://www.facebook.com/events/491813867546480/505785062816027/?notif_t=plan_mall_activity btw delinquentme | 12:40 |
| klafka | INTERNET CAT VIDEO FESTIVAL OF OAKLAND | 12:41 |
| klafka | gonna be so good | 12:41 |
| nmz787 | lol | 12:41 |
| nmz787 | amazing | 12:41 |
| delinquentme | oh jesus | 12:41 |
| delinquentme | so good. | 12:41 |
| brownies | what did Rick tell you? | 12:41 |
| klafka | nmz787: we have a psychedelic society of sf here | 12:41 |
| klafka | like if you were really interested i would go to stuff like an evolver meetup or like burner / psytrance events and talk to people | 12:42 |
| klafka | guaranteed to find someone | 12:42 |
| nmz787 | "I'd like to see the DMT-synthesizing gene's regulation studied more. The brain clearly needs the attention of genetic engineering, and that's going to be a wild ride." | 12:42 |
| klafka | in general psychedelic genomics is a field that is in its super infancy | 12:43 |
| nmz787 | yeah | 12:43 |
| brownies | klafka: thing is, those places are full of suspicious hippie nuts, not scientists | 12:43 |
| nmz787 | yeah | 12:43 |
| nmz787 | that | 12:43 |
| klafka | i would totally switch fields if i could be a psychedelic genomicist | 12:43 |
| nmz787 | let's do it | 12:44 |
| klafka | brownies: that's what you're going to find if you want to find a shaman for an ayahuasca journey | 12:44 |
| nmz787 | i'm a fresh biotech/bioinf B.S. (-3 classes) | 12:44 |
| klafka | maybe you want someone that does like psychedelic therapy ? | 12:44 |
| klafka | where they are an actual therapist | 12:44 |
| nmz787 | hmm | 12:44 |
| klafka | idk what do you want | 12:44 |
| nmz787 | outsource the work to them, just handle the genomics | 12:45 |
| klafka | you can just take ayahuasca with someone you trust as a trip sitter | 12:45 |
| klafka | that is experienced | 12:45 |
| nmz787 | guidance is the point of a shaman though | 12:45 |
| nmz787 | or therapist | 12:45 |
| klafka | yes | 12:45 |
| klafka | that's why i said it depends what you want out of it | 12:45 |
| klafka | that's how you choose your guide | 12:45 |
| klafka | if you don't want 'hippie nonsense' or perhaps a bit nicer 'spiritual discovery' | 12:46 |
| klafka | then you don't need a shaman | 12:46 |
| nmz787 | i read like 10 years ago on some weird web site that you could learn to edit your own DNA | 12:46 |
| nmz787 | that was pretty interesting | 12:46 |
| nmz787 | way before i knew much about DNA | 12:46 |
| nmz787 | so that would be cool to look into, since I talk about DNA synthesis alot | 12:46 |
| nmz787 | but i feel like there would be a LOT of searching through 'noise' when asking people about this | 12:47 |
| klafka | lol yes | 12:47 |
| klafka | nmz787: idk i am immediately intensely sceptical anytime someone talks about DNA in the psychedelic community | 12:47 |
| nmz787 | 'hmm, you hide you GM appendage well, I can't see it at all' | 12:47 |
| klafka | that is not an actual mol/cel biologist | 12:47 |
| nmz787 | 'oh you encoded insivibility for it too' | 12:47 |
| nmz787 | 'makes sense' | 12:47 |
| klafka | like terrence mckenna's theory of harmaline resonance with DNA | 12:48 |
| nmz787 | I can barely remember that one | 12:48 |
| nmz787 | recently i've really started to question the 'innate knowledge in the molecule' concepts | 12:48 |
| klafka | why? | 12:49 |
| nmz787 | well, it's only got so many degrees of difference from other molecules | 12:49 |
| nmz787 | so not that much more info inherent | 12:49 |
| klafka | i guess the knowledge is in the system | 12:49 |
| klafka | it's like going from a neuro transmitter/receptor view of the brain to a neural firing pattern view of the brain | 12:50 |
| kanzure | .... what. | 12:50 |
| nmz787 | I'm not convinced we can't do telepathy, so maybe these molecules could actually change brain circuits to resonate and communicate with 'greater consciousness' or the hive or whatever | 12:50 |
| nmz787 | hive mind | 12:50 |
| klafka | idk i have yet to see a convincing argument for telepathy | 12:51 |
| klafka | or a good example of telepathy existing | 12:51 |
| kanzure | electronic telepathy has already been demonstrated. | 12:51 |
| nmz787 | i did a bunch of research last year | 12:51 |
| nmz787 | not much out there | 12:51 |
| delinquentme | klafka, did I tell you <# | 12:51 |
| nmz787 | not a good test system developed | 12:51 |
| kanzure | i'm pretty sure warwick was the first one to demonstrate electronic telepathy with his wife's wrist implant. | 12:51 |
| klafka | what does electronic telepathy mean? | 12:51 |
| nmz787 | like, put person in a faraday cage and blast them with scanner freq EM from low to really high freq | 12:52 |
| nmz787 | and see if they feel anything other than heat | 12:52 |
| klafka | aah | 12:52 |
| kanzure | klafka: wireless communication over radio. | 12:52 |
| kanzure | but why are you guys bothering with "innate knowledge inside a molecule" nonsense. wtf? | 12:52 |
| nmz787 | or have some scanning transmitter helmet that you wear, and the message encoded on the carrier freq is always the same... some color or sound data... so when you see or hear that, you'll know there's resonance | 12:53 |
| nmz787 | kanzure: it's what a lot of hippy/shaman types say | 12:53 |
| superkuh | It isn't uncommon for people who identify as transhumanists to believe that extremely weak magnetic fields can somehow effect the brain. Usually Russians. This often leads to even worse talk of shared effects from geomagnetic events. | 12:53 |
| nmz787 | the best biophysical systems I found that looked a lot like electronics were the electric eel shock systems | 12:54 |
| nmz787 | basically like a voltage pump | 12:54 |
| delinquentme | isnt there some open source / rentable IC fabrication lab? | 12:55 |
| nmz787 | 1-way membranes aka diodes | 12:55 |
| kanzure | delinquentme: no, but there's two major companies that offer space on their wafers for ASICs and die packaging. also there's homecmos if you want to do it yourself. | 12:55 |
| delinquentme | or like a fab lab which does something less than holy-crap-intel-scale-utilization? | 12:55 |
| nmz787 | most brain freqs are damn low, but i wonder if that's not because we simply aren't checking the right freqs | 12:55 |
| nmz787 | there was a lot of russian data on the eyes emitting photons | 12:56 |
| delinquentme | kanzure, do you know of any processes in IC design for making micro / nano manipulators? | 12:56 |
| nmz787 | so more line-of-sight than broadcasting | 12:56 |
| nmz787 | delinquentme: micromanipulators are made by pulling glass capillary | 12:56 |
| nmz787 | delinquentme: IC wafer fabs pull crystals, so similar but not same | 12:56 |
| delinquentme | but I mean a process to etch manipulators through a chip-fab process | 12:57 |
| nmz787 | depends what manipulator you want | 12:58 |
| nmz787 | if it's for cells, then need to be hollow | 12:58 |
| nmz787 | so easier to pull and snap | 12:58 |
| nmz787 | maybe you could make layers | 12:58 |
| nmz787 | and have a boxy manipulator | 12:59 |
| delinquentme | and the design software? probs just something like cad? | 13:00 |
| kanzure | for wafer masks people tend to use things like autocad dxf :( | 13:01 |
| kanzure | also sometimes the masks are autogenerated from vlsi verilog/vhdl things. | 13:01 |
| kanzure | "Organovo Holdings, Inc., a company that designs and creates functional human tissue has announced at this year's Experimental Biology Conference that it has developed a 3D printing technique that is able to produce small samples of human liver tissue. They claim their new process allows for printing 500 micron thick liver tissue, amounting to 20 cell layers, which is able to produce cholesterol and some of the enzymes produced by the natural ... | 13:02 |
| kanzure | ... liver. The liver samples produced, the company said, can be used by researchers looking to test the efficacy of new drugs designed to treat liver diseases or to test side effects on the liver of drugs created for other purposes." | 13:02 |
| kanzure | hmm i'm not sure what the point is for testing purposes. how exactly similar are their tissues to actual human tissue? | 13:02 |
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| nmz787 | so this isn't that funny or witty http://memegenerator.net/instance/37253023 | 15:21 |
| nmz787 | i'm not sure how to do better | 15:21 |
| kanzure | http://www.joachim-breitner.de/blog/archives/593-The-carbondioxide-footprint-of-Debians-Haskell-packages.html | 15:28 |
| kanzure | "By now, Debian ships quite a lot of Haskell packages (~600). Because of GHC's ABI volatility, whenever we upload a new version of a library, we have to rebuild all libraries that depend on that. In particular, if we upload a new version of the compiler itself, we have to rebuild all Haskell library packages. So we have to rebuild stuff a lot. Luckily, Debian has a decent autobuilding setup so that I just need to tell it what to rebuild, and ... | 15:29 |
| kanzure | ... the rest happens automatically (including figuring out the actual order to build things)." | 15:29 |
| kanzure | "During the last four days a complete rebuild was happening, due to the upload of GHC 7.6.3. During these 2 days and 18 hours building 537 packages took 48 hours of build time and produced 15kg of CO2. That is 94% of all uploads and 91% the total build time. The numbers are lower for the whole of last year: 52% of uploads, 31% of build time and 57kg of CO2." | 15:29 |
| ParahSailin | lol | 15:31 |
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| ThomasEgi | and that is why i install precompiled packages. and not running on a source-and-self-compile distro | 16:07 |
| ThomasEgi | environmental reasons.. and lazyness. mainly lazyness. | 16:07 |
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| kanzure | someone posted some helpful things about the solidworks file format https://groups.google.com/forum/?fromgroups=#!topic/openmanufacturing/Fv2Ovmxnfyw | 16:57 |
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| nmz787 | paperbot: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5588008&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D5588008 | 17:21 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/d569853ecbe85c4c1d3e702510051ca3.pdf | 17:21 |
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| nmz787 | fenn: are you around? | 19:35 |
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| kanzure | don't ask to ask etc.. | 19:36 |
| kanzure | also see the corollary ("just ask") | 19:37 |
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| nmz787 | wasn't that a question? | 20:11 |
| nmz787 | i mean, i /did/ ask something | 20:11 |
| kanzure | yes but what about just saying what you need? | 20:11 |
| nmz787 | fenn: where are you these days? | 20:13 |
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| brownies | kanzure: hang on, i have a question about asking to ask. can i ask that here? | 20:37 |
| Juul | any good DNA day offers today? | 20:41 |
| kanzure | brownies: you forgot /quit to make it look realistic | 20:42 |
| yashgaroth | "offering a 50% discount on gBlocks™ Gene Fragments* for one day only. gBlocks Gene Fragments are double-stranded, sequence-verified genomic blocks up to 500 bp" | 20:42 |
| brownies | heh | 20:44 |
| kanzure | cambrian genomics recently raised a few million | 20:46 |
| kanzure | i think this is not the SBIR money from DARPA. | 20:46 |
| kanzure | "The novel aspect of the Cambrian Genomics approach comes from the fact that they make many thousands of copies of their sequence, ensuring that at least some proportion will have been made with the proper sequence." | 20:48 |
| kanzure | that's not novel.. that's a lie. | 20:48 |
| kanzure | "Cambrian Genomics brings in lasers only once the plate is covered with many thousands of DNA-carrying beads, and once each of the beads has been sequenced. With so many copies made, some predictable portion will have been made error-free, and an automated laser flits about over the plate and blasts any beads with a desired sequence off of the plate and into a collector. " | 20:49 |
| kanzure | so uh i don't remember that part | 20:49 |
| kanzure | i think fenn didn't know about that | 20:49 |
| kanzure | yashgaroth: verdict? | 20:49 |
| yashgaroth | man until I get a full tech brief on their process I'm gonna continue being skeptical | 20:50 |
| kanzure | it's just normal dna synthesis | 20:51 |
| kanzure | except they sequence each bead | 20:51 |
| yashgaroth | but how | 20:51 |
| kanzure | i'm sure plate sequencing is already a thing | 20:51 |
| kanzure | ... right? | 20:51 |
| yashgaroth | not as much for single molecules | 20:51 |
| kanzure | no they are beads | 20:51 |
| yashgaroth | with single molecules on them | 20:51 |
| yashgaroth | presumably you're running the same synthesis process on all the beads, but each single strand may have errors | 20:51 |
| kanzure | right | 20:51 |
| yashgaroth | so you have to find single molecules that have the correct sequence, which is hard | 20:52 |
| yashgaroth | since single-molecule sequencing is terribly error prone, and/or impossible when it's stuck to a huge bead | 20:52 |
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| kanzure | it's possible that they wash the beads and then sequence. dunno. | 20:53 |
| yashgaroth | well sure they can wash it | 20:53 |
| kanzure | anyway the laser part is the important detail. i didn't know they were using lasers to push beads around. | 20:53 |
| yashgaroth | when you're as cutting edge as cambrian, you gotta have a laser or two in there somewhere | 20:54 |
| kanzure | well, if you use magnets you end up with possible contamination | 20:55 |
| kanzure | unless you can time it right so that you levitate an object briefly, turn off the electromagnet, then have the bead fall into place somewhere. | 20:55 |
| nmz787 | they're using some sequence by template matching or something | 20:55 |
| nmz787 | template or ligtaion | 20:55 |
| nmz787 | 10mers though | 20:55 |
| nmz787 | the laser induced forward transfer is well known tech actually | 20:56 |
| kanzure | yes i'm aware it's well known tech | 20:56 |
| kanzure | but i didn't know they were using that idea in particular | 20:56 |
| nmz787 | and helicos does single molecule sequencing by synthesis on a plate with a microscope reading the seq | 20:57 |
| nmz787 | it's still not making things cheaper though, as far as I can tell | 20:57 |
| kanzure | yeah, but yashgaroth is claiming the method is impossible (or something) | 20:57 |
| nmz787 | they're just automating the existing pruning process | 20:57 |
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| kanzure | i don't remember the specific binding chemistry though | 20:58 |
| kanzure | antibody? biotin? who knows. | 20:58 |
| nmz787 | which binding? | 20:58 |
| nmz787 | i'm pretty sure it's just stuck in the think liquid layer | 20:58 |
| nmz787 | thin | 20:59 |
| nmz787 | emulsion | 20:59 |
| nmz787 | polonator tech | 20:59 |
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| nmz787 | (joe kaufman mentioned it was prob polonator tech, the night after i visited cambrian) | 20:59 |
| kanzure | prob? | 21:00 |
| yash | just sayin', single molecule reading by CCD or whatever is fine if you have many copies of a sample so you can figure out errors from individual molecules' sequences | 21:00 |
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| kanzure | nmz787: i think you should revisit the pacbio paper. they were specifically binding the enzyme to the bottom of the well with some linker chemistry. | 21:01 |
| nmz787 | probably* | 21:02 |
| nmz787 | kanzure: that's not helicos tech though | 21:02 |
| kanzure | yash: if your complaint is that individual beads will have millions of possibly-wrong sequences, then i could understand where you're coming from. maybe they get better-enough yields from this method than not doing it at all, so they view it as a net gain. | 21:02 |
| nmz787 | helicos just uses damn good fluorophores | 21:02 |
| nmz787 | i wish i could buy their reagent refill kit | 21:02 |
| nmz787 | or get a price on it | 21:03 |
| nmz787 | i have a simple way to fix the error much closer to the source, simply by gel filtering between synthesis steps | 21:04 |
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| yashgaroth | god damnit | 21:04 |
| kanzure | yash: if two beads have different error rates, just select the one with the better error rate. also you could do pcr and whichever sequence ends up winning could be sequenced, and then you can be sure about whether or not it's errored. | 21:04 |
| yashgaroth | why would different beads have different error rates | 21:05 |
| kanzure | "actual" error rate | 21:05 |
| kanzure | "observed" error rate i mean. | 21:05 |
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| yashgaroth | if you have to do pcr and amplify the sequence and then sequence it, you're not doing much better than traditional methods | 21:06 |
| kanzure | yeah nevermind. doesn't matter. when you do 40 cycles of PCR, your population is going to end up dominated by a winning sequence, and that's the one you sequence. and that one might have an error or not. | 21:06 |
| yashgaroth | I guess they could reduce the proportion of bad sequences but it's not groundbreaking | 21:06 |
| kanzure | well reducing the proportion of bad sequences might be grounbreaking if it actually reduces the cost of synthesis | 21:06 |
| kanzure | *groundbreaking | 21:07 |
| kanzure | of course, i wouldn't call it groundbreaking in that scenario anyway :) | 21:07 |
| ParahSail1n | you guys are talking about the laser printing of genes? | 21:08 |
| yashgaroth | I don't see why they have to be so damn secretive if they've got a patent, unless china or something | 21:08 |
| kanzure | it's not laser printing. | 21:08 |
| ParahSail1n | i should have put the quotation marks | 21:09 |
| ParahSail1n | what is their supposed technology anyway\ | 21:10 |
| kanzure | synthesis on a plate, then sequencing on a plate (i guess?), then using a laser to bump the beads off the plate for conjugation. | 21:11 |
| yashgaroth | it seems to be something about 'run traditional synthesis on beads, where there's a single strand on each bead somehow, then sequencing those individual strands' | 21:11 |
| kanzure | + ignore the beads that probably have a bad sequence | 21:11 |
| kanzure | yashgaroth: i don't think there's a single strand on each bead. | 21:11 |
| yashgaroth | well there better be because unless you're reading a single strand the result is useless | 21:11 |
| kanzure | nmz787: i'm not going to watch an entire video just to hear the three seconds of detail. could you just summarize what the actual method is? | 21:15 |
| ParahSail1n | is singularity university siai? | 21:20 |
| kanzure | no | 21:21 |
| kanzure | however, siai sold their branding to singularity university recently | 21:21 |
| kanzure | so the answer is "yes" in that sense.. | 21:21 |
| ParahSail1n | who is behind cambrian | 21:21 |
| kanzure | http://anselmlevskaya.com/ and george church | 21:22 |
| yashgaroth | george church is behind as in 'previously involved' | 21:22 |
| kanzure | i think the full list is sagar indurkhya, austen heinz, reese jones, john mulligan, anselm levskaya, and george church | 21:22 |
| kanzure | yeah who knows what george is actually up to | 21:22 |
| nmz787 | kanzure: actually they're using the oligomaker from azcobiotech | 21:22 |
| yashgaroth | not cambrian, that much we know | 21:22 |
| nmz787 | kanzure: the video was linked to the second | 21:23 |
| kanzure | what? | 21:23 |
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| nmz787 | the method is use this to make 150mer oligos http://www.azcobiotech.com/instruments/OligoArray.php | 21:24 |
| kanzure | no what does "linked to the second" mean? | 21:24 |
| nmz787 | attach to beads, do emulsion PCR to amp each oligo | 21:24 |
| nmz787 | do some template matching/ligation sequencing | 21:24 |
| nmz787 | for good matches, use laser to induce forward transfer to a plate below | 21:25 |
| kanzure | they are willing to do emulsion pcr in batch? alright.. | 21:25 |
| nmz787 | collect an aliquot from each well on output plate, do gibson, etc | 21:25 |
| ParahSail1n | i wonder if you could do bridge amplification on solid support ala illumina | 21:25 |
| nmz787 | the emulsion keeps the chemistry localized according to j kaufman | 21:25 |
| nmz787 | so each bead is clonal | 21:25 |
| kanzure | yeah i'm familiar with emulsion pcr but it was always a huge pain in the butt | 21:25 |
| ParahSail1n | and do the sequencing of clusters ala illumina | 21:25 |
| kanzure | how are they extracting beads from an emulsion? i don't get it. | 21:26 |
| ParahSail1n | and then pick out your beads with a laser | 21:26 |
| nmz787 | they also had an myseq or hiseq there | 21:26 |
| kanzure | i guess it wouldn't require too much more force if it was suspended in emulsion | 21:26 |
| ParahSail1n | emulsion pcr seems dubious when illumina's bridge amplification is established to work well | 21:27 |
| nmz787 | it doesn't seem to matter | 21:28 |
| ParahSail1n | i wonder if cambrian has any interesting ligation ideas | 21:28 |
| nmz787 | as long as it's clonal amp | 21:28 |
| kanzure | nah i'm sure they just use gibson assembly | 21:28 |
| ParahSail1n | that azco thing is pretty cool | 21:29 |
| ParahSail1n | the promise of .03 cents that is, couldnt say if there are deliverables yet | 21:30 |
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| kanzure | this is neat: | 21:37 |
| kanzure | http://www.seomoz.org/blog/machine-learning-and-link-spam-my-brush-with-insanity | 21:37 |
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| Mokstar | Howdy folks | 22:12 |
| Mokstar | Who was that fellow who was building NIR EEG systems? | 22:12 |
| ParahSail1n | kanzure is a huge fan of EEG | 22:18 |
| Mokstar | kanzure, do you know anything about NIR HEG? | 22:18 |
| kanzure | aaaaaah | 22:18 |
| kanzure | ParahSail1n: stop it people will believe you | 22:18 |
| kanzure | http://openoptogeneticsblog.org/?p=383 | 22:19 |
| kanzure | .title | 22:19 |
| yoleaux | 3D waveguide array for optogenetic neuronal stimulation | OpenOptogenetics | 22:19 |
| kanzure | iirc ed boyden had an infrared-related apparatus but i dunno if it was near-infrared or if it was HEG or EEG... i doubt it was EEG. | 22:20 |
| kanzure | btw don't listen to ParahSail1n, because i really don't like EEG. | 22:20 |
| Mokstar | yeah, you like scrambling people's eggs with ultrasound! :p | 22:20 |
| Mokstar | eeg = electrical, heg = hemoglobin | 22:21 |
| kanzure | oh maybe you are thinking of "functional near infrared optical brain imaging" | 22:22 |
| Mokstar | damn | 22:23 |
| Mokstar | did I say NIR EEG? | 22:23 |
| * Mokstar slaps himself. | 22:23 | |
| Mokstar | I blame... someone else. | 22:23 |
| Mokstar | I was gonna ask about what wavelength would work best, but then I just looked up the absorption spectrum of hemoglobin | 22:24 |
| kanzure | i don't know anyone doing fNIR things.. | 22:25 |
| kanzure | do i? i'm really confused. why have i not seen this? | 22:26 |
| kanzure | what sort of depth does it provide? this does not tell me many things: http://www.andrewpatrick.ca/wp-content/uploads/t004map.jpg | 22:26 |
| Mokstar | afaik it's pretty broad, I was interested in using it to suss regional frequencies | 22:27 |
| Mokstar | in combo with tDCS | 22:27 |
| kanzure | what does broad mean? | 22:27 |
| kanzure | paperbot: http://onlinelibrary.wiley.com/doi/10.1111/1469-8986.00053/abstract | 22:28 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/7b3e93b22179038ecf06b073c42a1c6b.txt | 22:28 |
| kanzure | paperbot: http://www.ingentaconnect.com/content/bpl/psyp/2003/00000040/00000004/art00004 | 22:28 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/7ed2f4f47eae18a301ac0a6c73944675.txt | 22:28 |
| Mokstar | whatever I think it means! | 22:28 |
| kanzure | man what's the point of paperbot if everything is blocked | 22:30 |
| Mokstar | scattering limits the precision | 22:30 |
| Mokstar | in terms of surface area | 22:30 |
| kanzure | paperbot is just a reminder of how much crap i can't read. | 22:31 |
| Mokstar | looking like 660nm | 22:39 |
| Mokstar | ... is that a twist tie? | 22:40 |
| Mokstar | http://bio-medical.com/products/heg-nir-headband.html | 22:40 |
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| Mokstar | Mechanistic claims are unsupported as no reverse causal relationship between blood flow increase and neuronal activity has been found yet [7] | 22:52 |
| Mokstar | :( | 22:52 |
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