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| kyknos | paperbot, http://www.ncbi.nlm.nih.gov/pubmed/4892006 | 08:49 |
|---|---|---|
| kyknos | paperbot, http://www.sciencedirect.com/science/article/pii/S0022283668800129 | 08:51 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/a9c23acc090628425ad893f38c5f7618.txt | 08:51 |
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| kanzure | well that's not right | 09:44 |
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| kanzure | "Coat variation in the domestic dog is governed by variants in three genes" http://www.bio.davidson.edu/COURSES/genomics/2011/Bio309_papers/Dog_coats.pdf | 09:55 |
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| kanzure | ParahSailin: special dna prep required before sending pig/doggy/bunny dna for whole genome sequencing? | 10:01 |
| ParahSailin | you can send gdna on ice to any sequencing core | 10:02 |
| kanzure | do i have to tell them the species? | 10:02 |
| ParahSailin | kanzure: in that paper, do they give rs#s? | 10:02 |
| ParahSailin | i find biologists are super-lazy about reporting rs#s in papers | 10:03 |
| ParahSailin | kanzure: you dont particularly need to tell them what the gdna is | 10:03 |
| kanzure | ehhh no they do not | 10:03 |
| kanzure | yeah, i agree with that lazyness assessment | 10:03 |
| ParahSailin | you can tell them fragment size you want, if you want paired end data | 10:03 |
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| ParahSailin | last week, i was trying to figure out what the rs#s corresponding to the different beta casein variants are | 10:05 |
| ParahSailin | nobody seems to have a fucking clue | 10:05 |
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| kanzure | ugh | 10:05 |
| ParahSailin | granted, they couldnt even bother to sequence an animal with a y chromosome for the umd 3.1 draft genome | 10:06 |
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| ParahSailin | "oh shit fuck, we sequenced a cow instead of a bull" | 10:06 |
| kanzure | all the pedigree bullshit in the animal breeding industries is really annoying | 10:06 |
| kanzure | even a tiny bit of dna magic would fix a lot of their problems | 10:06 |
| ParahSailin | "i guess theres nothing cool on the y chromosome anyway, lets just plough ahead" | 10:07 |
| kanzure | sheena: poke. see words above. | 10:08 |
| ParahSailin | if you can get a dog ear tag, im sure the biologists where i work would love to have dna quality better than hair follicles | 10:08 |
| ParahSailin | or maybe snip a bit off the end of the tail | 10:09 |
| sheena | ParahSailin: blood isnt enough? | 10:09 |
| ParahSailin | dried bloodspot is definitely better than hair follicle | 10:10 |
| ParahSailin | hm, actually i think they used cheek swabs | 10:10 |
| sheena | there are dog breeding things that are tracking/requiring dna sequencing on breeding dogs now, but im not sure the're using it for anything more than proof of ancestry | 10:10 |
| sheena | cheek swabs are typical in dog dna stuff, but a tubeo f blood is very easy to get from most dogs | 10:10 |
| ParahSailin | yeah nobody has a $99 microarray for 900001 dog snps | 10:11 |
| sheena | ParahSailin: is that for me? i do not understand your words | 10:11 |
| ParahSailin | there isnt 23andme for dog | 10:11 |
| kanzure | in that sentence you can parse snps as "traits" more or less | 10:12 |
| ParahSailin | tube of blood should be better than cheek swab | 10:12 |
| sheena | i can get you tubes of blood of dogs any time | 10:12 |
| sheena | there is the "guess your dog's breed based on its dna" for dogs | 10:13 |
| sheena | its about 100-200 bucks | 10:13 |
| sheena | some are 50 | 10:13 |
| ParahSailin | yeah one of my coworkers did that for his dogs | 10:14 |
| ParahSailin | oh, yeah these guys http://www.neogen.com/Agrigenomics/EquineCanine.html | 10:15 |
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| ParahSailin | if you're serious, do that beadchip | 10:15 |
| kanzure | this started with population genetic diversity questions | 10:16 |
| ParahSailin | its probably < 500 | 10:16 |
| sheena | ParahSailin: beadchip will give what information that might be useful? | 10:16 |
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| ParahSailin | you get 170k snps, so thats pretty good | 10:18 |
| sheena | do you know any pedigree software for tracking breeding? Pedigreedatabase.com is for dogs, something like that ? | 10:19 |
| gradstudentbot | Holy crap, I need to add that to my slide collection. | 10:19 |
| * sheena is lost | 10:19 | |
| ParahSailin | i dont know of public databases for animal microarrays | 10:20 |
| kanzure | is that dog-specific snps or what | 10:20 |
| sheena | http://www.kintraks.com/ | 10:20 |
| sheena | maybe that? | 10:20 |
| ParahSailin | kanzure: obviously | 10:20 |
| sheena | just to track parentage | 10:20 |
| ParahSailin | tracking your own animals? | 10:20 |
| sheena | right | 10:21 |
| sheena | my mom's rabbits | 10:21 |
| sheena | and her friends... they trade between 4 different "populations" to increase diversity | 10:21 |
| sheena | so would be nice to have everyone be able to contribute? | 10:21 |
| ParahSailin | you are gonna spend 200/rabbit for a beadchip? | 10:21 |
| sheena | no? | 10:21 |
| ParahSailin | those are like $5 animals | 10:21 |
| sheena | i think kanzure is talking about something else | 10:22 |
| sheena | i just want FOSS software to track my mom's bunny population parentage | 10:22 |
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| sheena | ideally it will accept a photo of each animal in the pedigree, calculate COIs, and be accessible to several people or have a sync feature of some sort | 10:22 |
| sheena | kanzure is talking about breeding dogs for better.. something? using DNA? | 10:22 |
| ParahSailin | coi? | 10:22 |
| ParahSailin | you dont really need dna for that, unless you dont know who the dad is | 10:23 |
| sheena | ParahSailin: correct. dna is not relevant to my question re sotware | 10:27 |
| sheena | kintraks looks good tho | 10:27 |
| ParahSailin | lol just have kanzure make you something | 10:27 |
| sheena | lol | 10:28 |
| sheena | ask him how that's worked out in the past ;) | 10:28 |
| kanzure | pretty well? | 10:29 |
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| gradstudentbot | Wasn't there a paper about that? | 10:31 |
| sheena | minusthe frustration and anger, sure ;) | 10:33 |
| kanzure | yeah but that's like my default state though | 10:33 |
| heath | win 2 | 10:37 |
| heath | whee, irssi | 10:37 |
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| delinquentme | kanzure, what are some of the more complex / interesting microfluidic devices you've seen? | 10:51 |
| delinquentme | the synthesizer was definitely one | 10:51 |
| kanzure | i think the sequencers were more complex | 10:52 |
| kanzure | gene_hacker would have some good answers | 10:54 |
| ParahSailin | unafold is quite a rathole | 10:56 |
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| delinquentme | so I had a chat w andrew hessel and he seems to think that an arbitrary pump / valve / resviour box would be interesting for microfluidics | 11:10 |
| delinquentme | ParahSailin, you're running this package for research purposes? | 11:24 |
| ParahSailin | sheena: you should domesticate the new world cottontails | 11:28 |
| kyknos | paperbot, http://www.researchgate.net/publication/9319978_STRUCTURE_OF_A_RIBONUCLEIC_ACID | 11:28 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/db1d7884f09daa5b8ed883f8efc55174.txt | 11:30 |
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| kyknos | paperbot, http://www.sciencemag.org/content/147/3664/1462.abstract | 11:34 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1126%2Fscience.147.3664.1462 | 11:34 |
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| ebowden | paperbot: http://informahealthcare.com/doi/pdf/10.1586/ern.11.1 | 12:03 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/e58cc6a89d5c839967353f9579771d22.txt | 12:03 |
| ebowden | paperbot: http://www.ncbi.nlm.nih.gov/pubmed/21651332 | 12:05 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1586%2Fern.11.1 | 12:05 |
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| kyknos | paperbot, http://www.nature.com/nature-newbio/journal/v236/n68/abs/newbio236198a0.html | 12:19 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2F10.1038%2Fnewbio236198a0 | 12:19 |
| kyknos | paperbot, broken link :( | 12:19 |
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| ebowden | paperbot http://www.sciencedirect.com/science/article/pii/S0028390808002256 | 12:28 |
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| ebowden | http://www.nature.com/nature-newbio/journal/v236/n68/abs/newbio236198a0.html | 12:29 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/8688d583313c30d41f3ba90c6a306aea.txt | 12:29 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2F10.1038%2Fnewbio236198a0 | 12:29 |
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| ebowden | paperbot: http://www.sciencedirect.com/science/article/pii/S0028390808002256 | 12:32 |
| ebowden | paperbot http://www.nature.com/nature-newbio/journal/v236/n68/abs/newbio236198a0.html | 12:32 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2F10.1038%2Fnewbio236198a0 | 12:32 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/e0384ac6a7fa35f9c0fae6d99ef44bc0.txt | 12:33 |
| ebowden | paperbot: http://www.nrcresearchpress.com/doi/pdf/10.1139/Y09-028 | 12:35 |
| gradstudentbot | Whatever, I'm really dating school anyway. | 12:35 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/d06eff404dd0fb94f6aa16018b4ceba6.txt | 12:36 |
| ebowden | paperbot: http://www.readcube.com/articles/10.3858/emm.2012.44.6.042 | 12:37 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/56427d01a42b59232f79f839d440e587.txt | 12:37 |
| ebowden | paperbot: http://www.sciencedirect.com/science/article/pii/S0014299908003725 | 12:41 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/1d51967ff2927f45400fd0f2c055ebd1.txt | 12:41 |
| justanotheruser | paging nsh | 12:46 |
| kanzure | that's not how you do it | 12:47 |
| justanotheruser | it isn't? | 12:47 |
| kanzure | nsh: channel 4 is mispronouncing your name | 12:47 |
| justanotheruser | wat | 12:47 |
| justanotheruser | nesh? | 12:48 |
| justanotheruser | as is gunesh | 12:48 |
| justanotheruser | *in | 12:48 |
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| kyknos | paperbot, http://www.sciencedirect.com/science/article/pii/0022283671901057 | 13:58 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/8efdadeaf02c77b1157ffd961a8af5d9.txt | 13:58 |
| kyknos | oh no give me the paper | 13:59 |
| bbrittain | ouch | 13:59 |
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| kyknos | paperbot, http://www.sciencedirect.com/science/article/pii/0022283671901057 | 14:41 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/9640cc19093d30bc2caba8a46a0dc421.txt | 14:41 |
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| delinquentme | kanzure, Y u no build me dis? http://nar.oxfordjournals.org/content/38/8/2514.full | 15:47 |
| kanzure | .title | 15:49 |
| yoleaux | A microfluidic oligonucleotide synthesizer | 15:49 |
| kanzure | actually i need to buy the chemicals | 15:49 |
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| delinquentme | what would you guys use to fab something like this??? | 15:49 |
| delinquentme | laser cutter? | 15:50 |
| gradstudentbot | My study reveals that people are awesome at memorizing insecure passwords. | 15:50 |
| kanzure | photolithography | 15:50 |
| kanzure | projector pointed at a stamp | 15:51 |
| kanzure | some su-8, some microwave-based plasma bonding thing | 15:51 |
| kanzure | maybe a little pdms somewhere in there | 15:51 |
| kanzure | uh.. you know. stuff. | 15:51 |
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| kanzure | also a spin coater | 16:04 |
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| ParahSailin | done | 17:45 |
| ParahSailin | fuck | 17:45 |
| kanzure | on a scale of 1 to 10 how much do you hate yourself now | 17:48 |
| ParahSailin | 9! | 17:49 |
| ParahSailin | (factorial) | 17:49 |
| kanzure | i haven't had much luck outsourcing refactoring work like that | 17:51 |
| ParahSailin | hells yeah i got wine in the fridge | 17:54 |
| ParahSailin | so how do you go back and remove curse words from commit messages | 17:56 |
| kanzure | git filter-branch | 17:58 |
| kanzure | --commit-filter | 17:59 |
| kanzure | oops i mean --msg-filter | 17:59 |
| kanzure | git filter-branch --msg-filter 'sed "s/fuck/turd eater/g"' -- --all | 18:01 |
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| delinquentme | kanzure, is phtolithography restricted to multi-million dollar machines? | 19:57 |
| kanzure | no | 20:00 |
| kanzure | you just shine some light at some shit and it photocures, that's not even $1000 | 20:01 |
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| dingo | ehe im doing git filter-branch now | 20:12 |
| dingo | merging some repos | 20:12 |
| kanzure | you can merge repos by git fetch and git merge if you're okay with merging in the entire history of the other repo | 20:13 |
| dingo | i gotta move the project folder contents to a sub-folder | 20:14 |
| dingo | using git filter-branch, after that, then yup, i just merge | 20:14 |
| delinquentme | is this using a premade machine or something you're fabbing? | 20:16 |
| kanzure | you point a projector at some liquid | 20:16 |
| kanzure | you can also use a camera and 35mm film but then the setup is a little more complicated | 20:18 |
| kanzure | http://diyhpl.us/~bryan/papers2/optics/photolithography/Fabrication%20of%20metallic%20microstructures%20using%20exposed,%20developed%20silver%20halide-based%20photographic%20film%20-%20Deng%20-%20Whitesides.pdf | 20:18 |
| kanzure | http://diyhpl.us/~bryan/papers2/optics/photolithography/Prototyping%20of%20masks,%20masters,%20and%20stamps%20or%20molds%20for%20soft%20lithography%20using%20an%20office%20printer%20and%20photographic%20reduction%20-%20Deng.pdf | 20:18 |
| kanzure | http://diyhpl.us/~bryan/papers2/optics/photolithography/Photomasks%20fabrication%20based%20on%20optical%20reduction%20for%20microfluidic%20applications.pdf | 20:19 |
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| kanzure | http://diyhpl.us/~bryan/papers2/optics/photolithography/Using%20patterns%20in%20microfiche%20as%20photomasks%20for%2010-micron-scale%20microfabrication%20-%20Deng%20-%20Whitesides.pdf | 20:19 |
| kanzure | etc | 20:19 |
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| delinquentme | say you're getting VC and you don't want to build one of these. | 20:37 |
| delinquentme | also im curious about things like this: | 20:37 |
| delinquentme | http://nar.oxfordjournals.org/content/38/8/2514/F1.large.jpg | 20:38 |
| delinquentme | how are the reactions restricted to binding a single nucleotide?? | 20:38 |
| kanzure | even if you're getting venture capital money you would still want to do it in house because the prototype turn-around time is way too long to work out the bugs | 20:39 |
| delinquentme | so this is why you guys are interested in it... because there are no cheap fast solutions for good iteration | 20:40 |
| delinquentme | save for maybe having access at some academic lab | 20:41 |
| kanzure | there was this stanford lab that was offering $400 per mold (per design) | 20:41 |
| kanzure | but they have shut down or stopped accepting non-campus money | 20:41 |
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| kanzure | i hope you got a good deal on the funding... you using "the vault"? | 20:45 |
| delinquentme | thiel? | 20:47 |
| delinquentme | nah no funding | 20:47 |
| kanzure | "the vault" is not a person. it's a reference to "the vault" during seed rounds. | 20:48 |
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| delinquentme | no idea what this is | 20:55 |
| kanzure | if you don't actually have a deal in progress then it doesn't really matter | 21:00 |
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| nmz787 | i'm pretty sure there is 23andme like service for dogs | 21:27 |
| nmz787 | for pedigree certification | 21:27 |
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| nmz787 | this might not give you the raw data, but its $60 at walmart http://mobile.walmart.com/ip/36142574?wmlspartner=wlpa&adid=22222222228024602309&wl0=&wl1=g&wl2=m&wl3=40341973952&wl4=&wl5=pla&wl6=78302346752&veh=sem | 21:28 |
| nmz787 | or presumably str profiling https://www.akc.org/dna/ | 21:30 |
| kanzure | "pedigree certification" sounds like a scam | 21:30 |
| kanzure | what are they going to do, time travel and get the genotypes of all the ancestors? fuck those assholes | 21:30 |
| nmz787 | here 170k snp panel http://www.neogen.com/Agrigenomics/EquineCanine.html | 21:30 |
| nmz787 | you guys's googling is lacking | 21:31 |
| kanzure | do they know what the snps correlate with | 21:31 |
| nmz787 | lmgtfy | 21:32 |
| nmz787 | lotsa hits for: dna dog pedigree snps | 21:33 |
| kanzure | that's not what i mean | 21:33 |
| kanzure | snps aren't just pedigree | 21:33 |
| nmz787 | so | 21:33 |
| nmz787 | its keyword searching | 21:33 |
| kanzure | snps can determine a bunch of the phenotype of a dog or anything else for that matter | 21:33 |
| kanzure | and i'm curious if anyone has done the studies to figure it out | 21:33 |
| kanzure | especially behavior snps that would be interesting | 21:33 |
| kanzure | like bite inhibition | 21:33 |
| nmz787 | Genetic background of aggressive behaviour in dogs - Acta ... | 21:35 |
| nmz787 | https://www.google.com/url?sa=t&source=web&rct=j&ei=4PbmU7WbB8mLyAS0yoCoAg&url=http://actavet.vfu.cz/pdf/201382040441.pdf&cd=3&ved=0CCoQFjAC&usg=AFQjCNEQTMesIbOWe8EoCmXkW7zejKGlMQ&sig2=CXNCUjooJ5Ry7tdod2fNhg | 21:35 |
| nmz787 | sry on phone which doesnt have instakled google crap stripping | 21:36 |
| nmz787 | search: dna dog snps aggression | 21:36 |
| kanzure | why are you saying these things to me | 21:37 |
| nmz787 | im just sayon to irc | 21:37 |
| nmz787 | idk who was asking | 21:37 |
| kanzure | my question wasn't about aggression, it was about the state of the collected data about doggy snps and their phenotypes | 21:38 |
| dingo | i will relay your chats to the internet | 21:38 |
| nmz787 | you said bite | 21:38 |
| nmz787 | which is pretty close to aggression | 21:38 |
| kanzure | i gave an example | 21:38 |
| kanzure | is that bad? | 21:38 |
| nmz787 | no | 21:38 |
| nmz787 | you just need to search that stuff to get the answers | 21:39 |
| kanzure | i am not going to search every conceivable phenotype, wtf | 21:39 |
| nmz787 | obv no one has mapped all dog snps to phenotype | 21:39 |
| nmz787 | and made a cyclopedia | 21:39 |
| kanzure | well i don't care about *all* necessarily | 21:39 |
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| kanzure | just those 170k | 21:39 |
| nmz787 | went to a biohacking village planning meeting here today | 21:40 |
| nmz787 | mlp wasnt there, butvsaw her last two nights | 21:41 |
| nmz787 | hung out with forrest | 21:41 |
| kanzure | which forrest? the reprap one or the cool one | 21:41 |
| nmz787 | and koeng | 21:41 |
| nmz787 | flanagan | 21:41 |
| nmz787 | i guess he was the cool one | 21:42 |
| kanzure | ok the cool one | 21:42 |
| nmz787 | from hou | 21:42 |
| nmz787 | seems like the village could become reality next year | 21:43 |
| nmz787 | good amount of interest | 21:43 |
| kanzure | what else? | 21:45 |
| kanzure | catch any malware? | 21:45 |
| nmz787 | not that i can tell | 21:45 |
| nmz787 | i am on my phone now | 21:45 |
| nmz787 | havent been on wifi at all, someone supposedly has a femtocell tho | 21:46 |
| nmz787 | i heard gmail gapps had its certs embedded tho | 21:46 |
| nmz787 | and that ssh woukd alert of key change | 21:46 |
| nmz787 | aka he normal mitm warning | 21:46 |
| nmz787 | forrest said his phone was | 21:47 |
| kanzure | yes but the really nasty stuff is "plug in my phone to get charged, have my nuclear launch codes stolen by the outlet" | 21:47 |
| nmz787 | haf some weord shit on it | 21:47 |
| nmz787 | hah | 21:47 |
| nmz787 | nah | 21:47 |
| nmz787 | not doing anything like that | 21:47 |
| nmz787 | one talk by a colleague was on using RF to blow up GGCIs | 21:48 |
| nmz787 | GFCIs | 21:48 |
| kanzure | nice to know maradydd isn't dead | 21:48 |
| nmz787 | went to a party in two-story hotel suite last night | 21:50 |
| nmz787 | idk waht | 21:50 |
| nmz787 | to do tonight | 21:50 |
| kanzure | go back and claim you lost your something | 21:51 |
| gradstudentbot | Where's my pellets? | 21:54 |
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| nmz787 | ugh this chromebook doesnt want to see my phone's files | 22:08 |
| nmz787 | ugh | 22:08 |
| nmz787 | even with droiddrive | 22:08 |
| nmz787 | i can see sr0 in dmesg | 22:08 |
| nmz787 | but cant mount it, says no medium found | 22:08 |
| nmz787 | and tho theyre both google products it cant do MTP | 22:09 |
| nmz787 | so f-ing dumb | 22:09 |
| kanzure | airdroid will show you the files over http | 22:10 |
| nmz787 | is that wifi hotspot? | 22:12 |
| nmz787 | cuz bluetooth on this phone/chromebook doesnt like to fileshare | 22:12 |
| -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 22:39 | |
| -!- gully_foyle_ja [~theghosto@pool-71-116-68-251.snfcca.dsl-w.verizon.net] has quit [Ping timeout: 250 seconds] | 22:41 | |
| -!- gully_foyle_ja [~theghosto@pool-71-116-68-251.snfcca.dsl-w.verizon.net] has joined ##hplusroadmap | 23:00 | |
| -!- drewbot [~cinch@ec2-54-204-222-14.compute-1.amazonaws.com] has quit [Remote host closed the connection] | 23:05 | |
| -!- drewbot [~cinch@ec2-107-21-140-100.compute-1.amazonaws.com] has joined ##hplusroadmap | 23:05 | |
| -!- petrushki [~asakharov@24.60.79.55] has joined ##hplusroadmap | 23:09 | |
| -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 23:33 | |
| -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 240 seconds] | 23:34 | |
| -!- Viper168_ is now known as Viper168 | 23:36 | |
| --- Log closed Sun Aug 10 00:00:30 2014 | ||
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