2013-07-10.log

--- Log opened Wed Jul 10 00:00:21 2013
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heathkanzure: is your copy of "molecular biology of the cell" 1.8gb?00:59
heaththe djvu is 63mb over here, but the pdf conversion made it 1.8gb01:00
heathpaperbot: molecular biology of the cell01:00
heathdo it01:00
* heath threatens paperbot with a .meow01:07
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* heath accepts his 1.8gb pdf and sleeps through sb6.001:08
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@kanzurebeep boop07:19
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chidobzz07:22
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@kanzure"A Japanese startup called Spiber Inc. said it has produced an artificial spider thread that it claims is equal to steel in tensile strength yet as flexible as rubber. The company hopes to spin enough of the thread for mass production within two years, potentially opening the door to creating lighter but stronger auto parts, surgical materials and bulletproof vests. Spiber plans to produce one metric ton, or 2,205 pounds, of spider silk by ...08:33
@kanzure... 2015. By November, it aims to triple its current monthly output to about 220 pounds. One promising venture was Montreal-based Nexia Biotechnologies, which engineered goats to produce milk containing spider's silk. The company, which raised $42.4 million in an initial public offering in 2000, folded in 2009 when it failed to make its research commercially viable. Since going public with its production technique last August, Spiber said it ...08:33
@kanzure... has received more than a hundred requests to collaborate on projects. With a 750-million-yen ($7.6 million) investment from auto-parts maker Kojima Press Industry Co., Spiber broke ground on a prototype center and pilot plant in the northwest Japanese city of Tsuruoka earlier this month. But it will face competition from Germany's AMSilk GmbH, which says it plans to scale up lab production of the spider-silk fiber it calls Biosteel. Its ...08:34
@kanzure... product also is made entirely from recombinant silk proteins that are processed via a spinning apparatus to recreate the structure of spider silk. Another competitor is Michigan-based Kraig Biocraft Laboratories Inc., which says it has genetically engineered silkworms that spin silk containing spider fiber. A small amount of spider protein can strengthen the normal silk produced by silkworms, it said."08:34
ParahSailinbeen hearing this shit for the last 20 years almost08:35
gradstudentbotSomeone's sitting at my bench space.08:36
@kanzurespiber seems sorta new so i dunno how you would have heard that for 20 years. goats, sure, 20 years. silkworm too.08:37
@kanzurei guess they don't say what their technique is08:37
@kanzurehow would you even know08:37
ParahSailinintuition08:39
@kanzurewhich technique do you predict they are using, then08:40
ParahSailinpaperbot: http://dx.doi.org/10.1007/s00210-002-0577-308:41
ParahSailinwhatever theyre doing to make silk proteins in macro amounts its not working08:44
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@kanzure"hackubator"10:19
@kanzuresee, this is why we shouldn't let jojack out on his own10:19
heathjshttp://ellingtonlab.org/blog/2012/11/09/on-apologetics/10:31
@kanzureoh yeah he totally fucking hates biobricks10:32
@kanzurejonathan_: can vouch for that, i think10:32
jonathan_biobricks are like arduino.  it's an educational tool for high school kids.10:33
jonathan_that's why he calls them "toys"10:33
@kanzurefwiw my time with him was fun and informative10:38
@kanzure"William also did his 3D Origami thang, but took it into new dimensions, so to speak, by examining the impact of DNA shape on cellular uptake"10:40
@kanzurehrm i didn't hear about that one10:40
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ParahSailini dont think they'll solve the age-old spidroin production problem until "basic" molecular genetics are way ahead from where they are now10:45
ParahSailinlike, maybe to the point of an hour to produce a 20kb circular plasmid from scratch10:46
@kanzurepaperbot: http://dx.doi.org/10.1007/s00210-002-0577-310:51
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@kanzureoops sorry about that10:51
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delinquentmeFUCK10:56
delinquentmefucking.10:56
gradstudentbotMy parents keep asking when I'm going to finish.10:57
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heathjshttps://www.youtube.com/watch?v=JtHgIJ6kalk&feature=player_detailpage#t=3362s11:51
heathjs.title11:51
yoleauxDo You Want To Live Forever? - YouTube11:51
gradstudentbotI don't think my PI remembers me.11:51
heathjstitle is misleading, it's the part of the video where richard miller and martin raff tear into aubrey11:52
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ParahSailinlol c++12:23
ParahSailini have the feeling that i should write my own version for when the boondoggle committee effort falls further behind schedule12:24
ParahSailinone of the guys was using some xml parsing library that required certain whitespace to parse correctly12:27
ParahSailinit didn't like the python xml.etree output, and i had to do xml.dom.minidom reparse and pretty output on that12:28
@kanzureyou should use xml pull parser or xmlpp or something12:31
ParahSailinand why we using xml instead of json? for serialization to/from php of course12:31
ParahSailinpresumably if there's xml in the php standard namespace, nobody can remember if it's camelCase or under_scores, so it's impossible to find in an array of 9001 items, so php wizards use xml instead12:33
gradstudentbotYou don't happen to have any more virgin flies, do you?12:34
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@kanzurejrayhawk: do you remember if zotero translation-server had a wacky build system on their own fault, or was it because gecko has a wacky build system?13:41
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jrayhawk_kanzure: IIRC they expected custom-patched binaries to be copied into the source directory, but I've already repressed most of what I learned from that experience.13:59
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@kanzurei just blew my mind up, i am collecting the pieces14:01
@kanzurethis is extremely cool:14:01
@kanzurehttps://wiki.gnome.org/Seed14:01
@kanzure"Seed is a library and interpreter, dynamically bridging (through GObjectIntrospection) the WebKit JavaScriptCore engine, with the GNOME platform."14:01
@kanzureit uses JavaScriptCore in the outer context (like phantomjs does)14:01
@kanzureand then it can use webkit because there's webkitgtk+ gobject bindings14:02
@kanzureapparently all the node developers ignored it because "oh maybe it will be useful for GUIs"14:02
@kanzurehttps://groups.google.com/forum/#!topic/nodejs/OFfKXdIbzYk14:02
@kanzurethe one downside that i see is that there's no require() implementation yet.. but it's only 100 or 200 lines of javascript to implement that.14:02
@kanzureso basically this should be compatible with all node modules14:03
@kanzureand node modules that use node-specific apis can be forced to work in seedjs using a trick similar to what substack did in browserify14:03
@kanzurehttps://git.gnome.org/browse/seed-examples/tree/14:04
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@kanzuresudo apt-get install seed; git clone git://git.gnome.org/seed-examples; cd seed-examples; seed json-reddit.js14:15
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@kanzurenmz787: http://smokinghotcoffee.com/posts/fertilab-thinkubator-is-bringing-diy-bio-hacking-to-the-startup-community-in-eugene-or14:30
@kanzurepeople to stalk: Matt Beaudet, Shula Jaron & Jason Boone14:31
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@kanzurei think we know boone?14:31
@kanzureoh they seem to be mostly large, slowly-loaded "infographics".. nevermind.14:32
@kanzurei can't tell if they actually have equipment or not14:32
@kanzurealso they don't seem to be an incubator. they charge membership fees. that's a coworking space, not an incubaotr. an incubator will usually fund you in exchange for equity or something.14:33
@kanzureman these guys are liars14:33
heath.title https://www.youtube.com/watch?v=lV3Yhi9ib3Y14:34
yoleauxNanotechnology: Moving Beyond Small Thinking, Chad Mirkin, Northwestern University - YouTube14:34
heathone of the better videos i've watched recently14:34
@kanzurethat's not hard to beat, you've been watching terrible synbio marketing pitches on youtube for like 3 weeks now14:36
heath:)14:42
nmz787what are revenue for public dna synthesis companies14:55
@kanzurewell the market size is <$1B ish14:55
@kanzureby market size i mean revenue14:56
@kanzurewell.. no. my numbers are 12 months old and shouldn't be trusted.14:56
nmz787do you have a list that i could plow through lexisnexis with?14:58
@kanzureno, but i have a list of synthetic biology companies like: amyris, atg biosynthetics, blue heron, dna2.0, febit, geneart, ginkgo bioworks, genentech, ls9, sloning biotechnology, synthetic genomics, mr.gene, ambrx, codexis, complete genomics, halcyon molecular, solayzyme, navigenics, sequesco, pacific biosciences, raindance, kaiima biofuels, gevo, verdezyne, eureka genomics, genia, compete genomics15:00
@kanzureoops, those turned into dna sequencing companies15:00
@kanzureand the last one (compete) is a dupe of another (complete)15:01
@kanzureidtdna15:01
@kanzurehmm http://hg.mozilla.org/incubator/offscreen/15:05
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jrayhawk_paperbot: http://www.sciencedirect.com/science/article/pii/S105381190500274015:10
paperbothttp://libgen.org/scimag4/10.1016/j.neuroimage.2005.04.023.pdf15:10
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nmz787kanzure: that web page is pretty uninforming15:21
nmz787i guess i have to watch their video15:21
nmz787i was actually planning to head down near Eugene this weekend15:21
@kanzurei didn't watch their video because it's video15:22
@kanzuresince they don't explicitly say they have equipment, my guess is that they have none15:22
@kanzureplus, since they are wrong about their corporate structure (they are not an incubator), i don't have a lot of faith in these people15:23
nmz787oh gosh, that video is an hour15:23
@kanzurehaha15:24
nmz787hmm, this almost sounds like they have stuff http://fertilabthinkubator.com/node/515:25
nmz787says they offer chemistry15:25
@kanzurethey are vague about what they actually have15:26
@kanzureand instead they have giant slowly-loading infographics15:26
@kanzureso my guess: they are boneheads15:26
nmz787ok emailed them15:27
nmz787yeah i couldn't copy paste their email addy15:27
nmz787life tech guy there http://www.linkedin.com/profile/view?id=76873282&authType=NAME_SEARCH&authToken=iC2r&locale=en_US&srchid=292975351373495306375&srchindex=1&srchtotal=8&trk=vsrp_people_res_name&trkInfo=VSRPsearchId%3A292975351373495306375%2CVSRPtargetId%3A76873282%2CVSRPcmpt%3Aprimary15:28
nmz787'Lead scientist for development of Qubit '15:29
nmz787http://www.google.com/patents/?vid=USPATD65398115:30
nmz787Fluorometer15:30
nmz787assigned to life tech15:30
@kanzureis it still active?15:30
nmz787hah, another of their ppl are from lifetech15:31
nmz787http://www.linkedin.com/pub/shula-jaron/5/30b/aa215:31
nmz787so they both have history or being managers15:32
nmz787Jason Boone is VP at this place floragenex which is at PSBA  http://www.linkedin.com/profile/view?id=187630138&authType=NAME_SEARCH&authToken=dc2Q&locale=en_US&srchid=292975351373495566508&srchindex=2&srchtotal=218&trk=vsrp_people_res_name&trkInfo=VSRPsearchId%3A292975351373495566508%2CVSRPtargetId%3A187630138%2CVSRPcmpt%3Aprimary15:33
nmz787but their tech doesn't look to flashy http://en.wikipedia.org/wiki/Restriction_site_associated_DNA_markers15:34
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nmz787so neither the interviewers nor the fertilab people realize biocurious used kickstarter15:38
nmz787'it would have been ahead of their time' [to use kickstarter]15:38
nmz787that was just around 13:30 into the video15:39
nmz787another 50 mins left15:39
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@kanzurethat's funny15:44
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nmz787heath: why aren't you telling newbs about the diyhpl.us faq?16:00
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heathhrm?16:00
nmz787on diybio16:02
@kanzureprobably because of how embarrassed we are about it16:02
@kanzureit hasn't improved much in years16:02
@kanzurei think jonathan_ is literally the only person other than me who has ever cared16:02
nmz787it improved last year16:02
@kanzurejonathan_: btw thanks for caring about the faq16:02
nmz787wasn't klafka helping you parse emails to questions?16:02
@kanzurehey that's a good idea16:03
nmz787?16:03
@kanzureparsing questions from my email dump16:04
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heathnmz787: i haven't said anything on diybio in a long time, it's almost turned into an rss feed for me16:07
heathhttps://benchling.com/splash16:10
heathwow, images instead of text16:10
heathfor the headers16:10
nmz787heath, are you not the william heath that just posted something?16:12
heathnope16:12
heathheath matlock16:12
nmz787ahh16:12
nmz787well16:12
@kanzureyeah, i have the same opinion of benchling as i do of synbiota16:12
nmz787sry!16:12
@kanzurehttps://synbiota.ca/welcome_page/welcome16:12
heathi'm aware of that page16:13
@kanzurehaha now it's a social network16:13
@kanzureawful16:13
@kanzure"Access and edit DNA - the software of life, from any web browser using our desktop-class Open Source app"16:13
@kanzurehatred16:13
heathhttps://github.com/Synbiota/GENtle216:13
@kanzurethere was this entire closed source component too. it was crazy. but why would i want to use a bad web ui on top of this?16:13
@kanzureit would be better if there was actually good non-ui software for editing genomes and stuff16:14
heathi don't think they are pursuing that idea anymore16:14
@kanzureinstead of everyone focusing on making terrible user interfaces that don't work or aren't useful16:14
@kanzureit's like trying to make vectornti except worse16:14
heathbenchling actually has funding, but the only email i found was for cory li through the whois of the site16:15
heathone of the two founders16:15
nmz787i thought synbiota was all open16:15
nmz787gentle2 is a nice start16:15
@kanzurenah there was some email where connor got really hostile iirc16:15
nmz787i've used gentle a bunch, and ApE, but never vectornti16:16
@kanzurevectornti was this junk installed on all the lab computers at ut austin16:16
heathi don't mind sites like benchling if they open source their main tools and they use git for version control16:16
@kanzureit's actually used a lot, there's like 20,000 papers that cite using it16:16
nmz787cool I am now a reviewer for the next open hardware summit talks!16:17
@kanzureheath: i'm not entirely sure if git is the correct option for genome version control. maybe fossil. dunno. but also, just because it's open source doesn't mean it's a good idea.16:17
nmz787just got the first 4 papers to review16:17
@kanzurenmz787: me too, did windell ask you?16:17
nmz787(talks)16:17
nmz787yeah16:17
@kanzurethat's sad. i was hoping it would be someone else.16:20
@kanzureis windell the only one asking people not in his immediate community?16:20
nmz787"we need to move all of our equipment and furniture from its current home at the Broadway Commerce Center (44 West Broadway)"16:24
@kanzureguess they might have equipment16:24
nmz787so fertilab used to be in the same bldg or maybeused space of floragenex16:24
nmz787(one of the founder's company)16:24
nmz787http://fertilabthinkubator.com/node/2616:24
nmz787'News'16:24
nmz787.title16:24
yoleauxBreaking news!!! We have a new home! | FertiLab16:24
@kanzurethe /node/26 stuff means they are probably using drupal :(16:25
@kanzureyep.. http://fertilabthinkubator.com/README.txt16:25
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nmz787homegirl wants fertilab to be the 'nexus' of startup in eugene16:25
nmz787software hardware biotech everything16:25
@kanzurewhy is it startup-related? it's just another membership-fee lab.16:25
nmz787it's really not any better than plaintext16:26
@kanzureincubators are usually those things that give you things in exchange for equity. sometimes payment.. but that would be a weird relationship ("you want our money and equity??")16:26
nmz787they said they have some $16:27
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nmz787mentioned something about scholarships or something to come and try a startup in eugene16:27
nmz787they have a vision to make it a GMO center of excellence, to test stuff for GMO16:31
nmz787apparently countries are banning wheat from oregon16:32
nmz787because some unallowed GMO strain was found growing somewhere it wasn't supposed to be16:33
nmz787or somewhere it wasnt expected16:33
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nmz787huh, so this biotech company was found violating animal rights http://www.aphis.usda.gov/foia/enforcement_actions/2012/August/Animal%20Welfare%20Act%20(AWA)/Complaints/CA07655-AC%20Santa%20Cruz%20Biotechnology%20Complaint_Redacted.pdf17:03
nmz787'in willful violation' is used several times there17:03
gradstudentbotThe grant got rejected.17:06
nmz787guess the company opened in 1991, and that pdf shows 5 years of violations17:07
nmz787so i guess the law enforcement here sucks or they make enough to simply continue paying fines17:07
nmz787which is weird, for things like a drivers license you can only have so many violations before they shut you down from driving17:08
nmz787hmm, now the moral decision, should I cancel my order with this company because of this17:08
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@kanzurenmz787: heath is not william heath17:26
@kanzurenmz787: these are two completely different people17:26
@kanzurenmz787: william heath is xp_prg (you might remember him from the logs)17:26
@kanzurenmz787: our heath is ybit (the not-evil one)17:26
@kanzurecheck out the sort of bullshit that this other one spews, "The greatest amount of innovation in the history of mankind is happening at igem: http://igem.org/Main_Page"17:27
@kanzurewho the hell thinks that17:27
gradstudentbotOh man, that's a great scrabble word. I got to write that down.17:29
delinquentmesooooo17:29
delinquentmeapparently sequencers ....17:30
delinquentmeare breaking chromosomes arbitrarily17:30
delinquentmeTHEN sequencing17:30
@kanzureyes17:30
@kanzureeven afm sequencing does that because you can't get 1 billion-long reads at a single time17:31
@kanzurealso because you need the parallelism or else it would take forever17:31
@kanzurecontigs, my friend..17:31
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nmz787well it appears sigma has the item for 2/3rd the price, so morally and logistically i can cancel that order17:36
@kanzurenmz787: just wanna make sure you're not confusing those two heaths17:51
ParaSa1linheath richards was the best batman17:52
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nmz787good thing i've only had them confused for a week or three18:57
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delinquentmebut the thing is ... if it wernt arbitrarily chopped19:21
delinquentmeit would have logic going IN19:21
delinquentmemaking assembly *way* cleaner19:21
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ybityou're welcome nmz78719:40
ybithow's your microfluidics project coming along?19:42
ybitwait, i think that may have been wrldpc19:42
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ybitnope that's you19:45
ybit.title https://www.youtube.com/watch?v=b6zpEyDvdRA19:45
yoleauxIntro to DNA, DNA synthesis, and microfluidics (Nathan McCorkle) - YouTube19:45
nmz787ybit: lol20:00
nmz787ybit: slowly, i just watched a video on COMSOL and microfluidics earlier20:00
nmz787ybit: gonna design one in autodesk inventor to show a local place who is willing to fab it for me20:01
nmz787so figure i'll try to throw it into COMSOL as well20:01
nmz787the video i watched earlier had a cool slide, showing diffusion times in different volumes from 1mm cube to 1 um cube... 1uL to 1 femtoliter20:02
nmz787500s ... 0.5ms20:02
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nmz787so i shouldn't have to worry about mixers!20:02
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nmz787huh, so Santa Cruz Biotech caused a stir when they bought a ranch years ago, well before the USDA violations were filed http://www.metroactive.com/papers/cruz/07.18.96/biofarm-9629.html20:22
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nmz787'Back Ranch Road' appears to be where they keep their goats...20:25
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ParaSa1linall my goats make is poop20:30
nmz787http://www.indybay.org/newsitems/2013/01/18/18730443.php?show_comments=120:32
nmz787.title20:32
yoleauxFederal Investigations Reveal Severe Neglect of Animals at Santa Cruz Biotechnology : Indybay20:32
gradstudentbotWhere are the thermometers?20:32
nmz787'First-Ever Lawsuit Under California Cruelty Law Filed Against Animal Research Lab in Santa Cruz20:32
nmz787'20:32
nmz787January 17, 201320:33
nmz787http://www.gtweekly.com/index.php/santa-cruz-news/santa-cruz-local-news/4629-animal-welfare-questioned.html20:33
nmz787.title20:33
yoleauxAnimal Welfare Questioned | Santa Cruz Good Times20:33
nmz78713 MARCH 201320:33
nmz787bad times in the Good Times... strange20:33
nmz787' It also has facilities in Dallas, Tex., Germany and Shanghai, China.'20:34
nmz787'According to a May 12 APHIS report from last year, an inspector identified a goat lying on its side bleating loudly, suffering from a severe case of pneumonia. It died in front of the inspector. In August of last year, an inspector reported a goat had such a low weigh that its ribs were protruding dramatically. When the inspector informed the company's staff, they did not provide treatment but were found later to have continued harvesting its blood.20:35
nmz787well, maybe the goats were making antibodies for emaciating illness?20:35
nmz787'On Oct. 31, APHIS inspectors discovered a fully operational production site operated by Santa Cruz Biotechnology called H7, just nine miles away from the main ranch. The existence of the site, which APHIS reports say housed 841 goats, several of which were severely sick, was previously denied by Santa Cruz Biotechnology personnel.'20:35
nmz787interesting20:36
nmz787'a goat lost 23 percent body weight due to an inability to eat properly after a rattlesnake bite to the face '20:37
nmz787i wonder if the bite was intentional though20:37
nmz787http://arstechnica.com/science/2013/01/why-would-a-biotech-company-keep-a-secret-herd-of-goats/20:37
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nmz787dang they made it to Nature http://blogs.nature.com/news/2011/04/antibody_provider_investigated.html20:50
nmz787"Budkie says the fines imposed by the USDA are so small theyre virtually meaningless, and that some companies lump the fines into the cost of doing business."20:51
nmz787"The Animal Welfare Act, passed in 1966, includes regulations for the treatment of warm-blooded animals involved in research  but excludes rats from the genus Rattus, and mice from the genus Mus."20:51
nmz787unfortunately as we recently learned a mouse only has 1-2mL of blood and is short-lived so isn't good for antibody production20:52
nmz787.wa rat blood volume20:52
yoleauxrat: maximum recorded blood mass (mass of blood as fraction of body mass): (data not available); Scientific name: Rattus20:53
nmz787pfft20:53
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Burninate.wa guinea pig blood volume21:02
yoleauxguinea pig: maximum recorded blood mass (mass of blood as fraction of body mass): (data not available); Scientific name: Cavia porcellus21:02
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Burninate.wa pig blood volume21:02
yoleauxdomestic pig: maximum recorded blood mass (mass of blood as fraction of body mass): (2.3 to 8.7)%; Scientific name: Sus domestica21:02
Burninatealso http://xkcd.com/434/21:03
Burninateoh21:05
Burninatenmz787 You didn't finish the paste21:05
Burninate"Excluded from the Act are birds, rats of the genus Rattus (laboratory rats), mice of the genus Mus (laboratory mice), farm animals, and all cold-blooded animals.[3]"21:06
BurninatePigs are farm animals.21:06
Burninateand have significant biological compatibility with humans21:07
Burninatewhy on Earth would you use goats?21:09
Burninatewith dere cuuuue widdwe faces21:10
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ParaSa1linmaybe pigs are dangerous for that sort of thing21:22
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ParaSa1linor maybe nobody wants to deal with pig shit21:28
ParaSa1linnobody ever got mauled to death and eaten after slipping in a sheep pen21:30
@kanzuredelinquentme: sequencing by short fragments isn't that big of a problem. this is why alignment exists.21:31
@kanzureParahSailin: man we really have to get on that antibody gravy train.21:34
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jonathan_sb6 stream?21:36
ParaSa1lini think it would be somewhat difficult to verify the functional activity of avastin21:36
@kanzurethat was yesterday21:36
ParaSa1linpaperbot, http://dx.doi.org/10.1002/anie.20130257721:38
paperbothttp://libgen.org/scimag5/10.1002/anie.201302577.pdf21:38
jonathan_so no sb6?  is that it :-(21:41
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nmz787paperbot: http://onlinelibrary.wiley.com/store/10.1002/anie.201302577/asset/201302577_ftp.pdf?v=1&t=hievp0s2&s=5cc03fa2279c49bc5a56780508c4c5d3968d9b7122:25
paperbothttp://libgen.org/scimag5/10.1002/anie.201302577.pdf22:25
nmz787bitchin22:26
nmz787ParaSa1lin: so you added some crazy stuff to paper bot? using that russian site?22:28
ParaSa1linindeed22:29
nmz787does it use a proxy?22:31
nmz787i wasn't able to use that russian site, and have since forgotten it's name22:31
ParaSa1linkanzure negotiated with sci-hub owner for limited access22:31
nmz787ooooo22:32
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