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| @kanzure | oof | 09:36 |
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| @kanzure | https://twitter.com/search?q=%23pdftribute&src=typd | 10:05 |
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| jrayhawk | Seth Roberts is on an anti-doctor spree lately | 11:19 |
| jrayhawk | he's an okay guy | 11:19 |
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| @kanzure | http://pdftribute.net/ twitter links from a hashtag. they are all sort of useless though since it's hard to predict what a t.co link points to. | 12:08 |
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| rigel | ohai | 13:11 |
| rigel | i was in here some months ago talking to some folks | 13:11 |
| rigel | i cant remember anyones name though | 13:11 |
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| @kanzure | rigel: you talked about animal care. | 13:22 |
| @kanzure | and something about refrigerators being impossible to build. | 13:22 |
| rigel | that is...strange | 13:22 |
| rigel | i do not remember that | 13:22 |
| rigel | perhaps i was drunk | 13:22 |
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| delinquentme | yashgaroth, happen to know where I could read more about the given FDA regulations when using a patients own stem cells? | 13:44 |
| rigel | ficking google with their fucking link bullshit | 13:45 |
| rigel | "stem cells" site:fda.gov | 13:45 |
| rigel | http://www.fda.gov/aboutfda/transparency/basics/ucm194655.htm | 13:46 |
| delinquentme | Stem cells, like other medical products that are intended to treat, cure or prevent disease, generally require FDA approval before they can be marketed. At this time, there are no licensed stem cell treatments. | 13:55 |
| delinquentme | however people in beverly hill are doing it | 13:55 |
| delinquentme | so this is quasi legal? | 13:55 |
| delinquentme | totally ILLEGAL? | 13:55 |
| rigel | i think there are some court cases about this | 13:56 |
| rigel | physicians can prescribe whatever the hell they want | 13:57 |
| rigel | FDA tests safety/efficacy and polices marketing | 13:57 |
| delinquentme | OHHH so its MARKETING? | 13:58 |
| delinquentme | you just cant market them if they're not approved in the FDA? | 13:58 |
| rigel | that is my understanding | 13:59 |
| rigel | off-label prescribing is huge, docs can prescribe whatever the hell they want for any reason | 13:59 |
| rigel | they might not get paid if the insurance company thinks it's hinky | 13:59 |
| rigel | or if it's a controlled substance | 13:59 |
| rigel | see also: neurontin settlement, GSK settlement (over paxil, iirc) | 14:00 |
| @kanzure | i think you can also get your medical license revoked if you prescribe terrible things | 14:01 |
| rigel | yeah, but that is also pretty rare | 14:01 |
| rigel | not getting reimbursed or DEA heat is usually a sifficient disincentive | 14:01 |
| delinquentme | i mean im super interested in this beauty market | 14:02 |
| delinquentme | people pay out the ass, they're willing to be early adopters | 14:02 |
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| delinquentme | @biome_data["native"]["temperate grassland"] = @name_indexed_ecosystems["temperate grassland"] | 14:33 |
| delinquentme | how DRY? | 14:33 |
| @kanzure | that looks awful | 14:35 |
| brownies | wtf? | 14:39 |
| delinquentme | HOW DRY | 14:43 |
| delinquentme | erma gurd. | 14:44 |
| delinquentme | y u no halp | 14:50 |
| delinquentme | instead poke w stick? | 14:50 |
| delinquentme | HURM?! brownies kanzure | 14:51 |
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| * brownies grumbles | 14:55 | |
| delinquentme | http://boingboing.net/2013/01/13/filabot-turn-scrap-plastic-in.html | 14:58 |
| delinquentme | looks super polished end product | 14:58 |
| @kanzure | delinquentme: what are you asking for help with | 15:00 |
| @kanzure | all i see is a question that is more of a statement about how un-DRY something is | 15:00 |
| delinquentme | so two hashes and I need to stick a hash kv pair from one hash to another | 15:01 |
| delinquentme | basically they've both got the same key ... and one is a storage hash ... and the other is the one which has the refined values | 15:02 |
| @kanzure | biome.grassland.temperature | 15:07 |
| @kanzure | if grassland is a biome, then i would recommend just making grassland a Grassland object | 15:08 |
| @kanzure | then you can do grassland.temperature | 15:08 |
| @kanzure | if a biome has a number of grasslands, there should be a biome.grasslands lister | 15:08 |
| delinquentme | ruby hashes should me accessible through Hash.key ? | 15:11 |
| @kanzure | there's a gem somewhere that can dump keys to attributes on an object but i forget its name | 15:17 |
| @kanzure | hashify? | 15:17 |
| delinquentme | hashy ? | 15:18 |
| @kanzure | ah, looks like OpenStruct ('ostruct') is a good way to do that | 15:20 |
| @kanzure | anyway, it'sj ust a trick really, not very dry. | 15:20 |
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| brownies | actually just regular Struct should be able to give you that, no? | 15:40 |
| @kanzure | haven't experimented with ruby in a month or two, i guess i can try that | 15:40 |
| * kanzure waits for irb to switch on | 15:40 | |
| @kanzure | (it's warming up) | 15:41 |
| @kanzure | "But what should the school do when Elsevier cuts them off?" | 16:02 |
| @kanzure | "Get more schools to do it. Get as many schools as possible to do it. How many schools would Elsevier be willing to cut off just to stop a few technically proficient users without university affiliations from accessing their stuff for free?" | 16:02 |
| @kanzure | well... i think elsevier would probably block everyone. | 16:02 |
| @kanzure | gene_hacker: hey. what's up? | 16:10 |
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| @kanzure | hmmm arxiv is starting membership fees this year | 16:13 |
| @kanzure | https://confluence.cornell.edu/download/attachments/127116484/arXiv+Business+Model.pdf?version=2&modificationDate=1349107159000 | 16:13 |
| brownies | i thought arxiv was the domain of hippies ? | 16:14 |
| rigel | kanzure: elsevier can wait it out. they are one of the most profitable companies in the world on a ROI basis | 16:14 |
| @kanzure | arxiv has always been severely underfunded | 16:14 |
| rigel | so i assume they are sitting on lots of cash | 16:14 |
| @kanzure | brownies: https://confluence.cornell.edu/display/culpublic/arXiv+Sustainability+Initiative | 16:15 |
| rigel | cf. "the market can stay irrational longer than you can stay solvent" | 16:15 |
| brownies | elsevier's ROI is only about 15-20% | 16:15 |
| rigel | that's pretty fucking high | 16:16 |
| brownies | er... maybe their ROI is higher. their margin is only 15-20% | 16:16 |
| @kanzure | "arXiv's operating costs for 2013-2017 are projected to average of $826,000 per year, including indirect expenses." | 16:16 |
| rigel | 2011 profit margin of 36% | 16:17 |
| rigel | that is insane | 16:17 |
| @kanzure | "The goal is to transition from the current three-year sustainability planning phase to a long-term model with clearly identified roles for CUL, the MAB, and the SAB by December 2012." | 16:17 |
| @kanzure | w3.org and mit.edu are both down? | 16:22 |
| yashgaroth | looks like it | 16:23 |
| nmz787 | genscript.com says its capacity is 4.5 Mbp/month | 16:43 |
| @kanzure | that's... not much. | 16:43 |
| @kanzure | i'm pretty sure a single cell can top that | 16:44 |
| nmz787 | psh | 16:44 |
| nmz787 | your grandma | 16:44 |
| nmz787 | grandma's cell couldn't top an e.coli | 16:44 |
| nmz787 | (sorry, that was supposed to be a random joke) | 16:45 |
| @kanzure | upvote this (arxiv's business model) http://news.ycombinator.com/item?id=5052539 | 16:45 |
| @kanzure | they are starting to charge "membership fees" this year starting jan 2013 | 16:45 |
| @kanzure | i can't help but think that the costs are a bit high though. $826k/year.. | 16:47 |
| brownies | i didn't even know it was a Cornell project. do they own it? | 16:48 |
| brownies | isn't that a bit... biased? | 16:48 |
| @kanzure | "The term e-print was adopted to describe the articles. Ginsparg was awarded a MacArthur Fellowship in 2002 for his establishment of arXiv." | 16:49 |
| @kanzure | "The annual budget for arXiv is $400,000 for 2010." haha... what. then how did it balloon. | 16:50 |
| @kanzure | "It has been announced that, beginning in September 2011, Cornell will completely take responsibility for the operation of the project, without the further participation of Ginsparg, who is quoted in the Chronicle of Higher Education as saying it "was supposed to be a three-hour tour, not a life sentence"" | 16:50 |
| brownies | rofl | 16:51 |
| brownies | what a delightfully optimstic metaphor on the world of academic publishing | 16:51 |
| @kanzure | the doubling is concerning to me. everyone holds up arxiv in such high light. | 16:51 |
| @kanzure | ostensibly this is because ginsparg isn't an idiot and has been managing arxiv well for these years. | 16:51 |
| rigel | value proposition! branding! | 16:52 |
| rigel | more buzzwords! more MBAs! | 16:52 |
| rigel | FULL SPEED AHEAD! | 16:52 |
| brownies | they appear to be doing more Things ? | 16:52 |
| brownies | i saw a note in the budget about them working on some open software this year that would be done next year | 16:52 |
| brownies | so this year they have 2.25 programmers and next year they have 1.5 | 16:53 |
| @kanzure | i would love to get a macarthur fellowship just for hosting pdfs | 16:53 |
| brownies | haha, yeah, seriously. | 16:53 |
| brownies | presumably only the first guy to host PDFs is going to get one though. | 16:53 |
| @kanzure | party pooper | 16:54 |
| rigel | macarthur fellowships for everyone! | 16:54 |
| joshcryer | What percentage of arXiv papers are crackpots? | 16:55 |
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| @kanzure | i wonder if the federal government could go after aaronsw's family for damages etc. | 17:11 |
| rigel | doubtful | 17:12 |
| yashgaroth | I almost wonder if they could sue the government for causing his death, but I severely doubt it | 17:14 |
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| joshcryer | They could, they wouldn't win though. | 17:22 |
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| @kanzure | "then you must condemn Aaron's actions for the same reason, for he did them anonymously also."... i don't think anonymity means what you think it means. | 17:44 |
| brownies | kanzure: source? | 17:44 |
| @kanzure | brownies: the troll at the top of http://news.ycombinator.com/item?id=5051885 | 17:45 |
| brownies | kanzure: hmph. | 17:52 |
| @kanzure | "I briefly worked at JSTOR during the the time Aaron was doing the massive downloads from JSTOR. I was not the principal engineer involved, but I did work on a daily basis with the person who was in charge." | 18:08 |
| @kanzure | http://unhandled.com/2013/01/12/the-truth-about-aaron-swartzs-crime/#comment-530 | 18:08 |
| @kanzure | "At the time, JSTOR had previously made arrangements with academics for large bulk downloads or transfers of documents." | 18:09 |
| @kanzure | (with huge licensing agreements i assume) | 18:09 |
| rigel | i read a good book on the history of this over the summer | 18:16 |
| rigel | goddamn, i wish i could remember the title | 18:18 |
| delinquentme | do we know of anyone whos had lipo? | 18:21 |
| delinquentme | I've heard its really really rough on the body | 18:21 |
| delinquentme | but a solid way to harvest fat for stem cells | 18:22 |
| @kanzure | you could just collect other cells and convert them to stem cells instead. | 18:22 |
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| delinquentme | kanzure, the reverting process is mostly just cytokines right? | 18:39 |
| delinquentme | but theres alot to be said about the environment and other complexities? | 18:40 |
| yashgaroth | transcription factors, cytokines, infinite patience | 18:40 |
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| delinquentme | "enhancer" == "promoter" ? | 18:42 |
| yashgaroth | no, enhancers regulate expression of genes within a large region surrounding them, promoters are tied to a single gene | 18:43 |
| yashgaroth | there are some similarities between them | 18:44 |
| yashgaroth | ...which I won't get in to, but basically no | 18:45 |
| delinquentme | Would it be a misnomer to ask what some of the more complex cells in the human body are? | 18:46 |
| yashgaroth | neurons | 18:46 |
| yashgaroth | any other type of cell is infinitely less complex than neurons | 18:47 |
| yashgaroth | and yes it is a misnomer, every cell is special and unique | 18:47 |
| yashgaroth | except kupffer cells, fuck those guys | 18:48 |
| delinquentme | infinitely less complex | 18:49 |
| delinquentme | thats a hell of a claim | 18:49 |
| yashgaroth | it sure is | 18:49 |
| delinquentme | I've looked at biovisions of normal cells and they're pretty damn complex ... neurons are that much different? | 18:49 |
| delinquentme | I mean its not the first time that my education has failed me | 18:50 |
| yashgaroth | oh they're all hella complex, but in terms of determining their function, yes | 18:50 |
| yashgaroth | every cell has an equally complex gene regulatory network | 18:50 |
| yashgaroth | since I'm not totally sure what you're asking, I'm afraid I must resort to grand sweeping generalizations | 18:51 |
| delinquentme | transcription factors ... SPIRAL along pieces of DNA?? | 18:53 |
| yashgaroth | they attach to DNA, usually within the grooves so that they can recognize specific motifs of base pairs, which form into a helix, so...sort of? | 18:54 |
| delinquentme | yeah I was watching this decent visualization video | 18:55 |
| delinquentme | I was wondering how it "knows" the sequence its after ... but the confirmation of the molecule would match to a given sequence | 18:55 |
| delinquentme | and thus transcription factors vary in length / shapes? | 18:56 |
| delinquentme | http://www.youtube.com/watch?v=MkUgkDLp2iE | 18:56 |
| yashgaroth | certain protein sequences are able to recognize certain dna sequences, and yes they do vary in length/shape/size/function/specificity | 18:56 |
| yashgaroth | oh I see what you mean, yes they are theorized to travel along the dna strand until they find their recognition sequence | 18:58 |
| delinquentme | and so obviously transcription isn't happening while the dna is bundled around histones | 18:58 |
| yashgaroth | not when it's tightly bound | 18:58 |
| yashgaroth | but yes back to your original question, enhancers are responsible for freeing dna from being bound to histones, so that promoters can come in and transcribe the genes | 18:59 |
| yashgaroth | generally speaking | 18:59 |
| yashgaroth | or rather they mediate the freeing | 19:00 |
| delinquentme | ahhh ok | 19:00 |
| delinquentme | check! enhancers work to unravel the chromatin to facilitate transcription | 19:01 |
| delinquentme | erm . or they are a first step , not to be confused with promoters which also aid in transcription | 19:02 |
| yashgaroth | yes, and there is again quite a bit of overlap between the two | 19:02 |
| delinquentme | however neither actually constructs the yield protein | 19:04 |
| yashgaroth | no that's ribosomes | 19:04 |
| delinquentme | well at least with TONS of complexity there are TONS of options and places to stick new operations in | 19:06 |
| yashgaroth | that's one way to think about it | 19:06 |
| delinquentme | and so the final output protein from the ribosome is kind of the active unit to get cells to do things | 19:07 |
| yashgaroth | ...sure | 19:07 |
| delinquentme | I know the yields can be varied ... but is cell signaling using these proteins ? | 19:08 |
| yashgaroth | like, signaling between cells? it's usually proteins, sometimes small molecules, but those molecules are made by proteins, so yeah | 19:10 |
| delinquentme | hormones != proteins | 19:11 |
| @kanzure | since when | 19:11 |
| yashgaroth | hormones are often proteins | 19:11 |
| delinquentme | oh ok | 19:11 |
| delinquentme | so what happens when we just dump said hormone on a cell | 19:11 |
| delinquentme | how does that differ from the cells actually producing / excreting that hormone? | 19:12 |
| yashgaroth | it shouldn't differ, all else being equal | 19:12 |
| delinquentme | ribosomes... basically all have the same molecular structure? | 19:13 |
| delinquentme | in a given species | 19:14 |
| yashgaroth | yes | 19:14 |
| nmz787 | so i just calculated microfluidic DNA synthesis should be 6-9 orders of magnitude cheaper than $ 0.28/bp | 19:15 |
| nmz787 | potentially 12 orders less | 19:15 |
| delinquentme | any new fun stuff on etching techniques? | 19:16 |
| nmz787 | lookin for a DLP projector for cheap to try using tha twith a microscope | 19:17 |
| nmz787 | add servos/steppers to the XY | 19:17 |
| nmz787 | but i'm applyin to PhD too | 19:18 |
| delinquentme | so is there alot of complexity in getting substances / proteins / dna from *outside* the cell ... into the nucleus of the cell where it can actually modify behavior? | 19:18 |
| nmz787 | so I would just use this lithography with FIB too | 19:18 |
| delinquentme | or does that depend on the approach you want to take? IE " throw some hormones at it ... and we dont have to worry about getting it INTO the nucleus " | 19:18 |
| nmz787 | i think so | 19:19 |
| nmz787 | but viruses and maybe that lipofectamine shit do it | 19:19 |
| delinquentme | ahh true | 19:19 |
| nmz787 | so its prob standard protocol | 19:19 |
| juri_ | mm. this channel is awesome; i learn a whole lot just reading the backlog. | 19:19 |
| yashgaroth | the point of hormones is that they act on cell receptors that transduce the signal to the nucleus | 19:19 |
| delinquentme | again. tons of ways to get stuff in | 19:19 |
| delinquentme | so if you want to get a cell to do more or less of its "normal thing" you can throw hormones / proteins at it | 19:20 |
| delinquentme | if you want it to do something novel ... IE create oil or something, you need to insert new DNA | 19:20 |
| yashgaroth | sometimes, depending on the type of cell | 19:20 |
| yashgaroth | oh and yes to your second question | 19:21 |
| @kanzure | juri_: your goal should be to supercede the awesomeness of this place | 19:21 |
| delinquentme | vectors ... they insert DNA into the cell membrane correct? not the nucleus? | 19:21 |
| delinquentme | kanzure, juri_ +1 | 19:21 |
| yashgaroth | non-viral vectors usually do | 19:21 |
| yashgaroth | viruses tend to transport it into the nucleus, at least with dna | 19:21 |
| delinquentme | oh theres multiple "vectors" ? | 19:21 |
| juri_ | kanzure: it is. however, i'm aware that we each have limits and specialties, so i'm really just trying to answer the question : for the skills of me, how do i add the knowlege of others to superceed what has been done before? | 19:22 |
| delinquentme | how do crossing of the cell membrane? | 19:22 |
| delinquentme | i feel like this is a heavy process... | 19:22 |
| yashgaroth | cationic liposomes filled with the deliverable that merge with the cell membrane, electroporation that opens holes in the membrane | 19:22 |
| yashgaroth | some cell-penetrating peptides/chemicals that are conjugated to your deliverable can transit across the membrane | 19:23 |
| delinquentme | yeah I know about only electroporation :P | 19:25 |
| delinquentme | there we go: http://en.wikipedia.org/wiki/File:Liposome.jpg | 19:26 |
| delinquentme | so the cell engineering process is kind of getting all these things together in a given package | 19:28 |
| yashgaroth | that stuff it pretty routine, the tough part is figuring out what genes you need to put in to make it go | 19:29 |
| delinquentme | erm or bio-engineering ... more generally. IE Getting the drug into its proper spot: within the liposome or within the lipid bilayer ... embedding the homing peptide | 19:30 |
| yashgaroth | that's the routine bit | 19:30 |
| delinquentme | what does that process look like? | 19:30 |
| yashgaroth | buy fectamine from lifetech, mix with dna, shake lightly, add to cells | 19:31 |
| delinquentme | hahaha | 19:31 |
| delinquentme | fuck yes! | 19:31 |
| delinquentme | that sounds easy | 19:32 |
| yashgaroth | you should see what lipofectamine costs | 19:32 |
| delinquentme | and then they just embed into the lipid bylayer rafts orrrr? | 19:32 |
| yashgaroth | no not the rafts; cationic lipids have a positive charge on the outside, while the cell membrane is negative, so they merge like two bubbles or something | 19:33 |
| yashgaroth | and thus your deliverable is inside the cytoplasm | 19:33 |
| delinquentme | so whats the advantage of lipofectamine vrs electroporation? I mean you're shocking sufficient cells to not kill ALL of them right? | 19:33 |
| yashgaroth | don't worry about lipid rafts you don't need to know about them | 19:33 |
| yashgaroth | electroporation works on a much smaller volume of cells, and is much less efficient, and more toxic | 19:33 |
| yashgaroth | since I have no idea what your end goal is I can't recommend one method specifically | 19:34 |
| delinquentme | toxic to the cells? to modifying the input proteins? | 19:34 |
| delinquentme | ( obv to cells ) | 19:35 |
| yashgaroth | toxic because you're electrocuting the cells | 19:35 |
| delinquentme | oh but if they recover they're peachy right? | 19:35 |
| yashgaroth | sure, mostly | 19:35 |
| delinquentme | O_o frankencell | 19:35 |
| delinquentme | so lipofectamine <<< costs? | 19:35 |
| delinquentme | im reading about how it works | 19:35 |
| yashgaroth | it's hella expensive, but when you're producing protein that costs exponentially more than its weight in gold, it's worthwhile | 19:36 |
| delinquentme | Oh you're saying you've got custom oligos n stuff so you need to ensure it works | 19:37 |
| delinquentme | so its just worth it | 19:37 |
| @kanzure | yashgaroth: why haven't i paid you to start up a random antibody company yet | 19:37 |
| yashgaroth | no oligos are cheap | 19:37 |
| yashgaroth | funny story kanzure, I'm 99% sure I'm starting at a tiny antibody company next week | 19:37 |
| yashgaroth | like two guys and me, makin' proteins and stuff | 19:37 |
| @kanzure | well, why not do your own | 19:37 |
| yashgaroth | lotta startup cost, lotta companies to compete with | 19:38 |
| yashgaroth | however at this company I'll actually be able to use equipment for my projects | 19:38 |
| @kanzure | i'm pretty sure the lab equipment startup cost for antibody production is <$50k | 19:38 |
| yashgaroth | my current place is locked down because it's clinical drug manufacture, but here I'll have a new fplc, incubator, the works | 19:38 |
| yashgaroth | man you spend 50k on an fplc | 19:38 |
| @kanzure | fourier penis liquid chromatography? | 19:39 |
| yashgaroth | fast protein, but close | 19:39 |
| @kanzure | fast protein. damn. | 19:39 |
| yashgaroth | not to mention leasing space, permits, the hundred chemicals you'll need a supply of, deep freezers, the works | 19:39 |
| yashgaroth | anyway the owner at this place was my boss at my last company, chill chinese dude | 19:40 |
| yashgaroth | so if I come in on the weekend and make a bunch of plasmid he won't mind/notice | 19:40 |
| rigel | are you going to be changing your nick to heisenberg? | 19:40 |
| rigel | because that's taken, apparently | 19:40 |
| yashgaroth | hey now plasmids ain't illegal yet | 19:41 |
| delinquentme | yashgaroth, lemme know if you need a shaker | 19:42 |
| delinquentme | $275 + tip | 19:42 |
| yashgaroth | anyway I'm quite pleased since the local diybio space keeps getting delayed and will have shit equipment in comparison | 19:42 |
| yashgaroth | no they've got shakers, and anyway I only need shaker-incubators | 19:42 |
| delinquentme | noted. | 19:42 |
| delinquentme | yashgaroth, where locate? | 19:43 |
| delinquentme | where LIVE HOME ADDRESS! | 19:43 |
| yashgaroth | san diego, natch | 19:43 |
| delinquentme | oh sweet my cousin just took a job there | 19:43 |
| yashgaroth | it's a nice town | 19:44 |
| yashgaroth | tell you what kanzure, if they catch me midnight splicin' I'll come to you, until then it's free equipment | 19:44 |
| delinquentme | ribosomes look like a jumbled mess | 19:45 |
| @kanzure | yashgaroth: i was once spending a weekend in a lab when the professor didn't think i'd be around. he gave me the weirdest stink eye when he discovered me working. | 19:45 |
| yashgaroth | haha | 19:45 |
| @kanzure | it was very bizarre, because most of the time they compel you to work constantly | 19:45 |
| delinquentme | OOOOOOOO http://rna.ucsc.edu/rnacenter/ribosome_images.html | 19:46 |
| yashgaroth | that's ribosomal RNA, a blow-up schematic, it doesn't look like that on the protein | 19:46 |
| rigel | one time i got really shitfaced and blacked out, apparently couldnt find my way home from the side of town i was on | 19:46 |
| rigel | i woke up on the couch at work | 19:46 |
| rigel | got a side-eye from a coworker, and a knowing look from the security guard | 19:47 |
| @kanzure | delinquentme: there are thousands of videos on youtube that illustrate how ribosomes operate | 19:47 |
| delinquentme | yashgaroth, this would be a primary structure right? | 19:48 |
| delinquentme | the 2nd and 3rd are the functional forms ja? | 19:49 |
| yashgaroth | those diagrams are technically secondary structure for the rRNA | 19:49 |
| yashgaroth | primary is just the sequence | 19:49 |
| rigel | dibosomes are crazy | 19:49 |
| delinquentme | ohhh ok ok | 19:49 |
| rigel | ribosomes even | 19:49 |
| yashgaroth | tertiary is how it's folded onto the ribosome protein | 19:49 |
| delinquentme | http://www.ks.uiuc.edu/Research/dbps/images/DBPribosomeSecY.png | 19:50 |
| rigel | dont they have a slightly different universal code or something | 19:50 |
| delinquentme | like look at that | 19:50 |
| delinquentme | its a freaking mess | 19:50 |
| rigel | no, im thinking trna | 19:50 |
| @kanzure | does it make financial sense to be shorting elsevier over a 10 or 20 year period? | 19:51 |
| @kanzure | i mean eventually they will die in a fire, right? | 19:51 |
| rigel | why are you trying to profit off of someone else's misfortune | 19:51 |
| yashgaroth | have you done some comparative analysis between pdf's from different proxies and providers to determine if they're watermarking? | 19:51 |
| rigel | arent options like the worst fucking gambling, er, investment vehicles you can buy | 19:51 |
| @kanzure | yashgaroth: many of their watermarks are very obvious, but no i haven't tried from e.g. nature | 19:52 |
| @kanzure | yashgaroth: i'd love to do that analysis though | 19:52 |
| yashgaroth | like, straight comparing every bit between pdf X downloaded from pdx and umb, and seeing if they differ at all | 19:52 |
| delinquentme | http://rna.ucsc.edu/rnacenter/images/figs/70s_atrna_labels.jpg | 19:52 |
| @kanzure | what i need most to get started is multiple copies of the same pdf | 19:52 |
| @kanzure | also, some publishers insert an entire front page with ip address info, so i will just remove that page in my analysis | 19:52 |
| rigel | you're not piping stuff through .ps and then back to pdf, and then re-adding metadata? | 19:52 |
| rigel | i thought i suggested that last time i was in here | 19:52 |
| rigel | its a lot easier to find/remove that shit if you do that | 19:53 |
| @kanzure | most papers dont have the metadata in the pdf anyway | 19:53 |
| rigel | wow, i am talking a lot of shit | 19:53 |
| @kanzure | additionally, it's worth knowing whether or not the pdfs are tampered with, rather than just being paranoid | 19:54 |
| @kanzure | i think overzealous paranoia is adorable, but it's not for me | 19:54 |
| @kanzure | let's pick a set of publishers to test it out on | 19:55 |
| @kanzure | i suggest: nature publishing group, sciencedirect, springer, wiley interscience | 19:56 |
| yashgaroth | bentham and ingenta, and whoever sciencemag's publisher is | 19:56 |
| delinquentme | http://rna.ucsc.edu/rnacenter/images/figs/50s_30s_labels.jpg and so people are labeling parts of this image in order to identify parts of these molecules? | 19:56 |
| @kanzure | http://www.nature.com/nmat/journal/v11/n9/full/nmat3357.html | 19:56 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Rapid%20casting%20of%20patterned%20vascular%20networks%20for%20perfusable%20engineered%20three-dimensional%20tissues.pdf | 19:56 |
| @kanzure | does anyone have another copy of that one? | 19:56 |
| delinquentme | is this to modify them? ... I'd guess this is akin to parts of a car? | 19:57 |
| delinquentme | and how much movement happens within that structure? | 19:57 |
| @kanzure | delinquentme: it's to study them in general. | 19:57 |
| yashgaroth | delinquentme, A P & E are the catalytic regions that add amino acids onto the growing chain | 19:57 |
| @kanzure | nmz787: can you get the umbc copy of that nature article? | 19:58 |
| @kanzure | erm.. umb | 19:58 |
| @kanzure | yashgaroth: can you pick out an article for bentham and ingenta? | 19:58 |
| delinquentme | yashgaroth, so those are definitely moving parts | 19:59 |
| yashgaroth | I'll need to check for journals shared by both unis, gimme a minute | 19:59 |
| yashgaroth | the whole protein is a moving part | 19:59 |
| delinquentme | is the rest of it functional? simply support structure? | 19:59 |
| yashgaroth | those are the parts responsible for recognizing the correct tRNA, adding its attached amino acid to the chain, and ejecting the empty tRNA, respectively | 20:00 |
| delinquentme | ok so transcriptic is doing plasmids ... plasmids are nothing more than circular DNA chains ... so they're *only* doing dna synthesis? | 20:01 |
| yashgaroth | I think they do splicing too | 20:01 |
| delinquentme | oh ok so putting a bunch of plasmids together | 20:01 |
| yashgaroth | sure | 20:03 |
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| yashgaroth | man UMB may have nature protocols but they've got shit-all from bentham/ingenta | 20:05 |
| @kanzure | another paper i'd like to try is | 20:07 |
| @kanzure | http://www.sciencedirect.com.proxy.lib.pdx.edu/science/article/pii/S0022283610011575 | 20:07 |
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| @kanzure | same md5sums on the nature papers | 20:10 |
| yash | excellent | 20:11 |
| yash | also, brb | 20:11 |
| @kanzure | same md5sums on sciencedirect papers | 20:11 |
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| delinquentme | http://www.knowledgeoftoday.org/2012/06/fda-cancer-industry-prevent-cure.html | 20:13 |
| delinquentme | so it sounds sensational .. but I'm seeing a few links to legit research down at the bottom... | 20:14 |
| superkuh | Automated detection and removal of those 1st page IP of downloader pages would be nice. I sometimes forget to do it with ghostscript. | 20:14 |
| delinquentme | and financially it could be a motivation ... but to say that theres sufficient money to be made that we keep killing people ... | 20:14 |
| delinquentme | ( via cancer ) thoughts? | 20:14 |
| @kanzure | superkuh: there are also other things that appear of course | 20:15 |
| @kanzure | i am having trouble finding examples in my collection :( | 20:15 |
| @kanzure | what was the exact text? it was something like "Downloaded by .. on date .. " | 20:15 |
| @kanzure | ooh this one is good | 20:16 |
| @kanzure | http://diyhpl.us/~bryan/papers2/Evaluation%20of%20the%20micro%20wobble%20motor%20fabricated%20by%20concentric%20build-up%20process.pdf | 20:16 |
| @kanzure | "Authorized licensed use limited to: University of Texas at Austin. Downloaded on July 22, 2009 at 15:50 from IEEE Xplore. Restrictions apply." | 20:17 |
| @kanzure | yeah that fucker's getting removed | 20:17 |
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| @kanzure | fenn: maybe you will find something for psychometrics here? http://psychopy.org/ | 20:23 |
| @kanzure | "/JS and /JavaScript indicate that the PDF document contains JavaScript. Almost all malicious PDF documents that I’ve found in the wild contain JavaScript (to exploit a JavaScript vulnerability and/or to execute a heap spray). Of course, you can also find JavaScript in PDF documents without malicious intend." | 20:26 |
| @kanzure | aaaahhhhhhh | 20:26 |
| @kanzure | who would think that's a good idea | 20:26 |
| @kanzure | http://blog.didierstevens.com/2008/04/29/pdf-let-me-count-the-ways/ | 20:27 |
| @kanzure | http://brundlelab.wordpress.com/2010/11/23/malware-pdf-analysis-of-a-very-simple-sample/ | 20:35 |
| rigel | you gotta think though, the delivery infrastructure for this stuff is not that smart | 20:36 |
| rigel | adding a ps line that indicates date, time, and ip before converting to pdf is about the best theyre going to be able to do | 20:36 |
| rigel | that functionality is widely distributed, but the incentive to get someone to build something more substantial is low | 20:37 |
| rigel | they know that academics share the ever loving shit out of journal articles | 20:37 |
| rigel | and an obvious line like "downloaded from" is like a shitty lock -- it's going to keep the honest people honest | 20:38 |
| @kanzure | so? | 20:38 |
| rigel | i just dont think you need to spend a lot of time analyzing this | 20:40 |
| @kanzure | it's not a lot of time | 20:41 |
| @kanzure | it's like five lines of code to remove the offending line from pdf files | 20:41 |
| yashgaroth | after what happened to aaron swartz a little caution isn't unfounded | 20:41 |
| rigel | he wasnt caught by jstor adding lines to the pdf | 20:42 |
| rigel | from what people are saying though, he didnt rate limit | 20:43 |
| yashgaroth | how he was caught is irrelevant, the point is that he was and what happened to him afterwards | 20:43 |
| rigel | removing the line, yeah | 20:43 |
| rigel | its just that you can go down the rabbit hole with this | 20:43 |
| rigel | downloading from two independent sources and sha1summing or whatever | 20:44 |
| yashgaroth | you only need to check each publisher once, maybe each journal if you wanna get intense | 20:45 |
| rigel | fair enough | 20:45 |
| @kanzure | if you can do malware detection on top of pdfs, you can do "evil lines of text" detection. | 20:45 |
| @kanzure | as far as i'm concerned those lines /are/ malware anyway | 20:46 |
| rigel | so the pyphantomjs thing is working out? | 20:46 |
| rigel | i remember thats something you were excited about before | 20:47 |
| rigel | i have not used it, not enough time to learn anything other than school | 20:47 |
| @kanzure | pyphantomjs doesn't entirely work at the moment | 20:51 |
| @kanzure | it needs some maintenance | 20:52 |
| rigel | meh | 21:06 |
| rigel | i want to pull my email off of this horrible archive system my institution has | 21:06 |
| rigel | archive it on an encrypted drive at home | 21:06 |
| rigel | but it is such a huge pain in the ass, with random links that dont appear until you mouseover them and double click | 21:07 |
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| juri_ | https://petitions.whitehouse.gov/petition/award-presidential-medal-freedom-aaron-swartz/n6Fcyn3V | 21:55 |
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| nmz787 | did you need some umb ezproxy tests? | 22:16 |
| yashgaroth | yeah I was hoping to compare the same pdf downloaded via two different libraries to see if we can detect a watermark and/or identifying information | 22:17 |
| nmz787 | ahh | 22:17 |
| nmz787 | link? | 22:17 |
| yashgaroth | had a hard time finding a bentham or ingenta journal that umb was subscribed to | 22:17 |
| @kanzure | i did nature and sciencedirect | 22:18 |
| nmz787 | ahh, did you get UMB creds yet? | 22:18 |
| @kanzure | i did it at another school | 22:18 |
| yashgaroth | cell is on elsevier and everyone's subbed to cell, try one of their papers | 22:18 |
| nmz787 | well since i'm not gonna do the md5 just give me a link to the cell paper you choose | 22:19 |
| yashgaroth | I just thought of them a second ago, gimme a minute | 22:19 |
| yashgaroth | http://www.sciencedirect.com/science/article/pii/S0092867412014110 I guess | 22:19 |
| nmz787 | i think watermark may depend on the publisher tho | 22:20 |
| yashgaroth | oh also mary-ann liebert, they publish a bunch of stuff | 22:20 |
| @kanzure | yeah sciencedirect wasn't adding a watermark | 22:20 |
| yashgaroth | that's why we need to do at least one per publisher | 22:20 |
| @kanzure | i already did check them | 22:20 |
| @kanzure | choose something else :P | 22:21 |
| @kanzure | ieee tends to slap on stuff | 22:21 |
| yashgaroth | uhh http://online.liebertpub.com/doi/pdfplus/10.1089/hum.2012.029 for liebert | 22:22 |
| yashgaroth | oh wait I don't think pdx is subscribed to them | 22:23 |
| yashgaroth | oh no it's just not current | 22:24 |
| nmz787 | here is the cell paper http://diyhpl.us/~nmz787/1-s2.0-S0092867412014110-main__UMB.pdf | 22:24 |
| nmz787 | so not that liebert link? | 22:25 |
| yashgaroth | ahh here we go http://dx.doi.org.proxy.lib.pdx.edu/10.1089/hum.2010.223 | 22:25 |
| nmz787 | that link didn't work with ezproxy anyway | 22:26 |
| yashgaroth | yeah I had to go through pdx's library site | 22:26 |
| nmz787 | that didn't work either | 22:26 |
| nmz787 | is liebert a database or what? | 22:26 |
| yashgaroth | no it's a publisher | 22:27 |
| nmz787 | ok lemme search UMB | 22:27 |
| yashgaroth | of such noteworthy journals as Rejuvenation Research | 22:27 |
| yashgaroth | http://go.galegroup.com.proxy.lib.pdx.edu/ps/publicationSearch.do?lm=&inPS=true&prodId=AONE&userGroupName=s1185784&method=doLinkDirectedSearch&searchType=AdvancedSearchForm&qt=PU~%22Human+Gene+Therapy%22~~DA~120111001~~IU~%2210%22~~VO~22 | 22:27 |
| yashgaroth | has somewhat direct links to pdfs | 22:27 |
| nmz787 | full text coverage for human gene therapy is December 1, 2007 - October 1, 2011 | 22:29 |
| yashgaroth | ok well since proxies don't work I can't go through UMB's library to find a random pdf | 22:29 |
| yashgaroth | pick one that looks fun | 22:30 |
| nmz787 | the link to the foamy virus vector paper for me is http://go.galegroup.com.ezproxy.lib.umb.edu/ps/retrieve.do?retrieveFormat=PDF_FROM_CALLISTO&inPS=true&prodId=AONE&userGroupName=mlin_b_umass&workId=PI-2EPC-2011-OCT00-IDSI-121.JPG%7CPI-2EPC-2011-OCT00-IDSI-122.JPG%7CPI-2EPC-2011-OCT00-IDSI-123.JPG%7CPI-2EPC-2011-OCT00-IDSI-124.JPG%7CPI-2EPC-2011-OCT00-IDSI-125.JPG%7CPI-2EPC-2011-OCT00-IDSI-126.JPG%7CPI-2EPC-2011-OCT00-IDSI-127.JPG%7CPI-2EPC-2011-OCT0 | 22:30 |
| yashgaroth | okay | 22:31 |
| nmz787 | that is the link to the iframe with the pdf in it | 22:31 |
| yashgaroth | do you have a save option for the pdf | 22:31 |
| nmz787 | here is the fulltext HTML with that PDF link in it http://go.galegroup.com.ezproxy.lib.umb.edu/ps/i.do?id=GALE%7CA272484716&v=2.1&u=mlin_b_umass&it=r&p=AONE&sw=w | 22:32 |
| nmz787 | yes | 22:32 |
| yashgaroth | these links are of minimal use to me without a UMB login | 22:32 |
| @kanzure | nmz787: your first ilnk was bad because it had some session crap in the url. | 22:32 |
| @kanzure | pdx.edu doesn't seem to have access to that anyway | 22:33 |
| nmz787 | http://diyhpl.us/~nmz787/A%20foamy%20virus%20vector%20system%20for%20stable%20and%20efficient%20RNAi%20expression%20in%20mammalian%20cells__UMB.pdf | 22:33 |
| yashgaroth | http://go.galegroup.com.proxy.lib.pdx.edu/ps/retrieve.do?retrieveFormat=PDF_FROM_CALLISTO&inPS=true&prodId=AONE&userGroupName=s1185784&workId=PI-2EPC-2011-OCT00-IDSI-121.JPG%7CPI-2EPC-2011-OCT00-IDSI-122.JPG%7CPI-2EPC-2011-OCT00-IDSI-123.JPG%7CPI-2EPC-2011-OCT00-IDSI-124.JPG%7CPI-2EPC-2011-OCT00-IDSI-125.JPG%7CPI-2EPC-2011-OCT00-IDSI-126.JPG%7CPI-2EPC-2011-OCT00-IDSI-127.JPG%7CPI-2EPC-2011-OCT0 | 22:33 |
| yashgaroth | 0-IDSI-128.JPG%7CPI-2EPC-2011-OCT00-IDSI-129.JPG%7CPI-2EPC-2011-OCT00-IDSI-130.JPG%7CPI-2EPC-2011-OCT00-IDSI-131.JPG&docId=GALE%7CA272484716&callistoContentSet=PER&isAcrobatAvailable=false | 22:33 |
| yashgaroth | hmm uh | 22:33 |
| @kanzure | "ApplicationError: Error Code:Exception while authenticating. (Click here for stack trace)" | 22:33 |
| yashgaroth | well it's on this page: http://go.galegroup.com.proxy.lib.pdx.edu/ps/publicationSearch.do?lm=&inPS=true&prodId=AONE&userGroupName=s1185784&method=doLinkDirectedSearch&searchType=AdvancedSearchForm&qt=PU~%22Human+Gene+Therapy%22~~DA~120111001~~IU~%2210%22~~VO~22 | 22:33 |
| @kanzure | "Cause: com.gale.presentation.framework.RequestException: Exception while authenticating" | 22:34 |
| @kanzure | "cause = "Failure Response from the server, response code: 500"" | 22:34 |
| @kanzure | "at com.gale.capm.application.auth.AuthenticationServicePrxHelper.authenticate(AuthenticationServicePrxHelper.java:48)" | 22:34 |
| nmz787 | i get "Log in to access Academic Onefile | 22:35 |
| nmz787 | Your product session has expired." | 22:35 |
| @kanzure | because they store the session id in the url that you pasted | 22:35 |
| @kanzure | or possibly in a cookie | 22:36 |
| @kanzure | userGroupName:mlin_b_umass | 22:36 |
| @kanzure | well that sounds wrong | 22:36 |
| nmz787 | if I modify this http://go.galegroup.com.ezproxy.lib.umb.edu/ps/i.do?id=GALE%7CA272484716&v=2.1&u=mlin_b_umass&it=r&p=AONE&sw=w | 22:37 |
| nmz787 | to proxy.lib.pdx | 22:37 |
| nmz787 | it asks for my library password, but my pass doesnt auth there | 22:37 |
| @kanzure | yes, that's not a pdx password prompt | 22:37 |
| @kanzure | don't type passwords into random forms that ask you to type in your password | 22:38 |
| nmz787 | kanzure: http://vikat.pdx.edu/search/a?a&searchtype=t&SORT=D&searcharg=human+gene+therapy&searchscope=5 | 22:38 |
| nmz787 | yeah i was able to navigate to the PDF from the library at pdx | 22:39 |
| nmz787 | http://diyhpl.us/~nmz787/A%20foamy%20virus%20vector%20system%20for%20stable%20and%20efficient%20RNAi%20expression%20in%20mammalian%20cells__PDX.pdf | 22:40 |
| nmz787 | http://www.teselagen.com/ | 22:43 |
| nmz787 | Here at TeselaGen, we are developing a revolutionary Biological Design Automation system, and currently testing our beta product with over 100 scientists and engineers. | 22:43 |
| @kanzure | oh great another proprietary pile of crap that i have to reverse engineer | 22:43 |
| yashgaroth | why even have a website if they don't have a single sentence about what it does | 22:44 |
| -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has joined ##hplusroadmap | 22:44 | |
| yashgaroth | ah http://synbiobeta.com/teselagen/ | 22:46 |
| yashgaroth | oh look mac cowell is doing http://genefoo.com/ | 22:51 |
| @kanzure | what happened to snplasergene | 22:51 |
| @kanzure | "personalpcr" i see.. | 22:51 |
| yashgaroth | haha "Genefoo was started in Winter 2013 in the industrial outskirts of San Francisco" | 22:52 |
| @kanzure | hah shopify | 22:53 |
| @kanzure | well whatever floats your boat | 22:53 |
| @kanzure | http://genefoo.myshopify.com/ | 22:53 |
| @kanzure | pfft tumblr. http://diybioftw.com/ | 22:53 |
| @kanzure | ok i give up on macowell. | 22:53 |
| yashgaroth | one year warranty on the pipettes, nothing on the pcr machine...hmm | 22:56 |
| bkero | kanzure: oshit, their office is about 3 blocks away from my office in Mountain View :P | 23:09 |
| -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving] | 23:16 | |
| -!- amphetamine [~dextro@unaffiliated/amphetamine] has joined ##hplusroadmap | 23:26 | |
| -!- AdrienG [~dextro@unaffiliated/amphetamine] has quit [Ping timeout: 276 seconds] | 23:30 | |
| @kanzure | "This information is top security. When you have read it, destroy yourself." | 23:30 |
| @kanzure | ah hell his irc bot is still going (datum) | 23:41 |
| -!- erasmus [~esb@unaffiliated/erasmus] has quit [Quit: Ciao a tutti!] | 23:42 | |
| bkero | What's it do? | 23:42 |
| bkero | kanzure: btw, /me waves from Vietnam. | 23:42 |
| @kanzure | bkero: i have some friends in saigon if you're looking to meet some programmers | 23:43 |
| bkero | kanzure: just came from there, down at an island now. With programmers. http://www.hackerbeach.org/ | 23:43 |
| bkero | I'd definitely be up for meeting them if I had any spare time up there though | 23:44 |
| @kanzure | i might have misunderstood. does that mean "next time" or "give me the names now"? | 23:59 |
| --- Log closed Mon Jan 14 00:00:30 2013 | ||
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