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[~eudoxia@r186-53-138-233.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 10:05 <@kanzure> https://twitter.com/search?q=%23pdftribute&src=typd 10:46 -!- strages_home [~strages@98.67.169.50] has joined ##hplusroadmap 11:01 -!- Thorbinator [~Thorbinat@76-14-130-152.rk.wavecable.com] has joined ##hplusroadmap 11:09 -!- Netsplit *.net <-> *.split quits: Thorbinator1 11:19 < jrayhawk> Seth Roberts is on an anti-doctor spree lately 11:19 < jrayhawk> he's an okay guy 11:36 -!- EnLilaSko [~Nattzor@unaffiliated/enlilasko] has quit [Ping timeout: 255 seconds] 11:37 -!- EnLilaSko [~Nattzor@unaffiliated/enlilasko] has joined ##hplusroadmap 11:38 -!- sylph_mako [~mako@103-9-42-1.flip.co.nz] has joined ##hplusroadmap 12:08 <@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. 12:29 -!- wizrobe [~aserid@c-76-23-254-105.hsd1.ct.comcast.net] has left ##hplusroadmap [] 12:30 -!- wizrobe [~aserid@c-76-23-254-105.hsd1.ct.comcast.net] has joined ##hplusroadmap 12:32 -!- qu-bit [~shroedngr@unaffiliated/barriers] has quit [Ping timeout: 272 seconds] 13:03 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 244 seconds] 13:11 -!- rigel [~pi@c-76-105-237-98.hsd1.or.comcast.net] has joined ##hplusroadmap 13:11 < 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 13:13 -!- qu-bit [~shroedngr@unaffiliated/barriers] has joined ##hplusroadmap 13:22 <@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 13:24 -!- AdrienG [~dextro@unaffiliated/amphetamine] has joined ##hplusroadmap 13:27 -!- AdrianG [~dextro@unaffiliated/amphetamine] has quit [Ping timeout: 256 seconds] 13:37 -!- wrldpc [~wrldpc@203.105.94.33] has quit [Quit: wrldpc] 13:43 -!- soylentbomb [~k@unaffiliated/soylentbomb] has quit [Quit: Leaving] 13:43 -!- delinquentme [~asdfasdf@c-24-3-73-35.hsd1.pa.comcast.net] has joined ##hplusroadmap 13:44 < delinquentme> yashgaroth, happen to know where I could read more about the given FDA regulations when using a patients own stem cells? 13:45 < rigel> ficking google with their fucking link bullshit 13:45 < rigel> "stem cells" site:fda.gov 13:46 < rigel> http://www.fda.gov/aboutfda/transparency/basics/ucm194655.htm 13:55 < 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? 13:56 < rigel> i think there are some court cases about this 13:57 < rigel> physicians can prescribe whatever the hell they want 13:57 < rigel> FDA tests safety/efficacy and polices marketing 13:58 < delinquentme> OHHH so its MARKETING? 13:58 < delinquentme> you just cant market them if they're not approved in the FDA? 13:59 < 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 14:00 < rigel> see also: neurontin settlement, GSK settlement (over paxil, iirc) 14:01 <@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 14:02 < 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 14:07 -!- ElixirVitae [~Shehrazad@unaffiliated/shehrazad] has quit [Ping timeout: 272 seconds] 14:09 -!- ElixirVitae [~Shehrazad@unaffiliated/shehrazad] has joined ##hplusroadmap 14:15 -!- Simurg [~Shehrazad@unaffiliated/shehrazad] has joined ##hplusroadmap 14:16 -!- ElixirVitae [~Shehrazad@unaffiliated/shehrazad] has quit [Ping timeout: 272 seconds] 14:24 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 14:24 -!- Simurg [~Shehrazad@unaffiliated/shehrazad] has quit [Ping timeout: 272 seconds] 14:24 -!- Simurg [~Shehrazad@unaffiliated/shehrazad] has joined ##hplusroadmap 14:33 -!- gene_hacker [~chatzilla@cpe-70-113-85-111.austin.res.rr.com] has joined ##hplusroadmap 14:33 < delinquentme> @biome_data["native"]["temperate grassland"] = @name_indexed_ecosystems["temperate grassland"] 14:33 < delinquentme> how DRY? 14:35 <@kanzure> that looks awful 14:39 < brownies> wtf? 14:43 < delinquentme> HOW DRY 14:44 < delinquentme> erma gurd. 14:50 < delinquentme> y u no halp 14:50 < delinquentme> instead poke w stick? 14:51 < delinquentme> HURM?! brownies kanzure 14:53 -!- EnLilaSko [~Nattzor@unaffiliated/enlilasko] has quit [Remote host closed the connection] 14:55 * brownies grumbles 14:58 < delinquentme> http://boingboing.net/2013/01/13/filabot-turn-scrap-plastic-in.html 14:58 < delinquentme> looks super polished end product 15:00 <@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 15:01 < delinquentme> so two hashes and I need to stick a hash kv pair from one hash to another 15:02 < 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 15:07 <@kanzure> biome.grassland.temperature 15:08 <@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 15:11 < delinquentme> ruby hashes should me accessible through Hash.key ? 15:17 <@kanzure> there's a gem somewhere that can dump keys to attributes on an object but i forget its name 15:17 <@kanzure> hashify? 15:18 < delinquentme> hashy ? 15:20 <@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. 15:21 -!- gene_hacker [~chatzilla@cpe-70-113-85-111.austin.res.rr.com] has quit [Ping timeout: 240 seconds] 15:30 -!- eudoxia [~eudoxia@r186-53-138-233.dialup.adsl.anteldata.net.uy] has quit [Read error: Connection reset by peer] 15:32 -!- augur [~augur@208.58.5.87] has joined ##hplusroadmap 15:37 -!- gene_hacker [~chatzilla@wireless-198-213-198-64.public.utexas.edu] has joined ##hplusroadmap 15:40 < 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 15:41 <@kanzure> (it's warming up) 16:02 <@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. 16:10 <@kanzure> gene_hacker: hey. what's up? 16:11 -!- joshcryer [~g@unaffiliated/joshcryer] has joined ##hplusroadmap 16:13 <@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 16:14 < 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 16:15 <@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% 16:16 < 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." 16:17 < 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." 16:22 <@kanzure> w3.org and mit.edu are both down? 16:23 < yashgaroth> looks like it 16:43 < nmz787> genscript.com says its capacity is 4.5 Mbp/month 16:43 <@kanzure> that's... not much. 16:44 <@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 16:45 < 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 16:47 <@kanzure> i can't help but think that the costs are a bit high though. $826k/year.. 16:48 < brownies> i didn't even know it was a Cornell project. do they own it? 16:48 < brownies> isn't that a bit... biased? 16:49 <@kanzure> "The term e-print was adopted to describe the articles. Ginsparg was awarded a MacArthur Fellowship in 2002 for his establishment of arXiv." 16:50 <@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"" 16:51 < 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. 16:52 < 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 16:53 < 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. 16:54 <@kanzure> party pooper 16:54 < rigel> macarthur fellowships for everyone! 16:55 < joshcryer> What percentage of arXiv papers are crackpots? 17:07 -!- gene_hacker [~chatzilla@wireless-198-213-198-64.public.utexas.edu] has quit [Ping timeout: 276 seconds] 17:11 <@kanzure> i wonder if the federal government could go after aaronsw's family for damages etc. 17:12 < rigel> doubtful 17:14 < yashgaroth> I almost wonder if they could sue the government for causing his death, but I severely doubt it 17:15 -!- ElixirVitae [~Shehrazad@unaffiliated/shehrazad] has joined ##hplusroadmap 17:16 -!- ElixirVitae is now known as BathWater 17:18 -!- Simurg [~Shehrazad@unaffiliated/shehrazad] has quit [Quit: Leaving] 17:22 < joshcryer> They could, they wouldn't win though. 17:27 -!- archbox_ [~archbox@unaffiliated/archbox] has joined ##hplusroadmap 17:29 -!- ElixirVitae [~Shehrazad@95.5.124.138] has joined ##hplusroadmap 17:29 -!- ElixirVitae [~Shehrazad@95.5.124.138] has quit [Changing host] 17:29 -!- ElixirVitae [~Shehrazad@unaffiliated/shehrazad] has joined ##hplusroadmap 17:29 -!- devrandom [~devrandom@gateway/tor-sasl/niftyzero1] has quit [Remote host closed the connection] 17:42 -!- archbox_ [~archbox@unaffiliated/archbox] has quit [Ping timeout: 255 seconds] 17:44 <@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? 17:45 <@kanzure> brownies: the troll at the top of http://news.ycombinator.com/item?id=5051885 17:52 < brownies> kanzure: hmph. 18:08 <@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 18:09 <@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) 18:16 < rigel> i read a good book on the history of this over the summer 18:18 < rigel> goddamn, i wish i could remember the title 18:21 < delinquentme> do we know of anyone whos had lipo? 18:21 < delinquentme> I've heard its really really rough on the body 18:22 < 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. 18:37 -!- qu-bit [~shroedngr@unaffiliated/barriers] has quit [Read error: Connection reset by peer] 18:39 < delinquentme> kanzure, the reverting process is mostly just cytokines right? 18:40 < delinquentme> but theres alot to be said about the environment and other complexities? 18:40 < yashgaroth> transcription factors, cytokines, infinite patience 18:41 -!- qu-bit [~shroedngr@unaffiliated/barriers] has joined ##hplusroadmap 18:42 < delinquentme> "enhancer" == "promoter" ? 18:43 < yashgaroth> no, enhancers regulate expression of genes within a large region surrounding them, promoters are tied to a single gene 18:44 < yashgaroth> there are some similarities between them 18:45 < yashgaroth> ...which I won't get in to, but basically no 18:46 < delinquentme> Would it be a misnomer to ask what some of the more complex cells in the human body are? 18:46 < yashgaroth> neurons 18:47 < 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 18:48 < yashgaroth> except kupffer cells, fuck those guys 18:49 < 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? 18:50 < 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 18:51 < yashgaroth> since I'm not totally sure what you're asking, I'm afraid I must resort to grand sweeping generalizations 18:53 < delinquentme> transcription factors ... SPIRAL along pieces of DNA?? 18:54 < 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? 18:55 < 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 18:56 < 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 18:58 < 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 18:59 < 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 19:00 < yashgaroth> or rather they mediate the freeing 19:00 < delinquentme> ahhh ok 19:01 < delinquentme> check! enhancers work to unravel the chromatin to facilitate transcription 19:02 < 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 19:04 < delinquentme> however neither actually constructs the yield protein 19:04 < yashgaroth> no that's ribosomes 19:06 < 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 19:07 < 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 19:08 < delinquentme> I know the yields can be varied ... but is cell signaling using these proteins ? 19:10 < yashgaroth> like, signaling between cells? it's usually proteins, sometimes small molecules, but those molecules are made by proteins, so yeah 19:11 < 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 19:12 < delinquentme> how does that differ from the cells actually producing / excreting that hormone? 19:12 < yashgaroth> it shouldn't differ, all else being equal 19:13 < delinquentme> ribosomes... basically all have the same molecular structure? 19:14 < delinquentme> in a given species 19:14 < yashgaroth> yes 19:15 < 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 19:16 < delinquentme> any new fun stuff on etching techniques? 19:17 < nmz787> lookin for a DLP projector for cheap to try using tha twith a microscope 19:17 < nmz787> add servos/steppers to the XY 19:18 < 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 " 19:19 < 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 19:20 < 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 19:21 < 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" ? 19:22 < 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 19:23 < yashgaroth> some cell-penetrating peptides/chemicals that are conjugated to your deliverable can transit across the membrane 19:25 < delinquentme> yeah I know about only electroporation :P 19:26 < delinquentme> there we go: http://en.wikipedia.org/wiki/File:Liposome.jpg 19:28 < delinquentme> so the cell engineering process is kind of getting all these things together in a given package 19:29 < yashgaroth> that stuff it pretty routine, the tough part is figuring out what genes you need to put in to make it go 19:30 < 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? 19:31 < yashgaroth> buy fectamine from lifetech, mix with dna, shake lightly, add to cells 19:31 < delinquentme> hahaha 19:31 < delinquentme> fuck yes! 19:32 < 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? 19:33 < 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 19:34 < 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? 19:35 < 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 19:36 < yashgaroth> it's hella expensive, but when you're producing protein that costs exponentially more than its weight in gold, it's worthwhile 19:37 < 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 19:38 < 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 19:39 <@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 19:40 < 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 19:41 < yashgaroth> hey now plasmids ain't illegal yet 19:42 < 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. 19:43 < 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 19:44 < 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 19:45 < 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 19:46 < 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 19:47 < 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 19:48 < delinquentme> yashgaroth, this would be a primary structure right? 19:49 < 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 19:50 < 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 19:51 <@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 19:52 <@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 19:53 < 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 19:54 <@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 19:55 <@kanzure> let's pick a set of publishers to test it out on 19:56 <@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? 19:57 < 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 19:58 <@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? 19:59 < 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? 20:00 < 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 20:01 < 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 20:03 < yashgaroth> sure 20:04 -!- gene_hacker [~chatzilla@wireless-206-76-91-95.public.utexas.edu] has joined ##hplusroadmap 20:05 < yashgaroth> man UMB may have nature protocols but they've got shit-all from bentham/ingenta 20:07 <@kanzure> another paper i'd like to try is 20:07 <@kanzure> http://www.sciencedirect.com.proxy.lib.pdx.edu/science/article/pii/S0022283610011575 20:10 -!- yash [~ffffff@cpe-66-27-118-94.san.res.rr.com] has joined ##hplusroadmap 20:10 <@kanzure> same md5sums on the nature papers 20:11 < yash> excellent 20:11 < yash> also, brb 20:11 <@kanzure> same md5sums on sciencedirect papers 20:11 -!- gene_hacker [~chatzilla@wireless-206-76-91-95.public.utexas.edu] has quit [Ping timeout: 252 seconds] 20:13 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Ping timeout: 276 seconds] 20:13 < delinquentme> http://www.knowledgeoftoday.org/2012/06/fda-cancer-industry-prevent-cure.html 20:14 < 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? 20:15 <@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 .. " 20:16 <@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 20:17 <@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 20:23 -!- yash is now known as yashgaroth 20:23 <@kanzure> fenn: maybe you will find something for psychometrics here? http://psychopy.org/ 20:26 <@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 20:27 <@kanzure> http://blog.didierstevens.com/2008/04/29/pdf-let-me-count-the-ways/ 20:35 <@kanzure> http://brundlelab.wordpress.com/2010/11/23/malware-pdf-analysis-of-a-very-simple-sample/ 20:36 < 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 20:37 < 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 20:38 < 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? 20:40 < rigel> i just dont think you need to spend a lot of time analyzing this 20:41 <@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 20:42 < rigel> he wasnt caught by jstor adding lines to the pdf 20:43 < 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 20:44 < rigel> downloading from two independent sources and sha1summing or whatever 20:45 < 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. 20:46 <@kanzure> as far as i'm concerned those lines /are/ malware anyway 20:46 < rigel> so the pyphantomjs thing is working out? 20:47 < 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 20:51 <@kanzure> pyphantomjs doesn't entirely work at the moment 20:52 <@kanzure> it needs some maintenance 21:06 < 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 21:07 < rigel> but it is such a huge pain in the ass, with random links that dont appear until you mouseover them and double click 21:36 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] 21:52 -!- delinquentme [~asdfasdf@c-24-3-73-35.hsd1.pa.comcast.net] has quit [Ping timeout: 272 seconds] 21:55 < juri_> https://petitions.whitehouse.gov/petition/award-presidential-medal-freedom-aaron-swartz/n6Fcyn3V 22:04 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has quit [Quit: Lost terminal] 22:07 -!- lichen [~lichen@c-24-21-206-64.hsd1.or.comcast.net] has joined ##hplusroadmap 22:09 -!- Viper168 [~Viper@node9.19.251.72.1dial.com] has joined ##hplusroadmap 22:09 -!- Viper168 [~Viper@node9.19.251.72.1dial.com] has quit [Changing host] 22:09 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 22:16 < nmz787> did you need some umb ezproxy tests? 22:17 < 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 22:18 <@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 22:19 < 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 22:20 < 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 22:21 <@kanzure> choose something else :P 22:21 <@kanzure> ieee tends to slap on stuff 22:22 < yashgaroth> uhh http://online.liebertpub.com/doi/pdfplus/10.1089/hum.2012.029 for liebert 22:23 < yashgaroth> oh wait I don't think pdx is subscribed to them 22:24 < 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 22:25 < 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 22:26 < 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? 22:27 < 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 22:29 < 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 22:30 < 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 22:31 < 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 22:32 < 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. 22:33 <@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 22:34 <@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)" 22:35 < 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 22:36 <@kanzure> or possibly in a cookie 22:36 <@kanzure> userGroupName:mlin_b_umass 22:36 <@kanzure> well that sounds wrong 22:37 < 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 22:38 <@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 22:39 < nmz787> yeah i was able to navigate to the PDF from the library at pdx 22:40 < nmz787> http://diyhpl.us/~nmz787/A%20foamy%20virus%20vector%20system%20for%20stable%20and%20efficient%20RNAi%20expression%20in%20mammalian%20cells__PDX.pdf 22:43 < 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 22:44 < 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 22:46 < yashgaroth> ah http://synbiobeta.com/teselagen/ 22:51 < yashgaroth> oh look mac cowell is doing http://genefoo.com/ 22:51 <@kanzure> what happened to snplasergene 22:51 <@kanzure> "personalpcr" i see.. 22:52 < yashgaroth> haha "Genefoo was started in Winter 2013 in the industrial outskirts of San Francisco" 22:53 <@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. 22:56 < yashgaroth> one year warranty on the pipettes, nothing on the pcr machine...hmm 23:09 < bkero> kanzure: oshit, their office is about 3 blocks away from my office in Mountain View :P 23:16 -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving] 23:26 -!- amphetamine [~dextro@unaffiliated/amphetamine] has joined ##hplusroadmap 23:30 -!- 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." 23:41 <@kanzure> ah hell his irc bot is still going (datum) 23:42 -!- 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. 23:43 <@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/ 23:44 < bkero> I'd definitely be up for meeting them if I had any spare time up there though 23:59 <@kanzure> i might have misunderstood. does that mean "next time" or "give me the names now"? --- Log closed Mon Jan 14 00:00:30 2013