| --- Log opened Sat Apr 13 00:00:02 2013 | ||
| --- Day changed Sat Apr 13 2013 | ||
| yashgaroth | do you have a protein sequence yet? | 00:00 |
|---|---|---|
| cory_ | yeah, this was on a MiSeq | 00:00 |
| ParahSail1n | miseq is kinda expensive, should have just outsourced to ucdavis or something | 00:00 |
| cory_ | no protein sequence yet, just got the sequencing data like 6 or 7 days ago | 00:01 |
| @kanzure | wtf? didn't you put in the request to beijing genomics institute like 2 years ago? | 00:01 |
| cory_ | well, some people at harvard offered to do all the sequencing for free so I took them up on the offer | 00:01 |
| ParahSail1n | cory_, when you get the server with the reads, send access instructions to ropoctl@gmail.com | 00:01 |
| ParahSail1n | cory_, ah fair enough | 00:01 |
| @kanzure | what happened to bgi doing the sequencing? | 00:01 |
| ParahSail1n | harvard prepared the libraries? | 00:02 |
| cory_ | yeah, but by the time we actually got the bugs growing BGI no longer wanted to collaborate | 00:02 |
| ParahSail1n | paired or single end, what read length | 00:02 |
| @kanzure | that's lame of bgi. | 00:02 |
| cory_ | well, it was going to be part of some project to sequence like 1000 bacterial genomes or somehting. They had already completed their goal by the time I had the bug. | 00:03 |
| @kanzure | maybe someone filled up their capacity. | 00:03 |
| cory_ | single-end, 150bp I think | 00:04 |
| ParahSail1n | quality scores past 100 are not great, but can't argue with free | 00:04 |
| ParahSail1n | if you give me those reads this weekend, i can run them through assembly and blast contigs | 00:05 |
| @kanzure | oh right, don't you have like a fleet of servers for assembly? | 00:06 |
| ParahSail1n | yes | 00:06 |
| cory_ | k, I'll see what I can come up with. | 00:06 |
| ParahSail1n | should not be hard to find a nitrogenase in the mess | 00:07 |
| yashgaroth | it seems they have the n-termini in the paper already | 00:08 |
| cory_ | the trick will be discerning the nitrogenase from CO-dehydrogenases and xanthine dehydrogenases, etc | 00:08 |
| ParahSail1n | i dont think thatll be the problem | 00:09 |
| cory_ | btw, those N-termini are wrong. From some direct communication with the authors I found out they screwed it up and accidentially sequenced some proteins from a different organism all together | 00:09 |
| cory_ | and of course they never bothered to fix it | 00:10 |
| ParahSail1n | heh yeah i wouldnt trust any wetlab stuff, especially when we got gbs of sequence data to play with | 00:10 |
| yashgaroth | well if you don't get anywhere with genome sequences, you can probably purify a good sample of the enzyme and get a few peptide fragments sequenced | 00:11 |
| cory_ | I should have a lot better sequencing data in a week or 2. the first run had like 6 different variations of the 16S sequence in it, so I know it's a mixture of multiple strains | 00:12 |
| ParahSail1n | you're looking for one gene, not nicely assembled scaffolds | 00:12 |
| ParahSail1n | you're pretty likely to get it out of there | 00:12 |
| ParahSail1n | so they're doing another miseq run on it? | 00:13 |
| cory_ | yeah | 00:13 |
| ParahSail1n | see if they can do 2x100 paired end | 00:13 |
| cory_ | oh right, it's HiSeq rather than MiSeq and I think they are doing paired ends this time | 00:14 |
| ParahSail1n | yeah thats good | 00:14 |
| ParahSail1n | what % of a lane? | 00:14 |
| cory_ | not sure, sorry | 00:14 |
| ParahSail1n | well it's definitely gonna be enough coverage | 00:14 |
| cory_ | anyways, I gotta get out of here. Gotta catch a flight early tomorrow morning. | 00:15 |
| cory_ | adios amigos | 00:16 |
| @kanzure | seeya | 00:16 |
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| @kanzure | i should trick him into showing up more often | 00:16 |
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| rigel | hey so | 01:06 |
| rigel | what should i be using to provide access to my entire house to my library resources? is there some way i can set up a forwarding proxy that will automatically log me in? | 01:07 |
| rigel | i find it a bit irritating to always be doing that, and want to allow my wife to access this stuff too | 01:07 |
| @kanzure | if you are willing to use firefox or chrome then you can use zotero which can autologin to ezproxy | 01:08 |
| rigel | i actually would rather do this via a proxy on my main server machine | 01:10 |
| rigel | rather than set up her account with my pwn | 01:10 |
| rigel | heh | 01:10 |
| rigel | pw even | 01:10 |
| @kanzure | you could use a bookmarklet that takes the current url and pastes it to http://ezproxy.lib.fuckyoucollege.edu/login?url=xyz and then you could have a proxy on your network that autologins when an ezproxy.lib.fuckyoucollege.edu is detected. | 01:10 |
| @kanzure | e.g. the proxy could attach a cookie without passing the cookie to the client | 01:10 |
| rigel | i would rather just pipe everything through http://my.server.lan/resource | 01:11 |
| @kanzure | here's how the sticky cookie would work without passing the cookie to the client: http://mitmproxy.org/doc/sticky.html | 01:11 |
| @kanzure | oh wait that's an awful example | 01:11 |
| @kanzure | this, https://github.com/cortesi/mitmproxy/blob/master/examples/stickycookies | 01:11 |
| @kanzure | i don't think passing every conceivable http request through a local proxy is a good idea for privacy reasons | 01:12 |
| rigel | explain? | 01:12 |
| @kanzure | which part :( | 01:13 |
| rigel | the privacy reasons part | 01:13 |
| @kanzure | it sounds to me like your idea of an optimal solution was "all outgoing http/https requests would go through a proxy and when the proxy detects the ezproxy url it will autologin" | 01:13 |
| rigel | no | 01:13 |
| rigel | what i mean is instead of going to the library resource page, i go to http://myserver.lan/resources that auto-logins and mitm's the resources | 01:14 |
| rigel | so, you want to look at articles? go to http://myserver.lan/resources and choose from that menu | 01:14 |
| @kanzure | mitmproxy/libmproxy can handle that quite easily with that stickycookie example | 01:15 |
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| @kanzure | although that's an http protocol level proxy, which is probably overkill | 01:15 |
| @kanzure | ezproxy was actually made for these situations heh | 01:16 |
| @kanzure | i have been fucking around with libmproxy all day so i have some serious mitmserver bias going on at the moment | 01:17 |
| @kanzure | *mitmproxy | 01:17 |
| @kanzure | i am busy replicating this at the moment http://blog.sabaini.at/2013/03/12/mocking-flask/ | 01:19 |
| rigel | https://sphotos-b.xx.fbcdn.net/hphotos-ash3/534183_313164078812216_1083341310_n.jpg this made me smile | 01:20 |
| nmz787 | cool to see cory's updates | 01:21 |
| @kanzure | so the advantage of the mitmproxy approach is that it will leave ezproxy's url rewriting in tact | 01:21 |
| @kanzure | plus it can just store a cookie to login to your university's resources without sending that cookie to the client | 01:22 |
| rigel | so i guess | 01:22 |
| @kanzure | the downside is that https would require installing a custom cert on your clients | 01:22 |
| rigel | how the fuck do i get a job doing this? | 01:22 |
| rigel | because this is a hell of a lot more fun than medical school so far | 01:22 |
| @kanzure | write lots of angry emails and hatemail | 01:22 |
| @kanzure | basically just copy my emails | 01:23 |
| rigel | i mean, i would love to take a few months to, you know, write a proper file explorer application that can use ssh key authentication to connect to my server at home | 01:23 |
| @kanzure | i wonder how ezproxy gets around the https problem.. wtf? | 01:24 |
| rigel | for android | 01:24 |
| @kanzure | brownies: ezproxy. https. how does that work? i might be too sleepy to be coherent. | 01:24 |
| rigel | there are no good fucking tools for android that are properly free and open source and what the fuck are people doing trying to sell me a goddamn ssh-enabled file manager that I CANT LOOK AT THE FUCKING CODE FOR HAVE YOU ASSHOLES NO CLUE WHAT SECURITY MEANS | 01:25 |
| rigel | i think i feel a rant coming on | 01:25 |
| @kanzure | ssh in terminal works fine on android. just use that to explore files. | 01:26 |
| rigel | oh, connectbot is fine | 01:26 |
| rigel | the variations of it are fine | 01:26 |
| @kanzure | or use mosh. or the connectbot version of mosh or w/e. | 01:26 |
| rigel | but they are cumbersome as hell to use to transfer files from a remote server | 01:26 |
| @kanzure | if you hate those things then i recommend installing debian in a chroot on your android device | 01:27 |
| @kanzure | possibly through lildeb or something else | 01:27 |
| rigel | i havent even rooted this thing despite having it for almost a year and a half | 01:27 |
| rigel | i wanted to not have to root it | 01:27 |
| @kanzure | which model? | 01:27 |
| rigel | gnex | 01:28 |
| @kanzure | holy crap my phone is three years old. why am i using this? | 01:28 |
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| brownies | kanzure: i don't know | 01:53 |
| brownies | kanzure: i think you'd need to middleman a cert authority in order to do anything meaningful? | 01:54 |
| @kanzure | maybe nobody is using https on ezproxy? | 01:54 |
| @kanzure | or maybe all ezproxy instances have a root cert?? | 01:55 |
| nmz787 | this is https https://login.ezproxy.rit.edu/login | 01:56 |
| nmz787 | i guess the next page (the journal) isn't | 01:56 |
| nmz787 | http://www.sciencedirect.com.ezproxy.rit.edu/science/article/pii/B0122267702028611 | 01:57 |
| @kanzure | try https://www.sciencedirect.com.ezproxy.rit.edu/science/article/pii/B0122267702028611 | 01:58 |
| nmz787 | exproxy session cookie present | 01:59 |
| @kanzure | not what i mean | 01:59 |
| @kanzure | https://www.oclc.org/support/services/ezproxy/documentation/cfg/ssl/certopts.en.html | 01:59 |
| nmz787 | nope your link didn't work | 01:59 |
| nmz787 | (no in chrome inspector, there's a cookie for exproxy) | 02:00 |
| @kanzure | it looks like they are doing self-signed certs, self-signed wildcard certs, CA-issued regular, and CA-issued wildcard | 02:00 |
| @kanzure | it would be interesting to scan the list of ezproxy libraries to see if any are using a CA-issued wildcard cert. | 02:01 |
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| @kanzure | jrayhawk: what would be the quickest way to scan https://raw.github.com/kanzure/ezproxy-urls/master/urls.txt to find which ones are paying for a CA-issued wildcard cert? | 02:02 |
| jrayhawk | openssl s_client -connect login.ezproxy1.lib.asu.edu:443 -quiet -CApath /etc/ssl/certs/ 2>&1 | grep 'CN = \*' | 02:04 |
| jrayhawk | grep -q if you just want the exit status | 02:05 |
| jrayhawk | though most of those URLs aren't https, so i am not super sure what you're after | 02:07 |
| @kanzure | i am just curious how most people are using ezproxy with https | 02:07 |
| @kanzure | for instance, https://www.sciencedirect.com.ezproxy.rit.edu/science/article/pii/B0122267702028611 | 02:08 |
| @kanzure | depending on how ezproxy.rit.edu is configured that will work in a variety of different ways | 02:08 |
| @kanzure | including "not at all" | 02:08 |
| @kanzure | relevant documentation words https://www.oclc.org/support/services/ezproxy/documentation/cfg/ssl/certopts.en.html | 02:09 |
| @kanzure | also.. it would be fun to sniff ezproxy http traffic for cookies. | 02:11 |
| jrayhawk | oh i guess you'd want to track the exit status of the openssl command as well | 02:16 |
| jrayhawk | eh, sleepy | 02:16 |
| @kanzure | me too. good night. | 02:17 |
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| nostack | dude i want to b superman | 02:19 |
| nostack | or like really fucking smart | 02:19 |
| nostack | like that move limitles | 02:20 |
| nostack | either way rly | 02:20 |
| nmz787 | http://en.wikipedia.org/wiki/Laser_capture_microdissection | 02:32 |
| nmz787 | I just watched the move Special | 02:32 |
| nmz787 | it was kinda the opposite of limitless | 02:32 |
| nmz787 | movie* | 02:32 |
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| superkuh | paperbot: http://pre.aps.org/abstract/PRE/v87/i4/e043104 | 05:43 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/a91d6e207e04d7c45bca29dcd274fbb2.txt | 05:43 |
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| @kanzure | "Based on testing to date, it looks like the merge branch merging in the BRL-CAD version of SCL to stepcode is ready to go live." | 08:27 |
| @kanzure | https://github.com/stepcode/stepcode/pull/227 | 08:27 |
| @kanzure | that is a tremendously huge merge | 08:27 |
| @kanzure | the u.s. military is serious business | 08:28 |
| @kanzure | essentially they have merged all of their changes to step class library from the original NIST version into this currently-maintained version of step class library | 08:29 |
| @kanzure | (because they had vendorized it for the longest time) | 08:30 |
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| @kanzure | hackerspaces.org is blowing up | 12:22 |
| @kanzure | they never figured out how to organize themselves | 12:22 |
| @kanzure | i'm not sure why they are a group anyway | 12:22 |
| @kanzure | it's nice that there's a way for different hackerspaces to communicate with each other | 12:22 |
| @kanzure | but i don't see why they are calling for a foundation to be incorporated? | 12:22 |
| @kanzure | an entire incorporated entity just to manage a mailing list ? | 12:23 |
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| ParahSail1n | i think that s thermoautotroph should not require H2 | 12:38 |
| ParahSail1n | CO and O2 should be adequate | 12:38 |
| ParahSail1n | growth rate of anything the requires gas fixation's gonna be slow though | 12:39 |
| jrayhawk | if they're hoping to expand operations, a financial umbrella for doing so would probably be nice. | 12:40 |
| @kanzure | On Sat, Apr 13, 2013 at 2:32 PM, Randall G. Arnold wrote: | 12:42 |
| @kanzure | > In the case of Makerspaces there is no real product, which actually benefits | 12:42 |
| @kanzure | > us. There is no corporate entity, really, to which we are beholden. On the | 12:42 |
| @kanzure | > surface, though, that means the absence of a single guiding force that | 12:43 |
| @kanzure | > identifies purpose. Some can say that in our world O'Reilly is or means to | 12:43 |
| @kanzure | > be that force... but as noted, they have a financial agenda of their own | 12:43 |
| @kanzure | > that may often get in the way of maker/hacker goals. | 12:43 |
| @kanzure | haha... "there is no real product, which actually benefits us" what? | 12:43 |
| @kanzure | jrayhawk: maybe, but at this point they are just being vague about what a foundation would do. | 12:43 |
| @kanzure | the most specific thing they have mentioned is collective insurance bargaining. | 12:43 |
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| @kanzure | jrayhawk: ok i told them it would be cool if they would organize to fund hacker activities (electronics, biology, whatever) in hackerspaces. maybe they will collectively organize around that idea. whatever. | 12:53 |
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| @kanzure | an ok discussion about phantomjs/webkit/qt/nodejs architecture things: https://groups.google.com/forum/?fromgroups=#!topic/phantomjs/bNjRI0anpi0 | 16:49 |
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| @kanzure | lesswrong public log: http://epi.ponzo.net:8080/?page=6115 | 16:56 |
| @kanzure | grab it before the lynch epitron | 16:56 |
| ParahSail1n | ? | 17:00 |
| @kanzure | *they lynch | 17:00 |
| @kanzure | epitron used to show up in here once in a while. i hate his title bot. | 17:01 |
| @kanzure | anyway, #lesswrong has a no logging policy | 17:03 |
| @kanzure | and the point is that those are logs that you can download | 17:03 |
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| ParahSail1n | they really are bronies i guess | 17:08 |
| @kanzure | haha you thought i was kidding, that's cute. | 17:10 |
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| eudoxia | oh no the logs are down | 18:08 |
| eudoxia | and why would #lesswrong have a no logging policy? | 18:09 |
| jrayhawk | peasants, pitchforks | 18:09 |
| jrayhawk | more uncharitably, moving privilege beyond scrutiny | 18:12 |
| jrayhawk | all the same thing, really | 18:12 |
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| ParahSail1n | because they're weird and cultish? | 18:26 |
| eudoxia | well my first guess was that they didn't want anyone recording the latin chanting when EY logged on | 18:27 |
| ParahSail1n | expecting robin hanson to give a positive review to that meta-medicine startup simply because of in-group affiliation is a pretty good indicator | 18:32 |
| rigel | god dammit, i need to start one of these weird pseudoscience cults | 18:38 |
| ParahSail1n | have you considered bayesology? | 18:40 |
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| brownies | meta-medicine? | 19:23 |
| @kanzure | something about getting desperately ill people to pay them to contact experts | 19:23 |
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| makoLime | brownies, they do extensive research on your ailment and approach finding what is actually the best treatment available, where as a regular GP would only find you the best treatment they're aware of, which is often much less effective. | 19:51 |
| brownies | huh | 19:55 |
| brownies | how odd | 19:56 |
| brownies | i always thought that's what a doctor already did | 19:56 |
| @kanzure | no far from it | 20:00 |
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| @kanzure | oh jeebus | 20:55 |
| @kanzure | i was looking through my mailing list subscriptions and found this https://groups.google.com/forum/?fromgroups#!forum/slwaterflow | 20:55 |
| @kanzure | seems to be aaronsw/guerilla open access things | 20:56 |
| @kanzure | haha content liberation front | 20:58 |
| @kanzure | oh weird they reference some of my 2008 emails | 20:59 |
| rigel | i reject the characterization of medicine/medicine | 20:59 |
| rigel | first, the US does not have "GPs" | 20:59 |
| rigel | er | 21:00 |
| @kanzure | wtf aaronsw did tor2web? | 21:00 |
| yashgaroth | what about PCPs | 21:00 |
| rigel | s|medicine/medicine|medicine/meta-medicine| | 21:00 |
| @kanzure | that's lame, why did he have to be the one to write tor2web | 21:00 |
| rigel | PCPs != GPs | 21:00 |
| rigel | the implication is that GPs have not done a residency, merely an internship year. you can only do that in a few states these days | 21:01 |
| rigel | there are plenty of PCPs that are lazy and do things like take drug company money or freebies | 21:02 |
| rigel | there are also plenty of PCPs that will in fact do that research you mention | 21:02 |
| rigel | and there are furthermore limits to evidence-based medicine, one of which is the aforementioned corrupting influence of drug companies on e.g. publication of studies | 21:03 |
| rigel | an editorial decision to publish by Science or Nature often has as part of the calculation how much revenue the publisher will make in reprints. so, of course that biases things in favor of the Newest and Best (even if it's not actually best) | 21:04 |
| rigel | pharma and device companies spend a lot of money on reprints | 21:04 |
| yashgaroth | or you can just go with 'controversial' like the lancet | 21:05 |
| rigel | the UK journals are not immune to this but some of them have been more willing to acknowledge it | 21:05 |
| rigel | theres a recent plos article that tried to look at how much revenue journal publishers made from reprints | 21:06 |
| rigel | BMJ and the Lancet, iirc, were the only ones to respond with data | 21:06 |
| yashgaroth | huh | 21:07 |
| rigel | i think that's in part because of the strong cultural influence of the NHS, at least up until it was recently, effectively cripped by Cameron et al | 21:07 |
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| ParahSail1n | thats pretty cool http://www.corning.com/lifesciences/us_canada/en/whats_new/cell_culture_and_bioprocess/flowell_plate.aspx | 21:29 |
| yashgaroth | the boys at corning have done it again | 21:31 |
| ParahSail1n | i think they acquired that from BD | 21:32 |
| yashgaroth | as long as they're priced competitively against 'get some poor undergrad to come in on weekends, inc.' | 21:33 |
| ParahSail1n | i dont think any grad student trusts undergrads with cell culture media changes | 21:40 |
| yashgaroth | maybe not cells finicky enough to require daily media replacement, true | 21:41 |
| ParahSail1n | anything mammalian really | 21:41 |
| yashgaroth | 293s are super forgiving if you can do sterile technique | 21:42 |
| ParahSail1n | "if you can do sterile technique" is what i'm getting at | 21:43 |
| yashgaroth | oh heh yeah | 21:44 |
| ParahSail1n | when contamination will set you back 4-6 months you do all the media changes yourself | 21:44 |
| yashgaroth | all my work with them has been in industry so I haven't become inured to primary cells and ESCs and all that fun | 21:46 |
| ParahSail1n | where contamination does not follow matter transmission rules, but simple line of sight through sealed, but transparent containers | 21:47 |
| ParahSail1n | what you do? | 21:47 |
| yashgaroth | montagnier was right, dna can teleport! | 21:47 |
| yashgaroth | me, I do/did 293 and cho cells for protein production | 21:47 |
| yashgaroth | little bit with cancer cell lines, but they're pretty hardy too | 21:48 |
| yashgaroth | and always an infinite supply of more cells | 21:48 |
| yashgaroth | though I never lost a flask to contamination, and we didn't even get to use pen/strep | 21:50 |
| ParahSail1n | i got run out of a collaborating lab because my cells looked funny (were not very attachy) and other people in the lab were having myco problems | 21:50 |
| ParahSail1n | lava tag magic contamination rules are real | 21:50 |
| ParahSail1n | if contaminated flask touches rack, germs get conducted into all other flasks | 21:51 |
| yashgaroth | and yet I worked in a place where half the people didn't use gloves in the hood | 21:52 |
| ParahSail1n | wow, seriously? | 21:52 |
| yashgaroth | yyyup | 21:52 |
| yashgaroth | for the laminar air flow is magic, you see | 21:53 |
| yashgaroth | these were PhDs too | 21:53 |
| ParahSail1n | id like to start playing with those cells again | 21:55 |
| yashgaroth | what kind were they? | 21:55 |
| ParahSail1n | HepG2 | 22:03 |
| ParahSail1n | i had them growing without serum | 22:03 |
| yashgaroth | like, you weaned them off? that'd explain the detaching pretty handily | 22:04 |
| ParahSail1n | yeah i was still in the process of weaning | 22:06 |
| ParahSail1n | started them in opti-mem (no serum) and they were pretty sticky then | 22:07 |
| ParahSail1n | weaned them from opti-mem into regular dmem | 22:07 |
| yashgaroth | I wonder how much money biotech as a whole would've saved if mad cow never existed | 22:09 |
| ParahSail1n | i wasnt using pen/strep either | 22:09 |
| yashgaroth | pen/strep is for the weak | 22:10 |
| ParahSail1n | without serum to buffer that stuff, it probably would have killed cells | 22:10 |
| ParahSail1n | mad cow, how so? | 22:11 |
| yashgaroth | all the old enzymes sourced from various parts of cows are a huge no-no for manufacturing nowadays | 22:11 |
| yashgaroth | so instead of pancreatic rnase or pepsin, you gotta use the expensive recombinant shit for production | 22:11 |
| ParahSail1n | that sucks | 22:12 |
| yashgaroth | not to mention serum-free media for your cell lines | 22:12 |
| ParahSail1n | well my cell lines worked perfectly well with fbs, i was just using medium that normally one would need fbs for cells to survive in | 22:13 |
| ParahSail1n | but yeah, fancy serum free media is expensive | 22:13 |
| yashgaroth | especially when you're doing a 20,000 liter batch of cells to make avastin, or whatever | 22:14 |
| ParahSail1n | so when they make avastin, what medium do they grow the cells in? | 22:15 |
| ParahSail1n | hamster ovary cells dont need serum, right? | 22:15 |
| yashgaroth | not anymore with the new serum-independent lines, but I bet they're a little sickly jonesing for dat sweet serum | 22:16 |
| ParahSail1n | what new serum independent lines do they have? | 22:18 |
| yashgaroth | I dunno the names, but there's probably several at this point | 22:20 |
| yashgaroth | ah yeah we had DG44 and S lines, those were both serum-free | 22:25 |
| yashgaroth | or maybe those weren't serum-free and we had to wean them, well whatever I never had to use FBS | 22:26 |
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| @kanzure | http://www.reddit.com/r/ReverseEngineering/comments/1c3gc5/the_first_level_of_super_mario_bros_is_easy_with/ | 22:48 |
| @kanzure | https://www.cs.cmu.edu/~tom7/mario/mario.pdf | 22:48 |
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