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phillyj | anyone know if github is a good place to use for project collaborations? I have no experience with this stuff. | 06:53 |
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kanzure | phillyj: for software or hardware, yes. | 08:24 |
kanzure | or website development | 08:24 |
kanzure | or papers written in TeX or w/e. | 08:24 |
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brownies | or... everything. | 08:31 |
kanzure | not really. i don't think you should throw .docx files into there. | 08:33 |
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phillyj | ok, cool | 09:02 |
phillyj | i've seen cathal put up lab protocols on it | 09:02 |
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eudoxia | paperbot: http://dl.acm.org/ft_gateway.cfm?id=1869462&ftid=845668&dwn=1&CFID=333425031&CFTOKEN=51878698 | 11:54 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/7a01e5a892a6d7a9f408df01905f9359.pdf | 11:54 |
eudoxia | paperbot: http://dl.acm.org/ft_gateway.cfm?id=1869526&ftid=845715&dwn=1&CFID=333425031&CFTOKEN=51878698 | 11:56 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/67845a4fb5b009259c389f90ab02c1c0.pdf | 11:56 |
heath | eudoxia: i'm curious now if those studies took into account haskell :) | 12:01 |
eudoxia | heh | 12:03 |
eudoxia | >While in correspondance to [8] Lisp seems to | 12:03 |
eudoxia | have a positive impact on development time, it also seems | 12:03 |
eudoxia | that programming in (the statically typed programming | 12:03 |
eudoxia | language) Haskell requires less effort than for example | 12:03 |
eudoxia | Ada. | 12:03 |
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kanzure | http://www.sciencedirect.com/science/activateaccess "To access ScienceDirect from outside your subscribing institutional IP range, your user account needs to be associated to your institution by validating your institutional email. Please enter your email address from the institution that offers you ScienceDirect (e.g. name@university.edu)." | 12:27 |
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kanzure | hmm. so find some holes in some universities, register an email account on a random mail server (not the official mail server), and profit? | 12:27 |
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archels | if you're already inside a box on the university network, just wget them | 12:47 |
kanzure | i wonder if i could route email to root@bryan.svcs.cs.pdx.edu through that form | 12:48 |
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archels | neither of my university mail addresses is even accepted | 12:49 |
kanzure | does your university subscribe to elsevier/sciencedirect? | 12:50 |
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archels | one I'm sure of, the other probably | 12:52 |
archels | (ru.nl, tue.nl) | 12:52 |
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kanzure | "Bryan: There was an off list discussion where we decided we liked google pages better than mediawiki." | 16:33 |
kanzure | uh.. well, i give them points for not liking mediawiki, but google pages seems like a step in the opposite direction. | 16:33 |
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kanzure | "The main problem was that not enough people were using the wiki. And since we were already comfortable using google docs to do collaborative editing, and google groups for the mailing list, I think it makes sense to switch to a somewhat better integrated platform." | 16:38 |
kanzure | how unfortunate. | 16:38 |
kanzure | gene_hacker: hi | 16:39 |
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eudoxia | kanzure: it only gets worse, doesn't it? | 16:44 |
kanzure | that's the east bay diybio group. voting for google lock-in. really mind boggling. | 16:45 |
kanzure | also, when did this happen? http://cia.vc/ | 16:45 |
kanzure | "CIA.vc, the open source "version control informant", was a source code commit notification service. It helped people collaborate more efficiently on open source projects, by broadcasting code changes over Internet Relay Chat." | 16:46 |
kanzure | "This project first went online back in 2003, when the internet was a very different place. Since then, IRC and Subversion have taken a back seat to Twitter and Github. For many people, the service offered by CIA would be just as relevant today as it was when the site first went live; but for myself as well as many former and potential supporters of the project, this sort of centralized fast-paced development just isn't as compelling. ... | 16:46 |
kanzure | ... Technology moves on, and I've personally moved on." | 16:46 |
kanzure | http://scanlime.org/2011/05/cia-vc-service-is-down-indefinitely/ | 16:46 |
kanzure | http://shadowm.rewound.net/blog/archives/245-CIA.vc-is-dead.html | 16:46 |
kanzure | .title https://lwn.net/Articles/518955/ | 16:46 |
yoleaux | CIA.vc shuts down [LWN.net] | 16:46 |
eudoxia | why did he have to call it CIA | 16:46 |
kanzure | pretty neat to see the source code up though http://code.google.com/p/cia-vc/source/browse/ | 16:48 |
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gene_hacker | know of any good hackerspaces in california kanzure? | 17:10 |
kanzure | noisebridge, los angeles biohackers, biocurious, sudo room | 17:11 |
kanzure | if you are willing to accept a commercial entity as an answer, then techshop too. | 17:12 |
gene_hacker | sudo room? | 17:12 |
gene_hacker | is hacker dojo any good | 17:12 |
kanzure | hacke rdojo is a bunch of office chairs | 17:12 |
kanzure | *hacker dojo | 17:12 |
gene_hacker | techshop is waaaaaay too expensive | 17:12 |
gene_hacker | that's what I thought | 17:12 |
kanzure | then you want noisebridge | 17:12 |
kanzure | biocurious is also useful but has no machining capability whatsoever | 17:13 |
kanzure | btw noisebridge is on irc in #noisebridge | 17:13 |
gene_hacker | definately visiting biocurious on their bioluminescent night | 17:14 |
gene_hacker | can one just drop into noisebridge? | 17:14 |
kanzure | if you are in san francisco then let us know, there's a few people in here who you should hang out with | 17:14 |
kanzure | yes you can just drop into noisebridge, but sometimes you have to complain loudly to be let in (either call someone you know, or find the doorbell, or something) | 17:14 |
gene_hacker | going to be in san francisco | 17:15 |
kanzure | also you should stop by langton labs and meet 3scan/cambrian genomics/other people | 17:15 |
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kanzure | hah you could meet up with carl crott (delinquentme).. he's been building his orbital shaker and liquid handler. | 17:16 |
kanzure | also Juul | 17:16 |
gene_hacker | what's langton labs? | 17:17 |
kanzure | communal living space for a group of molecular biologists and creative folks | 17:18 |
kanzure | houses http://3scan.com/ and http://cambriangenomics.com/ | 17:18 |
gene_hacker | cool | 17:18 |
kanzure | has some fun people like http://anselmlevskaya.com/ and http://craneium.net/ | 17:20 |
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delinquentme | paperbot, http://www.ncbi.nlm.nih.gov/pubmed?term=perspectives%20on%20whole%20organ%20assembly | 17:20 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/67ee5fb646ad3d800a9cbb08bea1c5b3.txt | 17:20 |
kanzure | delinquentme: hey, gene_hacker will be in SF soon and you should hang out with him | 17:20 |
delinquentme | gene_hacker, !!! | 17:21 |
gene_hacker | sup | 17:21 |
delinquentme | when are you gonna be in town??? | 17:21 |
gene_hacker | like saturday through tuesday | 17:21 |
delinquentme | aww fack. I'm getting back 6/6 | 17:21 |
gene_hacker | oh well | 17:22 |
kanzure | delinquentme: hook him up with some people? | 17:22 |
delinquentme | currently in pittsburgh | 17:22 |
gene_hacker | what sort of liquid handler are you making? | 17:22 |
delinquentme | gene_hacker, what are you into homeslice?? | 17:22 |
gene_hacker | not much as of yet | 17:22 |
delinquentme | gene_hacker, I wish it was made ... kanzure Im interested in one which can be fabbed on chip | 17:24 |
kanzure | gene_hacker does things like http://www.instructables.com/id/Build-a-Polar-3-D-Printer-from-Legos/ | 17:24 |
kanzure | or erm.. http://boingboing.net/2008/09/01/howto-make-a-3d-prin.html | 17:24 |
kanzure | honestly i forget the url | 17:24 |
gene_hacker | trying to get my master degree, trying to design a simple machine controller(as in relays) that can be 3d printed | 17:25 |
gene_hacker | trying to design some 3d printable relays, and looking for a way to print a fluid stepper motor | 17:25 |
kanzure | you should definitely go to biocurious at least for a little while. they might have an event on saturday or in the evenings. | 17:25 |
gene_hacker | so a microfluidic liquid handler then? | 17:26 |
gene_hacker | I assume you are using PDMS or something like that? | 17:27 |
delinquentme | gene_hacker, thats wild!! | 17:43 |
gene_hacker | what? | 17:44 |
delinquentme | the polar lego printer :D | 17:44 |
delinquentme | gene_hacker, yeah so the macro liquid handler I had I didn't like bc its not actually BUILDING on techniques which could get us mass reproducibility | 17:44 |
delinquentme | http://strong-flower-9013.herokuapp.com/ << LH002 | 17:45 |
delinquentme | SO microlfuidics + some integrated circuit scale manufacturing | 17:45 |
delinquentme | and you've got a hella replicable liquid handler for like 500 | 17:45 |
gene_hacker | nice | 17:45 |
gene_hacker | for invitro work? | 17:46 |
delinquentme | however im geeking out on replacement organs and cantilevers right now | 17:46 |
delinquentme | gene_hacker, yeah I mean unless you knwo someone whos cool with me attaching a 2x3x3 foot cube to their body | 17:46 |
delinquentme | Id be willing to do the implanting free of charge | 17:47 |
delinquentme | however they'd have to sign a bit of paperwork | 17:47 |
delinquentme | kanzure, whatchoo know about functionalized cantilevers in microfluidics for biomarker detection? | 17:47 |
delinquentme | I'm guessing you've got a research paper folder? | 17:48 |
gene_hacker | I was thinking more like nematodes and other biological models you can fit in a test tube | 17:48 |
gene_hacker | detecting a bacterium by it's weight? | 17:48 |
Viper168 | babies | 17:49 |
kanzure | gene_hacker: have you seen davidad's work on his nematode simulator? | 17:49 |
Viper168 | in really big test tubes | 17:49 |
kanzure | oh also kirka did a thing recently.. | 17:49 |
kanzure | http://fennetic.net/irc/kirka_worm_simulator.gif | 17:49 |
gene_hacker | yup | 17:49 |
gene_hacker | this? http://www.artificialbrains.com/openworm | 17:50 |
kanzure | that was 09:40 < kirka> If someone is interested here is my simple physical model of c.elegans http://anonymousdelivers.us/49074 | 17:50 |
kanzure | openworm is http://openworm.org/ | 17:51 |
kanzure | but davidad's things are at http://nemaload.davidad.org/ | 17:51 |
kanzure | oh come on now he's just showing off to us "David's research is personally funded by Larry Page, CEO of Google." | 17:52 |
gene_hacker | delinquentme there's this: http://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=1000&context=nanodocs | 17:52 |
kanzure | .title | 17:53 |
delinquentme | The fucking issue with *ALL* simulations is false negatives | 17:53 |
yoleaux | kanzure: Sorry, that doesn't appear to be an HTML page. | 17:53 |
delinquentme | no one has a good fucking answer for that. | 17:53 |
gene_hacker | and it | 17:53 |
delinquentme | we need actual testing. | 17:53 |
gene_hacker | 's probably cheaper to grow a whole bunch of nematodes and experiment on them than it is to simulate them | 17:54 |
delinquentme | gene_hacker, the sim is probably faster | 17:54 |
delinquentme | that is im guessing, is the primary advantage... but yes it seems like " false negative " is a dirty word around any simulation operation | 17:54 |
kanzure | gene_hacker: actually someone did that and uploaded 10,000 hours of video | 17:54 |
gene_hacker | where? | 17:55 |
kanzure | ftp://anonymous@ftp.mrc-lmb.cam.ac.uk/pub/tjucikas/wormdatabase/results-12-06-08/Laura%20Grundy | 17:55 |
kanzure | more information can be found here: http://wormbehavior.mrc-lmb.cam.ac.uk/ | 17:55 |
gene_hacker | sounds like a great training dataset | 17:55 |
kanzure | i haven't actually watched any percentage of these videos, so i can't comment on quality.. i hear it's okay. | 17:56 |
gene_hacker | for a computer I mean | 17:56 |
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delinquentme | kanzure, functionalized cantilevers? | 18:06 |
kanzure | dunno, look in http://diyhpl.us/~bryan/papers2/microfluidics/ | 18:06 |
delinquentme | any info .. or thoughts? I'd love a way to release the biomarkers post binding as well :D | 18:06 |
kanzure | i am busy fixing javascript things | 18:06 |
delinquentme | for paperboot? | 18:06 |
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kanzure | no not paperbot :( | 18:13 |
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yashgaroth | paperbot: http://www.nature.com/mt/journal/v21/n5/abs/mt201333a.html | 18:25 |
paperbot | HTTP 401 unauthorized http://www.nature.com/mt/journal/v21/n5/pdf/mt201333a.pdf | 18:25 |
yashgaroth | noooooo | 18:25 |
kanzure | yashgaroth: http://diyhpl.us/wiki/articles | 18:26 |
kanzure | yashgaroth: (try the russian one) | 18:26 |
yashgaroth | it sends me to a forums homepage? if you mean sci-hub | 18:27 |
kanzure | well first you need to be in russia | 18:28 |
yashgaroth | 1 sec | 18:29 |
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kanzure | set proxy to 109.198.126.112:8080 then try again | 18:29 |
kanzure | or 46.21.240.253:3128 | 18:29 |
yashgaroth | man I ain't got time to be setting proxies | 18:30 |
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kanzure | DoktorUnicorn: hello | 19:05 |
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heath | paperbot: http://onlinelibrary.wiley.com/doi/10.1002/anie.201005931/abstract | 19:53 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/3011fd5d1349d902d74ab0ecd92576d7.txt | 19:53 |
heath | paperbot: https://www.sciencemag.org/content/336/6085/1171.abstract | 19:53 |
paperbot | SSLError: [Errno 1] _ssl.c:504: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 632, in send) | 19:54 |
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kanzure | paperbot needs your help | 19:59 |
kanzure | paperbot needs people | 19:59 |
kanzure | because people need paperbot. ok this is a bad advertisement, but you get the idea. | 20:00 |
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kanzure | Juul: hey gene_hacker is coming through SF on saturday-tuesday, you fancy a time to meet up? he wanted to stop by noisebridge or some other hackerspace. | 20:10 |
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delinquentme | Juul, !!!!!!!!!!!!!!!!!!!!!!!!! | 20:15 |
* delinquentme hugs | 20:15 | |
Juul | hi delinquentme :) | 20:15 |
delinquentme | sooooo when we're talking about antibodies functionalized to a substrate... | 20:15 |
delinquentme | is there a way to say .. detach given analytes from the binding sites? | 20:16 |
delinquentme | I'd guess it can be done through a current change... | 20:16 |
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delinquentme | as I believe the impedance changes through the cantilever when additional alalytes attach | 20:17 |
delinquentme | hence we can measure the quantity of a given biomarker through a sample | 20:17 |
delinquentme | NOW... if they could be detached ... we've got an awesome system for marker-free detection | 20:17 |
delinquentme | ALSO I was thinking about a solution for type 1 diabetes | 20:18 |
delinquentme | apparently people have developed microfluidic wells with "molecular caps" which can be detached | 20:18 |
delinquentme | so i'm thinking what if you could implant someone with a chip full of insulin wells ... and sample blood glucose levels ... on spike address a cap from the well and release the insulin | 20:19 |
delinquentme | le blah. | 20:26 |
delinquentme | nobody larvs mar | 20:27 |
delinquentme | kanzure, hug? | 20:27 |
delinquentme | klafka, harg? | 20:27 |
kanzure | wait longer. not everyone can jump to action at once. i'm still bugging some debuggers for some other bugged bug things. | 20:28 |
delinquentme | does anyone know of a good bay area accountant? | 20:41 |
delinquentme | paperbot, http://www.ncbi.nlm.nih.gov/pubmed/11533645 | 20:43 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/1a2e3b414c2e1a6242e6cdc924196d6e.txt | 20:43 |
jrayhawk | T1Ds are also amylin and glycogen dysregulated | 20:44 |
Juul | delinquentme, that's interesting, do you have a link to the article about molecular caps? | 20:45 |
Juul | i'm not very well-versed in antibodies. | 20:45 |
delinquentme | Juul, Its in this book I picked up ... lemme see if I can find the ref for it | 20:45 |
delinquentme | but yeah they're individually addressable molecule tops which could be popped off | 20:45 |
delinquentme | the question is what would the refill process look like | 20:46 |
delinquentme | or like better yet! what if you could design a surface/skin mounted delivery system | 20:46 |
Juul | i think darpa has funded some research on that | 20:47 |
delinquentme | was reading about a process called anisotropic etching which researchers have used to create delivery systems which are JUST the right size for delivery w/o nerve end interaction | 20:47 |
delinquentme | IE painless and skin-mounted drug / substance delivery | 20:48 |
delinquentme | Juul, from what you know ... when we're talking about detaching an analyte from a bound docking surface | 20:53 |
delinquentme | that process... what would it be called? Any idea? | 20:53 |
kanzure | cleaving | 20:59 |
delinquentme | Dr. Thomas, I've come across a paper of yours and I'm wondering if your group has pursued any means to detach a given analyte from the functionalized cantilever. I'd guess that a given pulse of electricity would do the trick? | 21:00 |
delinquentme | that might sound slightly ignorant | 21:00 |
kanzure | you can usually wash away certain antibodies | 21:00 |
yashgaroth | elution | 21:02 |
kanzure | i was about to say "yashgaroth probably has some terminology, but he isn't around", but then i thought better of it because it would be disappointing, but you delivered. you delivered. | 21:02 |
yashgaroth | not sure how electrocution affects antibody binding | 21:02 |
yashgaroth | or how you read a microcantilever in a tiny chip | 21:03 |
yashgaroth | implanted chip, anyway | 21:03 |
kanzure | microcantilevers is how afm works, you bounce light off of them and read curvature. | 21:03 |
yashgaroth | cramming an afm into your arm seems like a hassle | 21:04 |
kanzure | most afm setups are big because people suck at stability | 21:04 |
kanzure | stabilization or w/e | 21:04 |
kanzure | not like financial stability. :( | 21:04 |
yashgaroth | also, developing a membrane that only lets in tiny molecules like glucose, and also somehow doesn't get encapsulated by the body | 21:04 |
kanzure | isn't that what dialysis cellulose membrane things do? | 21:05 |
yashgaroth | none of them have pores that small, and they would get encapsulated | 21:05 |
yashgaroth | I suppose if they block almost all proteins the pore size is mostly irrelevant | 21:06 |
yashgaroth | implantable or other constant-monitoring biomarker sensors are one of them holy grails | 21:07 |
kanzure | haven't we had digestable jpeg-transmitting capsules for a while now? | 21:07 |
delinquentme | yashgaroth, there are a few ways to read the cantilever | 21:08 |
yashgaroth | that's not actually inside the body if you take a strict biologist's view, the digestive tract is epithelial | 21:08 |
delinquentme | thats actually a really interesting way to make a hella small AFM... | 21:09 |
delinquentme | ahhh ok so mass / dampening | 21:09 |
kanzure | an afm cantilever is already small.. what do you think they do, poke atoms with a 5 foot pole? | 21:09 |
delinquentme | but the whole system isnt | 21:09 |
delinquentme | yashgaroth, the issue is though what if we've got 400 biomarkers we're detecting ... that means nearly a single wash step for every cantilever | 21:10 |
yashgaroth | well washing with acid or high salt or both will usually knock off most stuff | 21:11 |
kanzure | huh? i don't understand your setup. | 21:11 |
yashgaroth | wait, 400 different biomarkers? | 21:11 |
kanzure | most people just put biomarkers on a plate and then they look at the plate. | 21:11 |
delinquentme | electrocution sounds like it could work because you've already got interaction forces between analyte and the binding site ... give it sufficient energy and maybe it will cause some kind of bump to a new minima | 21:11 |
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kanzure | i think they even do this with cmos things | 21:11 |
yashgaroth | electricity will probably denature and/or destroy your protein | 21:12 |
delinquentme | yashgaroth, kanzure I'm thinking over what a microfluidic setup for tons of biomarkers | 21:12 |
delinquentme | yashgaroth, you're saying the one I've got on the cantilever as a binding site? | 21:12 |
delinquentme | I mean it depends on the protein | 21:12 |
yashgaroth | sure, that one | 21:12 |
heath | paperbot: http://pubs.acs.org/doi/abs/10.1021/nl103427w | 21:13 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Single-Molecule%20Kinetics%20and%20Super-Resolution%20Microscopy%20by%20Fluorescence%20Imaging%20of%20Transient%20Binding%20on%20DNA%20Origami.txt | 21:13 |
delinquentme | yashgaroth, you lame ;D | 21:13 |
delinquentme | ONES | 21:13 |
delinquentme | excruse | 21:13 |
delinquentme | http://en.wikipedia.org/wiki/Surface_plasmon_resonance | 21:14 |
delinquentme | I still fail to grok where the plasmon operation happens here | 21:14 |
delinquentme | operation = "interaction" | 21:14 |
yashgaroth | also note that all these super-awesome microfluidics and plasmon resonance analysis techniques take place with a machine that's bigger than most diabetics | 21:15 |
delinquentme | yashgaroth, currently yeah | 21:15 |
delinquentme | why though | 21:15 |
yashgaroth | I don't know, quantum shit | 21:15 |
delinquentme | hahahaha | 21:16 |
delinquentme | percieved value | 21:16 |
delinquentme | " if its the size of a fucking car they think they're getting more for their money " | 21:16 |
delinquentme | " Just throw a few lead bricks in it " | 21:16 |
delinquentme | SCIENCE! ( marketing ) | 21:17 |
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delinquentme | yashgaroth, I just posted that on FB :P | 21:22 |
heath | paperbot: http://www.nature.com/nnano/journal/v7/n6/full/nnano.2012.73.html | 21:25 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Molecularly%20self-assembled%20nucleic%20acid%20nanoparticles%20for%20targeted%20in%20vivo%20siRNA%20delivery.pdf | 21:25 |
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heath | paperbot: http://www.nature.com/ncomms/journal/v4/n4/full/ncomms2690.html | 22:16 |
paperbot | HTTP 401 unauthorized http://www.nature.com/ncomms/journal/v4/n4/pdf/ncomms2690.pdf | 22:16 |
heath | paperbot: https://www.sciencemag.org/content/335/6070/831 | 22:22 |
paperbot | SSLError: [Errno 1] _ssl.c:504: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 632, in send) | 22:22 |
kanzure | still don't know why that's a problem | 22:23 |
heath | https://www.microryza.com/ :: follow and fund research (kickstarter for science) | 22:26 |
kanzure | you are about two years slow | 22:26 |
kanzure | also they got into ycombinator this year | 22:26 |
heath | paperbot: https://www.sciencemag.org/content/338/6106/506.abstract | 22:29 |
paperbot | SSLError: [Errno 1] _ssl.c:504: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 632, in send) | 22:29 |
kanzure | i don't think you understand.. https on sciencemag.org isn't gonna work until someone fixes paperbot. | 22:29 |
heath | i was publically logging notes to myself... but i can just bring it to ##note-to-self | 22:32 |
heath | publicly rather* | 22:32 |
heath | http://wired.jp/2013/05/05/dnahackers/ | 22:35 |
heath | http://www.bio-x.cn/foldna/ :: a webserver for DNA nanostructure autoscaffold and autostaple | 22:58 |
heath | paper describing it: http://www.hindawi.com/journals/jnt/2012/453953/ | 22:58 |
heath | http://molbot.org/ :: molecular robotics research group | 23:04 |
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heath | Congressional Biomedical Research Caucus 2013 Briefing Series :: http://www.coalitionforlifesciences.org/cbrc/cbrc-briefings/cbrc-briefing-schedule | 23:17 |
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heath | https://www.sciencemag.org/content/328/5986/1662.abstract | 23:20 |
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