2013-05-29.log

--- Log opened Wed May 29 00:00:41 2013
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phillyjanyone 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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kanzurephillyj: for software or hardware, yes.08:24
kanzureor website development08:24
kanzureor papers written in TeX or w/e.08:24
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browniesor... everything.08:31
kanzurenot really. i don't think you should throw .docx files into there.08:33
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phillyjok, cool09:02
phillyji've seen cathal put up lab protocols on it09:02
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eudoxiapaperbot: http://dl.acm.org/ft_gateway.cfm?id=1869462&ftid=845668&dwn=1&CFID=333425031&CFTOKEN=5187869811:54
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/7a01e5a892a6d7a9f408df01905f9359.pdf11:54
eudoxiapaperbot: http://dl.acm.org/ft_gateway.cfm?id=1869526&ftid=845715&dwn=1&CFID=333425031&CFTOKEN=5187869811:56
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/67845a4fb5b009259c389f90ab02c1c0.pdf11:56
heatheudoxia: i'm curious now if those studies took into account haskell :)12:01
eudoxiaheh12:03
eudoxia>While in correspondance to [8] Lisp seems to12:03
eudoxiahave a positive impact on development time, it also seems12:03
eudoxiathat programming in (the statically typed programming12:03
eudoxialanguage) Haskell requires less effort than for example12:03
eudoxiaAda.12:03
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kanzurehttp://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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kanzurehmm. 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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archelsif you're already inside a box on the university network, just wget them12:47
kanzurei wonder if i could route email to root@bryan.svcs.cs.pdx.edu through that form12:48
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archelsneither of my university mail addresses is even accepted12:49
kanzuredoes your university subscribe to elsevier/sciencedirect?12:50
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archelsone I'm sure of, the other probably12:52
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
kanzureuh.. 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
kanzurehow unfortunate.16:38
kanzuregene_hacker: hi16:39
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eudoxiakanzure: it only gets worse, doesn't it?16:44
kanzurethat's the east bay diybio group. voting for google lock-in. really mind boggling.16:45
kanzurealso, 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
kanzurehttp://scanlime.org/2011/05/cia-vc-service-is-down-indefinitely/16:46
kanzurehttp://shadowm.rewound.net/blog/archives/245-CIA.vc-is-dead.html16:46
kanzure.title https://lwn.net/Articles/518955/16:46
yoleauxCIA.vc shuts down [LWN.net]16:46
eudoxiawhy did he have to call it CIA16:46
kanzurepretty neat to see the source code up though http://code.google.com/p/cia-vc/source/browse/16:48
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gene_hackerknow of any good hackerspaces in california kanzure?17:10
kanzurenoisebridge, los angeles biohackers, biocurious, sudo room17:11
kanzureif you are willing to accept a commercial entity as an answer, then techshop too.17:12
gene_hackersudo room?17:12
gene_hackeris hacker dojo any good17:12
kanzurehacke rdojo is a bunch of office chairs17:12
kanzure*hacker dojo17:12
gene_hackertechshop is waaaaaay too expensive17:12
gene_hackerthat's what I thought17:12
kanzurethen you want noisebridge17:12
kanzurebiocurious is also useful but has no machining capability whatsoever17:13
kanzurebtw noisebridge is on irc in #noisebridge17:13
gene_hackerdefinately visiting biocurious on their bioluminescent night17:14
gene_hackercan one just drop into noisebridge?17:14
kanzureif you are in san francisco then let us know, there's a few people in here who you should hang out with17:14
kanzureyes 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_hackergoing to be in san francisco17:15
kanzurealso you should stop by langton labs and meet 3scan/cambrian genomics/other people17:15
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kanzurehah you could meet up with carl crott (delinquentme).. he's been building his orbital shaker and liquid handler.17:16
kanzurealso Juul17:16
gene_hackerwhat's langton labs?17:17
kanzurecommunal living space for a group of molecular biologists and creative folks17:18
kanzurehouses http://3scan.com/ and http://cambriangenomics.com/17:18
gene_hackercool17:18
kanzurehas some fun people like http://anselmlevskaya.com/ and http://craneium.net/17:20
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delinquentmepaperbot, http://www.ncbi.nlm.nih.gov/pubmed?term=perspectives%20on%20whole%20organ%20assembly17:20
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/67ee5fb646ad3d800a9cbb08bea1c5b3.txt17:20
kanzuredelinquentme: hey, gene_hacker will be in SF soon and you should hang out with him17:20
delinquentmegene_hacker, !!!17:21
gene_hackersup17:21
delinquentmewhen are you gonna be in town???17:21
gene_hackerlike saturday through tuesday17:21
delinquentmeaww fack. I'm getting back 6/617:21
gene_hackeroh well17:22
kanzuredelinquentme: hook him up with some people?17:22
delinquentmecurrently in pittsburgh17:22
gene_hackerwhat sort of liquid handler are you making?17:22
delinquentmegene_hacker, what are you into homeslice??17:22
gene_hackernot much as of yet17:22
delinquentmegene_hacker, I wish it was made ... kanzure Im interested in one which can be fabbed on chip17:24
kanzuregene_hacker does things like http://www.instructables.com/id/Build-a-Polar-3-D-Printer-from-Legos/17:24
kanzureor erm.. http://boingboing.net/2008/09/01/howto-make-a-3d-prin.html17:24
kanzurehonestly i forget the url17:24
gene_hackertrying to get my master degree, trying to design a simple machine controller(as in relays) that can be 3d printed17:25
gene_hackertrying to design some 3d printable relays, and looking for a way to print a fluid stepper motor17:25
kanzureyou 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_hackerso a microfluidic liquid handler then?17:26
gene_hackerI assume you are using PDMS or something like that?17:27
delinquentmegene_hacker, thats wild!!17:43
gene_hackerwhat?17:44
delinquentmethe polar lego printer :D17:44
delinquentmegene_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 reproducibility17:44
delinquentmehttp://strong-flower-9013.herokuapp.com/  << LH00217:45
delinquentmeSO microlfuidics + some integrated circuit scale manufacturing17:45
delinquentmeand you've got a hella replicable liquid handler for like 50017:45
gene_hackernice17:45
gene_hackerfor invitro work?17:46
delinquentmehowever im geeking out on replacement organs and cantilevers right now17:46
delinquentmegene_hacker, yeah I mean unless you knwo someone whos cool with me attaching a 2x3x3 foot cube to their body17:46
delinquentmeId be willing to do the implanting free of charge17:47
delinquentmehowever they'd have to sign a bit of paperwork17:47
delinquentmekanzure, whatchoo know about functionalized cantilevers in microfluidics for biomarker detection?17:47
delinquentmeI'm guessing you've got a research paper folder?17:48
gene_hackerI was thinking more like nematodes and other biological models you can fit in a test tube17:48
gene_hackerdetecting a bacterium by it's weight?17:48
Viper168babies17:49
kanzuregene_hacker: have you seen davidad's work on his nematode simulator?17:49
Viper168in really big test tubes17:49
kanzureoh also kirka did a thing recently..17:49
kanzurehttp://fennetic.net/irc/kirka_worm_simulator.gif17:49
gene_hackeryup17:49
gene_hackerthis? http://www.artificialbrains.com/openworm17:50
kanzurethat was 09:40 < kirka> If someone is interested here is my simple physical model of c.elegans http://anonymousdelivers.us/4907417:50
kanzureopenworm is http://openworm.org/17:51
kanzurebut davidad's things are at http://nemaload.davidad.org/17:51
kanzureoh 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_hackerdelinquentme there's this: http://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=1000&context=nanodocs17:52
kanzure.title17:53
delinquentmeThe fucking issue with *ALL* simulations is false negatives17:53
yoleauxkanzure: Sorry, that doesn't appear to be an HTML page.17:53
delinquentmeno one has a good fucking answer for that.17:53
gene_hackerand it17:53
delinquentmewe 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 them17:54
delinquentmegene_hacker, the sim is probably faster17:54
delinquentmethat is im guessing, is the primary advantage... but yes it seems like " false negative " is a dirty word around any simulation operation17:54
kanzuregene_hacker: actually someone did that and uploaded 10,000 hours of video17:54
gene_hackerwhere?17:55
kanzureftp://anonymous@ftp.mrc-lmb.cam.ac.uk/pub/tjucikas/wormdatabase/results-12-06-08/Laura%20Grundy17:55
kanzuremore information can be found here: http://wormbehavior.mrc-lmb.cam.ac.uk/17:55
gene_hackersounds like a great training dataset17:55
kanzurei haven't actually watched any percentage of these videos, so i can't comment on quality.. i hear it's okay.17:56
gene_hackerfor a computer I mean17:56
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delinquentmekanzure, functionalized cantilevers?18:06
kanzuredunno, look in http://diyhpl.us/~bryan/papers2/microfluidics/18:06
delinquentmeany info .. or thoughts? I'd love a way to release the biomarkers post binding as well :D18:06
kanzurei am busy fixing javascript things18:06
delinquentmefor paperboot?18:06
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kanzureno not paperbot :(18:13
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yashgarothpaperbot: http://www.nature.com/mt/journal/v21/n5/abs/mt201333a.html18:25
paperbotHTTP 401 unauthorized http://www.nature.com/mt/journal/v21/n5/pdf/mt201333a.pdf18:25
yashgarothnoooooo18:25
kanzureyashgaroth: http://diyhpl.us/wiki/articles18:26
kanzureyashgaroth: (try the russian one)18:26
yashgarothit sends me to a forums homepage? if you mean sci-hub18:27
kanzurewell first you need to be in russia18:28
yashgaroth1 sec18:29
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kanzureset proxy to 109.198.126.112:8080 then try again18:29
kanzureor 46.21.240.253:312818:29
yashgarothman I ain't got time to be setting proxies18:30
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kanzureDoktorUnicorn: hello19:05
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heathpaperbot: http://onlinelibrary.wiley.com/doi/10.1002/anie.201005931/abstract19:53
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/3011fd5d1349d902d74ab0ecd92576d7.txt19:53
heathpaperbot: https://www.sciencemag.org/content/336/6085/1171.abstract19:53
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kanzurepaperbot needs your help19:59
kanzurepaperbot needs people19:59
kanzurebecause people need paperbot. ok this is a bad advertisement, but you get the idea.20:00
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kanzureJuul: 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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delinquentmeJuul, !!!!!!!!!!!!!!!!!!!!!!!!!20:15
* delinquentme hugs20:15
Juulhi delinquentme :)20:15
delinquentmesooooo when we're talking about antibodies functionalized to a substrate...20:15
delinquentmeis there a way to say .. detach given analytes from the binding sites?20:16
delinquentmeI'd guess it can be done through a current change...20:16
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delinquentmeas I believe the impedance changes through the cantilever when additional alalytes attach20:17
delinquentmehence we can measure the quantity of a given biomarker through a sample20:17
delinquentmeNOW... if they could be detached ... we've got an awesome system for marker-free detection20:17
delinquentmeALSO I was thinking about a solution for type 1 diabetes20:18
delinquentmeapparently people have developed microfluidic wells with "molecular caps" which can be detached20:18
delinquentmeso 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 insulin20:19
delinquentmele blah.20:26
delinquentmenobody larvs mar20:27
delinquentmekanzure, hug?20:27
delinquentmeklafka, harg?20:27
kanzurewait longer. not everyone can jump to action at once. i'm still bugging some debuggers for some other bugged bug things.20:28
delinquentmedoes anyone know of a good bay area accountant?20:41
delinquentmepaperbot, http://www.ncbi.nlm.nih.gov/pubmed/1153364520:43
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/1a2e3b414c2e1a6242e6cdc924196d6e.txt20:43
jrayhawkT1Ds are also amylin and glycogen dysregulated20:44
Juuldelinquentme, that's interesting, do you have a link to the article about molecular caps?20:45
Juuli'm not very well-versed in antibodies.20:45
delinquentmeJuul, Its in this book I picked up ... lemme see if I can find the ref for it20:45
delinquentmebut yeah they're individually addressable molecule tops which could be popped off20:45
delinquentmethe question is what would the refill process look like20:46
delinquentmeor like better yet! what if you could design a surface/skin mounted delivery system20:46
Juuli think darpa has funded some research on that20:47
delinquentmewas 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 interaction20:47
delinquentmeIE painless and skin-mounted drug / substance delivery20:48
delinquentmeJuul, from what you know ... when we're talking about detaching an analyte from a bound docking surface20:53
delinquentmethat process... what would it be called? Any idea?20:53
kanzurecleaving20:59
delinquentmeDr. 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
delinquentmethat might sound slightly ignorant21:00
kanzureyou can usually wash away certain antibodies21:00
yashgarothelution21:02
kanzurei 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
yashgarothnot sure how electrocution affects antibody binding21:02
yashgarothor how you read a microcantilever in a tiny chip21:03
yashgarothimplanted chip, anyway21:03
kanzuremicrocantilevers is how afm works, you bounce light off of them and read curvature.21:03
yashgarothcramming an afm into your arm seems like a hassle21:04
kanzuremost afm setups are big because people suck at stability21:04
kanzurestabilization or w/e21:04
kanzurenot like financial stability. :(21:04
yashgarothalso, developing a membrane that only lets in tiny molecules like glucose, and also somehow doesn't get encapsulated by the body21:04
kanzureisn't that what dialysis cellulose membrane things do?21:05
yashgarothnone of them have pores that small, and they would get encapsulated21:05
yashgarothI suppose if they block almost all proteins the pore size is mostly irrelevant21:06
yashgarothimplantable or other constant-monitoring biomarker sensors are one of them holy grails21:07
kanzurehaven't we had digestable jpeg-transmitting capsules for a while now?21:07
delinquentmeyashgaroth, there are a few ways to read the cantilever21:08
yashgaroththat's not actually inside the body if you take a strict biologist's view, the digestive tract is epithelial21:08
delinquentmethats actually a really interesting way to make a hella small AFM...21:09
delinquentmeahhh ok so mass / dampening21:09
kanzurean afm cantilever is already small.. what do you think they do, poke atoms with a 5 foot pole?21:09
delinquentmebut the whole system isnt21:09
delinquentmeyashgaroth, the issue is though what if we've got 400 biomarkers we're detecting ... that means nearly a single wash step for every cantilever21:10
yashgarothwell washing with acid or high salt or both will usually knock off most stuff21:11
kanzurehuh? i don't understand your setup.21:11
yashgarothwait, 400 different biomarkers?21:11
kanzuremost people just put biomarkers on a plate and then they look at the plate.21:11
delinquentmeelectrocution 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 minima21:11
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kanzurei think they even do this with cmos things21:11
yashgarothelectricity will probably denature and/or destroy your protein21:12
delinquentmeyashgaroth, kanzure I'm thinking over what a microfluidic setup for tons of biomarkers21:12
delinquentmeyashgaroth, you're saying the one I've got on the cantilever as a binding site?21:12
delinquentmeI mean it depends on the protein21:12
yashgarothsure, that one21:12
heathpaperbot: http://pubs.acs.org/doi/abs/10.1021/nl103427w21:13
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Single-Molecule%20Kinetics%20and%20Super-Resolution%20Microscopy%20by%20Fluorescence%20Imaging%20of%20Transient%20Binding%20on%20DNA%20Origami.txt21:13
delinquentmeyashgaroth, you lame ;D21:13
delinquentmeONES21:13
delinquentmeexcruse21:13
delinquentmehttp://en.wikipedia.org/wiki/Surface_plasmon_resonance21:14
delinquentmeI still fail to grok where the plasmon operation happens here21:14
delinquentmeoperation = "interaction"21:14
yashgarothalso note that all these super-awesome microfluidics and plasmon resonance analysis techniques take place with a machine that's bigger than most diabetics21:15
delinquentmeyashgaroth, currently yeah21:15
delinquentmewhy though21:15
yashgarothI don't know, quantum shit21:15
delinquentmehahahaha21:16
delinquentmepercieved value21:16
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
delinquentmeSCIENCE! ( marketing )21:17
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delinquentmeyashgaroth, I just posted that on FB :P21:22
heathpaperbot: http://www.nature.com/nnano/journal/v7/n6/full/nnano.2012.73.html21:25
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Molecularly%20self-assembled%20nucleic%20acid%20nanoparticles%20for%20targeted%20in%20vivo%20siRNA%20delivery.pdf21:25
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heathpaperbot: http://www.nature.com/ncomms/journal/v4/n4/full/ncomms2690.html22:16
paperbotHTTP 401 unauthorized http://www.nature.com/ncomms/journal/v4/n4/pdf/ncomms2690.pdf22:16
heathpaperbot: https://www.sciencemag.org/content/335/6070/83122:22
paperbotSSLError: [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
kanzurestill don't know why that's a problem22:23
heathhttps://www.microryza.com/ :: follow and fund research (kickstarter for science)22:26
kanzureyou are about two years slow22:26
kanzurealso they got into ycombinator this year22:26
heathpaperbot: https://www.sciencemag.org/content/338/6106/506.abstract22:29
paperbotSSLError: [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
kanzurei don't think you understand.. https on sciencemag.org isn't gonna work until someone fixes paperbot.22:29
heathi was publically logging notes to myself... but i can just bring it to ##note-to-self22:32
heathpublicly rather*22:32
heathhttp://wired.jp/2013/05/05/dnahackers/22:35
heathhttp://www.bio-x.cn/foldna/ :: a webserver for DNA nanostructure autoscaffold and autostaple22:58
heathpaper describing it: http://www.hindawi.com/journals/jnt/2012/453953/22:58
heathhttp://molbot.org/ :: molecular robotics research group23:04
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heathCongressional Biomedical Research Caucus 2013 Briefing Series :: http://www.coalitionforlifesciences.org/cbrc/cbrc-briefings/cbrc-briefing-schedule23:17
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heathhttps://www.sciencemag.org/content/328/5986/1662.abstract23:20
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--- Log closed Thu May 30 00:00:41 2013

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