2012-02-03.log

--- Log opened Fri Feb 03 00:00:45 2012
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@kanzurehttp://dangerousprototypes.com/2011/09/21/editorial-upverter-another-closed-source-vampire-exploits-open-hardware-for-ventrue-capital-pr-and-profit/06:33
@kanzureEditorial: Upverter, another closed source vampire exploits open hardware for ventrue capital, PR, and profit06:33
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@kanzuretime to spam this:07:03
@kanzurehttp://singularityu.org/launchpad/07:03
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@kanzureso i'm watching cosmos for the first time, and it's opening up with this crazy little segment against the cold war08:47
@kanzureas if this is a "please donate to help save kids in africa" ad08:47
@kanzurewtf08:47
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@kanzureGrrr_: it worked..09:29
Grrr_Ah, excellent.09:30
Grrr_So this inactivity is the norm?09:30
@kanzurejust say whatever you want to say09:33
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Mokbortolan_only YOU can prevent inactivity!09:37
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Grrr_lol09:42
Grrr_Okay...09:42
Mariu1. Serve the public trust09:42
Mariu2. Protect the innocent09:42
Mariu3. Uphold the law09:42
Mariu4. Ensure the safety of OCP senior staff members09:42
Grrr_What do you wish to achieve wrt to Transhumanism, and how?09:43
Mokbortolan_4.  Ensure the safey of OCP senior staff members^H^H^H^H^H^H^H^H^H09:44
Grrr_OCP?09:45
Mokbortolan_it's from a movie about a cyborg policeman09:46
MariuOCP stands for Omni Consumer Products, in that movie09:46
Mokbortolan_a corporate policeman in a city owned by a company named OCP09:46
Grrr_Anyone here familiar with Orion's Arm?09:51
MariuI'm a little09:51
Mariuan MMO09:51
Mokbortolan_I'm more familiar with his belt09:51
Mokbortolan_oh09:51
MariuBlade Runner ?09:52
MariuxD09:52
Urchinthere are people here who haven't seen RoboCop?09:52
Mokbortolan_or don't remember things abou tit09:52
Mokbortolan_my wife will watch a movie and not remember anything about it 6mo later09:53
Mokbortolan_drives me nuts09:53
Grrr_I've seen Robocop... It's just been a long time...09:53
Mokbortolan_So a pirate captain goes to the urologist09:54
Mokbortolan_he says to the doctor, "Arr, doc, ye gotta see this"09:54
Grrr_not an MMO, I'm referring to anders world building project.09:54
Mokbortolan_he pulls down his breeches to reveal a small ships wheel firmly lodged around the base of his genitals09:54
Mokbortolan_and exclaims painfully, "Arr! You gotta help me, it's drivin' me nuts!"09:55
UrchinGrrr_: yes, I'm familiar with OA09:55
Urchinnot it's latest developments09:56
UrchinI sort of got disilusioned with it when they dropped Creative Commons09:56
MariuI will try OA when I will have some time09:58
Urchindo they still cover the next 10500 years, or did they move a bit forward with their coverage?09:59
Grrr_Same time frame to the best of my knowledge.10:00
Grrr_Favorite Archailect?10:00
UrchinUrchinStar has the coolest name10:01
Urchinand I like Omegarapture10:01
UrchinKeter, possibly10:02
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Grrr_Yeah, Keter or The Transcend for me.10:05
UrchinOmegarapture because he's one of us10:05
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Grrr_Can someone explain to me -  I'm a newcomer to this channel - why so many say nothing?10:09
Mokbortolan_they're saving up their wistom10:09
OmegaHuh what10:09
Mokbortolan_wisdom10:09
Mariulol10:09
eudoxiayou mean that there's no activity or some users have been idle for sixteen years?10:09
Mokbortolan_any minute now, they'll bust out with some incredibly profound statement that they've been putting together for weeks10:09
@kanzureGrrr_: because we are always online10:10
OmegaI think most of the people that are always online just have bouncers10:10
UrchinGrrr_: we just leave our irc clients online all the time10:10
OmegaOr... you could do that I guess.10:10
Urchinmine is running in a screen on a shell server10:11
Urchinand has racked up a 53 day uptime10:12
* eudoxia reads the logs10:12
eudoxiathe Silk God is cool too10:12
Urchinsilk god?10:12
eudoxiare: favorite archailect10:12
UrchinI had to google it10:13
Urchinthey probably added it after I stopped paying attention to OA10:13
eudoxiaOA could move much faster if it was more of a Wiki thing10:14
MariuI think of Bentusi as an advanced species10:15
UrchinOA requires a fleshing out of every article in a discussion, and discussing that much physics and stuff that way is not the best thing in wiki format10:16
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fennwhen they came for the cyborgs there was no-one left to stand up for me.11:13
@kanzurehi fenn11:17
fenn"Mice fed the chemical resveratrol are impervious to the harmful effects of a high-fat diet"   i keep reading this and wondering what the harmful effects of a high fat diet actually are11:25
fennif anything11:25
fennalso, nature's citations don't even show the title of the paper, wtf are they thinking11:26
@kanzuresome citation forms- like in chemistry journals- exclude titles11:26
@kanzureso it's only a list of authors, a date and maybe a journal abbreviation11:26
Urchinsome big journals require that to save space11:27
@kanzurebecause bytes cost so much11:27
fennwe are running out of electrons after all11:27
@kanzurehttp://groups.google.com/group/diybio/browse_thread/thread/64ad8acd3c47043a11:27
fennthey are using them all up in those wasteful atom smashers11:27
@kanzure> "And we invest a lot in infrastructure, the tags and metadata attached to11:27
@kanzure> each article that makes it discoverable by other researchers through search11:27
@kanzure> engines, and that links papers together through citations and subject11:27
@kanzure> matter.11:28
@kanzure> All of that has changed the way research is done today and makes it more11:28
@kanzure> efficient. That's the added value that we bring."11:28
fennwow thanks guys11:28
fennmaybe you could OCR your fucking documents too11:28
* fenn goes to sleep11:32
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delinquentmeZOMG12:17
delinquentmeHIO ALL12:17
delinquentme<3 <3 <312:17
MariuxD12:17
Mariuhey delinquentme12:17
delinquentmeso theres a new innocentive challenge12:23
delinquentmehttps://www.innocentive.com/ar/workspace/challengeDetail?challenge=993272012:23
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uniqanomaly"The Solvers are not required to transfer exclusive intellectual property rights to the Seeker.  Rather, by submitting a proposal, the Solvers grants to the Seeker a royalty-free, perpetual, and non-exclusive license to use any information included in this proposal"12:42
uniqanomalyACTIVE SOLVERS: 69312:42
uniqanomalyright12:42
uniqanomalyhttps://www.innocentive.com/ar/challenge/993282112:43
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delinquentmeits marked as an active solver if you accept the terms to see the entirety of the project13:07
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Mariulater guys13:31
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@kanzurewho is doing lucidant polymers?15:17
@kanzure"providing custom polymer matrices for biological separations"15:18
@kanzureeh..15:18
@kanzure"Our core technical expertise is in polyacrylamide chemistry.  Lucidant can synthesize linear or cross-linked polyacrylamides, as bulk powders or nanoparticles, to customer specs.  If you have an existing need or a novel application, call us with your requirements."15:18
JayDuggerGood evening, everyone.17:14
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delinquentmekanzure, lets do it in here18:52
* delinquentme evil grin18:52
delinquentmeso all that watermark shit is ehhh18:53
@kanzuredelinquentme: http://singularityu.org/launchpad18:53
delinquentmegenerated (obv) on the fly and interted into the papers18:53
@kanzureyes if you look at the pdf files you will see some other metadata inserted18:53
@kanzurelike "AdobeWatermarkerPdf2001"18:53
delinquentmeso would it be hard at all to just forcibly *take* them outside of their normal operating system?18:54
delinquentmeideally legal is awesome18:54
@kanzurewhat?18:54
@kanzureyou mean, manually scan the papers?18:54
delinquentmei mean just break the system so that they're not watermarking18:55
@kanzureno. it's not that hard to remove the watermarks, but it's a little hard to tell if you got all of it18:55
@kanzurelike the visible watermarks are easy to remove18:55
@kanzuredelete the relevant pdf object, boom it no longer shows up18:55
@kanzurebut what about that other compressed data in a non-visible element. trickier to tell.. i need to figure out the compression scheme :x18:55
delinquentmeoh so there are effectively individual layers and you can remove what you need18:57
delinquentmecool!18:57
@kanzureyes that's how pdf works18:58
@kanzureexcept when they are assholes and make the watermark a part of the image18:58
@kanzurego pick out say, an elsevier paper19:02
@kanzureand try to find the watermarks19:02
@kanzurehttp://diyhpl.us/~bryan/papers2/19:02
delinquentmeok you're telling me that the watermarks arent an issue19:04
delinquentmeOSCAR4, OPSIN, ChemicalTagger  << these are the chemical parsers19:05
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delinquentmekanzure, once a researcher submits a paper19:13
delinquentmethey still own that paper right?19:13
Stee|this depends on the journal in some cases19:13
Stee|in many cases no19:13
Stee|they can't publish that 'exact' paper again19:13
delinquentmeStee|, what if we wanted an excerpt of that journal19:13
Stee|basically, try emailing the dude19:13
Stee|there's a chance that his university paid the fee to be able to distribute the article as much as they want19:14
Stee|or back-door, they simply don't care19:14
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delinquentmeate some delicious ass ice cream ... now im freezing my ass off #firstworldproblems20:26
@kanzuredelinquentme: http://gnusha.org/logs/2011-06-10.log shows some of the watermark removal stuff20:28
@kanzure13:35 < kanzure> hmm some journals are using this to watermark their pdfs: http://www.appligent.com/stamppdf-batch20:28
@kanzure13:35 < kanzure> heh "StampPDF Batch starts at $1,995.00 (USD) for a single server with up to 4 cores"20:28
@kanzure13:57 < kanzure> also, for removing a first page with IP address info (like from IOP):20:28
@kanzure13:57 < kanzure> pdftk input.pdf cat 2-end output.pdf20:28
@kanzure13:59 < kanzure> 104/105.pdf have been moved into http://diyhpl.us/~bryan/papers2/neuro/ultrasound/manual-watermark-removal-example.zip (but i'll probably delete this too)20:28
@kanzurei posted some python file somewhere.. uh..20:29
delinquentmeok so you've got some code that begins to work around this stuff20:29
@kanzureask and ye shall receive (if i happen to remember where i put it)20:30
JayDuggerDoesn't that pdftk remove the entire first page, and not the watermark?20:34
@kanzureyes20:42
@kanzurethe watermark code is the stuff i haven't remembered where i put20:42
@kanzure1:21 < kanzure> well i used imagemagick in the past (via 'convert') to dump pdf to images and then move signatures by coordinates or otherwise blank shit out20:44
@kanzure11:21 < streety> fair enough, makes sense with context20:44
@kanzure11:53 < kanzure> ah here's one:20:44
@kanzure11:53 < kanzure> http://diyhpl.us/~bryan/papers2/Patterning%20design%20in%20color%20at%20the%20submicron%20scale.pdf20:44
@kanzure11:53 < kanzure> see left-hand side20:44
@kanzure11:58 < kanzure> some of the pdf obj streams seem to be zipped20:44
delinquentmemuh feet r cold20:44
@kanzure12:16 < kanzure> using that same file, try this:20:45
@kanzure12:16 < kanzure> cat temp.pdf | grep -a "Length " | sort | uniq -c | sort -k2nr20:45
delinquentmemust invent foot warmer first20:45
@kanzure12:16 < kanzure> as you can see, they repeat the watermark four times (once for each page)20:45
@kanzure12:17 < kanzure> in this case lines 63-67 inclusive are the watermark on the first page20:45
@kanzure12:20 < kanzure> iirc pypdf can handle FlateDecode?20:45
@kanzure12:21 < streety> I'm not using pypdf, I think that was the package then returned text but no spaces between words20:45
@kanzure12:21 < streety> I'm using pdfminer instead.  It was a pain to get my head around how it worked but generally produces good output20:45
@kanzure12:31 < kanzure> cat objstream.dat | python -c'import sys;import zlib;data=sys.stdin.read();print zlib.decompress(data)'20:45
@kanzure12:37 < kanzure> also that's probably just the display of the text and doesn't actually remove the compressed text from the file20:45
@kanzure12:41 < kanzure> the objects with "Length 40" in this file are the pdf/display commands20:45
@kanzure12:42 < kanzure> the objects like on line 6, 13, 19 and 25 are the "Downloaded by" lines20:45
@kanzure12:57 < kanzure> "Producer:       Acrobat Distiller Command 3.01 for Solaris 2.3 and later (SPARC)"20:45
@kanzure12:57 < kanzure> acs is running on solaris?20:45
@kanzurelatex-over-http collaboration stuff https://www.sharelatex.com/20:57
@kanzureah http://scribtex.com/ has git integration20:58
delinquentmekanzure,  >> http://en.wikipedia.org/wiki/RNA_polymerase_II22:04
delinquentmewhats the II part about?22:04
yashgarothdifferentiates it from the other ones22:06
delinquentmeyashgaroth, so you22:07
delinquentmere  saying that there are 2 kinds of polmerase?22:07
yashgarothof rna pol, there are several, as with dna pol22:07
yashgarothrna pol 2 is the 'interesting' one22:08
* delinquentme sits quietly22:09
delinquentmeyars. go on.22:09
yashgarothwell uh, the other rna pols just make short RNAs like tRNA and RNAi22:10
yashgarothpol 2 makes mRNA for translation22:11
yashgarothwhy...do you ask?22:11
delinquentmewell it just struck me as weird that there are 2 kinds22:11
@kanzurethere are many kinds of polymerase molecules22:11
@kanzurein humans i think there's at least 20 or 40.. something like that22:12
delinquentmeoh and I just learned about TRANSCRIPTION FACTORS!22:12
delinquentme>_<22:12
@kanzuredelinquentme: you should watch an ocw class about molecular biology22:12
@kanzuremolecular biology is much more enjoyable when you're not being tested on random kinetic equations22:12
yashgarothhaha if you think a dozen variants of pol is weird, there are tens of thousands of G-protein coupled receptors22:12
@kanzuregcmp stuff?22:13
@kanzureerm22:13
@kanzurehttp://en.wikipedia.org/wiki/Cyclic_guanosine_monophosphate22:13
@kanzurehttp://en.wikipedia.org/wiki/G_protein-coupled_receptor22:14
@kanzurenevermind22:14
delinquentmeyashgaroth, kanzure article worth reading?22:14
@kanzurewikipedia22:14
yashgarothmolecular biology of the cell22:14
@kanzurethere might be an ok review somewhere, but wikipedia is ok for this sorta high-level stuff22:14
delinquentmeah! so these are cellular receptors22:15
@kanzurethere are many types of receptors22:15
@kanzureall sorts of things are classified as 'integral proteins'22:15
@kanzurehttp://en.wikipedia.org/wiki/Integral_membrane_protein22:15
@kanzurewell, i guess i should clarify that an integral protein doesn't have to be the actual receptor22:16
@kanzureit's rather the channel22:16
delinquentmean "integral protein" is something which crosses the cellular membrane?22:16
@kanzure"A transmembrane protein (TP) is a protein that goes from one side of a membrane through to the other side of the membrane. Many TPs function as gateways or "loading docks" to deny or permit the transport of specific substances across the biological membrane, to get into the cell, or out of the cell as in the case of waste byproducts. As a response to the shape of certain molecules these "freight handling" TPs may have special ways of folding up or22:16
yashgarothor just embedded in the membrane, it doesn't have to necessarily cross all the way22:17
delinquentmecheck22:17
@kanzuresee bacteriorhodopsin22:17
delinquentmeI've heard germany has alot of vocational school22:17
delinquentmes22:17
delinquentmei wonder if they've got one for bleeding edge biolofy22:18
delinquentmebiology**22:18
yashgarothare you in germany?22:19
@kanzuredelinquentme: i didn't really have that much special biology training,22:19
delinquentmepittsburgh22:19
@kanzurejust read some textbooks, watch videos that don't suck22:20
delinquentmetrue true22:20
@kanzuremost textbooks can be read in a week tops if you're not doing homework from it (fucking hell)22:20
@kanzureat least in biology22:20
yashgarothit's true22:20
delinquentmekanzure, I guess i need to work on spee dreading?22:20
delinquentmespeed* reading22:20
yashgarothwhat do you aim to learn about biology?22:21
@kanzuredelinquentme: well the average high school graduate reads 400 wpm,22:21
@kanzurethe average college grad reads 600-700 wpm22:21
@kanzurei recommend getting up to 900-1100 wpm..22:22
@kanzure"While the average adult reading rate is 250 words per minute with 70% comprehension,[3] speed reading programs typically claim that improvements to 500 words per minute or more while maintaining or improving comprehension are possible."22:23
@kanzurewtf... 250?22:23
@kanzure500 wpm isn't that hard22:23
delinquentmenever been tested on comprehension22:23
delinquentmeyashgaroth, I want to get a job working on regen medicine22:24
@kanzureno you don't22:24
@kanzurei know you too well.22:24
delinquentmesomething having to do w genomics22:25
delinquentmeehh web apps and all the other shit is ...22:25
delinquentmemeh.22:25
@kanzureyou want to play with cool toys, do good work and not have to put up with bs22:25
@kanzurethat's not a job22:25
@kanzureweb apps are a job too22:25
@kanzurebut i'm pretty sure you don't want to do those anymore22:25
yashgarothhaha that's my job22:25
delinquentmeyashgaroth, you're a programmer?22:25
@kanzureyashgaroth: me too.. except also android, iphone, windows22:25
yashgarothfuck no, I'm in biochemistry22:26
yashgarothmostly protein production22:26
delinquentmeyashgaroth, where at?22:26
delinquentmeSV?22:26
yashgarothif by SV you mean sorrento valley, then you're very close22:27
delinquentmeoh so sandiego then?22:27
yashgarothyup22:27
delinquentmenot bad i applied @ organovo22:27
delinquentmehella cool company22:27
yashgarothah yes I've heard of them22:28
delinquentmeprinting body parts man!22:28
delinquentmeall for it22:28
yashgarothI don't make anything bigger than 250 kilodaltons usually22:29
yashgarothunless you count plasmids, which I don't22:29
delinquentmeyashgaroth, so you're kind of a biochemist22:30
delinquentmederp22:30
delinquentmeits close to bed time22:30
delinquentme:D22:30
yashgarothI'm classically a molecular biologist, but I go where jobs take me22:30
@kanzuresleep is for poor people22:30
yashgaroth"poors"22:30
delinquentmeyashgaroth, so daily tools are...?22:31
Mokbortolan_grow me a patch of retina that I can insert under my skin with some NGF so I can use it as a data input channel22:31
yashgarothFPLC mostly, TC hoods22:31
delinquentmeMokbortolan_, Advanced cell tech has that22:31
delinquentmeFPLC?22:31
Mokbortolan_little lasers'd do great22:31
delinquentmerelated to HLPC?22:31
@kanzureyou don't just patch in neurons like that :P22:31
yashgarothyes, but bigger22:32
yashgarothHPLC is mostly for analysis, FPLC for large-scale purification22:32
Mokbortolan_that's just another problem to overcome22:32
yashgarothyou've got two retinas already, surely you can spare one for data input22:32
Mokbortolan_no, I need those for looking around22:32
@kanzureuse your tongue instead22:32
Mokbortolan_the tongue works pretty good22:33
delinquentmeMokbortolan_, there are already brain - memory interfaces22:33
delinquentmeand you dont need a retina22:33
Mokbortolan_but then you have a hard time talking22:33
@kanzuredelinquentme: ?22:33
delinquentmejust diodes in your skull22:33
@kanzurememory interfaces?22:33
delinquentmekanzure, i've already showed u this :D22:33
@kanzureyou mean ted berger's stuff?22:33
@kanzurethe artificial hippocampus algorithms?22:33
delinquentmehttp://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CCgQFjAA&url=http%3A%2F%2Fwww.nytimes.com%2F2011%2F06%2F17%2Fscience%2F17memory.html&ei=PdEsT8q7AcLc0QG_04nsCg&usg=AFQjCNEomEnRkXxgaEDwK8VSSyEWksg-lA22:33
delinquentmedeadwyler22:34
delinquentmeawesome last name22:34
delinquentmeyashgaroth, where'd you go to school and what level of degree?22:34
@kanzurewell berger is at least cited in there22:34
delinquentmei want a phd in 3 years22:34
yashgarothUW-Seattle, BS22:34
Mokbortolan_I doubt the electrodes they used to attach it were designed to last a human's lifespan... but I guess that's also just another problem to overcome22:34
delinquentmeoh22:34
@kanzuredelinquentme: go get a phd in some third world country, done22:35
@kanzurejust show up and hand them money22:35
@kanzurewhy the hell do you want the degree?22:35
yashgarothI may do a phd but I don't wanna work 12 hour days and/or 8 years, for scraps22:35
delinquentme^^^^22:35
@kanzuredelinquentme: if you actually have research you need to do, you should just do it22:36
Mokbortolan_http://www.gizmag.com/retinal-stem-cell-transplant/21210/22:36
@kanzureregardless of a doctorate attached to it.22:36
delinquentmekanzure, agreed22:38
delinquentmeI simply dont have research to do yet22:38
@kanzurei thought you wanted to do lab automation :(22:38
@kanzurereally, i think cheap lab automation is super important22:38
@kanzurecompared to the phd pyramid scheme22:39
yashgarothhey man undergrads are way cheaper than most equipment22:39
@kanzurenot at my rates :322:39
delinquentmeso ive got to go out read lots of research and begin designing experiments22:40
yashgarothwell, get the basics down first22:43
delinquentmeyashgaroth, im kind of anti the traditional learning model22:45
@kanzurewhy experiments?22:45
delinquentmegranted programming isnt biology22:45
@kanzurei mean, why not pick something like, "i want to build x" and just build that22:46
delinquentmekanzure, i mean just something novel / useful22:46
@kanzurenovel or useful pick one :P (kidding)22:46
delinquentmeanother option is to go find experiments and attempt to recreate them22:46
yashgarothif you just jump into current research you'll have a difficult time, I still do22:46
delinquentmeyashgaroth, oh for sure ... lots of googling22:47
delinquentmebut you can highlight >> right click >> google <highlighted text>22:47
delinquentmeill get it sorted :D22:47
yashgarothaight22:47
delinquentmeyashgaroth, thats bad ass though22:48
delinquentmeFLPC22:48
delinquentmethats like *PRODUCTION* level chemical development22:48
yashgarothwell that is what I'm doing with it22:48
* delinquentme knows what hes squeezing one off to tonight22:48
delinquentme:P22:49
delinquentmeyeah man thats hella cool22:49
delinquentmeOK IM OUT KIDS22:49
delinquentme6 hours22:49
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@kanzuredid he just..22:52
@kanzurewhat22:52
yashgarothI don't know if he was implying shitting or masturbation, and frankly I don't wanna know22:52
ybityashgaroth: don't read this: he meant masturbation22:56
yashgarothwell, I suppose that's the preferable one22:56
@kanzuredamn it ybit22:56
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@kanzureoh shit23:21
@kanzurethis guy i'm talking with is senior manager of product dev at pacbio23:21
yashgarothheh, pacbio23:22
@kanzureapparently they use c# to run their sequencer23:22
@kanzure:/23:22
@kanzurehmm how do i absorb his brain23:25
@kanzuremaybe i could make it out like i'm a clueless-but-stellar software person that he decides to hire23:25
klafkahey kanzure  or anyone else good w/ mongo?23:29
klafkatell them i bought stock in them so don't suck23:29
yashgarothyou poor bastard23:29
klafkaah well23:30
@kanzureklafka: i've kicked around mongodb once or twice.. don't know if i'm stellar or not23:30
klafkaah23:30
klafkai have a bunch of bson files23:30
klafkaand i want to query one of them23:30
@kanzurea-ha23:30
@kanzurethat's how i knew this guy23:30
@kanzurehis name seemed familiar23:30
@kanzurehttp://diyhpl.us/~bryan/papers2/polymerase/Real-time%20DNA%20sequencing%20from%20single%20polymerase%20molecules%20-%202009.pdf23:30
@kanzurehe's a co-author on that paper. that's how i know his name.23:30
--- Log closed Sat Feb 04 00:00:07 2012

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