| --- Log opened Tue Mar 12 00:00:25 2013 | ||
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| @kanzure | hmm "Craig Rouskey here. I'm working on a Phage project through Sudo Room and am wondering if we can order these plates through Biocurious." | 00:07 |
|---|---|---|
| @kanzure | so does this mean it's a langton phage project or an actual phage project | 00:08 |
| @kanzure | maybe it's a phage phage project | 00:13 |
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| @kanzure | http://www.ulalaunch.com/site/docs/publications/Integrated%20Vehicle%20Propulsion%20and%20Power%20System%20for%20Long%20Duration%20Cyrogenic%20Spaceflight%202011.pdf | 01:01 |
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| archels | Some researchers, in the perceived absence of any real | 04:54 |
| archels | theoretical understanding of the observed behaviour, prefer | 04:54 |
| archels | to adopt a purely empirical approach. They are content to | 04:54 |
| archels | represent the data with mathematical formulae which, in | 04:54 |
| archels | themselves, do not necessarily have any physical meaning. | 04:54 |
| archels | *zing* | 04:54 |
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| archels | Figure 11: The wearer sensing one of the experi- | 05:32 |
| archels | menters approaching from behind and throwing a | 05:32 |
| archels | cardboard shuriken. | 05:32 |
| archels | science. | 05:32 |
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| nmz787 | paperbot: http://www.sciencedirect.com/science/article/pii/S014067361360598X | 10:20 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Atherosclerosis%20across%204000%20years%20of%20human%20history%3A%20the%20Horus%20study%20of%20four%20ancient%20populations.txt | 10:20 |
| nmz787 | paperbot: http://pdn.sciencedirect.com.proxy.lib.pdx.edu/science?_ob=MiamiImageURL&_cid=271074&_user=1694017&_pii=S014067361360598X&_check=y&_origin=article&_zone=toolbar&_coverDate=2013--12&view=c&originContentFamily=serial&wchp=dGLzVlt-zSkzS&md5=44462997f6ef868c989ee481bbe6d810&pid=1-s2.0-S014067361360598X-main.pdf | 10:21 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/2621d84075498767606cf78265907fb4.txt | 10:21 |
| nmz787 | weird | 10:21 |
| nmz787 | sciencedirect is showing me the full text, but not the PDF | 10:21 |
| nmz787 | fulltext-images | 10:21 |
| nmz787 | wow sciencedirect seems currently broken | 10:24 |
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| ParahSailin | [DIYbio] Do enzymes really need to be "frozen"? | 13:05 |
| ParahSailin | not if your time has no value | 13:05 |
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| kanzure | asimov.freenode.net is experiencing a netsplit i think | 13:16 |
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| kanzure | "This paper claims that all the restriction enzymes they tested maintained their activity at room temperature for a week, and most maintained activity for a full year:" | 13:26 |
| kanzure | paperbot: http://www.biotechniques.com/multimedia/archive/00011/00293st06_11772a.pdf | 13:27 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/af96bd839f3a7057171014f33c07e1f1.pdf | 13:27 |
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| kanzure | ParahSailin: what about thermostable enzymes? | 13:37 |
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| kanzure | ParahSailin: don't the catalogs have those? are they not popular? do they just not work? | 13:38 |
| kanzure | eh so this is what max more has been working on: http://www.wiley.com/WileyCDA/WileyTitle/productCd-1118555961,descCd-tableOfContents.html | 13:42 |
| kanzure | "The Transhumanist Reader: Classical and Contemporary Essays on the Science, Technology, and Philosophy of the Human Future" | 13:42 |
| kanzure | i've seen most of these essays before, but i'm having a hard time figuring out if these are updated, edited, or just copy-pasta. i am also not sure of the value of throwing lots of essays together and charging $80 for it.. | 13:45 |
| kanzure | "A good first step is this book, which collects the smartest thinking available concerning the inevitable conflicts, challenges and opportunities arising as we re-invent ourselves. It's a core text for anyone making the future." | 13:47 |
| kanzure | i am surprised that kevin kelly would write that last sentence about this book. over-statement i think.. you can totally ignore this book and still build tons of really important things. | 13:47 |
| ParahSailin | kanzure: thermostable means they can keep activity if you get them hot | 13:54 |
| ParahSailin | kanzure: at room temperature, all proteins go stale | 13:54 |
| ParahSailin | kanzure: sure you can get away with leaving a tube out on your bench overnight, but it still has a noticeable decrease in activity | 13:55 |
| kanzure | surely someone has tried to optimize a polymerase enzyme based on this | 13:57 |
| kanzure | no, not it.. "Preservation of nucleic acids for polymerase chain reaction after prolonged storage at room temperature." | 13:58 |
| kanzure | not quite.. "Room temperature stable polymerase chain reaction mixture for detection of hepatitis B virus." | 13:58 |
| kanzure | jrayhawk: where are the piny .deb files? | 14:03 |
| kanzure | i notice there are some on gnusha:/home/jrayhawk/ but hopefully there's something on the web | 14:03 |
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| ParahSailin | kanzure: but why would you? | 14:31 |
| ParahSailin | refrigeration exists | 14:31 |
| kanzure | haha: | 14:34 |
| kanzure | 2010-02-10.log:23:08 < fenn> ah well at least they sell bitcoins via paypal | 14:34 |
| kanzure | 2010-02-10.log:23:12 < fenn> currently $0.0038/bitcoin | 14:34 |
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| ParahSailin | heh | 14:38 |
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| jrayhawk | kanzure: I don't really do releases. You can feel free to git clone and ./builddebs.sh | 14:51 |
| jrayhawk | I probably should. | 14:51 |
| kanzure | because lazy, or because responsibility avoidance? | 14:55 |
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| jrayhawk | Mostly because at this point every other commit is worth a release, so the concept of a "release" is rather arbitrary | 15:32 |
| jrayhawk | but i suppose i could still build debs for all of them | 15:32 |
| jrayhawk | I actually have a proper PGP key, now | 15:32 |
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| jrayhawk | http://pgp.surfnet.nl:11371/pks/lookup?op=vindex&search=0xDF9C3BE0FEEDBEEF | 15:33 |
| jrayhawk | http://pgp.surfnet.nl:11371/pks/lookup?op=vindex&search=0xFEEDBEEF is better, i guess | 15:34 |
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| augur | has anyone considered building a visual augment that uses the buzzer array input? | 15:35 |
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| Juul | kanzure, craig rouskey is my housemate :) | 15:56 |
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| kanzure | 0xFEEDBEEF now you're just showingo ff | 16:06 |
| kanzure | *showing off | 16:06 |
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| nmz787 | paperbot: http://ac.els-cdn.com.proxy.lib.pdx.edu/S014067361360598X/1-s2.0-S014067361360598X-main.pdf?_tid=007f622e-8b6c-11e2-a580-00000aacb35e&acdnat=1363130855_6d11ee28adca262b6fe340c79a39a200 | 16:24 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/94d7961328aae9d579722c4e1859b4dd.pdf | 16:24 |
| nmz787 | jrayhawk: ^ | 16:25 |
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| nmz787 | paperbot: http://www.sciencedirect.com.proxy.lib.pdx.edu/science/article/pii/S014067361360598X#ecomp10 | 16:26 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Atherosclerosis%20across%204000%20years%20of%20human%20history%3A%20the%20Horus%20study%20of%20four%20ancient%20populations.pdf | 16:26 |
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| nmz787 | the actual page has some videos embedded with flash of the CT scans | 16:26 |
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| kanzure | squidbot@googlegroups.com, BioCurious Printer Hacking <biocurious-printer-hacking@googlegroups.com>, biocurious-robo-biohacking@googlegroups.com, biocurious-bioinfo-hacking@googlegroups.com, biocurious-helpers@googlegroups.com, innercircle@biocurious.org | 16:59 |
| kanzure | blerg why is there an "innercircle" anyway | 16:59 |
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| JayDugger | Good evening, everyone. | 18:25 |
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| superkuh | paperbot: http://apl.aip.org/resource/1/applab/v102/i8/p082601_s1 | 18:33 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Macroscale%20refrigeration%20by%20nanoscale%20electron%20transport.pdf | 18:34 |
| superkuh | 5 blank pages. | 18:34 |
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| jrayhawk | most of those are solidly agricultural, but the unangan one is interesting. high latitude means low vitamin c, low vitamin d, and high oxidative stress from smoke and PAHs. | 18:39 |
| jrayhawk | traditional aleutians were actually fairly free of heart disease; were they better adapted either genetically or behaviorally? | 18:40 |
| jrayhawk | i.e. organ meat prizing, raw food eating, sunlight-worshipping, etc. | 18:41 |
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| kanzure | 5 blank pages.. erm. | 18:54 |
| kanzure | nope it looks right to me | 18:54 |
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| superkuh | Oh. It must be evince viewer stuff on my end. Thanks. | 18:57 |
| superkuh | This is what I get for updating poppler to try to get the latest GNOME Tracker to compile. | 18:59 |
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| kanzure | superkuh: to be fair, someone pointed out that many of the pdfs that pdfparanoia spits out are not exactly "valid". | 19:34 |
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| superkuh | I get the same blank 5 pages on multiple independent computers with different OSes and readers (evince/xpdf, Zathura, and even Acrobat). | 19:34 |
| kanzure | (aip.org is one of the few watermarks that pdfparanoia is working with) | 19:34 |
| superkuh | What do you use that renders it? | 19:35 |
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| kanzure | chrome :( | 19:35 |
| superkuh | Even GIMP gives me nothing. | 19:35 |
| kanzure | i don't know which rendering engine chrome uses. | 19:35 |
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| kanzure | this is troubling. | 19:36 |
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| superkuh | pdftotext fails (same libs as xpdf/evince). Only access is via $ strings | less | 19:36 |
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| kanzure | we're talking about this one, right? http://diyhpl.us/~bryan/papers2/paperbot/Macroscale%20refrigeration%20by%20nanoscale%20electron%20transport.pdf | 19:37 |
| superkuh | Yeah. | 19:37 |
| superkuh | This is the third paper I've had it happen with. | 19:37 |
| kanzure | i'm certain the problem is with pdfparanoia. what it's doing isn't exactly "pdf-format-friendly". | 19:37 |
| superkuh | I can accept the occasional failure to convert in the name of safety. | 19:38 |
| kanzure | https://github.com/kanzure/pdfparanoia/blob/master/pdfparanoia/plugins/aip.py | 19:38 |
| kanzure | he added a verbosity flag | 19:38 |
| kanzure | maybe using pdfparanoia with -v -v will reveal something interesting in this instance | 19:39 |
| kanzure | i guess i should fetch you the original version | 19:39 |
| kanzure | superkuh: http://diyhpl.us/~bryan/papers2/paperbot/pdfparanoiasucks.pdf | 19:41 |
| superkuh | Thanks. | 19:41 |
| kanzure | remember kids: always use science protection | 19:42 |
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| SphericalMouse_ | Hope to do a GA teardown at biocurious in a month or two | 20:01 |
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| kanzure | GA? | 20:12 |
| @fenn | chrome has a different rendering engine than 99% of open source tools out there, which all use ghostscript/xpdf | 20:18 |
| @fenn | noticed this when images weren't displaying in google books pdfs | 20:18 |
| @fenn | says something like Error in JPX stream | 20:20 |
| kanzure | pc load letter? the fuck does that mean? | 20:20 |
| SphericalMouse_ | illumina genome analyzer (DNA sequencer) | 20:24 |
| kanzure | when you do the teardown please get a copy of the ROM so we can poke at it | 20:25 |
| SphericalMouse_ | the rom? It just runs off a computer. | 20:26 |
| SphericalMouse_ | the old models are all basically off the shelf hardware | 20:26 |
| kanzure | there are no microcontrollers? | 20:27 |
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| SphericalMouse_ | maybe something. but for the most part they were very unintegrated pieces of hardware. as in, they run via serial commands and take pictures from a scientific camera to the computer | 20:28 |
| kanzure | yes but something is interpreting those serial commands | 20:28 |
| SphericalMouse_ | yes, it is the syringe pump and laser | 20:28 |
| SphericalMouse_ | kloen brand pumps, I believe | 20:29 |
| kanzure | so it's pwm straight from serial? | 20:29 |
| SphericalMouse_ | i'm overstating the case, there is some custom PCB on the inside, but mostly you could build a GA straight up | 20:30 |
| SphericalMouse_ | you can get the pumps to run straight off of serial | 20:30 |
| SphericalMouse_ | I thinks its basically pumps, valves, laser illumination, camera | 20:31 |
| SphericalMouse_ | and stage | 20:31 |
| SphericalMouse_ | these things only put out like 80 mega bases of data | 20:32 |
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| kanzure | anyway, if there is a custom PCB inside, with a chip, please grab the ROM during the teardown.. | 20:34 |
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| SphericalMouse_ | is this some kind of stuxnet ploy? | 20:36 |
| kanzure | no. i'm just curious about illumina's software. also it would be cool to find any security issues. | 20:37 |
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| kanzure | also you can look at existing software and then write better things | 20:38 |
| kanzure | you could even say.. i'm biocurious about it. | 20:38 |
| @fenn | "i'm in ur sequencer, analyzin ur genomes" | 20:39 |
| SphericalMouse_ | well, the GA's are years out of date, but like I said, the core of the software is running on the PC | 20:39 |
| kanzure | sure send that over too | 20:39 |
| kanzure | i think there's a few downloads on the illumina site | 20:39 |
| SphericalMouse_ | that is where is interpretation is done | 20:39 |
| kanzure | but they don't host everything | 20:39 |
| kanzure | yes i'm aware of that | 20:39 |
| SphericalMouse_ | i'll see what I can do | 20:45 |
| kanzure | thank you | 20:46 |
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| ParahSail1n | you need any stuff from illumina site that requires a customer account? | 21:02 |
| ParahSail1n | they dont have anything too special-- CASAVA and OLB, but CASAVA is kinda shitty | 21:03 |
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| kanzure | here's some lifetech stuff i found once: http://diyhpl.us/~bryan/irc/lifetech/5500/instrument-server-methods/ | 21:06 |
| kanzure | http://diyhpl.us/~bryan/irc/lifetech/5500/instrument-server-methods/robotics.mod.txt | 21:06 |
| kanzure | this was in one of the installable binaries from their site | 21:06 |
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| kanzure | for their 5500 genetic analyzer | 21:06 |
| kanzure | they even have a way to upload new firmware: | 21:07 |
| kanzure | http://diyhpl.us/~bryan/irc/lifetech/5500/instrument-server-methods/firmwareupgrade.mod.txt | 21:07 |
| kanzure | and an example protocol: http://diyhpl.us/~bryan/irc/lifetech/5500/instrument-server-methods/example.mod.txt | 21:08 |
| kanzure | ... well i thought it was neat. | 21:27 |
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| kanzure | "Back in February, the FDA officially gave the go-ahead for use of the OsteoFab Patient Specific Cranial Device (OPSCD) in the United States. First, the bone in question is scanned to create a CAD file. Then polyetherketoneketone (PEKK) is put down in countless layers by the Oxford Performance Materials (OPM) company in Connecticut to create a replacement part that fits perfectly. Unlike metallic materials, this plastic is radiolucent, ... | 22:12 |
| kanzure | ... allowing X-rays to pass through. When the OPSCD is in place, doctors will still be able to X-ray the patients. In addition, the OPSCD is osteoconductive, so it can work as scaffolding for growth of the patient’s own bones." | 22:12 |
| kanzure | "On March 4, the first surgery using this method in the United States was completed successfully. OPM estimates 300 to 500 patients in the US need skull replacements every month." | 22:12 |
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| kanzure | hm "We're using WARC (Web Archive) which is an official ISO File Format standard - which the Internet Archive's Wayback Machine can use. It's also a pretty good and nice format for archiving web pages in general." | 22:44 |
| kanzure | i didn't know .warc had an iso specification | 22:44 |
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| jrayhawk | http://www.youtube.com/watch?v=ns2oS1WXDvc pretty inspiring | 23:27 |
| --- Log closed Wed Mar 13 00:00:26 2013 | ||
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