--- Log opened Tue Mar 12 00:00:25 2013
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00:07 <@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."
00:08 <@kanzure> so does this mean it's a langton phage project or an actual phage project
00:13 <@kanzure> maybe it's a phage phage project
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01:01 <@kanzure> http://www.ulalaunch.com/site/docs/publications/Integrated%20Vehicle%20Propulsion%20and%20Power%20System%20for%20Long%20Duration%20Cyrogenic%20Spaceflight%202011.pdf
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04:54 < 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*
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05:32 < 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.
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10:20 < 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
10:21 < 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
10:24 < nmz787> wow sciencedirect seems currently broken
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13:05 < ParahSailin> [DIYbio] Do enzymes really need to be "frozen"?
13:05 < ParahSailin> not if your time has no value
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13:16 < kanzure> asimov.freenode.net is experiencing a netsplit i think
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13:26 < 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:"
13:27 < 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
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13:37 < kanzure> ParahSailin: what about thermostable enzymes?
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13:38 < kanzure> ParahSailin: don't the catalogs have those? are they not popular? do they just not work?
13:42 < 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"
13:45 < 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..
13:47 < 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.
13:54 < ParahSailin> kanzure: thermostable means they can keep activity if you get them hot
13:54 < ParahSailin> kanzure: at room temperature, all proteins go stale
13:55 < 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
13:57 < kanzure> surely someone has tried to optimize a polymerase enzyme based on this
13:58 < 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."
14:03 < 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
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14:31 < ParahSailin> kanzure: but why would you?
14:31 < ParahSailin> refrigeration exists
14:34 < 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
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14:38 < ParahSailin> heh
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14:51 < jrayhawk> kanzure: I don't really do releases. You can feel free to git clone and ./builddebs.sh
14:51 < jrayhawk> I probably should.
14:55 < kanzure> because lazy, or because responsibility avoidance?
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15:32 < 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
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15:33 < jrayhawk> http://pgp.surfnet.nl:11371/pks/lookup?op=vindex&search=0xDF9C3BE0FEEDBEEF
15:34 < jrayhawk> http://pgp.surfnet.nl:11371/pks/lookup?op=vindex&search=0xFEEDBEEF is better, i guess
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15:35 < augur> has anyone considered building a visual augment that uses the buzzer array input?
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15:56 < Juul> kanzure, craig rouskey is my housemate :)
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16:06 < kanzure> 0xFEEDBEEF now you're just showingo ff
16:06 < kanzure> *showing off
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16:24 < 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
16:25 < nmz787> jrayhawk: ^
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16:26 < 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
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16:26 < nmz787> the actual page has some videos embedded with flash of the CT scans
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16:59 < 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
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18:25 < JayDugger> Good evening, everyone.
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18:33 < superkuh> paperbot: http://apl.aip.org/resource/1/applab/v102/i8/p082601_s1
18:34 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Macroscale%20refrigeration%20by%20nanoscale%20electron%20transport.pdf
18:34 < superkuh> 5 blank pages.
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18:39 < 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.
18:40 < jrayhawk> traditional aleutians were actually fairly free of heart disease; were they better adapted either genetically or behaviorally?
18:41 < jrayhawk> i.e. organ meat prizing, raw food eating, sunlight-worshipping, etc.
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18:54 < kanzure> 5 blank pages.. erm.
18:54 < kanzure> nope it looks right to me
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18:57 < superkuh> Oh. It must be evince viewer stuff on my end. Thanks.
18:59 < superkuh> This is what I get for updating poppler to try to get the latest GNOME Tracker to compile.
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19:34 < kanzure> superkuh: to be fair, someone pointed out that many of the pdfs that pdfparanoia spits out are not exactly "valid".
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19:34 < 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)
19:35 < superkuh> What do you use that renders it?
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19:35 < kanzure> chrome :(
19:35 < superkuh> Even GIMP gives me nothing.
19:35 < kanzure> i don't know which rendering engine chrome uses.
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19:36 < kanzure> this is troubling.
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19:36 < superkuh> pdftotext fails (same libs as xpdf/evince). Only access is via $ strings | less
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19:37 < 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".
19:38 < 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
19:39 < 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
19:41 < kanzure> superkuh: http://diyhpl.us/~bryan/papers2/paperbot/pdfparanoiasucks.pdf
19:41 < superkuh> Thanks.
19:42 < kanzure> remember kids: always use science protection
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20:01 < SphericalMouse_> Hope to do a GA teardown at biocurious in a month or two
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20:12 < kanzure> GA?
20:18 <@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
20:20 <@fenn> says something like Error in JPX stream
20:20 < kanzure> pc load letter? the fuck does that mean?
20:24 < SphericalMouse_> illumina genome analyzer (DNA sequencer)
20:25 < kanzure> when you do the teardown please get a copy of the ROM so we can poke at it
20:26 < SphericalMouse_> the rom? It just runs off a computer.
20:26 < SphericalMouse_> the old models are all basically off the shelf hardware
20:27 < kanzure> there are no microcontrollers?
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20:28 < 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
20:29 < SphericalMouse_> kloen brand pumps, I believe
20:29 < kanzure> so it's pwm straight from serial?
20:30 < 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
20:31 < SphericalMouse_> I thinks its basically pumps, valves, laser illumination, camera
20:31 < SphericalMouse_> and stage
20:32 < SphericalMouse_> these things only put out like 80 mega bases of data
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20:34 < kanzure> anyway, if there is a custom PCB inside, with a chip, please grab the ROM during the teardown..
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20:36 < SphericalMouse_> is this some kind of stuxnet ploy?
20:37 < kanzure> no. i'm just curious about illumina's software. also it would be cool to find any security issues.
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20:38 < 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.
20:39 <@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
20:45 < SphericalMouse_> i'll see what I can do
20:46 < kanzure> thank you
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21:02 < ParahSail1n> you need any stuff from illumina site that requires a customer account?
21:03 < ParahSail1n> they dont have anything too special-- CASAVA and OLB, but CASAVA is kinda shitty
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21:06 < 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
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21:06 < kanzure> for their 5500 genetic analyzer
21:07 < 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
21:08 < kanzure> and an example protocol: http://diyhpl.us/~bryan/irc/lifetech/5500/instrument-server-methods/example.mod.txt
21:27 < kanzure> ... well i thought it was neat.
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22:12 < 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."
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22:44 < 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
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23:27 < jrayhawk> http://www.youtube.com/watch?v=ns2oS1WXDvc pretty inspiring
--- Log closed Wed Mar 13 00:00:26 2013