--- Log opened Tue Feb 05 00:00:51 2013
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01:13 < gnusha> https://secure.diyhpl.us/cgit/paperbot/commit/?id=715b73db Joe Rayhawk: Add phenny and translation-server as submodules.
01:13 < gnusha> paperbot: reload papers
01:13 < paperbot> gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-24 02:03:09)
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01:14 <@kanzure> jrayhawk: thank you
01:14 <@kanzure> https://github.com/kanzure/pdfparanoia
01:14 < eleitl> Morning.
01:15 < eleitl> How would you structure a Nerdnite talk about cryonics? The leitmotif is Futurama.
01:15 < eleitl> we need a way to keep the idiots entertained, while providing enough meat for the technical types
01:15 <@kanzure> jrayhawk: actually it should be the paperbot branch of git://github.com/kanzure/translation-server.git but i forget how to specify a branch or change a submodule uri
01:16 < jrayhawk> Ah, okay
01:19 < eleitl> Fry memes seem like a good hangup
01:19 < eleitl> Plus, Akbar'n'Jeff cryonics hut.
01:19 <@kanzure> too much reddit
01:19 < eleitl> Remember, we've got a bunch of idiots to entertain, too.
01:20 < eleitl> We have to be 'hip' (ack, ptui).
01:21 < eleitl> I think we should also mention destructive brain scan.
01:22 < eleitl> Vitrification, of course.
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01:22 < eleitl> Emphasize need to moar research.
01:22 < gnusha> https://secure.diyhpl.us/cgit/paperbot/commit/?id=24fcf417 Joe Rayhawk: translation server submodule: switch over to kanzure's github and the paperbot branch specifically
01:22 < gnusha> paperbot: reload papers
01:22 < paperbot> gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-24 02:03:09)
01:22 <@kanzure> hooray
01:22 <@kanzure> the illusion of progress!
01:22 < jrayhawk> that's the spirit!
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01:27 < eleitl> so, I get no advice
01:27  * eleitl <-- sad panda
01:27 <@kanzure> eleitl: we're not exactly a media company
01:28 <@kanzure> when i make presentations, i think about what i would want to see if i was in the audience and bored out of my mind
01:28 <@kanzure> usually this means the most detail i can possibly muster
01:28 <@kanzure> most presentations seem to assume i'm a moron
01:28 < eleitl> audience is bimodal
01:28 < eleitl> so we have two narratives at the same time
01:29 < eleitl> one to make technical people perk up, other to engage people, reddit/imgur-style.
01:29 < eleitl> it's a tool of recruitment, but in an entertaining way
01:29 < eleitl> remember, I'm a 46 year old guy with no clue how young people work
01:30 < jrayhawk> i suspect attempting to appear hip and with it will backfire
01:31 < eleitl> do normal nerds watch Futurama?
01:31 < eleitl> audience is Nerd Nite, but in Germany
01:31 < eleitl> we'
01:31 <@kanzure> eh just copy ccc and you'll be good to go
01:32 < eleitl> we're trying to address these 5 people out of 500 who have clue
01:32 < eleitl> I've never seen a CCC event
01:32 < eleitl> nor Futurama, for that matter
01:32 < jrayhawk> The problem with culture is that it's highly highly contextual, and attempting to emulate it by copying superficial elements of it will only make you stand out like a sore thumb.
01:32 < eleitl> yes
01:33 < eleitl> is the reddit/imgur culture relevant to german geeks?
01:33 < eleitl> if yes, I can connect
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01:38 < jrayhawk> Or, rather, attempting to integrate with members of a culture by using superficial elements from that culture runs very strong risk of underestimating the depth of context and meaning of those elements to a degree insulting to those members.
01:38 < eleitl> dude
01:38 < eleitl> do german nerds do futurama?
01:38 < eleitl> that's all I need to know
01:38 < jrayhawk> No idea!
01:39 < eleitl> somebody fetch me a german nerd
01:40 < jrayhawk> kanzure why are there a bunch of external binary build products in /home/bryan/code/paperbot/translation-server
01:40 <@kanzure> external=?
01:40 < jrayhawk> or, rather, in /home/bryan/code/paperbot/translation-server/build
01:40 < jrayhawk> things like libnss shared objects
01:40 < jrayhawk> which really seem like they should be, you know, shared objects
01:41 < jrayhawk> in /usr/lib
01:41 <@kanzure> i see, yeah i don't know about those
01:41 <@kanzure> i assume build.sh pooped them out
01:42 <@kanzure> by the way, gecko is huge and ridiculous
01:43 < jrayhawk> http://gnusha.org/~jrayhawk/irc/paperbotbuild.txt pooping looking unlikely
01:44 < jrayhawk> and yes, the mozilla project has always been an utter pig to build
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01:45 < eleitl> it seems mozilla is committing suicide
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01:47 <@kanzure> jrayhawk: xulrunner-sdk was a symlink
01:47 <@kanzure> to /home/bryan/local/gecko-sdk/xulrunner-sdk
01:47 < jrayhawk> uuugh
01:48 <@kanzure> because translation-server's readme told me to and i wasn't thinking straight
01:48 <@kanzure> feel free to move gecko-sdk to wherever, but afaik there's no package for that.
01:48 < jrayhawk> uh... xulrunner-dev perhaps?
01:50 <@kanzure> worth a shot, i think there were packaging problems but i don't remember.
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01:57 < jrayhawk> this build system is an atrocity
01:57 < eleitl> firefox?
01:57 < jrayhawk> No, translation-server.git
01:59 <@kanzure> "In devops, there only one build system, it is be call Perl."
02:00 <@kanzure> eleitl: context is https://twitter.com/DEVOPS_BORAT
02:02 < jrayhawk> i guess i will go to sleep and decide on how much of this lunacy i really want to tackle
02:02 <@kanzure> jrayhawk: what's currently broken?
02:03 <@kanzure> xulrunner-dev doesn't work out of the box with this?
02:03 < jrayhawk> i should not have to copy around shared libraries ever
02:05 < jrayhawk> if [ -e "$XULRUNNERSDKDIR/bin/xpcshell.exe" ]; then
02:05 < jrayhawk> ah, windows users. suddenly all is clear.
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02:07 <@kanzure> windows support was added to build.sh >12 months after it was written
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02:53 <@kanzure> aip and ieee are working
02:53 <@kanzure> https://github.com/kanzure/pdfparanoia
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03:06 <@kanzure> paperbot: http://intl.pnas.org/content/early/2013/01/30/1215501110/suppl/DCSupplemental
03:06 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/fbd7212c4676d5076a49af19adf81d79.txt
03:06 <@kanzure> paperbot: http://intl.pnas.org/content/early/2013/01/30/1215501110.abstract
03:06 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/S-nitrosylated%20SHP-2%20contributes%20to%20NMDA%20receptor-mediated%20excitotoxicity%20in%20acute%20ischemic%20stroke.pdf
03:10 < archels> eleitl: re that "two worms, same brains" thing, they obviously do not have "identical brain cells" as NewScientist writes
03:11 < archels> paperbot: http://www.sciencedirect.com/science/article/pii/S0092867412015000
03:11 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/System-wide%20Rewiring%20Underlies%20Behavioral%20Differences%20in%20Predatory%20and%20Bacterial-Feeding%20Nematodes.pdf
03:15 < archels> the reconstruction is beautiful http://turingbirds.com/temp/P.%20pacificus.%20reconstruction%20(Bumbarger%20et%20al.%20Neuron%202013).jpg
03:17 < eleitl> obviously
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04:14 < eleitl> that's a pretty worm
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08:51 < strages_work> http://prospect.rsc.org/blogs/cw/2013/02/04/quantum-chemistry-takes-on-virtual-reality/ neat application of haptic feedback
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09:16 < ephialtes480> paperbot: http://www.mitpressjournals.org/doi/abs/10.1162/0011526054622015
09:16 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/490ea454a4b2969c003cd07d32167ffa.txt
09:17 < ephialtes480> http://www.mitpressjournals.org/doi/pdf/10.1162/0011526054622015
09:17 < ephialtes480> paperbot: http://www.mitpressjournals.org/doi/pdf/10.1162/0011526054622015
09:17 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/5e74b13008997b5a78da2ad81fd07317.pdf
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09:27 < ephialtes480> brilliant...
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10:58 < nmz787> so supposedly unlocking phones is now seen as copyright infringement?
10:59 < nmz787> if skipping a chapter in a book isn't illegal, why should skipping the network check code be illegal?
11:05 < ThomasEgi> money..
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12:04 <@kanzure> neat, i'm a cypherpunk now https://twitter.com/_cypherpunks_/status/298861862441857024
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12:13 < nmz787> nice
12:14 <@kanzure> @maradydd wrote "@_cypherpunks_ oh hey I know that guy. He does good work."
12:14 <@kanzure> hooray meredith likes my work
12:15 < ielo> wow
12:15 < ielo> tried to get relationship advice from people on irc
12:16 < ielo> worst idea ever
12:18 < Mariu> oh, kanzure .. did you see the Cyberpunk 2077 trailer on YouTube ?
12:20 <@kanzure> no
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12:28 < nmz787> kanzure: well she's saying you do good work, that doesn't mean she likes it :P
12:28 <@kanzure> aww
12:28 <@kanzure> dreams = crushed
12:30 < Mariu> :p
12:37 < nmz787> paperbot: http://www.sciencedirect.com/science/article/pii/S1567576910002092
12:37 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Dietary%20garlic%20%28.txt
12:38 < nmz787> paperbot: http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=272179&_user=1694017&_pii=S1567576910002092&_check=y&_origin=article&_zone=toolbar&_coverDate=2010--31&view=c&originContentFamily=serial&wchp=dGLzVlS-zSkWb&pid=1-s2.0-S1567576910002092-main.pdf&_valck=1&md5=b2c94ff1536366d67cc4366cfaeae97f&ie=/sdarticle.pdf
12:38 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/8e4c3fe9a8336d045c001672ca34d8b1.txt
12:38 <@kanzure> hmm
12:38 < nmz787> paperbot: http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=272179&_user=1694017&_pii=S1567576910002092&_check=y&_origin=article&_zone=toolbar&_coverDate=2010--31&view=c&originContentFamily=serial&wchp=dGLzVlS-zSkWb&pid=1-s2.0-S1567576910002092-main.pdf
12:38 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/dc952baf17a7f692376d750bdecc83a2.txt
12:39 <@kanzure> no access?
12:39 < nmz787> o
12:39 < nmz787> no
12:39 < nmz787> lemme try my other schools
12:39 < nmz787> i really need to get a printer so i can send in my CMU reg papers
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12:49 < nmz787> so chandni's laptop randomly turned off last night
12:49 < nmz787> i think it's something with the batter, since it works with the wall attached
12:50 < nmz787> jrayhawk: this might interest you http://nathanmccorkle.com/pdf/Dietary%20garlic%20(Allium%20sativum)%20lectins,%20ASA%20I%20and%20ASA%20II,%20are%20highly%20stable%20and%20immunogenic.pdf
12:50 < nmz787> jrayhawk: tell me if it is, I can't tell if the immunigenisis is bad or not
12:50 < jrayhawk> hot damn
12:53 < jrayhawk> oh, yes, figure 1 looks to be the important one
12:54 < jrayhawk> "highly stable" does not appear to mean "cooking stable"
12:55 < jrayhawk> this appears to be consistent with my experience; unboiled garlic fucks me up a bit.
12:57 < nmz787> jrayhawk: so what would the immunogens do if the immune system didn't mess with them?
12:58 < nmz787> jrayhawk: i guess what I'm really wondering is, if the shit is potent and fucks up cells (and that's why the body sets off in response to it) then would you wanna dose with raw garlic if you were sick?
12:58 < nmz787> like stomach infection
12:59 <@kanzure> http://blog.okfn.org/2013/02/05/we-need-an-open-database-of-clinical-trials/
13:00 <@kanzure> http://www.alltrials.net/
13:01 < nmz787> "s. It is of interest to note
13:01 < nmz787> here that a garlic protein with sequence similarity to the lectin ASA II
13:01 < nmz787> has been shown to possess both hemagglutination and cysteinyl
13:01 < nmz787> protease activity"
13:04 < nmz787> agglutination: 1. The act or process of agglutinating; adhesion of distinct parts.
13:04 < nmz787> "Since stability of proteins in the GI tract could be another
13:04 < nmz787> important parameter for immunogenic response, we have looked
13:04 < nmz787> into the stability of garlic lectins ASA I and ASA II in SGF. Garlic lectins
13:04 < nmz787> are resistant to peptic digestion in vitro as determined by SDS-PAGE
13:04 < nmz787> and hemagglutination assay"
13:06 < nmz787> ". ASA I was found to retain 80100% activity
13:06 < nmz787> at all pH values tested. On the other hand, ASA II retains 100% activity
13:06 < nmz787> at pH 6 and 8, 40% at pH 10 and 12, and 25% at pH 2 and 4. The
13:06 < nmz787> hemagglutination activity of both ASA I and ASA II was retained at
13:06 < nmz787> 60 C for 30 min, but was completely lost at 100 C incubation"
13:09 < nmz787> a friend says his grandfather ate a clove or two of raw garlic along with nuts and grapefruit for breakfast every morning
13:12 < Mariu> ate ?
13:12 < Mariu> what changed ?
13:16 < EnLilaSko> http://www.kickstarter.com/projects/461687407/kickstarter-open-source-death-star
13:17 < chris_99> lol
13:18 < ThomasEgi> i'd so laught if they get the money together
13:18 < ThomasEgi> sitting on 20mio to buy chicken wire
13:18 < chris_99> hehe
13:19 < chris_99> i'm glad it's open source, should someone wish to duplicate their efforts
13:19 <@kanzure> sudo apt-get install death-star
13:19 < EnLilaSko> :D
13:19 <@kanzure> ERR: The death star is not fully operational.
13:19 < Mariu> LOL
13:19 <@kanzure> alderaan shot first, etc.
13:19 < ThomasEgi> unmet dependencies
13:19 < ThomasEgi> can't get iron
13:20 < ThomasEgi> you may want to update your source lists
13:20 <@kanzure> http://nerdapproved.com/wp-content/uploads/2011/09/alderaan-shot-first.gif
13:22 < Mariu> lol
13:22 < Mariu> =]
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13:28 < ephialtes480> brilliant kickstarter project.
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13:36 < nmz787> https://petitions.whitehouse.gov/petition/secure-resources-and-funding-and-begin-construction-death-star-2016/wlfKzFkN
13:38 <@kanzure> fuck the death star, let's do a dyson swarm or something
13:38 < jrayhawk> nmz787: there's likely to be some variance in response due to differences in genetics, adaptive immunity, gut flora, and intestinal permeability. Garlic is really complicated chemically and it's entirely reasonable to postulate that it has effects on the gut biome both directly and through immunomodulation based on its prevalence and success in traditional medical practices (see also: garlic enema).
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13:43 < jrayhawk> lectins have a wide variety of effects; you'd have to study the particular lectin. Some of them are fairly innocuous.
13:44 < nmz787> huh
13:44 < nmz787> garlic enema eh
13:44 < jrayhawk> Not something I've ever done, but they do have some clinical trials.
13:45 < nmz787> i've heard of using coffe
13:45 < nmz787> and doing fecal transfer
13:45 < ArmilusDajjal> coldpress coffee
13:45 < ArmilusDajjal> not regular coffee
13:45 < ArmilusDajjal> the tannic acid will give you the shite
13:46 < nmz787> ahh
13:46 < nmz787> kanzure: I can't seem to track down the authors current info for this http://diyhpl.us/~bryan/papers2/paperbot/SU-8%20thick%20photoresist%20processing%20as%20a%20functional%20material%20for%20MEMS%20applications.pdf
13:47 < nmz787> kanzure: the email given is bad now
13:47 < nmz787> kanzure: and I want to contact them
13:50 <@kanzure> hmm. this one will require some advanced sleuthing.
13:54 <@kanzure> nmz787: try looking for patents by these guys. they seem to not have any papers after 2002 but maybe there's patents.
13:59 < nmz787> kanzure: do you know anyone looking for a remote scientific programmer?
14:00 < nmz787> i need some income to funnel into projects now that I have lab space... i don't need much $ since the lab is really relaxed with when they will want me to pay (if I start making money or getting in their way)
14:00 <@kanzure> i dunno if enthought does remote
14:00 < nmz787> (which is far off, and if i'm making money, well geez that's the point of me experimenting)
14:01 <@kanzure> but enthought would be enriching for you i think
14:01 <@kanzure> or anyone in here i guess
14:02 <@kanzure> i regularly get blasted by recruiters but never for explicitly scientific things.
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14:05 < juri_> if its remote free software, keep me in mind, please. ;)
14:06 < nmz787> juri_: what kind of projects would you be interested in working on?
14:06 < nmz787> by free do you mean you'd work for free?
14:07 < juri_> nmz: no. ;)
14:07 <@kanzure> juri_: i've been meaning to tell you this for a while, but you should be aware that if your goal is to optimize for cash income that your requirement of gpl-licensed software work is not necessarily beneficial towards that goal.
14:07 < juri_> I'm a Free Software developer.
14:08 < juri_> right now, i've specialied in OpenEMR, virtualization technologies (author of createvm), i'm wicked with file conversions (big into XSLT/SED), and quite a 3d printer geek.
14:08 < nmz787> kanzure: know this person https://twitter.com/skry
14:08 <@kanzure> eww xslt
14:08 < nmz787> kanzure: ?
14:09 < nmz787> exSlut
14:09 < juri_> kanzure: tell me something i don't know. i used to make GOOD money as a software developer. then i developed morals. ;)
14:09 <@kanzure> nmz787: no i don't seem to know this person
14:10 < juri_> at one point, i was the youngest MCSE in the nation.
14:11 < juri_> this was a while ago. ;)
14:13 < juri_> everything i've written since i was ~20 was licensed under the GPL, and 95% of that made it online.
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14:14 <@kanzure> On Tue, Feb 5, 2013 at 3:47 PM, Peter Murray-Rust <pm286@cam.ac.uk> wrote:
14:14 <@kanzure> > I use Apache FOP.  We should be able to:
14:14 <@kanzure> > * read PDF into SVG
14:14 <@kanzure> > * remove the rubbish
14:14 <@kanzure> i can't seem to find how to use apache fop to write a pdf
14:15 <@kanzure> > * write the primitives back into PDF. We might get font problems so you may
14:15 <@kanzure> http://xmlgraphics.apache.org/fop/dev/#doc
14:15 <@kanzure> it looks like this is possibly xslt related? http://xmlgraphics.apache.org/fop/fo/size.fo
14:16 < juri_> looks like fun. ;)
14:16 <@kanzure> well pete is suggesting this as an alternative to my https://github.com/kanzure/pdfparanoia
14:17 <@kanzure> so i'm trying to figure out how to actually make it work
14:17 < juri_> xslt + sed is fun. i can certainly see that applying to a pdf stream.
14:18  * juri_ takes a peek.
14:18 <@kanzure> juri_: can you look at pdfparanoia and see if you can duplicate the results in xslt?
14:18 <@kanzure> or erm, i mean, possibly using something less evil
14:18 <@kanzure> here's the gist of how it works:
14:18 <@kanzure> https://github.com/kanzure/pdfparanoia/blob/master/tests/test_aip.py
14:18 <@kanzure> https://github.com/kanzure/pdfparanoia/blob/master/pdfparanoia/plugins/aip.py
14:19 <@kanzure> basically i use pdfminer to find /FlateDecode streams in a pdf file that contain suspicious text
14:19 <@kanzure> then i use manually delete the offending obj/endobj lines from the lines of the pdf file,
14:19 <@kanzure> https://github.com/kanzure/pdfparanoia/blob/master/pdfparanoia/eraser.py
14:20 < juri_> i'll take a look.
14:20 < juri_> i've got three customers asking for time, plus i'm sick.. but being sick gives me some leway. ;P
14:21 < ephialtes480> kanzure does that account for majority of ways watermarking is done? Are there significant exceptions?
14:21 <@kanzure> ephialtes480: it currently works for IEEE and AIP but others need to be added
14:22 < juri_> ... less evil than xslt? sacrelige. ;)
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14:27 < juri_> well, i can certainly do the job in less lines than you have here.
14:27 <@kanzure> tell me more
14:27 < juri_> but for your purposes, i don't think that would be as maintainable.
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14:30 <@kanzure> juri_: well, what is the idea?
14:31 < juri_> the approac i would use is to tokenize the stream as lines you're interested in, and lines you're not. you're doing object removal.
14:31 < juri_> so, use sed to encode all lines in <boringline>"sometesthere"</boringline>, except the ones that match your interesting regex (object definitions).
14:32 <@kanzure> the text is encoded in some format inside the pdf, so sed can't pull that out with a regex unless something preprocesses it first
14:32 < juri_> slap a header and footer on it, and you have an xml document. now, do a xslt transform that just responds to all the blocks you're interested by looking through your filter rules, and spit the rest out verbatim.
14:33 < juri_> hmm. i'm tempted to just do a hex encode of the lines, for sed to handle.
14:35 < nmz787> juri_: if you did that, please comment how to do it for other arbitraty sed commands, so if i have a pdf with a different search requirement, i can reuse your code easily
14:35 < juri_> really, step 1 for me is always 'convert to a dumb xml format'.
14:35 <@kanzure> once you convert to a dumb xml format, how do you get it back to pdf?
14:36 < juri_> that's the xml transform.
14:36 < juri_> it just does writes of all the data back.
14:36 <@kanzure> is there an existing xml transform that works to convert xml to pdf?
14:36 < juri_> I've done this a ton with X12 formatted data. anything that has a concept of 'lines', basically.
14:36 < juri_> xml is not a 'real' format that way.
14:36 < juri_> your concept is sheared.
14:36 <@kanzure> pdfquery uses pdfminer to dump a pdf into xml via lxml, and lxml then dumps to an xml format that currently can't be converted back to pdf.
14:37 < juri_> interesting.
14:37 <@kanzure> adobe has a pdfxml format, but it is nothing like the xml that lxml dumps for pdfquery.
14:37 < ephialtes480> kanzure - let us say I wanted to add support for another kind of watermark - looking at the raw text of an example PDF, I see a suspect FlateDecode at the top which may be the watermark:
14:37 < ephialtes480> <</Type/XObject/Resources<</ProcSet [/PDF /Text /ImageB /ImageC /ImageI]/Font<</F1 2 0 R>>>>/Subtype/Form/BBox[0 0 414 648]/Matrix [1 0 0 1 0 0]/Length 126/FormType 1/Filter/FlateDecode>>stream
14:37 < juri_> yea, xml is not a format, think of it more as a linewise encoding.
14:37 < ephialtes480> followed by some binary code
14:37 < ephialtes480> and "endstream" end object etc.
14:37 < ephialtes480> deleting this manually produces a garbled PDF, what is the catch here? reproducing some stream code of same length?
14:37 < juri_> right. thats a line. and the next line not matching any regex, would get encoding with 'boringdata'.
14:39 < juri_> the act of using XSLT to transform your (now) xml file back into a pdf would also use a 'xslt library' of functions to remove the target data.
14:39 < juri_> i usually just use sed to break data into sections, and pull out atributes i'm interested in handling in the xslt.
14:39 <@kanzure> ephialtes480: you picked the wrong one :)
14:40 <@kanzure> ephialtes480: you have to start with the line that begins with "<number> 0 obj<<" and then delete up to and including the following "endobj"
14:40 <@kanzure> ephialtes480: if your pdf comes out garbled, you deleted the wrong object
14:40 < juri_> here, let me paste an example.
14:41 <@kanzure> ephialtes480: another hint is that most of these watermarks seem to be the same between each page, so the size of the FlateDecode object will be the same each time. so if you see an object that isn't repeated on each page, chances are it isn't the watermark.
14:41 < ephialtes480> thx, trying now!
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14:45 < juri_> http://pastebin.com/vsRMzNJC
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14:45 <@kanzure> you wrote all of those regular expressions just now?
14:48 < juri_> oh goodnes no.
14:48 < juri_> that's about two days of work.
14:49 < ephialtes480> kanzure success...
14:49 <@kanzure> ephialtes480: now write it up into python
14:49 < juri_> well, that, and: http://pastebin.com/izZgpNuf
14:49 <@kanzure> ephialtes480: aip.py and ieee.py both work very similarly, they search for specific text and then make a list of object ids that need to be removed
14:50 < ephialtes480> k, added to the list of todos...forked for now, thanks will issue pull requests if I complete a functioning one...
14:51 <@kanzure> ephialtes480: it's really simple to write, if it takes you more than 10 minutes let me know
14:51 < juri_> http://www.open-emr.org/wiki/index.php/X12_837p_Reference
14:51 < juri_> that's a prser, ane un-parser for the file format i just posted.
14:52 < juri_> so that i, a lazy human, can edit the file format (which is very non-human-editable) in a text editor.
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14:52 < juri_> now, the reason i was showing that, is that the xslt there and the SED do the same job, just forward / reverse.
14:53 < juri_> xml is a good intimediary for binary formats, that's why its so readily used to replace them.
14:54 < juri_> you don't need to really adhere to any kind of written format or spec to make something that is very useful, and you can make decisions about transforming the data in XSLT.
14:54 <@kanzure> xml is a /good/ intermediary for binary formats? hrm.
14:55 <@kanzure> i haven't used xml like that before.
14:55 < juri_> the XSLT can be very sequence-picky, and show all of the data, some of the data, or even generate just messages instead of the output of the file. its pure transform, and a functional language. the sed is strictly serialized.
14:56 < juri_> xml is a great replacement for binary formats.. as long as you do not care about CPU time. ;)
14:57 < jrayhawk> or storage efficiency
14:57 < juri_> agreed.
14:58 < juri_> but once something is in xml (and really, all of it, which it sounds like you're having problems with), transforms are relatively simple, if wordy.
14:58 < jrayhawk> or robustness to syntax errors, or ability to do timely random access
14:58 < jrayhawk> really why are we using xml again
14:59 < juri_> I'm the author of the "xml form generator', which takes an XML file as input in openemr, generates some 7 different PHP files, a SQL file, and other fluff, to add a form into the OpenEMR system. the forms are simple, and have resulted in a lot of interchange between medical practitioners. you can imagine, writing all of that PHP with xslt gets both complicated, and simple.
15:00 < jrayhawk> aaaaa
15:00 <@kanzure> yeah that's a dumb way to do that
15:00 <@kanzure> have you heard of ORMs
15:00 < juri_> the real win in that case is you don't administrate 7*N_FORMS php pages hand written for security problems.
15:01 <@kanzure> most of the modern orm libraries do form generation for you, so you only have to maintain the core library and some minor templates for when you insist on differences in the form infrastructure.
15:01 < juri_> i've written an xml-only interface. upstream is insuficiently comfortable with xml to accept it.
15:01 < juri_> nothing about OpenEMR is modern.
15:01 <@kanzure> what's funny is that i call it modern but i'm pretty sure perl has been doing that for >15 years
15:02 < juri_> parts of openemr are that old.
15:03 < jrayhawk> i can see justifying what you've done under entirely practical New Jersey Style principles, but claiming it has quality architecture just makes you look like a lunatic
15:03 < juri_> it has a higher quality archetecture than what was there.
15:04 < juri_> i don't consider it 'good'.
15:04 < ephialtes480> kanzure, could you post an example of one of the aip files (for comparison)
15:04 <@kanzure> ephialtes480: there is an example in the tests/samples/aip/ folder
15:04 < jrayhawk> '14:53 < juri_> xml is a good intimediary for binary formats' was more the thing at issue
15:04 < ephialtes480> ah
15:04 < juri_> i mean, hell, i just removed all of the popups from the program.. and it will take a programatic act of a diety to remove frames from it.
15:05 <@kanzure> ephialtes480: the unit tests can be used to confirm that it is working
15:05 < jrayhawk> haha
15:05 <@kanzure> juri_: maybe you should take a page out of gnu's book and use lots of small programs and services instead of monolithic monolithicness
15:05 < juri_> jrayhawk: i enjoy it, and find it a fun aproach. ;)
15:05 <@kanzure> then you could install parts of the system via a package manager
15:06 < juri_> there's a movement to do that in openemr, but i fear it is going to fail.
15:06 <@kanzure> how many users does openemr have?
15:06 < juri_> i was happy just to get 'disable' buttons for the features my customers don't need.
15:06 < juri_> thousands of clinics, unfortunately.
15:06 <@kanzure> that's not much.
15:07 < juri_> its a lot for the way the project is (not) run.
15:08 < juri_> still, focusing on your problem, i guess the first question i have, is you say you have a PDF -> XML parser. do you know if all the data 'made' it to the xml format?
15:09 <@kanzure> i'm not confident enough in pdfparanoia at the moment to run it on my entire pdf collection
15:09 <@kanzure> there might be false positives
15:09 <@kanzure> and then suddenly entire sections of my documents might be missing
15:09 < nmz787> kanzure: why are you talking about xml if you have it working in pdfminer (or whatever pdf paranoia is using)
15:10 <@kanzure> nmz787: curiosity
15:14 < juri_> well, if you knew all of the data made it into the xml format, I'd be willing to pull it back out to create a file, as well as help convert your transforms into xslt. I'm a xslt geek. I don't enjoy writing the equivilent of that sed script, written by someone else however. ;)
15:14 < juri_> s/enjoy writing/enjoy fixing/
15:15 < ephialtes480> kanzure you get "Redistribution subject to AIP license or copyright" from the binary stream data. is that getting decoded by pdfminer methods?
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15:17 <@kanzure> ephialtes480: yes that is decoded by pdfminer
15:18 < ephialtes480> ok, we are looking at more than 10 minutes :) I am tracing back your method calls to pdfminer, and am reading up on pdfminer so I can first decode the stream data I need to identify. the PDF has a lot of FlateDecodes that are not connected to watermark
15:19 <@kanzure> to be honest, the quickest way to do this might be copy-and-paste of the aip.py version
15:19 <@kanzure> then change the text it is looking for
15:19 < ephialtes480> right, but need to find the text it is look for
15:19 < ephialtes480> which is in binary
15:19 < ephialtes480> or whatever, and need to decode with pdfminer, no?
15:20 < ephialtes480> This key line: if "Authorized licensed use limited to: " in data:
15:20 < ephialtes480>                         evil_ids.append(objid)
15:20 < ephialtes480> you are getting that quote from somewhere, and it isn't readable by simply opening the file
15:21 < ephialtes480> (it shows when opening the file regularly but there may be extra spaces, etc.)
15:23 < ephialtes480> thanks for now! later...
15:24 <@kanzure> i got the quote by looking at the watermark with my eyeballs
15:24 <@kanzure> it's visible on the bottom of each page
15:24 <@kanzure> there are not extra spaces really
15:25 <@kanzure> watermarks like that are applied in a very consistent manner by a pdf server that is pasting those in each time you download a pdf
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15:39 < nmz787> hah jimmy kimmel announced on national TV to his 10th grade history teacher (who told him he would never amount to anything if he kept screwing around) that he was just about to high-five the president
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16:12 <@kanzure> alibaba was acquired by yahoo?
16:12 < nmz787> when?
16:12 < nmz787> yahoo was the first auction site right?
16:12 <@kanzure> http://www.crunchbase.com/company/alibaba
16:12 <@kanzure> looks like there might be an upcoming alibaba ipo
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16:33 < nmz787> hah it says 'Offices
16:33 < nmz787> edit
16:33 < nmz787> united states of america
16:33 < nmz787> 6/F Chuangye Mansion, East Software Park
16:33 < nmz787> No.99 Huaxing Road
16:33 < nmz787> Hangzhou, 310099, CHN
16:33 < nmz787> Read more: http://www.crunchbase.com/company/alibaba#ixzz2K4gjmmLO'
16:33 < nmz787> pretty sure hangzhou is not continental U.S.
16:33 <@kanzure> man i hate things that inject shit into pastes
16:35 < nmz787> this lab equipment isn't priced too much http://www.tedpella.com/histo_html/unicore.htm
16:35 < nmz787> it's actually priced like normal people tools are
16:35 < nmz787> reasonably
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17:57 <@kanzure> so is FlateDecode referencing the deflate algorithm?
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18:37 <@kanzure> yashgaroth: how much does a CRO cost to make.
18:37 < yashgaroth> uhhh
18:38 < yashgaroth> depends on the line of work, though I can't speak to specifics there, whether you're including operating expenses
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18:40 < yashgaroth> like for a generic protein company maybe 200k upfront for equipment, plus 40k/BS 80k/PhD per year, and space runs about 2-3k per month
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18:43 <@kanzure> "Pfizer has decided to outsource pretty much everything except early discovery to two leading CROs—Icon (Hubbard’s former employer) and Parexel, Hubbard says."
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18:43 < yashgaroth> oh man I just found out quintiles is owned by bain capital
18:44 < klafka> wow 80k/phd
18:44 < klafka> that sucks
18:44 <@kanzure> who is offering 80k/phd?
18:44 < yashgaroth> also, GMP and clinical trial stuff is way more expensive than generic R&D CROs
18:44 <@kanzure> sure
18:44 <@kanzure> i'm not as interested in the clinical trial CROs
18:45 < yashgaroth> that's an average starting salary for a PhD, maybe a bit lowball but someone will take it
18:45 < yashgaroth> plenty of PhDs out of work that are flooding out of grad school
18:45 < klafka> in what fields?
18:45 < yashgaroth> bio
18:45 < klafka> ...
18:46 < yashgaroth> not like UCSF grads or whatever, but if you want "a PhD" you can get one for that
18:46 <@kanzure> and a phd dropout will be cheaper
18:46 < klafka> sssh
18:46 < klafka> well
18:46  * klafka is more and more glad he went back to computers
18:46 <@kanzure> klafka: eh you have >6 months of industry experience, nobody remembers your phd work anymore.
18:46 < yashgaroth> sure, but you want a PhD on the "about us" page so people will go "oh okay they have a PhD it's okay to send them money"
18:47 < klafka> aah
18:47 < klafka> hah that's actually true kanz
18:47 < klafka> kanzure:
18:47 <@kanzure> yashgaroth: i've been thinking about just dumping $20,000 into a company to do scienceexchange.com things
18:48 < yashgaroth> I do have in "in" with the CEO of assaydepot, in that he bought me a sandwich yesterday
18:48 <@kanzure> kevin?
18:48 < yashgaroth> *an
18:48 < yashgaroth> yep
18:49 <@kanzure> so he seems to be selling assaydepot licenses to pharma companies for $250k/year
18:49 < yashgaroth> selling licenses in what sense?
18:49 <@kanzure> an instance
18:49 <@kanzure> erm.. i guess you wont know what an instance is either.
18:50 <@kanzure> in the software world, you can license access to a service, or sell bytes, or do lots of other things.
18:50 < yashgaroth> a dungeon created for your party to raid? no
18:50 < nmz787> kanzure: what do you mean dump $20k into
18:50 <@kanzure> nmz787: i mean, i don't have a lot of interest in making transgenic mouse strains, but if it's good business why not
18:50 < yashgaroth> oh so they pay 250k and get a la carte services from anyone on assaydepot?
18:50 <@kanzure> no
18:51 <@kanzure> they pay 250k and they get the assaydepot software for managing their own internal labs
18:51 < yashgaroth> ohhhh
18:51 <@kanzure> http://diyhpl.us/wiki/transcripts/startup-science-2012/kevin-lustig-assay-depot
18:51 <@kanzure> "Secondly we built this company without VC funding. The last company I founded in 2001 I raised $170 million. It was a terrible idea. We were well-paid. But it came back to bite us in the ass. Good luck. What we've done is that we've gone out and raised money from friends and family. I got my mother to kick in some money."
18:51  * klafka is going to play with pandas
18:51 <@kanzure> "It puts pressure on you when your mother puts in money. We are profitable as of this year. It's only now that we're going to go out and actually raise VC money, but instead of giving up 70% of the company like in my first go, we're going to give up 10% or 20% this time to maintain control."
18:51 <@kanzure> "Our solution has been to take the public web based lab, for use by anyone, that we have availabel for free of charge, and turn it into an enterprise solution for pharma companies. "
18:51 <@kanzure> "So we have private web based labs for pfizer, johnson and others, and these companies are using this platform- 10,000 scientists within each company to coordinate all of their research activities."
18:51 < yashgaroth> oh like an internal lab management software
18:52 <@kanzure> "$250,000/license for pharma companies and charge through in the nose for integrations"
18:52 < klafka> yeah
18:52 < klafka> give them a solutions engineer!
18:52 < klafka> or solutions architect!
18:52 <@kanzure> sounds like a buzzword klafka
18:52 < klafka> with high billable rates
18:52 < klafka> integrations engineer
18:52 < klafka> whatever
18:52 < yashgaroth> solutions hacker
18:52 <@kanzure> (TM) (R)
18:52 < nmz787> kanzure: their site has totally different prices advertised from what it says when you click on it
18:53 < nmz787> mass spec $10, then i click and it says $100
18:53 < klafka> a technical person to implement your too complex software in their archaic systems
18:53 < klafka> mass spec for 10 is too cheap
18:53 < klafka> or seems a bit too cheap
18:53 <@kanzure> nmz787: assaydepot is like scienceexchange sorta, i think they have this public site just for people who don't have an assaydepot license
18:53 < yashgaroth> depends on the mass spec method
18:53 < klafka> fair enough
18:53 < yashgaroth> that is still like at-cost though
18:53 < nmz787> but literally it says $10 then
18:54 < nmz787> $100
18:54 < klafka> man i hate when i'm too tired and i keep going back and forth between 3 things even though i know what i need to actually do
18:54 < nmz787> https://www.scienceexchange.com/
18:54 < nmz787> klafka: i do that when i'm not tired
18:54 <@kanzure> "[CROs is a] very fragmented industry with the top 10 controlling 56.1% of the market in 2008[10] and down to 55% in 2009.[11][12] One estimate had the size of the market set to reach $24 billion in 2010[13] and set to grow at a rate of 8.5% through 2015.[14]"
18:54 < yashgaroth> $100 is pretty standard for protein MS
18:54 < klafka> yeah
18:54 < klafka> i know we get drugs gc/ms analyzed for like 140
18:54 < nmz787> kanzure: so you want to invest in scienceexcahnge, or pay $20k for some experiments you have in mind
18:54 <@kanzure> no i don't want to invest in scienceexchange
18:54 <@kanzure> no i don't want to pay for experiments
18:55 <@kanzure> neither of those things are what i said :p
18:55 < nmz787> 18:47 <@kanzure> yashgaroth: i've been thinking about just dumping $20,000 into
18:55 < nmz787>                  a company to do scienceexchange.com things
18:55 <@kanzure> yes, a CRO-like entity
18:55 < nmz787> sound like you wanna spend $20k on lab science
18:55 <@kanzure> huh?
18:55 < yashgaroth> like, buy a genetic analyzer and sell sequencing services?
18:56 < nmz787> CRO?
18:56 <@kanzure> yashgaroth: probably not "genetic analysis" because that market is going down constantly.
18:56 < yashgaroth> or an HPLC and sell analysis
18:56 < klafka> what is the cost to sequence a genome btw now?
18:56 <@kanzure> yashgaroth: and, even if it was something economically stable, i wouldn't want to do it myself either (i have better things to be doing)
18:56 < klafka> is it down to 100 bucks yet?
18:56 < klafka> (sequence not assemble)
18:56 < klafka> did the rate of change of sequencing costs flatten out yet?
18:57 < yashgaroth> $100 is higher than the cost of the hard drive they'd send it to you on
18:57 < klafka> yeah
18:57 <@kanzure> sequencing is not predicted to flatten any time soon
18:57 < klafka> that's why i said sequence not assemble
18:57 < klafka> :P
18:57 < yashgaroth> yeah yeah
18:58 < yashgaroth> ok so kanzure what did you mean then, if not our guesses?
18:59 <@kanzure> yashgaroth: your guess was right (HPLC might be ok)
18:59 < yashgaroth> ah okay then
18:59 <@kanzure> i'm still trying to figure out if it's good business or not
19:00 < yashgaroth> if you're located in a big biotech hub city, and have a decent operator to run it, then you could make some money
19:00 < yashgaroth> offering pickup for samples, high-quality analysis/expertise, and fast results, why would anyone spring for their own HPLC and operator
19:02 <@kanzure> how much are people making on that at the moment, though?
19:02 <@kanzure> i don't even know how much demand there is for random hplc runs
19:02 < yashgaroth> no idea, I've never had to hire an HPLC; it's certainly an investment on your part though
19:03 < nmz787> HPLC is usually run by a dude who takes care of other big machines too
19:03 < nmz787> or helps grad students set up runs for them to process
19:03 < nmz787> so he prob makes 40-55k
19:03 < yashgaroth> true, it's not that hard to run; I was mostly scaling down from some sort of mass spec business
19:03 <@kanzure> i bet i could get an hplc on credit, heh
19:04 <@kanzure> i'm also sure i could find someone to pay <$20/hour who would be reliable
19:04 < yashgaroth> anyway if I knew how to start a biotech services business I'd just do that
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19:04 < yashgaroth> ehh maybe
19:05 <@kanzure> well i think that's what all the people who get fired from roche do
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19:05 < nmz787> kanzure: too bad portland isn't a hub city or you'd have an operator :P
19:05 < yashgaroth> everyone gets fired from roche, it's like a rite of passage
19:05 < klafka> why is that?
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19:05 < yashgaroth> why is what
19:05 < klafka> does everyone get fired from roche
19:05 < klafka> or so many people
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19:06 < yashgaroth> no, that's more accurate as 'laid off', and 'from genentech/pfizer/GSK'
19:06 <@kanzure> right
19:06 < yashgaroth> roche is pretty good about not shedding people constantly
19:06 < yashgaroth> except from the companies they acquire
19:07 < klafka> i have an old roommate whose been working at genentech for like 5 years
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19:07 < klafka> since he got out of college
19:07 < yashgaroth> I have several colleagues who are ex-bay area genentech
19:13 <@kanzure> "the entrepreneur's guide to a biotech startup" http://www.evelexa.com/resources/EGBS4_Kolchinsky.pdf
19:16 <@kanzure> "Promoting your instrument as having a smaller "footprint" (area it takes up on the floor or bench) can differentiate it from competing products."
19:16 <@kanzure> geeze
19:17 <@kanzure> "A more attractive alternative may be the Razor Blade model; sell or lease the instrument cheaply but charge for disposables."
19:17 <@kanzure> yep.. i think that's why ABI was suing customers for using alternative reagents.
19:17 < yashgaroth> everyone does that shit
19:17 < klafka> uhh
19:17 < klafka> how is that legal?
19:17 < klafka> do you sign a contract
19:18 <@kanzure> i dunno, go read the court documents
19:18 < klafka> otherwise?
19:18 < cpopell> Some might.
19:18 <@kanzure> i don't recall who won that lawsuit
19:18 < yashgaroth> well, everyone does the 'charge out the ass for disposables/reagents', the suing is a bit much
19:21 <@kanzure> "Typical medical device products may have gross margins from 55%-70%." aww yeah.
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19:35 <@kanzure> equipment loans http://www.nature.com/bioent/building/infra/082004/full/bioent821.html
19:37 <@kanzure> no crap? "Negotiating leases on many individual pieces of equipment is time-consuming and daunting and, furthermore, in the biotech industry there is little justification for having the flexibility to return leased equipment. "
19:44 <@kanzure> fenn: this might be interesting background material for bayh-dole things, http://www.nature.com/bioent/view/102004/full/bioent832.html
20:10 < streety> kanzure: just noticed you asked me about pdfminer, not really used it since putting that repository on github. I managed to alter someone elses code to do roughly what I wanted  but that was the limit of my understanding
20:10 < streety> sorry I can't be more help
20:11 <@kanzure> thanks anyway. pdfparanoia is working for now.
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20:22 <@kanzure> "When Lin and a partner opened Explora’s doors, the company had two employees and occupied 1,500 square feet of space. Now, it employs 17 full-time workers and covers 33,000 square feet of office and lab space at three locations in the region."
20:22 <@kanzure> "The work requires a small animal research lab, known as a vivarium, which can cost several hundred thousand dollars to set up and about $200,000 annually to staff, Lin said."
20:22 <@kanzure> so 2 employees and 1500 sq ft is probably not going to be $200k/year
20:23 < yashgaroth> for rent and salaries? maybe half
20:25 <@kanzure> also, 33,000 sq ft of rats is a lot of rats
20:26 < yashgaroth> I really don't want to think about the smell
20:26 <@kanzure> maybe they have engineered some bacteria to make rat poo smell like lady farts
20:27 < yashgaroth> we can give it an air of wintergreen, that's about the state of the art
20:36 <@kanzure> did anyone commercialize that btw? the less stinky ecoli strain?
20:37 <@kanzure> iirc they won some igem prizes and then went back to their soulless lab jobs
20:38 < yashgaroth> I don't know if they designed the wintergreen synthase or whatever it was
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21:22 < nmz787> yay i installed gnu emacs for windows, and it solved my problem!
21:25 < nmz787> kanzure: would you have any idea of how to merge drivers from other ROMs into something like this http://themikmik.com/showthread.php?12584-ROM-PrimOG-Preview-1-5-6-2-12-_-Patch-Sense-4-0a-ICS-4-0-3
21:38 <@kanzure> well, drivers can be loaded into the android kernel so i think you can just distribute the .ko files or whatever?
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--- Log closed Wed Feb 06 00:00:52 2013