--- Log opened Tue Feb 05 00:00:51 2013 | ||
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gnusha | https://secure.diyhpl.us/cgit/paperbot/commit/?id=715b73db Joe Rayhawk: Add phenny and translation-server as submodules. | 01:13 |
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gnusha | paperbot: reload papers | 01:13 |
paperbot | gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-24 02:03:09) | 01:13 |
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@kanzure | jrayhawk: thank you | 01:14 |
@kanzure | https://github.com/kanzure/pdfparanoia | 01:14 |
eleitl | Morning. | 01:14 |
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 | 01:15 |
jrayhawk | Ah, okay | 01:16 |
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. | 01:19 |
eleitl | We have to be 'hip' (ack, ptui). | 01:20 |
eleitl | I think we should also mention destructive brain scan. | 01:21 |
eleitl | Vitrification, of course. | 01:22 |
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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! | 01:22 |
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eleitl | so, I get no advice | 01:27 |
* eleitl <-- sad panda | 01:27 | |
@kanzure | eleitl: we're not exactly a media company | 01:27 |
@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 | 01:28 |
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 | 01:29 |
jrayhawk | i suspect attempting to appear hip and with it will backfire | 01:30 |
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 | 01:31 |
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 | 01:32 |
eleitl | is the reddit/imgur culture relevant to german geeks? | 01:33 |
eleitl | if yes, I can connect | 01:33 |
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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! | 01:38 |
eleitl | somebody fetch me a german nerd | 01:39 |
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 | 01:40 |
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 | 01:41 |
@kanzure | by the way, gecko is huge and ridiculous | 01:42 |
jrayhawk | http://gnusha.org/~jrayhawk/irc/paperbotbuild.txt pooping looking unlikely | 01:43 |
jrayhawk | and yes, the mozilla project has always been an utter pig to build | 01:44 |
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eleitl | it seems mozilla is committing suicide | 01:45 |
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@kanzure | jrayhawk: xulrunner-sdk was a symlink | 01:47 |
@kanzure | to /home/bryan/local/gecko-sdk/xulrunner-sdk | 01:47 |
jrayhawk | uuugh | 01:47 |
@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? | 01:48 |
@kanzure | worth a shot, i think there were packaging problems but i don't remember. | 01:50 |
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jrayhawk | this build system is an atrocity | 01:57 |
eleitl | firefox? | 01:57 |
jrayhawk | No, translation-server.git | 01:57 |
@kanzure | "In devops, there only one build system, it is be call Perl." | 01:59 |
@kanzure | eleitl: context is https://twitter.com/DEVOPS_BORAT | 02:00 |
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? | 02:02 |
@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 | 02:03 |
jrayhawk | if [ -e "$XULRUNNERSDKDIR/bin/xpcshell.exe" ]; then | 02:05 |
jrayhawk | ah, windows users. suddenly all is clear. | 02:05 |
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@kanzure | windows support was added to build.sh >12 months after it was written | 02:07 |
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@kanzure | aip and ieee are working | 02:53 |
@kanzure | https://github.com/kanzure/pdfparanoia | 02:53 |
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@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 | 03:06 |
archels | eleitl: re that "two worms, same brains" thing, they obviously do not have "identical brain cells" as NewScientist writes | 03:10 |
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 | 03:11 |
archels | the reconstruction is beautiful http://turingbirds.com/temp/P.%20pacificus.%20reconstruction%20(Bumbarger%20et%20al.%20Neuron%202013).jpg | 03:15 |
eleitl | obviously | 03:17 |
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eleitl | that's a pretty worm | 04:14 |
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strages_work | http://prospect.rsc.org/blogs/cw/2013/02/04/quantum-chemistry-takes-on-virtual-reality/ neat application of haptic feedback | 08:51 |
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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 | 09:16 |
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 | 09:17 |
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ephialtes480 | brilliant... | 09:27 |
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nmz787 | so supposedly unlocking phones is now seen as copyright infringement? | 10:58 |
nmz787 | if skipping a chapter in a book isn't illegal, why should skipping the network check code be illegal? | 10:59 |
ThomasEgi | money.. | 11:05 |
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@kanzure | neat, i'm a cypherpunk now https://twitter.com/_cypherpunks_/status/298861862441857024 | 12:04 |
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nmz787 | nice | 12:13 |
@kanzure | @maradydd wrote "@_cypherpunks_ oh hey I know that guy. He does good work." | 12:14 |
@kanzure | hooray meredith likes my work | 12:14 |
ielo | wow | 12:15 |
ielo | tried to get relationship advice from people on irc | 12:15 |
ielo | worst idea ever | 12:16 |
Mariu | oh, kanzure .. did you see the Cyberpunk 2077 trailer on YouTube ? | 12:18 |
@kanzure | no | 12:20 |
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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 | 12:28 |
Mariu | :p | 12:30 |
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 | 12:37 |
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 | 12:38 |
@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 | 12:39 |
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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 | 12:49 |
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 | 12:50 |
jrayhawk | oh, yes, figure 1 looks to be the important one | 12:53 |
jrayhawk | "highly stable" does not appear to mean "cooking stable" | 12:54 |
jrayhawk | this appears to be consistent with my experience; unboiled garlic fucks me up a bit. | 12:55 |
nmz787 | jrayhawk: so what would the immunogens do if the immune system didn't mess with them? | 12:57 |
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 | 12:58 |
@kanzure | http://blog.okfn.org/2013/02/05/we-need-an-open-database-of-clinical-trials/ | 12:59 |
@kanzure | http://www.alltrials.net/ | 13:00 |
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" | 13:01 |
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" | 13:04 |
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" | 13:06 |
nmz787 | a friend says his grandfather ate a clove or two of raw garlic along with nuts and grapefruit for breakfast every morning | 13:09 |
Mariu | ate ? | 13:12 |
Mariu | what changed ? | 13:12 |
EnLilaSko | http://www.kickstarter.com/projects/461687407/kickstarter-open-source-death-star | 13:16 |
chris_99 | lol | 13:17 |
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 | 13:18 |
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 | 13:19 |
ThomasEgi | you may want to update your source lists | 13:20 |
@kanzure | http://nerdapproved.com/wp-content/uploads/2011/09/alderaan-shot-first.gif | 13:20 |
Mariu | lol | 13:22 |
Mariu | =] | 13:22 |
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ephialtes480 | brilliant kickstarter project. | 13:28 |
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nmz787 | https://petitions.whitehouse.gov/petition/secure-resources-and-funding-and-begin-construction-death-star-2016/wlfKzFkN | 13:36 |
@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). | 13:38 |
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jrayhawk | lectins have a wide variety of effects; you'd have to study the particular lectin. Some of them are fairly innocuous. | 13:43 |
nmz787 | huh | 13:44 |
nmz787 | garlic enema eh | 13:44 |
jrayhawk | Not something I've ever done, but they do have some clinical trials. | 13:44 |
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 | 13:45 |
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 | 13:46 |
nmz787 | kanzure: the email given is bad now | 13:47 |
nmz787 | kanzure: and I want to contact them | 13:47 |
@kanzure | hmm. this one will require some advanced sleuthing. | 13:50 |
@kanzure | nmz787: try looking for patents by these guys. they seem to not have any papers after 2002 but maybe there's patents. | 13:54 |
nmz787 | kanzure: do you know anyone looking for a remote scientific programmer? | 13:59 |
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) | 14:00 |
@kanzure | but enthought would be enriching for you i think | 14:01 |
@kanzure | or anyone in here i guess | 14:01 |
@kanzure | i regularly get blasted by recruiters but never for explicitly scientific things. | 14:02 |
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juri_ | if its remote free software, keep me in mind, please. ;) | 14:05 |
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? | 14:06 |
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. | 14:07 |
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: ? | 14:08 |
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 | 14:09 |
juri_ | at one point, i was the youngest MCSE in the nation. | 14:10 |
juri_ | this was a while ago. ;) | 14:11 |
juri_ | everything i've written since i was ~20 was licensed under the GPL, and 95% of that made it online. | 14:13 |
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@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 | 14:14 |
@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 | 14:15 |
juri_ | looks like fun. ;) | 14:16 |
@kanzure | well pete is suggesting this as an alternative to my https://github.com/kanzure/pdfparanoia | 14:16 |
@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. | 14:17 |
* 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 | 14:18 |
@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 | 14:19 |
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 | 14:20 |
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 | 14:21 |
juri_ | ... less evil than xslt? sacrelige. ;) | 14:22 |
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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. | 14:27 |
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@kanzure | juri_: well, what is the idea? | 14:30 |
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). | 14:31 |
@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. | 14:32 |
juri_ | hmm. i'm tempted to just do a hex encode of the lines, for sed to handle. | 14:33 |
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? | 14:35 |
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. | 14:36 |
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'. | 14:37 |
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 :) | 14:39 |
@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. | 14:40 |
@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! | 14:41 |
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juri_ | http://pastebin.com/vsRMzNJC | 14:45 |
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@kanzure | you wrote all of those regular expressions just now? | 14:45 |
juri_ | oh goodnes no. | 14:48 |
juri_ | that's about two days of work. | 14:48 |
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 | 14:49 |
ephialtes480 | k, added to the list of todos...forked for now, thanks will issue pull requests if I complete a functioning one... | 14:50 |
@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. | 14:51 |
juri_ | so that i, a lazy human, can edit the file format (which is very non-human-editable) in a text editor. | 14:52 |
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juri_ | now, the reason i was showing that, is that the xslt there and the SED do the same job, just forward / reverse. | 14:52 |
juri_ | xml is a good intimediary for binary formats, that's why its so readily used to replace them. | 14:53 |
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. | 14:54 |
@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. | 14:55 |
juri_ | xml is a great replacement for binary formats.. as long as you do not care about CPU time. ;) | 14:56 |
jrayhawk | or storage efficiency | 14:57 |
juri_ | agreed. | 14:57 |
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 | 14:58 |
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. | 14:59 |
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. | 15:00 |
@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 | 15:01 |
juri_ | parts of openemr are that old. | 15:02 |
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. | 15:03 |
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. | 15:04 |
@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 | 15:05 |
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. | 15:06 |
juri_ | its a lot for the way the project is (not) run. | 15:07 |
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? | 15:08 |
@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) | 15:09 |
@kanzure | nmz787: curiosity | 15:10 |
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/ | 15:14 |
ephialtes480 | kanzure you get "Redistribution subject to AIP license or copyright" from the binary stream data. is that getting decoded by pdfminer methods? | 15:15 |
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@kanzure | ephialtes480: yes that is decoded by pdfminer | 15:17 |
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 | 15:18 |
@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? | 15:19 |
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 | 15:20 |
ephialtes480 | (it shows when opening the file regularly but there may be extra spaces, etc.) | 15:21 |
ephialtes480 | thanks for now! later... | 15:23 |
@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 | 15:24 |
@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 | 15:25 |
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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 | 15:39 |
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@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 | 16:12 |
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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 | 16:33 |
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 | 16:35 |
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@kanzure | so is FlateDecode referencing the deflate algorithm? | 17:57 |
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@kanzure | yashgaroth: how much does a CRO cost to make. | 18:37 |
yashgaroth | uhhh | 18:37 |
yashgaroth | depends on the line of work, though I can't speak to specifics there, whether you're including operating expenses | 18:38 |
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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 | 18:40 |
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@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." | 18:43 |
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yashgaroth | oh man I just found out quintiles is owned by bain capital | 18:43 |
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 | 18:44 |
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 | ... | 18:45 |
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" | 18:46 |
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 | 18:47 |
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 | 18:48 |
@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. | 18:49 |
@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 | 18:50 |
@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 | 18:51 |
@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 | 18:52 |
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 | 18:53 |
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 | 18:54 |
@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? | 18:55 |
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? | 18:56 |
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 | 18:57 |
yashgaroth | ok so kanzure what did you mean then, if not our guesses? | 18:58 |
@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 | 18:59 |
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 | 19:00 |
@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 | 19:02 |
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 | 19:03 |
@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 | 19:04 |
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yashgaroth | ehh maybe | 19:04 |
@kanzure | well i think that's what all the people who get fired from roche do | 19:05 |
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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? | 19:05 |
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yashgaroth | why is what | 19:05 |
klafka | does everyone get fired from roche | 19:05 |
klafka | or so many people | 19:05 |
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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 | 19:06 |
klafka | i have an old roommate whose been working at genentech for like 5 years | 19:07 |
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klafka | since he got out of college | 19:07 |
yashgaroth | I have several colleagues who are ex-bay area genentech | 19:07 |
@kanzure | "the entrepreneur's guide to a biotech startup" http://www.evelexa.com/resources/EGBS4_Kolchinsky.pdf | 19:13 |
@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 | 19:16 |
@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 | 19:17 |
@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 | 19:18 |
@kanzure | "Typical medical device products may have gross margins from 55%-70%." aww yeah. | 19:21 |
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@kanzure | equipment loans http://www.nature.com/bioent/building/infra/082004/full/bioent821.html | 19:35 |
@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. " | 19:37 |
@kanzure | fenn: this might be interesting background material for bayh-dole things, http://www.nature.com/bioent/view/102004/full/bioent832.html | 19:44 |
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 | 20:10 |
@kanzure | thanks anyway. pdfparanoia is working for now. | 20:11 |
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@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 | 20:22 |
yashgaroth | for rent and salaries? maybe half | 20:23 |
@kanzure | also, 33,000 sq ft of rats is a lot of rats | 20:25 |
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 | 20:26 |
yashgaroth | we can give it an air of wintergreen, that's about the state of the art | 20:27 |
@kanzure | did anyone commercialize that btw? the less stinky ecoli strain? | 20:36 |
@kanzure | iirc they won some igem prizes and then went back to their soulless lab jobs | 20:37 |
yashgaroth | I don't know if they designed the wintergreen synthase or whatever it was | 20:38 |
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nmz787 | yay i installed gnu emacs for windows, and it solved my problem! | 21:22 |
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 | 21:25 |
@kanzure | well, drivers can be loaded into the android kernel so i think you can just distribute the .ko files or whatever? | 21:38 |
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