--- Day changed Sat Aug 08 2009 00:34 < nchaimov> dfdfdf 00:35 -!- nchaimov [n=cowtown@c-24-21-45-17.hsd1.wa.comcast.net] has quit [] 00:39 < kanzure> fenn: http://heybryan.org/~bbishop/docs/pong.txt 00:44 -!- nchaimov [n=cowtown@c-24-21-45-17.hsd1.wa.comcast.net] has joined #hplusroadmap 00:48 < kanzure> added some papers: http://heybryan.org/books/Biology/neuro/ 00:51 < kanzure> hrm things seem to be all messed up .. 00:51 < kanzure> http://heybryan.org/books/Biology/neuro/neuro/ 00:51 < kanzure> guess I'll fix that eventually 01:01 < genehacker> MWAHAHAHAHAHAHAHAHA 01:01 < genehacker> microfluidics is awesome 01:03 < genehacker> you can put a whole bunch of reactors on the same chip 01:05 < genehacker> page 207 of that book contains something that could be used for a dna synth 01:13 < genehacker> valveless valving for taking samples from different reactors so the composition can be analyzed 01:18 < genehacker> kanzure are you present at the moment? 01:20 < genehacker> nvm 02:46 < genehacker> probably won't work for DNA synthesis 02:46 < genehacker> re needs to be higher for those things to work 04:53 -!- genehacker [n=noko@pool-173-57-41-223.dllstx.fios.verizon.net] has quit [Read error: 113 (No route to host)] 04:59 -!- freedom_ [n=freedom@195.216.211.175] has quit [Read error: 104 (Connection reset by peer)] 05:18 -!- QuantumG [n=qg@nuclear.biodome.org] has quit [Remote closed the connection] 05:23 -!- QuantumG [n=qg@nuclear.biodome.org] has joined #hplusroadmap 08:01 -!- marainein [n=marainei@220.253.35.140] has joined #hplusroadmap 08:41 < kanzure> what? http://www.google.com/search?q=%22Full+text+access+provided+to+Googlebot+Access+by+Web+Services.%22&ie=utf-8&oe=utf-8&aq=t&rls=org.debian:en-US:unofficial&client=iceweasel-a 08:42 < kanzure> "Full text access provided to Googlebot Access by Web Services" 09:04 < kanzure> heh 09:04 < kanzure> "Finite-elements model of the developing cerebral hemisphere" 09:05 < kanzure> (from a model for the development of cortical convolutions) 09:11 -!- marainein [n=marainei@220.253.35.140] has quit ["Ex-Chat"] 09:11 < kanzure> heh tensegrity models of gyrification and cortical folding due to mechanical tension 09:30 < kanzure> "The increased predictability observed under surface-based registration suggests that the location of V1 is more accurately predicted by the cortical folds than by the shape of the brain embedded in the volume of the skull." 09:30 < kanzure> (from Accurate prediction of V1 location from cortical folds in a surface coordinate system 09:34 < kanzure> so is the inferior precentral sulcrus (IFJ) the same thing as the prefrontal orbitolateral regions? 09:38 < kanzure> er I guess I meant to say "dorsolateral prefrontal cortex" 09:48 < kanzure> http://en.wikipedia.org/wiki/Psychological_refractory_period 09:52 < kanzure> http://brainmap.org/scribe/index.html "Scribe is the BrainMap application that is used to extract coordinates and meta-data from a published functional neuroimaging study and enter it in our database." 09:53 < kanzure> hm. sleuth might be useful (maybe) 10:00 < kanzure> takes a while to download search results 10:00 * ybit wants to see an example of scribe 10:01 < ybit> 01:03 < genehacker> page 207 of that book contains something that could be used for a dna synth 10:01 < ybit> what book was genehacker referring to? 10:08 < ybit> it was some microfluidics books he mentioned allowing others to torrent?... 10:08 < ybit> http://filebin.ca/ayxuh 10:08 < ybit> i think 10:09 < ybit> wtf kind of file is that 10:09 < ybit> http://filebin.ca/ordqrh is the first part i believe 10:09 < ybit> zip 10:09 < ybit> -_- .zip would be nice 10:11 < ybit> oh 10:12 * ybit is jealous some people can scan two pages at once 10:13 < ybit> 11:48 < fenn> like CRC handbook, but for manufacturing 10:13 < ybit> Chemical Rubber Company handbook of chemistry and physics 10:13 < ybit> that's the only book which comes up 10:14 < ybit> is that what you were referencing? 10:16 < drazak> lol 10:17 < ybit> Pussy Beer: "Pussy Beer is an alcoholic beverage created from using Candida yeast from a vaginal yeast infection to create fermentation in a custom mash consisting of vaginal lubrication, menses, and rice. " 10:17 -!- kardan_ [n=kardan@p54BE3C9C.dip.t-dialin.net] has joined #hplusroadmap 10:17 < ybit> http://wiki.xkcd.com/irc/Pussy_Beer 10:17 -!- kardan| [n=kardan@p54BE670A.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] 10:18 < drazak> lol 10:20 < ybit> someone's rofling about crc book and i don't know why 10:22 < drazak> it's fucking impossible to find shit in the crc handbook of physics and chemistry 10:22 < drazak> motherfucking impossible 10:22 < ybit> :) 10:22 < drazak> you need to take a class on using it 10:56 -!- ybit [n=ybit@unaffiliated/ybit] has quit ["leaving"] 10:59 -!- ybit [n=ybit@unaffiliated/ybit] has joined #hplusroadmap 11:50 < ybit> df -h 11:50 -!- ybit [n=ybit@unaffiliated/ybit] has quit ["leaving"] 11:51 -!- ybit [n=ybit@unaffiliated/ybit] has joined #hplusroadmap 11:52 < kanzure> ybit: yes, CRC is a classic 11:54 < kanzure> there are various copies of it floating around the web 11:58 -!- genehacker [n=noko@pool-173-57-41-223.dllstx.fios.verizon.net] has joined #hplusroadmap 12:18 * kanzure really wants to find a gene silencing + beta-catenin + cerebral cortex paper. 12:18 < kanzure> "A recent study suggests that the regulation of cortical size might involve phospholipids, by showing that their addition to cultured embryonic mouse cortices increases cortical size and induces folds resembling gyri." 12:32 < kanzure> huh ncravens hangs out in #openkollab 13:07 < genehacker> ??? 13:07 < genehacker> wow 13:07 < genehacker> the potential between the cell wall and surroundings can get to 130 volts 13:08 < genehacker> cytoplasm an surroundings 13:08 < fenn> no way 13:10 < kanzure> maybe you mean mV 13:12 -!- tropology [n=michael@adsl-76-223-1-47.dsl.chcgil.sbcglobal.net] has joined #hplusroadmap 13:13 < kanzure> hey tropology 13:13 < kanzure> fenn: http://88proof.com/synthetic_biology/blog/wp-content/uploads/2009/06/protolexer1.png 13:13 < tropology> hi 13:13 < kanzure> what's up? 13:14 < tropology> was in #openkollab, thought I'd explore 13:14 -!- kanzure changed the topic of #hplusroadmap to: skdb - "apt-get but for hardware" http://adl.serveftp.org/skdb/ http://adl.serveftp.org/skdb.git/ 13:14 < kanzure> tropology: yeah I was surprised that nathan was on irc 13:14 < kanzure> he doesn't seem to understand what skdb is 13:15 < kanzure> and I don't seem to understand why he needs to make "openkollab" 13:15 < tropology> cool stuff 13:15 < tropology> any work there with wifi, etc? 13:15 < tropology> a few years back was trying to get community wireless more active in openhardware concept 13:18 < tropology> why dont you think it would be nec. or useful? 13:19 < kanzure> what's wrong with openmanufacturing? 13:19 < kanzure> why not just use that 13:20 < tropology> I need to get up to speed on what is/was happening there .. 13:20 < tropology> lots of folk startring from very different places but after something similar 13:20 < kanzure> well if you want it condensed, the first four links on this page are probably helpful: 13:20 < kanzure> http://heybryan.org/om.html 13:21 < tropology> thanks, gave quick glance will read more soon .. and will joni th e google grop 13:22 < tropology> I've been coming at this from several contexts myself .. arrived at a number of the same or related realizations .. 13:22 < tropology> my contexts included community organizing, local npo/community oorganizations , coalitions of same, community networking, community tech, and community wireless amomg other things 13:23 < tropology> everything just began bleeding together 13:24 < tropology> wow, still on the first of 4 == great stuff 13:27 < tropology> thanks for the orientation 13:27 < kanzure> no problem 13:28 < kanzure> but most of the work was Eric Hunting 13:30 * tropology begins memory game with daughter 13:44 -!- tav [n=tav@92.27.171.10] has joined #hplusroadmap 13:44 < tropology> :) 13:48 < kanzure> hey tav 13:50 < kanzure> fenn: will you fix the isinstance()/complement error? 13:50 < kanzure> er nevermind 13:52 < CIA-38> skdb: kanzure * r 9c2f747a39ec / (core/interface.py pymates/pymates.py): fix complement compatibility check in core/interfaces.py 13:55 < kanzure> should mate_parts() fuse objects together? 13:55 < kanzure> or should it return all objects, or what? it currently modifies the shapes of the inputs 13:55 < kanzure> but this was apparently not expected functionality? or something? 13:57 -!- gerryg [n=gerry@74.0.57.156] has joined #hplusroadmap 14:01 < genehacker> nope fenn 14:01 < genehacker> volts 14:02 < genehacker> or whatever a nernst potential is 14:15 < fenn> mate_parts should return the transformation, and then something else should display the transformation applied to that part 14:19 < fenn> re: interface complement; isinstance(other, self.complement) really makes more sense because it encompasses subclassed interfaces 14:19 < fenn> even though lego is broken atm 14:20 < kanzure> a nernst potential is in mV 14:21 < fenn> that's what i figured 14:27 < kanzure> fenn: can you add some more legos with step files to data.yaml for motivational purposes? 14:28 < fenn> hold yer horses 14:44 < kanzure> why isn't cp -p the default? 14:44 < kanzure> or scp -p? 14:45 < fenn> because you haven't added to .bashrc 14:45 < fenn> 14:46 < genehacker> ok 14:48 < CIA-38> skdb: fenn * r 4787abd600e1 /packages/lego/ (grammar.yaml interfaces.py): finish translating grammar to dict format 14:48 < fenn> er, the code to use that doesnt exist yet 14:49 < kanzure> er why are the URLs at the top not in a urls: attribute list? :p 14:49 < kanzure> also, line 15 you have a stray apostrophe 14:49 < kanzure> which messes up my vim highlighting- not sure if yaml will complain 14:49 < kanzure> huh yaml doesn't complain 14:49 < kanzure> the vim yaml syntax highlighter might suck 14:50 < kanzure> ah there was a bug report for it 14:52 < kanzure> didn't fix it 14:53 * kanzure blames Clark Evans 14:55 < kanzure> git://github.com/trans/yaml_vim.git 14:58 < fenn> do you really want metadata in every file? 14:59 < fenn> those are just notes for my reference later 14:59 < fenn> lugnet has nothing to do with the grammar besides hosting pretty pictures of the examples (method which i'll be writing shortly) 15:12 < CIA-38> skdb: kanzure * r 357220943669 /packages/bearing/metadata.yaml: bearing/metadata.yaml changed to match metadata for the threads package 15:38 < kanzure> genehacker: did you post in /r9k once about me? 15:48 < drazak> wtf is r9k? 15:53 < genehacker> did I? 15:53 < genehacker> why? 15:53 < genehacker> no 15:54 < genehacker> what happened? 15:54 < kanzure> drazak: on 4chan 15:55 < kanzure> oh well. someone sent an email to openmanufacturing and said that he found out about me on /r9k because someone posted a link to my homepage 15:55 < genehacker> and? 15:56 < genehacker> does he want to join us? 15:56 < genehacker> or do we have a troll problem? 15:57 < kanzure> no it's fine 15:58 < kanzure> I replied to him: http://groups.google.com/group/openmanufacturing/msg/7ee9a44355752417 15:59 < genehacker> oh the tech tree person 15:59 < genehacker> I think that was me 15:59 < genehacker> they might be useful to us 15:59 < kanzure> who is they? 16:00 < genehacker> no the tech tree guy 16:19 < fenn> post_init_hook never gets called; how have packages been getting their path? 16:19 < fenn> since package.unix_name never gets set 16:20 < fenn> (fwiw i think unix_name is a stupid idea; the package name should always be unix compatible) 16:20 < kanzure> ybit: the system I have in mind lets you view a web page only once, construct a scraper in it via the the GUI of your usual web browsing experience, extract data into yaml, then consequently do some cron-scheduled task on the data that is burped back, do some stuff on /dev etc. 16:20 < kanzure> erl 16:20 < kanzure> hm 16:21 < kanzure> fenn: skdb.py Package.path() 16:21 < fenn> i remember gene posting about skdb in some sort of 'time traveler from the future chats with 4chan for the lulz' thread 16:21 < kanzure> it checks if there is a unix name and if not, sets it as the name for the moment 16:21 < kanzure> however I agree that all names should be unix compatible 16:21 < kanzure> so I'm fine with you doing away with that 16:21 < kanzure> and replacing it with just the regular name 16:21 < fenn> right now it just checks assert hasattr(self, "unix_name") 16:21 < kanzure> well you can delete that then :) 16:21 < fenn> anyway.. fixing 16:24 < fenn> bah isalpha doesn't even do what you say 16:25 < kanzure> proof? 16:25 < fenn> 'fo_o'.isalpha() 16:25 < fenn> False 16:27 < kanzure> wasn't I using isalnum() ? 16:27 < kanzure> huh that doesn't work to 16:27 < kanzure> *too 16:29 < fenn> ^[a-zA-Z0-9_]*$ 16:29 < fenn> something like that 16:29 < kanzure> how about dashes? 16:30 < kanzure> and periods? 16:30 < fenn> keep em comin 16:31 < kanzure> + 16:31 < kanzure> and possibly \ but that's questionable 16:31 < fenn> no 16:31 < fenn> why +? 16:31 < kanzure> wouldn't want it anyway 16:32 < kanzure> I was thinking of my recent sudo apt-get install libgtk+ call 16:32 < fenn> superpackage++ 16:32 < fenn> i think it's lame 16:32 < kanzure> I don't think anyone will miss it 16:32 < fenn> packaging nazis ftw 16:32 < kanzure> "rawr you may *NOT* have those symbols in your package name!" 16:33 < fenn> somebody's gotta do it 16:37 < genehacker> shoot 16:38 < genehacker> I accidently sewed through tubing 16:39 < drazak> do you guys want to make me some primers? 16:41 < kanzure> what happened to your script? 16:41 < drazak> well, I only need one primer, atm, and my script is still in the works, but i wanted to see if someone else could make me this primer because i'm not sure how to find a UTR of a gene 16:42 < drazak> if i know have to find the untranslated region i'd do it 16:42 < drazak> :P 16:42 < kanzure> and it's not on genebank? 16:43 < drazak> i need a primer for 100-150 basepairs of one of the UTR of smooth muscle actin alpha 16:44 < kanzure> what's a UTR exactly? 16:44 < kanzure> don't give me bio crap, just say what you want 16:45 < drazak> it's the untranslated reigon 16:45 < kanzure> there's no reason for dna to be translated 16:45 < drazak> it's part of a gene that's turned into mRNA but not into a polypeptide 16:46 < kanzure> isn't there some codon that says whether or not that should happen? 16:47 < drazak> AUG is the start codon of a translated sequence 16:47 < kanzure> and the stop codon? 16:48 * kanzure tries to remember 16:48 -!- ecd [n=ecd@adsl-226-143-118.int.bellsouth.net] has joined #hplusroadmap 16:48 < drazak> AAUAAA 16:48 < kanzure> hey ecd 16:48 < ecd> hi! 16:48 < fenn> what about packages of all digits (no letters) 16:48 < kanzure> nice to see you show up 16:48 < kanzure> fenn: up to you. I see no reason to allow it. 16:48 < ecd> nice to be greeted immediately :) 16:48 < fenn> well, it'd be easier to allow it 16:48 < kanzure> ecd: we're wired in to the channel or something 16:48 < kanzure> fenn: maybe we can just "strongly discourage it" 16:49 < kanzure> or "strongly make fun of the practice" 16:49 < fenn> hm 16:49 < fenn> can we hire a professional heckler? 16:49 < drazak> lol 16:49 < ecd> ("Fantastic, I will eat your brain" - I have a friend who said something like that, who also seems "wired into the channel") 16:49 < kanzure> you mean a mother? 16:50 < drazak> kanzure said that, ecd 16:50 < kanzure> ecd: brains don't taste as good as you might think 16:50 < ecd> aye draz 16:50 < ecd> thanks for the tip, kanzure! 16:50 < kanzure> speaking of which, ecd, this was a recent find: http://adl.serveftp.org/papers/Regulation%20of%20cerebral%20cortical%20size%20by%20control%20of%20cell%20cycle%20exit%20in%20neural%20precursors.pdf.png 16:51 < kanzure> the brain on the right is a transgenic brain 16:51 < ecd> I had just looked at that in the "papers archive" 16:51 < ecd> how are you spying on me? 16:51 < ecd> real-time log monitoring? 16:52 < kanzure> yes, bot it's usually just bots 16:53 < ecd> so who has volunteered for brain enlargement treatment? 16:53 < kanzure> most of us 16:53 < kanzure> actually brain size isn't necessarily the real trick 16:54 < ecd> pardon my sluggishness, i'm relatively new to all this. what IS the real trick? quantity and fidelity of connections? 16:55 < kanzure> the real trick is not assuming you know the real trick :p 16:56 < ecd> far be it from me! 16:56 < kanzure> more tools would be helpful 16:56 < ecd> for investigating brains? or are you talking about collaboration stuff? 16:56 < kanzure> brains 16:57 < ecd> are you talking new tools/techniques, or actually having some of your own? 16:57 < kanzure> what is the difference? 16:57 < ecd> (tools, taht is) 16:57 < kanzure> as a sysadmin of my brain, I really have only these big bulky hands with which to do work with- so I need to acquire more tools and maybe build more. 16:58 < ecd> what do you have in mind? 16:58 < genehacker> direct interface to a computer for more control perhaps? 16:58 < ecd> Any progress anywhere in that regard? 16:59 < kanzure> in vivo dna synthesizer on a chip and virus bioreactor on a chip, implantable microelectrode arrays, sandboxing of neural stem cell cultures, "weather monitoring" such as by MRI reporter genes, 16:59 < kanzure> or fluorescent protein reporters of membrane potentials, gene silencing capabilities, 17:00 < ecd> haha, where do you want to start? or where have you already? 17:00 < kanzure> rTMS/tDCS, do-it-yourself fMRI/MRI/CT/PET scanners, etc. 17:00 < kanzure> ecd: well this is kind of why I'm doing skdb too 17:00 < ecd> anyone building? or still not enough info out there? 17:00 < kanzure> yes there are people building some of these devices 17:00 < kanzure> a few people I know have rTMS setups 17:01 < ecd> using them? getting results as advertised? 17:01 < kanzure> another fellow has herself a tDCS setup that she's been meaning to get back into the habit of working on 17:01 < kanzure> what results? 17:01 < nsh> stimulation of the transcraminums 17:02 < nsh> i would imagine 17:02 < kanzure> hi nsh :) 17:02 < nsh> yo 17:02 < kanzure> one fellow reported tingling sensations 17:02 < ecd> no memory/ability enhancements? 17:02 < ecd> (and no negative side effects yet?) 17:02 < kanzure> be very careful when asking that question 17:03 < kanzure> it's not entirely obvious what an "enhancement" might be 17:03 < kanzure> at this point I'm more interested in augmentations that might lead to enhancements 17:03 < ecd> such as? 17:03 < kanzure> a brain-computer interface is an augmentation in my book 17:03 < kanzure> but not necessarily an "enhancement" (whatever that means) 17:03 < kanzure> it might be an enhancement, but you shouldn't bet on it 17:04 < kanzure> what I'm trying to say is that intelligence/enhancement are just fuzzy words and nobody has a clear definition 17:04 < kanzure> so let's avoid them :) and carry on instead 17:04 < ecd> is memory a fuzzy word too? 17:05 < kanzure> dunno, I have read a lot of papers where memory is tested- and there are some simple ways to "test" different forms of memory 17:05 < ecd> (not being sassy) do i recall correctly: tms had some effect on memory? 17:05 < kanzure> like the "repeat a list of words" test 17:06 < kanzure> or the recent rapamycin tests regarding mice that had a ridiculously high percentile improvement in long-term visual memory 17:06 < kanzure> there are many TMS articles out there so I'm not sure which one you're talking about 17:06 < kanzure> http://heybryan.org/books/papers/open-rtms/ <-- here's some rTMS papers 17:06 < ecd> all i've heard is through pop sci-type articles and a friend who works in a lab 17:06 < kanzure> ouch. 17:07 < kanzure> don't you wish you had more tools to play with to see for yourself? 17:07 < genehacker> popsci as in the magazine? 17:07 < ecd> your site is a goldmine, thanks for hosting all that by the way 17:07 < ecd> hell yes 17:07 < ecd> hence my "tech tree" project 17:07 < genehacker> or or journals that advertise a lot? 17:07 < kanzure> I really think you might be working on the same thing as us, ecd 17:07 < ecd> general journals, gene 17:07 < kanzure> we just don't call it a tree because it's sometimes more of a graph 17:07 < ecd> more like "wanting to work" 17:07 < ecd> yeah 17:07 < kanzure> heh wanting to work 17:07 < ecd> exactly. i've been looking for decent graph databases 17:08 < kanzure> there are a few libraries that manipulate graphs 17:08 < ecd> (hard to invest the time it seems to require given my limited abilities and the demands of citizenship (money, etc.)) 17:08 < kanzure> but none that do dependency resolution algorithms really except smartpm 17:08 < kanzure> so I added some code to skdb for dependency resolution in the dep/ folder 17:08 < genehacker> oh good so you do read journals 17:08 < kanzure> it's not quite functional yet but it should give an idea as to what we have in mind for resolving multiple dependencies of different types on different tech/hardware 17:09 < ecd> where i can. i've been wanting to camp the local college library for access to some tech journals 17:09 < genehacker> which is good for figuring out how to make self-replicating automata 17:09 < genehacker> go for it 17:09 < genehacker> COLLEGE LIBRARIES ROCK 17:09 < ecd> are you all in school/professionals? 17:09 < kanzure> no 17:09 < genehacker> I am in school 17:10 < genehacker> but we're hardly professionals 17:10 < ecd> hah 17:10 < ecd> spoken proudly? :P 17:11 < genehacker> kanzure you're doing lego at the moment correct? 17:11 < kanzure> one idea I was toying around with a few years ago was this idea of using neural stem cell cultures to sandbox possible alterations to my brain that I might want to make 17:11 < kanzure> genehacker: fenn is, I'm in here acting like I'm social though 17:13 < ecd> (kanzure, on my account? or are there other brains in here you want to consume?) 17:13 < kanzure> what? 17:13 < ecd> "Acting like i'm social" 17:13 < genehacker> another idea I'm toying around with is a gene synthesizer to make the components necessary to do stuff like neural stem cell cultures 17:13 < kanzure> ecd: yes I should probably be acting like I'm working instead of acting like I'm being social 17:14 < ecd> then by all means! 17:14 < kanzure> secretly I'm this angry old man trapped in this old kid's body or something (not sure if I got my story straight this time) 17:14 < fenn> hum. what is Package.load supposed to do? 17:14 < kanzure> but anyway, no, I'm happy to be talking 17:14 < fenn> kanzure you're too naive to be an old man trapped in a kid's body 17:15 < kanzure> am I angry enough? 17:15 < fenn> not really, but why do old people have to be angry? 17:15 < kanzure> dementia? 17:15 < ecd> most old guys i know/knew are/were pretty chill 17:15 < kanzure> ok ok 17:15 < kanzure> fenn: I think it was supposed to be for loading stuff from data.yaml 17:15 < fenn> right, but, what is all the k,v stuff about? 17:16 < genehacker> you could cultivate insanity kanzure 17:16 < genehacker> it gets you evil genius points 17:16 < kanzure> genehacker: bah 17:17 < kanzure> fenn: the idea was that in data.yaml there might be multiple parts listed 17:17 < kanzure> so one of the parts might be "bob: !screw" 17:17 < kanzure> so this would set the screw's name attribute to "bob" 17:17 < fenn> oh, right 17:17 < fenn> what are only_classes? 17:17 < kanzure> data.yaml might have multiple objects listed 17:18 < kanzure> so if you want only the screw tags, then just say "screw" or something 17:18 < kanzure> er pass the screw class (screw_package.Screw) as only_classes 17:18 < fenn> hm 17:18 < kanzure> and then you'll get back only the screws 17:18 < fenn> i think that should be done with isinstance 17:18 < kanzure> this method is kind of stupidly structured 17:18 < fenn> and load should just load the file 17:18 < kanzure> it should be def load_data() 17:18 < kanzure> not def load(content) 17:18 < kanzure> no reason to make the user pass some content.. 17:18 < kanzure> it should know where the package_path is and where data.yaml can be found 17:19 < fenn> ok; is "source data:" always the right tag for data.yaml 17:19 < fenn> er, mapping key 17:19 < kanzure> if you're happy with the name "source data" in metadata.yaml yeah 17:19 < fenn> i'm not entirely happy with the idea of one data file 17:19 < kanzure> how about an attribute in metadata.yaml called "catalog" 17:19 < fenn> oh it's a list 17:20 < kanzure> ok nevermind 17:20 < kanzure> should be fine 17:20 < kanzure> for Package.load_data how do you specify which file to load, then? 17:20 < kanzure> I was hoping for Package.load_data() to just work automagically 17:20 < kanzure> (and spit out the objects/data) 17:21 < fenn> loads all in source data 17:21 < kanzure> ok 17:21 < kanzure> how about a particular source data file, then? 17:21 < kanzure> named parameter that is set to None, if None then load_all ? 17:21 < fenn> just do package.load(package_file(whatever)) 17:21 < kanzure> what? 17:21 < fenn> or skdb.load 17:21 < kanzure> why 17:21 < fenn> package_file hasnt been committed yet 17:22 < kanzure> package.load_data() #returns all source data 17:22 < fenn> i needed a way to load grammar.yaml inside of the lego package 17:22 < fenn> but i didnt know the local path 17:22 < kanzure> package.load_data("data.yaml") #returns source data only from data.yaml in the package 17:22 < fenn> so package_file finds the path of a file in a package 17:22 < kanzure> where is package_file defined 17:23 < fenn> skdb.py global namespace 17:23 < kanzure> then what are yuo passing it? 17:23 < fenn> package_file('lego', 'grammar.yaml') 17:23 < kanzure> meh 17:23 < kanzure> if you commit I'll make it slightly more pythonic 17:23 < fenn> how so, please elaborate 17:24 < fenn> i should just shut up and commit 17:24 < kanzure> Package.path() could take a parameter (filename) and spit out the path 17:24 < fenn> no 17:24 < fenn> won't work 17:24 < kanzure> why not 17:24 < kanzure> if there's no parameter given, then just do the default behavior (package path) 17:24 < fenn> you're in the middle of constructing the package 17:24 < fenn> just hang tight and look at the code when i'm done 17:25 < fenn> the real problem is i'm getting None for package name somewhere in this process 17:25 < fenn> even though it's defined in metadata.yaml 17:26 < kanzure> what's worng with os.path.dirname(os.path.abspath(__file__)) in where-ever you're trying to load grammar.yaml? 17:26 < fenn> it's gross 17:26 < kanzure> :p you're gross 17:26 < fenn> and doesn't do any checks or anything 17:27 < kanzure> ecd: so anyway, I'm guessing you checked out the repository? 17:27 < ecd> browsing now 17:35 < fenn> when a !package gets loaded from yaml its name is empty, so when it gets initialized unix_name fails (it doesnt have the right data anyway) 17:35 < fenn> how do i call check_unix_name after the data gets stuffed? 17:37 < kanzure> post_init_call? 17:38 < fenn> right, it works now for some reason 17:38 < fenn> _-_ 17:44 < kanzure> hahaha "Manipulating gene expressions by electroporation in the developing brain of mammalian embryos." 17:44 < kanzure> "We have also performed EP in developing fetuses in utero guided by ultrasound image" 17:45 < kanzure> hm there has to be a use for transient gene expression during cerebrogenesis (or whatever you call it) 17:46 < ecd> is this a paper you've uploaded? 17:46 < kanzure> localized accelerated regions of growth of neurons I guess 17:46 < kanzure> ecd: one moment and I'll put it up 17:46 < ecd> ty 17:46 < ecd> (though i've near-zero bio knowledge, still sounds interesting...) 17:47 < kanzure> ttp://adl.serveftp.org/papers/Manipulating%20gene%20expressions%20by%20electroporation%20in%20the%20developing%20brain%20of%20mammalian%20embryos.pdf 17:47 < kanzure> er 17:47 < kanzure> http://adl.serveftp.org/papers/Manipulating%20gene%20expressions%20by%20electroporation%20in%20the%20developing%20brain%20of%20mammalian%20embryos.pdf 17:48 < kanzure> so I wonder if anyone has built as stereotactic frame for human fetuses 17:48 < kanzure> "Mussen devised the first stereotactic frame intended for human use in 1918." 17:49 < ecd> for fetuses... how much jostling can fetuses tolerate without ill-effect? 17:49 < kanzure> they squeeze through a fucking vagina 17:49 < ecd> and how many women would let you build a frame in their womb? 17:50 < kanzure> who said anything about using a woman's womb? ectogenetic tanks, man :p 17:50 < kanzure> (only half kidding) 17:50 < ecd> hah. ...how far away? 17:50 < kanzure> kuwabara was doing that in the late 90s in japan but died and nobody continued his wokr 17:50 < kanzure> *work 17:50 < kanzure> however it was only for rats IIRC or goats(?) 17:50 < ecd> wow *internets* 17:51 < kanzure> search also for "artificial womb" and "artificial uterus" 17:51 < ecd> aye 17:51 < kanzure> aha, here we go: http://en.wikipedia.org/wiki/Artificial_uterus 17:52 < kanzure> "Another form of artificial uterus is one in which tanks are filled with amniotic fluid which is maintained at body temperature, and the embryonic umbilical cords are attached to external pumps which regulate nutrient intake and waste outflow. " 17:53 < kanzure> hrm surely someone has done fetal neurosurgery before 17:53 < kanzure> how have they done it without a stereotactic frame? 17:53 < ecd> i can search, yeah, but do you know offhand how "complete" the knowledge is of embryo development & such? 17:54 < kanzure> there's a large body of knowledge about embryogenesis if that's what you're asking 17:55 < kanzure> however there are not many people working on artificial wombs or verifying formulae for wombs 17:55 < drazak> kanzure: I'll ask my uncle, he was trained as a developmental biologist, they do fetal surgery and all that 17:55 < kanzure> ok thanks 17:56 < kanzure> the reason why I'm looking for a frame is so that I can figure out whether or not this is feasible or just speculation 17:59 < kanzure> ah they use ventriculosubgaleal shunts (VSG shunts) 18:00 < ecd> man, no shortage of motiviation to work on skdb and such... 18:00 < kanzure> http://www.scielo.br/img/revistas/acb/v22n3/03f1.jpg 18:01 < kanzure> what species is that? 18:04 < ecd> it's not in the paper? 18:04 < kanzure> the image 18:05 < ecd> quoting from the paper: "Twelve mixed breed Hampshire sheep were obtained from an external breeder." 18:05 < ecd> whoops, obviously "Twelve _pregnant_..." 18:06 < kanzure> the image I just linked to :p was saying that "they use VSG shunts" where they=neurosurgeons, not the paper's authors, sorry for the confusion 18:08 < ecd> Still confused, sorry... what species were you asking about? 18:09 < kanzure> the one in the image from the scielo.br link 18:09 < kanzure> nevermind 18:10 < ecd> You were making a joke that the paper's authors were pregnant sheep? :P 18:11 < ecd> Also, how do you read all these papers? Can you just read really fast (practice, or (+) natural ability), or do you have some techniques? 18:12 < kanzure> well the trick is to ignore the bullshit 18:12 < kanzure> but usually I read only the techniques and methods or more if I'm looking for more details 18:13 < kanzure> usually it's more about reading for feasibility information .. "ouch, that looks like a tool I won't be able to make or get my hands on, screw that" 18:13 < kanzure> this narrows down the possibility space quite a bit as you can imagine 18:13 < ecd> heh, hence the anger 18:13 < kanzure> sure 18:14 < ecd> have you built any of the Gingery stuff? (In addition to all the books, I have a pile of clay I dug out of the yard, and an old vacuum cleaner motor, and that's my progress on the furnace.) 18:15 < kanzure> fenn: you want to take that one? 18:15 < ecd> I take it fenn's more mechanically inclined? 18:16 < kanzure> what? 18:16 < kanzure> he built the gingery lathe and something else that I'm forgetting 18:16 < kanzure> but I thikn he'd like to talk about it himself 18:16 < fenn> eh 18:17 < ecd> not exciting? 18:17 < fenn> http://fennetic.net/machines/lathe_modifications 18:18 < fenn> why dont we have tab completion for http location bar yet? :P 18:19 < fenn> query the server for a list of possible urls 18:19 < kanzure> or even just over your history 18:19 < fenn> naw that just gets you a bunch of porn 18:20 < kanzure> you have porn that will match for "lathe"? 18:20 < kanzure> what the fuck man 18:20 < ecd> that's what the ladies call me 18:20 * fenn hides 18:20 < ecd> take that how you will 18:20 < ecd> also, what do you folks use to organize your bookmarks? 18:20 < ecd> just firefox/whatever's built-in search stuff? 18:21 < fenn> bookmarks really ought to be tagged rather than sorted 18:21 < kanzure> http://heybryan.org/bookmarking.html <- an old rant on bookmarking 18:21 < fenn> konqueror doesn't do tags so i'm sort of screwed there 18:21 < kanzure> kbookmarkeditor and firefox and konqueror all crash with my bookmarks these days 18:21 < kanzure> opera is able to load them up with sufficient RAM on a machine, but that's not ideal 18:21 < kanzure> I was thinking of moving to flatfile bookmarks a while back 18:22 < kanzure> should probably get around to doing that I guess :) 18:22 < fenn> ecd: if you're interested in gingery you might enjoy looking around fennetic.net/machines/ 18:23 < fenn> i havent done much with it in a couple years; eventually skdb will import that info 18:23 < ecd> excellent, thanks 18:23 < kanzure> fenn: push yet? 18:23 < fenn> wah 18:24 < fenn> ConstructorError: could not determine a constructor for the tag '!lego_feature' 18:24 < fenn> wtf 18:24 < kanzure> once things get more stable we won't have to push all the time 18:24 < kanzure> weren't you loading a lego_feature object the other day? 18:24 < fenn> it's in metadata.yaml 18:25 -!- kardan_ [n=kardan@p54BE3C9C.dip.t-dialin.net] has quit [Read error: 60 (Operation timed out)] 18:25 < fenn> i mean data.yaml. why is it loading data.yaml? gah 18:53 -!- kardan| [n=kardan@p54BE3C9C.dip.t-dialin.net] has joined #hplusroadmap 19:03 < CIA-38> skdb: fenn * r f4444609eb6c /packages/lego/grammar.yaml: now its a dict of lego.Feature objects 19:03 < CIA-38> skdb: fenn * r b6b0fe10999f /core/interface.py: Interface should be FennObject 19:03 < CIA-38> skdb: fenn * r 8822456e1611 /core/yamlcrap.py: new overlay function for merging objects 19:03 < CIA-38> skdb: fenn * r 5f834520c0bd /core/skdb.py: new functions package_file and load_data; clean up a lot of old file handling code 19:03 < CIA-38> skdb: fenn * r f2c40961610f /packages/lego/ (data.yaml grammar.yaml interfaces.py lego.py metadata.yaml): lego feature grammar works now 19:19 -!- MichaelMaranda [n=Michael@76.223.1.47] has joined #hplusroadmap 19:20 -!- MichaelMaranda [n=Michael@76.223.1.47] has quit [] 19:30 < fenn> sigh. 19:30 < fenn> 'foo' in 'foobar' 19:30 < fenn> True 19:30 < fenn> so 'stud' is compatible with 'anti stud cup' because it contains the string 'stud' 19:43 -!- kardan [n=kardan@p54BE3C9C.dip.t-dialin.net] has joined #hplusroadmap 20:18 < genehacker> ???/ 20:19 < genehacker> stud? 20:19 < genehacker> are you abstracting that high 20:29 < genehacker> oh I get it 20:49 -!- ecd [n=ecd@adsl-226-143-118.int.bellsouth.net] has quit [" HydraIRC -> http://www.hydrairc.com <- Go on, try it!"] 20:54 < CIA-38> skdb: kanzure * r a4ff523f295b /pymates/pymates.py: fix gp_Ax1 orientation parameters and fix list index error in random.randint in pymates 21:13 < ybit> kanzure: i like it (your web browsing exp. idea) 21:19 < fenn> web browsing exp? 21:21 < kanzure> fenn: just an idea to make tabs go away until they are needed 21:21 < fenn> who was ecd? 21:21 < kanzure> the guy I replied to on om 21:27 < ybit> s/exp/system *shrug* 21:28 * ybit doesn't like how beer makes him clumsy 21:28 * ybit would prefer adderall 21:28 < ybit> damn my doc for thinking i need straterra right now -_- 21:29 < ybit> for that sacha girl to be so on top of her email, she sure is taking a long time to respond to me 21:32 < ybit> it's okay though, i'm guessing the scripts she writes about our some of the ones she maintains like remember.el or something like that 21:45 < CIA-38> skdb: kanzure * r 72a288d439bb / (3 files in 2 dirs): key bindings and cycling through different possible combinations of legos (need to implement options() next) 21:48 -!- katsmeow-afk is now known as katsmeow 21:49 < genehacker> hmmm... now I wonder if there are plants that can make nitrous oxide 21:49 < katsmeow> they'd have been popular in the 60's 21:49 < kanzure> nitrogen cyclers? 21:50 < genehacker> plants that make NOx 21:50 < genehacker> and some sort of fuel 21:51 < genehacker> then mix them and take off like a rocket 21:54 < genehacker> or perhaps make some sort of cellulose based potato cannon 21:59 -!- katsmeow is now known as katsmeow-afk 22:08 < ybit> genehacker: what's the name of this microfluidics book you keep talking about 22:14 < genehacker> kanzure has it 22:14 < genehacker> microfluidics history and applications or something 22:14 < genehacker> let me check 22:15 < genehacker> Microfluidics History, Theory, and Applications 22:19 < kanzure> it's on the server 22:19 < kanzure> er, on adl 22:25 -!- kardan| [n=kardan@p54BE3C9C.dip.t-dialin.net] has quit [Remote closed the connection] 22:25 < kanzure> huh ldraw uses a 3x3 matrix 22:30 < fenn> boo 22:30 < fenn> oh wait, nevermind 22:51 < kanzure> sorta kinda have a ldr-to-python converter written 22:55 < genehacker> 3x3 matrix of what? 22:55 < genehacker> crystal structure? 22:56 < genehacker> I mean lego crystal structure can be quite simple 22:59 < fenn> probably position and two orientation vectors 23:00 < genehacker> rotation? 23:00 < fenn> right 23:00 < fenn> orientation == rotation more or less 23:00 < genehacker> euler angles not a quaternion? 23:00 < fenn> yeah 23:01 < fenn> i never figured out quaternions (bad explanations probably) 23:01 < genehacker> BUT THOSE ARE SUSCEPTIBLE TO GIMBAL LOCK? 23:01 < fenn> oh noes 23:01 < genehacker> I haven't either fenn 23:01 < genehacker> do you know the apollo spacecraft was too? 23:01 < fenn> actually orientation vectors don't have gimbal lock 23:01 < genehacker> they had to do special maneveuring to avoid those conditions 23:07 < fenn> Two interpolate between two quaternions, you must interpolate linearly over the surface of the unit hypersphere in four dimensions. 23:07 < fenn> i wonder if i'm supposed to get some sort of enlightenment from that 23:08 < genehacker> the missile knows where it is because it knows where it isn't 23:08 < fenn> there is no missile 23:08 < genehacker> I saw a very funny presentation on missile guidance 23:09 < genehacker> whose unstated purpose was to completely misinform people on missile guidance 23:09 < fenn> e2 is great 23:09 < genehacker> ??? 23:09 < fenn> "quaternion" links to "Everything2 23:09 < fenn> erm 23:09 < genehacker> awesome 23:09 < fenn> "quaternion" links to "roll me over and fuck me again" 23:12 < genehacker> rotation freaks me out 23:15 < fenn> definitive article on the subject http://everything2.com/title/Teenage+genius+computer+hacker+myth 23:17 < genehacker> how big is everything 23:25 < genehacker> http://nostarch.com/mg_electricity.htm 23:25 < genehacker> maybe there's a manga guide to matrix math 23:25 < fenn> i remember when this was funny http://onastick.net/sitz/images/webphone.html 23:28 -!- MichaelMaranda [n=Michael@adsl-76-223-1-47.dsl.chcgil.sbcglobal.net] has joined #hplusroadmap