--- Day changed Fri Aug 07 2009 00:00 < genehacker> jonathan cline? 00:00 < kanzure> yes 00:00 * kanzure sleeps 01:42 < CIA-38> skdb: fenn * reb98868077f8 /core/settings.py: / might not be correct path separator 01:42 < CIA-38> skdb: fenn * r25ecdbcd2c19 /packages/lego/ (grammar.yaml interfaces.py): towards a universal lego description language, F.F. Whiffletoe; 2009. wiley and sons ltd. 04:23 -!- marainein [n=marainei@220.253.58.67] has joined #hplusroadmap 05:19 -!- marainein [n=marainei@220.253.58.67] has quit [Read error: 110 (Connection timed out)] 06:38 < kanzure> can anyone find a copy of "Die Cytoarchitektonik der Hirnrinde des erwachsenen Menschen"? 06:40 < kanzure> english translation of the title: "Cytoarchitectonics of the Adult Human Cerebral Cortex" 06:40 < kanzure> "Two years later, a shorter version, “Zellaufbau der Großhirnrinde” ("The Cellular Architecture of the Cerebral Cortex") was published and translated into French, Italian and English " 06:41 < kanzure> aha: http://content.karger.com/ProdukteDB/produkte.asp?Aktion=showproducts&ProduktNr=233045&searchWhat=books 06:41 < kanzure> that was the 2008 republication 06:41 < kanzure> http://en.wikipedia.org/wiki/Cytoarchitectonics 06:50 < CIA-38> brain: kanzure master * rb480e1f / human_brain.yaml : brodmann areas, general references, search terms, cross-referencing 06:59 < CIA-38> brain: kanzure master * r51c2fb1 / human_brain.yaml : brodmann-area-4 improved - http://bit.ly/SroTh 07:00 < CIA-38> brain: kanzure master * rfbc3b99 / human_brain.yaml : licensing information - http://bit.ly/tvOiq 07:03 < kanzure> meh. 07:03 < kanzure> all of these localization prefixes *suck* 08:18 < kanzure> timschmidt says he'll be cad'ing up the aluminum gingery forge 08:21 < CIA-38> brain: kanzure master * r066467e / human_brain.yaml : lateral hypothalamus reorganization re: supraoptic-nucleus - http://bit.ly/2RwKB 08:23 -!- timschmidt_ [n=chatzill@c-24-11-81-207.hsd1.mi.comcast.net] has joined #hplusroadmap 08:23 < timschmidt_> howdy 08:23 < timschmidt_> So I'm thinking I'm going to start CADing the gingery machines and post results to openmanufacturing 08:23 < ybit> hi there timschmidt_ 08:24 < ybit> sounds like a plan 08:24 < ybit> that would be nice to have 08:24 < timschmidt_> I've also been sourcing steel and AL perf tube, and if I find a decent source, I'll be kitting up my wrench-buildable CNC machine. 08:25 < ybit> kanzure: did you ever find "Cytoarchitectonics of the Adult Human Cerebral Cortex" 08:27 < ybit> glad to have an update from you timschmidt_, i've been wondering what's been in the works over there 08:27 < timschmidt_> in the middle of moving, but still finding time to get things done 08:28 < ybit> looking at my backups from 2 years ago, maybe 10% are even worth my time 08:29 * ybit is off to scan more of mprg 08:29 < timschmidt_> ? 08:29 < ybit> timschmidt_: just a random bit from me, if you stay around long enough, you'll notice it happens often 08:29 < timschmidt_> :) 08:30 < timschmidt_> I find that personal backups are mostly cruft as well, but that last 10% is very valuable. 08:30 < timschmidt_> enough so to justify keeping the cruft around just in case. 08:31 < ybit> alright see you guys on the ssh tunneled flip-side in just a bit 08:43 -!- kardan| [n=kardan@p54BE3550.dip.t-dialin.net] has joined #hplusroadmap 08:47 -!- kardan [n=kardan@p54BE3550.dip.t-dialin.net] has joined #hplusroadmap 08:47 -!- kardan [n=kardan@p54BE3550.dip.t-dialin.net] has quit [Read error: 104 (Connection reset by peer)] 09:35 < kanzure> ybit: no, I didn't find it 09:36 < CIA-38> brain: kanzure master * r6d39d68 / sandbox/placement.yaml : attempts at figuring out how to organize everything - http://bit.ly/35tS18 09:36 < CIA-38> brain: kanzure master * r4d9dddc / sandbox/placement.yaml : keeping some of the better options - http://bit.ly/6Gsk2 09:36 < CIA-38> brain: kanzure master * r1fa1720 / sandbox/directions.yaml : directions (various planes, posterior/anterior, etc.) - http://bit.ly/kfhE 09:36 < CIA-38> brain: kanzure master * reb7987a / sandbox/directions.yaml : added complements and some basic grammar rules - http://bit.ly/rmXyn 09:41 < fenn> brick1 = skdb.load(open('lego/data.yaml'))['parts'][0] 09:41 < fenn> brick2 = skdb.load(open('lego/data.yaml'))['parts'][0] 09:41 < fenn> pymates.start(); pymates.mate_parts(brick1, brick2) 09:42 < kanzure> http://neurolex.org/wiki/Main_Page ? 09:42 < kanzure> ok I'll run that 09:42 < CIA-38> skdb: * r530fdfcaf53e / (import_tools/heeks_coords.py packages/lego/data.yaml): it's point, not origin. add pointer to interface's part. not happy about this 09:42 < CIA-38> skdb: * rbbe8618758de /packages/lego/data.yaml: typo 09:42 < CIA-38> skdb: * r377b4c55a2ca /pymates/pymates.py: Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb 09:42 < CIA-38> skdb: * r8d89f97016a2 /pymates/pymates.py: Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb 09:42 < CIA-38> skdb: * r2b6dd658d54b / (4 files in 3 dirs): Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb 09:42 < CIA-38> skdb: * rfb20481f70f6 /packages/lego/interfaces.py: oops 09:43 < kanzure> timestamps please 09:43 < kanzure> "from skdb.packages import lego" didn't work for you? 09:44 < fenn> go away 09:52 < kanzure> where should CAD loading code go? 09:52 < kanzure> in Part()? 09:52 < kanzure> or in pymates.py somewhere random? 09:54 < kanzure> fenn: ok it works actually 09:54 < kanzure> fenn: the problem is that you need to run brick1.load_CAD() 09:55 < kanzure> after I push 09:55 < fenn> why doesn't it just do that automatically? 09:55 < CIA-38> skdb: kanzure * rdf7a0a83b009 /pymates/pymates.py: syntax error with numpy 09:55 < kanzure> fenn: because I didn't know about the try-statement 09:55 * kanzure goes to add it 09:56 < kanzure> it seems that there is a path error however in the current code 09:56 < kanzure> it can be resolved by setting the path to the step file in the lego/data.yaml file to be "packages/lego/something.stp" 09:57 < kanzure> or by fixing load_CAD() ideally 09:57 < kanzure> huh why isn't the initializer running for Part()? 09:57 < kanzure> didn't I do this yesterday? where a FennObject calls the __init__() method? 09:57 < kanzure> __init()__ 09:58 < fenn> __init__() 09:58 < kanzure> er, yes 09:59 -!- kardan_ [n=kardan@p54BE670A.dip.t-dialin.net] has joined #hplusroadmap 10:00 < ybit> kanzure: what are your plans for the brain coordinate system? 10:00 < kanzure> ybit: did you see human_brain.yaml yet? 10:00 < ybit> yup, good stuff 10:00 < kanzure> maybe the coordinates and voxels or bounding boxes would be some attributes for particular regions 10:01 < kanzure> or, more usefully, the mapping could go the other way (bounding boxes -> region names) 10:01 < ybit> 09:56 < kanzure> er, yes 10:01 < ybit> 09:56 < kanzure> er, yes 10:01 < ybit> argh 10:01 < ybit> right click pastes it seems in putty 10:03 < kanzure> I could have sworn I added something like cls.__init__() yesterday 10:09 < fenn> why are the args to Package commented out? 10:09 < ybit> this is a ghetto setup i have going on here, the scanner lid is taped to the drawer, the book is held down by a pack of 50 cd-rs and a bottle of 100 fl oz dish detergent 10:10 < kanzure> fenn: because at some point we were calling Package.__init__() or something in yamlcrap.py (not Package in particular, just cls.__init__() or something) 10:10 < kanzure> but for some reason that's not there today? I don't know how this happened 10:10 < ybit> it works and my left arm isn't cramping 10:10 < kanzure> the only thing that comes to mind is that yesterday I mentioned something about not having checked an automerge 10:10 < kanzure> maybe something got deleted during an automerge? 10:10 < ybit> timschmidt_: ^ see random 10:10 < ybit> happens all the time 10:10 < timschmidt_> gotcha 10:12 < ybit> kanzure: how's uzbl working out for you? have you tried any of the scripts? anyone else using it? 10:12 -!- kardan| [n=kardan@p54BE3550.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] 10:13 < kanzure> brick2.files = ["packages/lego/brick_thick_round.stp"] 10:13 < CIA-38> skdb: fennetic.net> * r7c30198c622a /core/ (skdb.py units.py): FennObject classes should take no arguments, i guess 10:13 < CIA-38> skdb: fennetic.net> * r7e429188e2ad /pymates/pymates.py: Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb 10:13 < fenn> bah 10:13 < kanzure> then pymates.mate_parts(part1=blah, part2=blah) 10:13 < ybit> i've got a nice setup at the house with uzbl using the grid select xmonad module to handle tabs 10:13 < kanzure> grid select? 10:14 < ybit> http://blog.clemens.endorphin.org/2008/11/xmonad-gridselect.html 10:15 < fenn> grid select is only useful if your windows have proper titles 10:16 < fenn> at least show an icon or something 10:16 < ybit> you can tag your windows with titles 10:16 -!- freedom_ [n=freedom@195.216.211.175] has joined #hplusroadmap 10:16 < fenn> oh, yeah, right. ~ 10:16 -!- Phreedom [n=freedom@195.216.211.175] has quit [Read error: 113 (No route to host)] 10:16 < kanzure> fenn: yesterday you suggested that I write some code to make something happen when it's loaded into yaml 10:17 < kanzure> so I did, and I made FennObject always call the init method of the cls 10:17 < kanzure> and I even said "yay" afterwards 10:17 < fenn> ok 10:17 < kanzure> now where is that code? 10:17 < fenn> is it in the log? 10:17 < ybit> and i've yet to try this, but i'm planning on grouping the tabs using color sequence and grid alighment according to subject 10:17 < fenn> git log -p 10:17 < fenn> group according to subject == workspace 10:18 < ybit> workspace 2 = tabbed webspace 10:18 < fenn> webspace? 10:18 < ybit> i just made it up 10:18 < fenn> webspace 2.0? 10:18 < ybit> :) 10:19 < fenn> next you'll be trying to sell me a cloud manager 10:19 < kanzure> ybit: you should let groups of tags be managed by particular agents/daemons 10:19 * fenn has visions of tags being dipped in boiling mud and eaten alive by devils 10:20 < fenn> why is this regex returning "fennetic.net>" instead of "fenn"? ($user) = $author =~ /<(.*?)[@ ]/ 10:20 < kanzure> what is the value of $user and $author? 10:20 < kanzure> why is there a space after the @? 10:21 < fenn> this line gets split and put into author author fenn 1249656073 -0500 10:21 < fenn> split(/ /, $line, 2) 10:22 < fenn> er, the line was "author fenn blah blah" 10:22 < kanzure> well it's expecting < 10:22 < ybit> hi freedom_ 10:22 < fenn> shouldnt that put "fenn" into author in the first place? 10:22 < kanzure> no 10:22 < kanzure> the regex explicitly wants < 10:22 < kanzure> did you write this expression? 10:22 -!- timschmidt__ [n=chatzill@c-24-11-81-207.hsd1.mi.comcast.net] has joined #hplusroadmap 10:22 < fenn> sort of 10:23 < fenn> it was /<(.*?)@/ 10:23 < kanzure> that's stupid 10:23 * fenn adds do this: /author (.*?) <(.*?)@/ 10:23 < kanzure> but do whatever you have to do to make it greedy or not greedy 10:23 < kanzure> not sure which one it should be 10:24 < kanzure> you want the one after "author", not the crap in the brackets 10:24 < fenn> i'm not sure other people's fields look like mine 10:24 < kanzure> I think mine looks like this: 10:24 < kanzure> author kanzure 10:25 < kanzure> so it gets "kanzure" from the email address 10:25 < kanzure> which happens to be the username as well 10:25 < kanzure> so it looks like it passed 10:25 < kanzure> no, wait, that doesn't explain how it handles Smari's commits. 10:26 < fenn> what does git cat-fileauthor Smári McCarthy 1248649606 +0000 10:26 < fenn> oops 10:27 < fenn> $author =~ /author (.*?) wasn't in git log -p 10:28 < fenn> you must not have committed it then 10:28 < fenn> just rewrite it alreday 10:28 < kanzure> ah the problem is with part.py /me fixes 10:35 < kanzure> the problem is that the __init__ is being called before all of the attributes are assigned 10:37 < fenn> i think that's what you want 10:37 < fenn> because otherwise init will set everything to None (usually) 10:37 < kanzure> I'm trying to add load_CAD() to the init 10:37 < kanzure> so I've added a __post_init__() 10:37 < fenn> maybe you want post_setstate_hook instead 10:40 -!- timschmidt_ [n=chatzill@c-24-11-81-207.hsd1.mi.comcast.net] has quit [Read error: 110 (Connection timed out)] 10:49 < kanzure> __setstate__ is never being called 11:11 < kanzure> import skdb; import skdb.pymates as pymates; from skdb.packages import lego; import yaml 11:11 < kanzure> brick1 = skdb.load(open('packages/lego/data.yaml'))['parts'][0] 11:12 < kanzure> it's all custom code 11:12 < kanzure> various prints for debugging 11:12 < fenn> what do you get for foo = skdb.load(open('packages/lego/metadata.yaml')).urls 11:12 < kanzure> an error because files isn't a list 11:13 < fenn> ok fix your code and try again 11:13 < kanzure> you were the one telling me not to edit part.py I might add :p 11:13 < kanzure> dict object has no attribute "urls" 11:13 < kanzure> I think you meant ["urls"] 11:13 < fenn> no 11:14 < fenn> it should return a package object 11:14 < kanzure> KeyError: "!Peg" 11:14 < fenn> you get that when loading? 11:14 < kanzure> yes 11:14 < fenn> works for me, so must be whatever you just did 11:15 < fenn> i get KeyError: "!Peg" when i do yaml.dump(foo) 11:15 < kanzure> I get: ValueError: invalid null reference in method 'TopoDS_Shape___eq__', argument 2 of type 'TopoDS_Shape const & 11:16 < kanzure> oh 11:16 < fenn> i bet that just means you passed it an empty file 11:16 < kanzure> it's trying to print out "shapes" 11:16 < kanzure> so it's not playing nicely with yaml and opencascade 11:18 < fenn> i also get empty lists before return in from_yaml 11:18 < fenn> maybe yaml constructs the objects top-down 11:18 < kanzure> does this crap happen on last week's commits? 11:19 < fenn> what crap? 11:19 < kanzure> not loading sequences 11:19 < kanzure> I don't think yaml does that because yaml.load("blah:\n-blah1\n-blah2") does not give you a blank 11:19 < fenn> sequences work fine, just not in the middle of from_yaml 11:19 < fenn> for me, with today's code 11:20 < fenn> skdb.load blows up the second time you run it 11:21 < kanzure> I'm fairly certain it didn't do that last week 11:29 < CIA-38> skdb: * rb29b50a58e4a /core/yamlcrap.py: fix check for tag in yaml_multi_constructors 11:30 < fenn> stupid bot 11:33 < kanzure> Use of uninitialized value $user in concatenation (.) or string at /var/www/skdb.git/ciabot_git.pl line 193. 11:34 < CIA-38> skdb: * r1d470e57e700 /core/ (part.py yamlcrap.py): debugging core 11:34 < CIA-38> skdb: * ra4314b01c523 /core/yamlcrap.py: Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb 11:46 < fenn> in fennobject: return cls() is where cls.__init__() is called 11:48 < kanzure> why is process a scalar :p 11:49 < fenn> it's not 11:53 * fenn looks expectantly at CIA-38 11:55 < CIA-38> skdb: test test * rster /core/yamlcrap.py: Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb 11:58 < kanzure> rster? 12:00 < kanzure> fenn: you can test perl with perl -e 12:01 < fenn> perl question: wtf does $foo =~ /blah(.*)blah/ do? 12:01 < kanzure> matches anything in between blah and blah, and sets foo to that anything 12:02 < fenn> well, it doesn't 12:02 < fenn> print($author."\n"); $author =~ /(.*) kanzure 1249662478 -0500 12:03 < fenn> kanzure 1249662478 -0500 12:03 < fenn> is '<' special? 12:07 < kanzure> ($use_this_part) = $some_string =~ s/^(.*) i shouldnt have to do this? $foo =~ s/(.*) <.*/\1/; 12:08 < kanzure> perl -e "\$foo = 'blahhelloblah '; (\$blah2) = \$foo =~ /^(.*) skdb: kanzure test * r ster /core/yamlcrap.py: Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb 12:13 -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: bkero 12:13 < kanzure> ($blah) = $str = regex 12:14 -!- Netsplit over, joins: bkero 12:15 < kanzure> kinda need __setstate__ to work 12:20 < kanzure> I'm still concerned that __setstate__ isn't being set 12:22 < CIA-38> skdb: kanzure * r d409ee45efed / (core/part.py pymates/pymates.py): move around load_CAD call 12:22 < kanzure> \1 better written as $1 at /var/www/skdb.git/ciabot_git.pl line 160. 12:23 < fenn> any particular reason why? 12:23 < kanzure> that was what perl told me 12:23 < fenn> well since everything else uses \1 i tend to use \1 12:26 < CIA-38> skdb: kanzure * r c536faad9d19 /core/ (part.py yamlcrap.py): cleaning up print statements 12:37 < drazak> kanzure: who is tito whatever and what does he do? 12:38 < kanzure> he's a surfer/model in california 12:38 < kanzure> he claims to be starting a company called "Pearl Biotech" for open source diybio hardware 12:38 < kanzure> however his company has failed to produce schematics for a gel box in the past year and a half 12:38 < kanzure> so I'm not really convinced :( 12:38 < kanzure> he used to be on the Brown University iGEM team 12:39 < drazak> huh 12:39 < drazak> so has he really spent much time in a lab? 12:39 < drazak> I mean, the iGEM thing is time in a lab, but it's not that much 12:40 < kanzure> he claims that his team constructed some lab equipment 12:40 < kanzure> but he ran away when I asked him to elaborate 12:40 < kanzure> honestly I think he's a load of crap 12:40 < drazak> me too 12:40 < drazak> I see him posting shit 12:40 < drazak> but he never actually explains everything 12:40 < drazak> he's very vague 12:41 < kanzure> the only reason I don't call him out is that he's good friends with mac 12:41 < kanzure> and they both want to hate me very badly 12:41 < kanzure> so if I call him out and call his stuff shit, that will backlash easily 12:41 < drazak> of course you probably think I'm full of shit 12:41 < kanzure> if you want to call him out, by all means 12:41 < drazak> nah 12:41 < kanzure> to a lesser extent than tito 12:41 < drazak> I've made two posts on the list 12:41 < kanzure> so? 12:41 < drazak> give it a few hundred posts 12:41 < kanzure> oh 12:41 < kanzure> okay 12:41 < drazak> and then I'll call him out 12:42 < drazak> man, I'm gonna have so many dishes of MSCs 12:42 < drazak> I dunno what to do with them? 12:42 < drazak> 4 dishes plain, 4 with fibronectin, 4 with collagen, 4 with laminin 12:49 < kanzure> yeah he's full of it 12:49 < kanzure> http://www.pearlbiotech.com/2~ 12:49 < kanzure> er 12:49 < kanzure> http://www.pearlbiotech.com/ 12:49 < kanzure> that's clearly a CAD file 12:49 < kanzure> it's even in the file name of the image 12:49 < kanzure> and there's a "buy it now" button 12:49 < kanzure> so much for diybio 13:00 < kanzure> the development branch of bpython seems somewhat stable 13:05 < kanzure> import skdb; import skdb.pymates as pymates; from skdb.packages import lego; import yaml; brick1 = skdb.load(open("packages/lego/data.yaml"))["parts"][0]; brick1.load_CAD(); 13:05 < kanzure> AttributeError: 'Lego' object has no attribute 'package' 13:05 < kanzure> the fix is to do skdb.load_package("lego") first 13:05 < kanzure> is this expected? 13:12 < kanzure> I think skdb.dump() should cleverly get rid of any attribute named "package" or something- so that we don't get a recursion error from yaml 13:13 < fenn> i think you should think of a better way to do it 13:13 < kanzure> bah 13:13 < kanzure> fine. 13:14 < fenn> does load_package('package') do import package? 13:14 < kanzure> load_package is in the same file as the class Package 13:15 < fenn> no, i mean does load_package('foo') do import foo 13:15 < kanzure> no 13:16 < fenn> shouldnt it? 13:16 < kanzure> no 13:16 < kanzure> it calls skdb.load() 13:16 < kanzure> and does a few other things 13:16 < kanzure> it should read the package based off of the metadata 13:16 < fenn> well this string 'foo' ought to be somewhere 13:16 < kanzure> oh I've fixed it 13:16 < kanzure> just let me come up with a witty commit message 13:17 < CIA-38> skdb: kanzure * r 0d5261b17be6 / (core/part.py core/skdb.py packages/lego/data.yaml): got rid of some nasty recursion 13:37 < fenn> screw/metadata.yaml has classes: [screw.Screw, threads.Thread] 13:40 < kanzure> lego_package = skdb.load_package("lego") 13:40 < kanzure> some_new_screw = lego_package.Screw() 13:41 < kanzure> loaded_screw = skdb.open(open("packages/lego/data.yaml"))["parts"][0] 13:42 < kanzure> er, sorry 13:42 < kanzure> loaded_screw = skdb.load(open("packages/lego/data.yaml"))["parts"][0] 13:42 < ybit> tito's cad file is a google sketchup file 13:42 < kanzure> where? 13:43 < ybit> http://www.pearlbiotech.com/wp-content/uploads/2009/05/pearl_biotech-gel_box_cad.skp 13:43 < ybit> in the hardware tab 13:43 < kanzure> so after all this time of me asking him 13:43 < kanzure> and he could have just given me a link? 13:43 < kanzure> or said "it's on the site" 13:43 < kanzure> but he didn't? what does this mean? 13:44 < kanzure> 鮻쫊琢 awesome file format 13:45 < fenn> why would lego_package have Screw? 13:46 < kanzure> because I don't want to say lego_pack.lego.lego.lego.lego.my.ego 13:46 < kanzure> it currently works btw 13:48 < fenn> this works atm: foo = skdb.load_package('lego'); foo.Lego() 13:48 < kanzure> right 13:49 < kanzure> oh 13:49 < kanzure> screw 13:49 < kanzure> yes, lego_package would not have Screw 14:13 < drazak> rawr ncbi is slow 14:23 < CIA-38> skdb: fenn * r fecb6ed58b39 / (3 files in 3 dirs): rewrite import_package_classes, restructure metadata for required classes and modules 14:26 < CIA-38> skdb: kanzure * r 96b3048a949c /pymates/ (pymates.py rapid-test.py): pymates works with packages now, see rapid-test.py or run the contents of rapid-test.py in a pymates/shell.sh session 14:26 < kanzure> drazak: you can download ncbi via ftp.ncbi.nih.gov or something 14:27 < kanzure> fenn: NameError: global name 'new_import_package_classes' is not defined 14:28 < CIA-38> skdb: fenn * r a28c44592214 /core/skdb.py: oops 14:28 < CIA-38> skdb: fenn * r b49390702423 /pymates/ (pymates.py rapid-test.py): Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb 14:30 < kanzure> fenn: why don't my parts have package_path in them now? 14:30 < kanzure> AssertionError: Part.load_CAD doesn't have its package loaded. 14:31 < kanzure> /home/kanzure/code/skdb/core/part.pyc in load_CAD(self) 14:40 < fenn> how is package_path not the same as Package('foo').path()? 14:42 < kanzure> how does it know what package it is from 14:42 < kanzure> if you don't tell it? 14:43 < fenn> package_path is just some conglomination of os.path calls 14:43 < fenn> based on settings.py and the string passed to load_package 14:43 < kanzure> so what 14:43 < fenn> Package.path() appears to be the same thing? 14:44 < kanzure> so what? 14:44 < kanzure> part does not inherit from Package 14:44 < kanzure> it's ok, I've fixed it 14:44 < fenn> no wait, tell me what's going on 14:46 < kanzure> you just forgot to do setattr(module, "package_path", package_path) is all 14:46 < kanzure> hm and that didn't fix it 14:46 < fenn> but don't you want path in your Part objects? 14:47 < kanzure> no, I want package_path in my Part objects 14:47 < fenn> where does Part get package_path? 14:47 < kanzure> import_package_class 14:47 < kanzure> import_package_classes 14:48 < fenn> but Part doesnt have anything to do with import_package 14:48 < kanzure> why the hell not 14:48 < kanzure> what have you done to it 14:48 < fenn> untangled it 14:48 < kanzure> and fucked it up in the process 14:48 < fenn> yep 14:48 < kanzure> .. 14:48 < kanzure> so how is this better? 14:48 < fenn> it's not tangled 14:49 < kanzure> your clairvoyance hasn't given you the stolen data plans 14:49 < kanzure> Admiral Motti: "Don't try to frighten us with your sorcerer's ways, Lord Vader. Your sad devotion to that ancient religion has not helped you conjure up the stolen data tapes, or given you clairvoyance enough to find the Rebel's hidden fortre..." 14:49 < fenn> so, er.. is Part supposed to be in package.classes? 14:49 < kanzure> no 14:50 < kanzure> wait, what is package.classes? 14:50 < kanzure> Package.classes ? 14:50 < fenn> i dont see anything about Part in load_package in any revision 14:50 < fenn> it's just a list of classes from metadata 15:17 < genehacker> speaking of stolen dataplans, I'm willing to bet that the deathstar's cad files are all in .iges and you could easily fit those on a droids 20 tb datadrive 15:21 < genehacker> http://www.youtube.com/watch?v=5sVOSlUn7e0 15:24 < genehacker> inefficient but entertaining 15:40 < CIA-38> skdb: kanzure * r 14169113bb60 /core/skdb.py: cleanup 15:42 < CIA-38> skdb: fenn * r 60697322e6b4 / (9 files in 3 dirs): fix various package loading bugs; moved threads to a new package 15:42 < CIA-38> skdb: fenn * r 12ef8923beca /core/skdb.py: Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb 15:45 < CIA-38> skdb: kanzure * r 728ae6016175 /core/part.py: make load_CAD work with the new Part().__class__.package attribute 16:04 < CIA-38> skdb: fenn * r dd3a5c3a4e3d / (3 files in 2 dirs): probably busted, bryan's fault if so :P 16:15 -!- kardan_ [n=kardan@p54BE670A.dip.t-dialin.net] has quit [Remote closed the connection] 16:20 < drazak> kanzure: that's stupid 16:20 < drazak> kanzure: also: why would I want to download NCBI to a work computer that I don't even ahve a login for yet 16:21 < genehacker> download NCBI? 16:21 < genehacker> good idea 16:21 < drazak> bad idea 16:21 < drazak> it's motherfucking giant 16:21 < genehacker> I've got some worries about will become of them in the event of the zombie apocalypse 17:00 < bkero> Psh 17:00 < bkero> NCBI's not that big 17:00 < bkero> I've got 150 LTO-4 tapes sitting on my desk. 17:02 < genehacker> what are those? 17:02 < bkero> 2TB tapes 17:02 < genehacker> what do you mean 2 TB tapes? 17:02 < bkero> 2000GB can fit on each tape. 17:03 < genehacker> you mean to tell me that you have 300 TBs of data 17:03 < bkero> Well, they're blank now 17:03 < bkero> But I will 17:04 < genehacker> wow 17:04 < genehacker> do you seed bkero? 17:05 < genehacker> you could download nearly every song and every computer game 17:06 < kanzure> nearly!~ 17:08 < genehacker> so kanzure you are downloading NCBI? 17:08 < genehacker> the whole thing? 17:09 < genehacker> I think that is a rather good idea 17:09 < genehacker> there is a high probability that access to NCBI could be restricted in the future 17:12 < kanzure> I have offshore servers that have complete backups of NCBI 17:12 < kanzure> also complete backups of the korean equivalent of NCBI 17:14 < genehacker> excellent 17:14 < genehacker> just as planned 17:14 < kanzure> 05:27:50 omg/user: jules: i have heard that there is a programming language from japan whe re the programs are made entirely out of adjunctions 17:14 < genehacker> do you know why NCBI might become restricted in the future? 17:14 < kanzure> ybit: have you considered letting daemons manage tabs? 17:27 < fenn> cute robots 17:27 < fenn> i wonder who fills up the little pans of stuff 17:28 -!- kardan| [n=kardan@p54BE670A.dip.t-dialin.net] has joined #hplusroadmap 17:50 < kanzure> fenn: internet might be slow for a few minutes 17:50 < kanzure> complain if it's an issue 17:50 < fenn> wah! 17:51 < fenn> i wonder if "kelly alioth drinkwater" really is her real name 17:51 < kanzure> heh is it wrong that I wondered if "alioth" was what was supposed to be weird with that? 17:52 < kanzure> alioth is the name of some uk scientific paper retrieval service / proxy-ealy 17:52 < kanzure> *dealy 17:52 < fenn> it's a star, and also some prominent debian development server 17:52 < fenn> (Epsilon Ursae Majoris). It derives from the Arabic alyat, "fat tail of a sheep" 17:54 < kanzure> "The "End of Greatness" is an observational scale discovered at roughly 100 Mpc (roughly 300 million lightyears) where the lumpiness seen in the large-scale structure of the universe is homogenized and isotropized as per the Cosmological Principle. The superclusters and filaments seen in smaller surveys are randomized to the extent that the smooth distribution of the universe is visually apparent. It wasn't until the redshift surveys of the 1990s were completed that this scale could accurately be observed.[3]" 17:54 < fenn> apparently it's not her real name (if anyone cared) 17:55 < fenn> the Cosmological Principle is that everything is boring if you look far enough away? 17:56 < kanzure> galaxyfilament.org is available 17:57 < fenn> sign me up scotty 18:16 < fenn> "Medical Algorithms"? 18:17 < fenn> also, since when did 'full text' turn into 'download pdf' 18:18 < fenn> "A medical algorithm is any formula, score, scale, diagram, or computational technique that is useful in healthcare. Examples of medical algorithms include the Glasgow coma scale, TNM stage in oncology, and predictive risk factors for heart disease." 18:19 < fenn> 13500 spreadsheets seems a little excessive 18:22 < fenn> bah. why do they want me to register 18:23 < kanzure> what's sad is that health decisions are sometimes made based off of these spreadsheet macros 18:24 < fenn> i think it's a good idea (not sure about the implementation) 18:32 < kanzure> nice numbers: http://en.wikipedia.org/wiki/Cortical_minicolumn 18:33 < kanzure> er, what? # Thalamic input (1 axon) reaches 100–300 minicolumns. 18:36 < kanzure> units '635 microns^2 * 2 * 10^8' 'm^2' 18:37 < kanzure> so 0.127 m^2 of minicolumnar surface area 18:37 < kanzure> not sure how to calculate the effective surface area due to a certain number of gyri or sulcri (folds) 18:47 < kanzure> "we determined that the deep layers of gyri are just as densely populated with neurons as the deep layers of sulci. And because the deep layers of gyri are thicker, there are actually more neurons under a unit area in gyri than in sulci." 18:48 < kanzure> "Moreover, the shapes of individual neurons differ depending on where in the cortex they reside. Neurons situated in the deep layers of gyri, for example, are squeezed from the sides and appear elongated. In contrast, neurons located in the deep layers of sulci are stretched and look flattened. The shapes of these cells are consistent with having been modified by mechanical forces as the cortex folded. It will be an intriguing challenge to figure out whether such systematic differences in the shapes of neurons in gyri and sulci also affect their function." 18:48 < kanzure> http://www.scientificamerican.com/article.cfm?id=sculpting-the-brain&page=3 18:50 < kanzure> "People diagnosed with autism also exhibit abnormal cortical convolutions. Specifically, some of their sulci appear to be deeper and slightly out of place as compared with those of healthy subjects." 18:52 < kanzure> query: sulci gene expression 18:52 < kanzure> not getting much 18:57 < kanzure> "cerebral gyrification" heh 18:58 < kanzure> "genetic contributions to human gyrification" - http://www.jneurosci.org.ezproxy.lib.utexas.edu/cgi/content/full/25/34/7840 19:03 < kanzure> "gyral flattening and sulcral narrowing" leads to cerebral edema? hrm.. 19:06 < fenn> "overclocked computers have been observed to exhibit abnormal features such as pronounced heatsinks and blue LED's" 19:06 < fenn> (my opinion of neuroanatomy) 19:24 < kanzure> a test of the mechanical folding hypothesis: http://cercor.oxfordjournals.org.ezproxy.lib.utexas.edu/cgi/content/abstract/1/5/426 19:33 < CIA-38> brain: kanzure master * r452542f / human_brain.yaml : neocortex, mess stuff up - http://bit.ly/VNOiF 19:33 < CIA-38> brain: kanzure master * ra30b513 / human_brain.yaml : sulci and gyrification - http://bit.ly/8Nt2n 19:33 < kanzure> "Regulation of cerebral cortical size by control of cell cycle exit in neural precursors" 19:33 < kanzure> http://adl.serveftp.org/papers/Regulation%20of%20cerebral%20cortical%20size%20by%20control%20of%20cell%20cycle%20exit%20in%20neural%20precursors.pdf 19:38 < kanzure> fun search query: "transgenic brains" 19:38 < genehacker> kanzure can I get those papers on neural matrices or something 19:38 < genehacker> part of the brain that keeps track of where things are that we were talking about the other day 19:41 < kanzure> what? 19:41 < kanzure> about keeping track of what you were talking about? 19:41 < genehacker> no of stuff in a 3d space 19:42 < kanzure> oh the cat thing 19:42 < kanzure> hm 19:42 < genehacker> I think that was it 19:42 < kanzure> didn't save any papers yesterday :(* 19:43 < kanzure> http://www.sciencemag.org.ezproxy.lib.utexas.edu/cgi/content/abstract/297/5580/365 19:44 < kanzure> enlarged diagram: http://www.sciencemag.org.ezproxy.lib.utexas.edu/content/vol297/issue5580/images/large/se2820695003.jpeg 19:44 < fenn> scary 19:47 < kanzure> ok stolen: http://adl.serveftp.org/papers/Regulation%20of%20cerebral%20cortical%20size%20by%20control%20of%20cell%20cycle%20exit%20in%20neural%20precursors.pdf.png 19:48 < fenn> bonus points for whoever figures out where the nose went, and what those little wormy things are 19:49 < genehacker> blargh 19:49 < genehacker> that's not what I'm looking for 19:50 < genehacker> time to start logging chat I guess 19:50 < fenn> $$ but still neato http://www.voxel-man.de/3d-navigator/brain_and_skull/images/bs_ventrikel-englisch.jpg 19:51 -!- genehacker_ [n=chatzill@pool-173-57-41-223.dllstx.fios.verizon.net] has joined #hplusroadmap 19:57 < genehacker> it's not stolen, it's copied 19:58 < genehacker_> chatzilla can logchat right? 19:58 < fenn> "The data may be bought on tape or downloaded free of charge; one has to specify the intended use and sign a license agreement that allows NLM to use and modify the resulting application. NLM can cancel the agreement at any time, at which point the user has to erase the data files." 19:58 < fenn> (re: visible human project) 19:59 < fenn> genehacker_: here's a nickel, kid. get yourself a real IRC client 19:59 < genehacker_> A NICKEL? 19:59 < fenn> 20:00 < genehacker> a link to sourceforge would have been better 20:01 < fenn> sudo apt-get install irssi 20:02 < fenn> or at least x-chat, jeez 20:02 < genehacker> I've been logging chat the whole time 20:02 < genehacker> and I didn't even know it 20:02 < fenn> god bless those engineers at the CIA 20:03 -!- genehacker_ [n=chatzill@pool-173-57-41-223.dllstx.fios.verizon.net] has quit ["ChatZilla 0.9.85 [Firefox 3.0.13/2009073022]"] 20:06 < fenn> woah 20:06 < fenn> http://en.wikipedia.org/wiki/File:Vishumancolor.jpg 20:07 < genehacker> what's the res on that? 20:07 < fenn> it didnt look that good in 1998 20:07 < genehacker> yeah 20:08 < fenn> i never noticed the scars or messed up nose or tattoos 20:29 < genehacker> the guy they scanned was a prisoner 20:31 < fenn> so much for getting the data 20:32 < genehacker> you don't need a nose now do you? 20:45 < fenn> the visible human data isn't online anywhere 20:48 < genehacker> WHAT? 21:13 < kanzure> ASPM genes? 21:13 < kanzure> "human accelerated regions" (HARs) 21:13 < kanzure> hah 21:17 < fenn> 5~count me skeptical 21:18 < genehacker> genes that change a lot? 21:18 < fenn> i dont believe there's anything special about human biology 21:20 < genehacker> me either 21:20 < kanzure> "Recent acceleration of human adaptive evolution" 21:25 < genehacker> oh that paper? 21:25 < genehacker> that says our genomes are changing faster 21:27 < kanzure> CDK5RAP2, CENPJ, ASPM, microcephalin, ADCYAP1, AHI1 (for axon guidance), FOXP2, SHH (sonic hedgehog), MAOA, MRG, GLUD1, GLUD2, opsin, MYH16, PDYN, HAR1 21:58 < kanzure> axon guidance receptor gene ROBO1 22:01 < drazak> I know a bit about SHH 22:02 < genehacker> and not the videogame character I assume? 22:03 < drazak> it's a signaling gene 22:03 < drazak> related to wnt and stat iirc 22:20 < genehacker> yeah I know 22:29 < kanzure> "Turning blood into brain" ? 22:29 < drazak> craq 22:30 < drazak> hemapoeitic cells aren't related to the neural lineage 22:38 < genehacker> ??? 22:39 < kanzure> Neural stem cell culture expansion 22:39 < kanzure> under VEGF receptor blockade 22:39 < kanzure> hm. 22:39 < kanzure> who was complaining about VEGF the other day? 22:44 < drazak> me 22:44 < drazak> we do a lot of work with vegf 22:45 < drazak> and my uncles thesis was on it 22:46 < drazak> what' 22:46 < drazak> er, what'd they do, make a siRNA for VEGFR2? 22:47 < drazak> or did they use an inhibitor? 22:47 < drazak> and were they nerual crest stem cells? 22:51 < ybit> 17:12 < kanzure> ybit: have you considered letting daemons manage tabs? 22:52 < ybit> explain 22:55 < kanzure> huh type 1 diabetes solved by transplantable pancreatic islets 22:57 < ybit> don't try avoiding this topic :D 22:59 < drazak> kanzure: can you link me to the paper where they did this, I'm very interested, and would also like to share it with my PI and someone else in my lab 23:01 < drazak> not the diabetes paper 23:01 < drazak> the other one 23:16 < kanzure> 1Instituto de Neurociencias de Alicante. Universidad Miguel Hernández-CSIC, Campus de San Juan, Apt 18, San Juan de Alicante, Alicante 03550, Spain 23:16 < kanzure> Gene delivery into mouse retinal ganglion cells by in utero electroporation 23:16 < kanzure> http://www.pubmedcentral.nih.gov.ezproxy.lib.utexas.edu/articlerender.fcgi?tool=pmcentrez&artid=2080638 23:16 < kanzure> oh look it's CC 23:16 < kanzure> even though it's close to torturous 23:19 -!- doubting-thomas [n=Vox@97.93.221.49] has joined #hplusroadmap 23:19 < doubting-thomas> Hello. 23:21 < kanzure> Hey doubting-thomas. 23:21 < kanzure> what's up? 23:22 < doubting-thomas> Just bored, yourself? 23:22 < kanzure> ybit: different daemons/agents could manage tabs differently. 23:22 < kanzure> doubting-thomas: reading some neuroscience. 23:22 < drazak> kanzure: dude you're nuts, that doesn't even mention vegf 23:23 < kanzure> drazak: that's not what the paper was 23:23 < kanzure> it's long gone 23:23 < drazak> well find it for me 23:23 < drazak> it existed once 23:23 < drazak> ! 23:24 < kanzure> just search for "under VEGF receptor blockade" 23:24 -!- doubting-thomas [n=Vox@97.93.221.49] has quit ["Leaving"] 23:24 < genehacker> don't electroporators use aluminium plates? 23:25 < drazak> sometimes 23:25 < kanzure> IIRC, you can do electroporation with a needle 23:26 < genehacker> never heard of it 23:26 < genehacker> is it a titanium needle? 23:27 < genehacker> I need a titanium or copper needle 23:28 < drazak> kanzure: it's been known for a long time that vegf is related to neurogenesis, what happens is that nerved and endothelium grow into eachother in cell culture conditions for angiogenesis 23:29 < genehacker> so what can we do with all of this? 23:29 < genehacker> build brain bots? 23:29 < drazak> 3 or 4 of the reviews that i've read mention that as a problem with invitro vascularization of tissue 23:29 < genehacker> growing blood vessels in tissue culture? 23:30 < genehacker> now you have my attention 23:30 < drazak> uhm 23:30 < drazak> well it's been known that if you want to grow skeletal muscle as more than a monolayer or unstable myotube, you have to vascularize it 23:30 < drazak> so basically you have endothelial cells, smooth muscle cells, and soem sort of basement membrane 23:31 < drazak> well, the basement membrane is extraneous 23:31 < drazak> what happens is if you coculture smooth muscle and endothelial cells, the endothelial cells start to form a vascular network 23:31 < drazak> however it's not a stable network until it has regressed and rebuilt itaself atleast once, and then it's not transplantable 23:33 < drazak> so there ahve been other methods worked on of getting the endothelial cells to from entworks 23:33 < drazak> different growth factors is on e of the major ways 23:33 < drazak> reduced serum, hypoxia, etc 23:35 < genehacker> hypoxia induces angiogenesis? 23:35 < drazak> yes 23:36 -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: QuantumG, fenn, Ian_Daniher 23:36 -!- Netsplit over, joins: Ian_Daniher, fenn 23:36 -!- Netsplit over, joins: QuantumG 23:36 < drazak> the rationale is that hypoxia induces angiogenesis because when you ahve an injury that lowers bloodflow the network tries to reform, the cells are in a state of hypoxia when bloodflow is interupted 23:38 < genehacker> that makes sense 23:38 < drazak> yup 23:38 < drazak> i can send you a bunch of reviews about angio and vasculargenesis