| --- Day changed Fri Aug 07 2009 | ||
| genehacker | jonathan cline? | 00:00 |
|---|---|---|
| kanzure | yes | 00:00 |
| * kanzure sleeps | 00:00 | |
| 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. | 01:42 |
| -!- marainein [n=marainei@220.253.58.67] has joined #hplusroadmap | 04:23 | |
| -!- marainein [n=marainei@220.253.58.67] has quit [Read error: 110 (Connection timed out)] | 05:19 | |
| kanzure | can anyone find a copy of "Die Cytoarchitektonik der Hirnrinde des erwachsenen Menschen"? | 06:38 |
| 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 " | 06:40 |
| 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 | 06:41 |
| CIA-38 | brain: kanzure master * rb480e1f / human_brain.yaml : brodmann areas, general references, search terms, cross-referencing | 06:50 |
| CIA-38 | brain: kanzure master * r51c2fb1 / human_brain.yaml : brodmann-area-4 improved - http://bit.ly/SroTh | 06:59 |
| CIA-38 | brain: kanzure master * rfbc3b99 / human_brain.yaml : licensing information - http://bit.ly/tvOiq | 07:00 |
| kanzure | meh. | 07:03 |
| kanzure | all of these localization prefixes *suck* | 07:03 |
| kanzure | timschmidt says he'll be cad'ing up the aluminum gingery forge | 08:18 |
| CIA-38 | brain: kanzure master * r066467e / human_brain.yaml : lateral hypothalamus reorganization re: supraoptic-nucleus - http://bit.ly/2RwKB | 08:21 |
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| 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_ | 08:23 |
| 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. | 08:24 |
| ybit | kanzure: did you ever find "Cytoarchitectonics of the Adult Human Cerebral Cortex" | 08:25 |
| 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 | 08:27 |
| ybit | looking at my backups from 2 years ago, maybe 10% are even worth my time | 08:28 |
| * 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_ | :) | 08:29 |
| 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. | 08:30 |
| ybit | alright see you guys on the ssh tunneled flip-side in just a bit | 08:31 |
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| -!- kardan [n=kardan@p54BE3550.dip.t-dialin.net] has quit [Read error: 104 (Connection reset by peer)] | 08:47 | |
| kanzure | ybit: no, I didn't find it | 09:35 |
| 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 | 09:36 |
| 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) | 09:41 |
| 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 | 09:42 |
| kanzure | timestamps please | 09:43 |
| kanzure | "from skdb.packages import lego" didn't work for you? | 09:43 |
| fenn | go away | 09:44 |
| kanzure | where should CAD loading code go? | 09:52 |
| kanzure | in Part()? | 09:52 |
| kanzure | or in pymates.py somewhere random? | 09:52 |
| kanzure | fenn: ok it works actually | 09:54 |
| kanzure | fenn: the problem is that you need to run brick1.load_CAD() | 09:54 |
| 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 | 09:55 | |
| 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" | 09:56 |
| 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()__ | 09:57 |
| fenn | __init__() | 09:58 |
| kanzure | er, yes | 09:58 |
| -!- kardan_ [n=kardan@p54BE670A.dip.t-dialin.net] has joined #hplusroadmap | 09:59 | |
| 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 | 10:00 |
| 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 | 10:01 |
| kanzure | I could have sworn I added something like cls.__init__() yesterday | 10:03 |
| 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 | 10:09 |
| 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 | 10:10 |
| 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)] | 10:12 | |
| 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? | 10:13 |
| ybit | http://blog.clemens.endorphin.org/2008/11/xmonad-gridselect.html | 10:14 |
| fenn | grid select is only useful if your windows have proper titles | 10:15 |
| fenn | at least show an icon or something | 10:16 |
| ybit | you can tag your windows with titles | 10:16 |
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| 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 | 10:16 |
| 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 | 10:17 |
| 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 | :) | 10:18 |
| 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 | 10:19 | |
| 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 @? | 10:20 |
| fenn | this line gets split and put into author author fenn <fennetic.net> 1249656073 -0500 | 10:21 |
| fenn | split(/ /, $line, 2) | 10:21 |
| fenn | er, the line was "author fenn <fennetic.net> 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 | 10:22 |
| fenn | it was /<(.*?)@/ | 10:23 |
| kanzure | that's stupid | 10:23 |
| * fenn adds <? | 10:23 | |
| kanzure | 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 | 10:23 |
| 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 <kanzure@gmail.com> | 10:24 |
| 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. | 10:25 |
| fenn | what does git cat-fileauthor Smári McCarthy <smari@hilbert.(none)> 1248649606 +0000 | 10:26 |
| fenn | oops | 10:26 |
| fenn | $author =~ /author (.*?) </; | 10:27 |
| kanzure | wasn't in git log -p | 10:27 |
| 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 | 10:28 |
| kanzure | the problem is that the __init__ is being called before all of the attributes are assigned | 10:35 |
| 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 | 10:37 |
| -!- timschmidt_ [n=chatzill@c-24-11-81-207.hsd1.mi.comcast.net] has quit [Read error: 110 (Connection timed out)] | 10:40 | |
| kanzure | __setstate__ is never being called | 10:49 |
| 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] | 11:11 |
| 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 | 11:12 |
| 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 | 11:13 |
| 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 | 11:14 |
| 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 & | 11:15 |
| 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 | 11:16 |
| 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? | 11:18 |
| 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 | 11:19 |
| fenn | skdb.load blows up the second time you run it | 11:20 |
| kanzure | I'm fairly certain it didn't do that last week | 11:21 |
| CIA-38 | skdb: * rb29b50a58e4a /core/yamlcrap.py: fix check for tag in yaml_multi_constructors | 11:29 |
| fenn | stupid bot | 11:30 |
| kanzure | Use of uninitialized value $user in concatenation (.) or string at /var/www/skdb.git/ciabot_git.pl line 193. | 11:33 |
| 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 | 11:34 |
| fenn | in fennobject: return cls() is where cls.__init__() is called | 11:46 |
| kanzure | why is process a scalar :p | 11:48 |
| fenn | it's not | 11:49 |
| * fenn looks expectantly at CIA-38 | 11:53 | |
| CIA-38 | skdb: test test * rster /core/yamlcrap.py: Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb | 11:55 |
| kanzure | rster? | 11:58 |
| kanzure | fenn: you can test perl with perl -e | 12:00 |
| fenn | perl question: wtf does $foo =~ /blah(.*)blah/ do? | 12:01 |
| kanzure | matches anything in between blah and blah, and sets foo to that anything | 12:01 |
| fenn | well, it doesn't | 12:02 |
| fenn | print($author."\n"); $author =~ /(.*) </; print($author."\n"); | 12:02 |
| fenn | kanzure <kanzure@gmail.com> 1249662478 -0500 | 12:03 |
| fenn | kanzure <kanzure@gmail.com> 1249662478 -0500 | 12:03 |
| fenn | is '<' special? | 12:03 |
| kanzure | ($use_this_part) = $some_string =~ s/^(.*)</; | 12:07 |
| fenn | i shouldnt have to do this? $foo =~ s/(.*) <.*/\1/; | 12:07 |
| kanzure | perl -e "\$foo = 'blahhelloblah <blah@gmail.com>'; (\$blah2) = \$foo =~ /^(.*)</; print \$blah2; print \"\n\"; print \$foo; print \"\n\";" | 12:08 |
| CIA-38 | skdb: kanzure test * r ster /core/yamlcrap.py: Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb | 12:12 |
| -!- Netsplit simmons.freenode.net <-> irc.freenode.net quits: bkero | 12:13 | |
| kanzure | ($blah) = $str = regex | 12:13 |
| -!- Netsplit over, joins: bkero | 12:14 | |
| kanzure | kinda need __setstate__ to work | 12:15 |
| kanzure | I'm still concerned that __setstate__ isn't being set | 12:20 |
| 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. | 12:22 |
| 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 | 12:23 |
| CIA-38 | skdb: kanzure * r c536faad9d19 /core/ (part.py yamlcrap.py): cleaning up print statements | 12:26 |
| drazak | kanzure: who is tito whatever and what does he do? | 12:37 |
| 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 | 12:38 |
| 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 | 12:39 |
| 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 | 12:40 |
| 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 | 12:41 |
| 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 | 12:42 |
| 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 | 12:49 |
| kanzure | the development branch of bpython seems somewhat stable | 13:00 |
| 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? | 13:05 |
| 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 | 13:12 |
| fenn | i think you should think of a better way to do it | 13:13 |
| kanzure | bah | 13:13 |
| kanzure | fine. | 13:13 |
| fenn | does load_package('package') do import package? | 13:14 |
| kanzure | load_package is in the same file as the class Package | 13:14 |
| fenn | no, i mean does load_package('foo') do import foo | 13:15 |
| kanzure | no | 13:15 |
| 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 | 13:16 |
| CIA-38 | skdb: kanzure * r 0d5261b17be6 / (core/part.py core/skdb.py packages/lego/data.yaml): got rid of some nasty recursion | 13:17 |
| fenn | screw/metadata.yaml has classes: [screw.Screw, threads.Thread] | 13:37 |
| kanzure | lego_package = skdb.load_package("lego") | 13:40 |
| kanzure | some_new_screw = lego_package.Screw() | 13:40 |
| kanzure | loaded_screw = skdb.open(open("packages/lego/data.yaml"))["parts"][0] | 13:41 |
| 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? | 13:42 |
| 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? | 13:43 |
| kanzure | 鮻쫊琢 awesome file format | 13:44 |
| fenn | why would lego_package have Screw? | 13:45 |
| kanzure | because I don't want to say lego_pack.lego.lego.lego.lego.my.ego | 13:46 |
| kanzure | it currently works btw | 13:46 |
| fenn | this works atm: foo = skdb.load_package('lego'); foo.Lego() | 13:48 |
| kanzure | right | 13:48 |
| kanzure | oh | 13:49 |
| kanzure | screw | 13:49 |
| kanzure | yes, lego_package would not have Screw | 13:49 |
| drazak | rawr ncbi is slow | 14:13 |
| CIA-38 | skdb: fenn * r fecb6ed58b39 / (3 files in 3 dirs): rewrite import_package_classes, restructure metadata for required classes and modules | 14:23 |
| 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 | 14:26 |
| kanzure | fenn: NameError: global name 'new_import_package_classes' is not defined | 14:27 |
| 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 | 14:28 |
| 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. | 14:30 |
| kanzure | /home/kanzure/code/skdb/core/part.pyc in load_CAD(self) | 14:31 |
| fenn | how is package_path not the same as Package('foo').path()? | 14:40 |
| kanzure | how does it know what package it is from | 14:42 |
| kanzure | if you don't tell it? | 14:42 |
| 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? | 14:43 |
| 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 | 14:44 |
| 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? | 14:46 |
| 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 | 14:47 |
| 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 | 14:48 |
| 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 | 14:49 |
| 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 | 14:50 |
| 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 | 15:17 |
| genehacker | http://www.youtube.com/watch?v=5sVOSlUn7e0 | 15:21 |
| genehacker | inefficient but entertaining | 15:24 |
| CIA-38 | skdb: kanzure * r 14169113bb60 /core/skdb.py: cleanup | 15:40 |
| 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 | 15:42 |
| CIA-38 | skdb: kanzure * r 728ae6016175 /core/part.py: make load_CAD work with the new Part().__class__.package attribute | 15:45 |
| CIA-38 | skdb: fenn * r dd3a5c3a4e3d / (3 files in 2 dirs): probably busted, bryan's fault if so :P | 16:04 |
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| 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 | 16:20 |
| 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 | 16:21 |
| bkero | Psh | 17:00 |
| bkero | NCBI's not that big | 17:00 |
| bkero | I've got 150 LTO-4 tapes sitting on my desk. | 17:00 |
| 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. | 17:02 |
| 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 | 17:03 |
| genehacker | wow | 17:04 |
| genehacker | do you seed bkero? | 17:04 |
| genehacker | you could download nearly every song and every computer game | 17:05 |
| kanzure | nearly!~ | 17:06 |
| genehacker | so kanzure you are downloading NCBI? | 17:08 |
| genehacker | the whole thing? | 17:08 |
| 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 | 17:09 |
| kanzure | I have offshore servers that have complete backups of NCBI | 17:12 |
| kanzure | also complete backups of the korean equivalent of NCBI | 17:12 |
| 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? | 17:14 |
| fenn | cute robots | 17:27 |
| fenn | i wonder who fills up the little pans of stuff | 17:27 |
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| kanzure | fenn: internet might be slow for a few minutes | 17:50 |
| kanzure | complain if it's an issue | 17:50 |
| fenn | wah! | 17:50 |
| 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? | 17:51 |
| 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" | 17:52 |
| 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) | 17:54 |
| fenn | the Cosmological Principle is that everything is boring if you look far enough away? | 17:55 |
| kanzure | galaxyfilament.org is available | 17:56 |
| fenn | sign me up scotty | 17:57 |
| fenn | "Medical Algorithms"? | 18:16 |
| fenn | also, since when did 'full text' turn into 'download pdf' | 18:17 |
| 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." | 18:18 |
| fenn | 13500 spreadsheets seems a little excessive | 18:19 |
| fenn | bah. why do they want me to register | 18:22 |
| kanzure | what's sad is that health decisions are sometimes made based off of these spreadsheet macros | 18:23 |
| fenn | i think it's a good idea (not sure about the implementation) | 18:24 |
| kanzure | nice numbers: http://en.wikipedia.org/wiki/Cortical_minicolumn | 18:32 |
| kanzure | er, what? # Thalamic input (1 axon) reaches 100–300 minicolumns. | 18:33 |
| kanzure | units '635 microns^2 * 2 * 10^8' 'm^2' | 18:36 |
| 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) | 18:37 |
| 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." | 18:47 |
| 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 | 18:48 |
| 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." | 18:50 |
| kanzure | query: sulci gene expression | 18:52 |
| kanzure | not getting much | 18:52 |
| kanzure | "cerebral gyrification" heh | 18:57 |
| kanzure | "genetic contributions to human gyrification" - http://www.jneurosci.org.ezproxy.lib.utexas.edu/cgi/content/full/25/34/7840 | 18:58 |
| kanzure | "gyral flattening and sulcral narrowing" leads to cerebral edema? hrm.. | 19:03 |
| 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) | 19:06 |
| kanzure | a test of the mechanical folding hypothesis: http://cercor.oxfordjournals.org.ezproxy.lib.utexas.edu/cgi/content/abstract/1/5/426 | 19:24 |
| 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 | 19:33 |
| 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 | 19:38 |
| kanzure | what? | 19:41 |
| kanzure | about keeping track of what you were talking about? | 19:41 |
| genehacker | no of stuff in a 3d space | 19:41 |
| 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 :(* | 19:42 |
| kanzure | http://www.sciencemag.org.ezproxy.lib.utexas.edu/cgi/content/abstract/297/5580/365 | 19:43 |
| kanzure | enlarged diagram: http://www.sciencemag.org.ezproxy.lib.utexas.edu/content/vol297/issue5580/images/large/se2820695003.jpeg | 19:44 |
| fenn | scary | 19:44 |
| kanzure | ok stolen: http://adl.serveftp.org/papers/Regulation%20of%20cerebral%20cortical%20size%20by%20control%20of%20cell%20cycle%20exit%20in%20neural%20precursors.pdf.png | 19:47 |
| fenn | bonus points for whoever figures out where the nose went, and what those little wormy things are | 19:48 |
| genehacker | blargh | 19:49 |
| genehacker | that's not what I'm looking for | 19:49 |
| 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 | 19:50 |
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| genehacker | it's not stolen, it's copied | 19:57 |
| 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) | 19:58 |
| fenn | genehacker_: here's a nickel, kid. get yourself a real IRC client | 19:59 |
| genehacker_ | A NICKEL? | 19:59 |
| fenn | </dilbert> | 19:59 |
| genehacker | a link to sourceforge would have been better | 20:00 |
| fenn | sudo apt-get install irssi | 20:01 |
| 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 | 20:02 |
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| fenn | woah | 20:06 |
| fenn | http://en.wikipedia.org/wiki/File:Vishumancolor.jpg | 20:06 |
| genehacker | what's the res on that? | 20:07 |
| fenn | it didnt look that good in 1998 | 20:07 |
| genehacker | yeah | 20:07 |
| fenn | i never noticed the scars or messed up nose or tattoos | 20:08 |
| genehacker | the guy they scanned was a prisoner | 20:29 |
| fenn | so much for getting the data | 20:31 |
| genehacker | you don't need a nose now do you? | 20:32 |
| fenn | the visible human data isn't online anywhere | 20:45 |
| genehacker | WHAT? | 20:48 |
| kanzure | ASPM genes? | 21:13 |
| kanzure | "human accelerated regions" (HARs) | 21:13 |
| kanzure | hah | 21:13 |
| fenn | 5~count me skeptical | 21:17 |
| genehacker | genes that change a lot? | 21:18 |
| fenn | i dont believe there's anything special about human biology | 21:18 |
| genehacker | me either | 21:20 |
| kanzure | "Recent acceleration of human adaptive evolution" | 21:20 |
| genehacker | oh that paper? | 21:25 |
| genehacker | that says our genomes are changing faster | 21:25 |
| kanzure | CDK5RAP2, CENPJ, ASPM, microcephalin, ADCYAP1, AHI1 (for axon guidance), FOXP2, SHH (sonic hedgehog), MAOA, MRG, GLUD1, GLUD2, opsin, MYH16, PDYN, HAR1 | 21:27 |
| kanzure | axon guidance receptor gene ROBO1 | 21:58 |
| drazak | I know a bit about SHH | 22:01 |
| genehacker | and not the videogame character I assume? | 22:02 |
| drazak | it's a signaling gene | 22:03 |
| drazak | related to wnt and stat iirc | 22:03 |
| genehacker | yeah I know | 22:20 |
| kanzure | "Turning blood into brain" ? | 22:29 |
| drazak | craq | 22:29 |
| drazak | hemapoeitic cells aren't related to the neural lineage | 22:30 |
| genehacker | ??? | 22:38 |
| 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? | 22:39 |
| drazak | me | 22:44 |
| drazak | we do a lot of work with vegf | 22:44 |
| drazak | and my uncles thesis was on it | 22:45 |
| drazak | what' | 22:46 |
| drazak | er, what'd they do, make a siRNA for VEGFR2? | 22:46 |
| drazak | or did they use an inhibitor? | 22:47 |
| drazak | and were they nerual crest stem cells? | 22:47 |
| ybit | 17:12 < kanzure> ybit: have you considered letting daemons manage tabs? | 22:51 |
| ybit | explain | 22:52 |
| kanzure | huh type 1 diabetes solved by transplantable pancreatic islets | 22:55 |
| ybit | don't try avoiding this topic :D | 22:57 |
| 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 | 22:59 |
| drazak | not the diabetes paper | 23:01 |
| drazak | the other one | 23:01 |
| 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 | 23:16 |
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| doubting-thomas | Hello. | 23:19 |
| kanzure | Hey doubting-thomas. | 23:21 |
| kanzure | what's up? | 23:21 |
| 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 | 23:22 |
| 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 | ! | 23:23 |
| kanzure | just search for "under VEGF receptor blockade" | 23:24 |
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| genehacker | don't electroporators use aluminium plates? | 23:24 |
| drazak | sometimes | 23:25 |
| kanzure | IIRC, you can do electroporation with a needle | 23:25 |
| genehacker | never heard of it | 23:26 |
| genehacker | is it a titanium needle? | 23:26 |
| genehacker | I need a titanium or copper needle | 23:27 |
| 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 | 23:28 |
| 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? | 23:29 |
| 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 | 23:30 |
| 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 | 23:31 |
| 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 | 23:33 |
| genehacker | hypoxia induces angiogenesis? | 23:35 |
| drazak | yes | 23:35 |
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| 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 | 23:36 |
| genehacker | that makes sense | 23:38 |
| drazak | yup | 23:38 |
| drazak | i can send you a bunch of reviews about angio and vasculargenesis | 23:38 |
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