--- Day changed Wed Aug 12 2009
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01:18 < genehacker> what
01:18 < genehacker> 's giy
01:18 < genehacker> what is git?
02:49 -!- katsmeow is now known as katsmeow-afk
03:12 < timschmidt__> git is a version control application
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09:35 < CIA-38> skdb: kanzure * r b23f03b7ba40 /doc/todo/TODO: more todo added
09:35 < CIA-38> skdb: kanzure * r 21302447f47a /pymates/pymates.py: prototypes for some possibly useful methods in pymates
09:35 < CIA-38> skdb: kanzure * r 9c22864c8f59 /doc/proposals/biology-protocol-ontology.yaml: fixed some lines in the biology protocol ontology proposal
09:35 < CIA-38> skdb: kanzure * r a6aa23665497 /pymates/rapid-test.py: modified pymates rapid-test a while ago, committing
09:35 < CIA-38> skdb: kanzure * r 3e21023750c4 /taxonomy.yaml: added biology protocol ontology to skdb/taxonomy.yaml, see the proposal dir for a possibly more useful file
09:35 < CIA-38> skdb: kanzure * r ca1f21fb92ea /pymates/tests.py: cleaned up pymates unit tests (in pymates/tests.py)
09:35 < CIA-38> skdb: kanzure * r 54aa32554049 /clients/skdb-get.py: preliminary skdb-get.py prototype- does not do anything yet
09:35 < CIA-38> skdb: kanzure * r 3e74f3444f27 / (5 files in 2 dirs): Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb
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09:42 < kanzure> tools and reagents according to Nature Protocols: http://adl.serveftp.org/papers/tools-and-reagents--nature-protocols.html
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10:02 < CIA-38> skdb: fenn * r 4916aa82c290 /core/interface.py: documentation
10:02 < CIA-38> skdb: fenn * r 3330ea4c92ef /geom/geom.py: python property stuff.. this probably doesn't work at all
10:02 < CIA-38> skdb: fenn * r 88b6a3a43976 /packages/lego/grammar.yaml: attempt to quantify lego interface functionality
10:02 < CIA-38> skdb: fenn * r b15a3afb8c04 /unittests/test_geom.py: half of a unit test
10:06 < fenn> foo.IsEqual(gp_Pnt(0,0,0), Precision().Confusion()) == 1
10:06 < fenn> where foo = gp_Pnt(0,0,0)
10:13 < kanzure> tuition paid :/
10:30 < kanzure> fenn: http://adl.serveftp.org/papers/repositoryData.png
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11:38 < kanzure> fenn: http://www.civfanatics.com/images/civ3/tech%20tree/c3c_ancient.jpg
11:38 < kanzure> or, rather
11:38 < kanzure> http://www.civfanatics.com/images/civ3/tech%20tree/c3c_industrial.jpg
11:38 < kanzure> or perhaps even better:
11:38 < kanzure> http://www.civfanatics.com/images/civ3/tech%20tree/c3c_modern.jpg
11:38 < kanzure> (the last two links are the better ones)
11:39 < kanzure> http://home.comcast.net/~pmm1/games/civ3_tech_tree_rev100.gif
11:45 < ybit> http://cloud.github.com/downloads/yoshiki/yaml-mode/yaml-mode-0.0.4.tar.gz
11:45 < ybit> ^_^
11:46 < ybit> there's a mode for everything
11:46 < ybit> http://yaml-mode.clouder.jp/
11:46 < kanzure> http://adl.serveftp.org/lab/techtrees/
11:46 < ybit> http://github.com/yoshiki/yaml-mode/tree/master
11:47 < kanzure> many of these are completely stupid however, so be careful with those images
11:56 < fenn> uh oh
12:06 < CIA-38> skdb: fenn * r 746d7b3f90e3 /doc/dependency-tree.svg: drool
12:06 < CIA-38> skdb: fenn * r f7e301782985 / (4 files in 4 dirs): Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb
12:10 < draz|lab> kanzure: who is johnathon cline?
12:16 < kanzure> jonathan is an odd guy who lives in the attic of the molecular biology building across the street from where I am atm
12:23 < ybit> why was the dependency-tree.svg removed?
12:25 < kanzure> removed?
12:26 < ybit>  fenn * r 746d7b3f90e3 /doc/dependency-tree.svg
12:26 < ybit> the r stands for removed iirc
12:27 < kanzure> r stands for revision
12:28 < kanzure> fenn made the r go to the left because you can't copy r3840180187204hdfoahfd but you can copy r 304108r4afoljdaf8148
12:28 < kanzure> user interface crap re: irc clients :/
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12:30  * ybit wonders why it's not in the repo browser on github
12:30 < ybit> http://github.com/kanzure/skdb/tree/01df6b3bb73e08b2a5fc4f0302721b5424f10479/doc
12:31 < kanzure> sorry, let me push
12:32 < kanzure> ok have fun
12:32 < kanzure> but you should also consider using http://adl.serveftp.org/git/gitweb.cgi
12:32 < ybit> so ..cia is following adl's git repo?
12:33 < kanzure> yes
12:33 < ybit> guess i should change the origin then
12:33 < ybit> git remote -v  
12:33 < ybit> origin	git://github.com/kanzure/skdb.git
12:34 < kanzure> git remote add origin 
12:34 < kanzure> git remote rm some_old_name_goes_here
12:35 < ybit> the adl remote name ..git or http://?
12:35 < kanzure> er
12:35 < kanzure> for your situation, do this:
12:35 < kanzure> git remote rm origin; 
12:35 < kanzure> git remote add origin http://adl.serveftp.org/skdb.git/
12:35 < kanzure> or, alternatively, since you have ssh:
12:36 < ybit> so it's http
12:36 < kanzure> git remote add origin ssh://ybit@adl.serveftp.org/var/www/skdb.git/
12:37 < ybit> ah, good point since i will have to do that later anyway
12:41  * ybit is going to convert diyhplus_org.org into yaml. it's similar to trans-tech.yaml in that it includes relevant technology, but it also includes how to organize groups to more quickly finish the projects
12:42 < ybit> with yaml-mode, it's just as easy to fold as it is in org-mode
12:44 < kanzure> ybit: maybe you could just start editing trans-tech.yaml instead?
12:44 < kanzure> since that already exists and such
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12:45 < ybit> if you don't mind me adding the diyhplus hackerspace organizing part
12:46 < kanzure> not really
12:46 < CIA-38> skdb: kanzure * r b1df996169b2 / (core/part.py geom/geom.py unittests/test_geom.py): added a Transform class, wrote (passing) unit tests for it in test_geom.py
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12:46 < ybit> alright then, trans-tech.yaml it is
13:02 < kanzure> http://news.slashdot.org/comments.pl?sid=1333265&cid=29034715 "Nobody is going to put you in the GNU/Death Camps."
13:02 < kanzure> "So you admit they exist then.
13:02 < kanzure> You are correct, nobody will put you in them. Indeed, you must assemble the GNU/Death Camp yourself. The chain-link fence, razor wire, etc. are available for you to use under the terms of the GNU/DCL. If you are having trouble with assembly or use of GNU/Death Camps, don't even think about posting questions here unless you've RTFM, googled it and searched the mailing list archives."
13:03 < bkero> What is Richard Stallman's position at this GNU/Death camp?
13:08 < kanzure> funny how people like to hate on RMS as if he's crazy
13:09  * kanzure fully expects splicer to come in here now and tell me how crazy RMS is (and by extension, /me)
13:18  * bkero doesn't hate RMS.
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13:18 < bkero> Nothing wrong with GNU
13:22 < kanzure> except how people don't understand that project
13:23 < ybit> kanzure: :P
13:23 < ybit> 13:05  * kanzure fully expects splicer to come in here now and tell me how crazy RMS is (and by extension, /me)
13:23 < draz|lab> kanzure: does he know anything?
13:24 < draz|lab> well uhm, RMS is crazy
13:27  * ybit barks like an insane loon at draz|lab 
13:27 < ybit> draz|lab: i know he created the biopunk forum, can't recall if he knows much bio though
13:28 < ybit> he's highly defensive of mac & co
13:28 < draz|lab> ... awesome
13:29 < ybit> </sarcasm> i'm assuming
13:30 < ybit> speak of mac&co believing in gnu death camps, kanzure, did he ever put a link to the git repo on diybio.org?
13:32 < kanzure> no
13:32 < strages> gnu death camps?
13:32 < strages> wtf?
13:32 < kanzure> strages: it was a quote from slashdot
13:32 < ybit> hi strages 
13:32 < draz|lab> ah yes
13:32 < kanzure> strages: http://news.slashdot.org/comments.pl?sid=1333265&cid=29034715
13:33 < draz|lab> gnu death camps
13:33 < strages> hey ybit
13:33 < draz|lab> kanzure: so does jcline know anything?
13:33 < kanzure> does anyone know anyone at the Chinese WTA?
13:33 < kanzure> draz|lab: yes
13:33 < kanzure> draz|lab: one week he decided to read all of the microfluidic EWOD papers and subsequently build a device
13:33 < draz|lab> not bad
13:34 < any44613385> While the study showed deficits in facial reading among recovered alcoholics, the small number of subjects means that the study could not answer the question of whether the problem is a result of alcoholism or whether people who become alcoholics already had difficulty with facial cues.
13:34 < kanzure> he seems to have a background in EE and bio at the same time
13:34 < draz|lab> apparently I'm the only one in this lab that could do westerns properly the first time
13:34 < draz|lab> hmph
13:34 < any44613385> "The upshot, really, is that people who have had serious alcoholism problems sometime in the past, they could be misreading facial cues," said Ksenija Marinkovic, assistant professor in residence in the radiology department at the University of California, San Diego. "Not everybody is able to read facial cues in the same way."
13:34 < kanzure> draz|lab: I need an ontology or way of organizing a few thousand biology lab protocols
13:35 < any44613385> this smells like a commonality to aspergers, in some yet-unknown fashion
13:35 < draz|lab> kanzure: do a tree, like you would for taxonomy, start with qualitative or quantitative, then what it detects, then accuracy
13:35 < kanzure> any44613385: there was a study once that I read that pinpointed the region responsible for facial issues in aspergers
13:36 < kanzure> draz|lab: "what it detects" ?
13:36 < kanzure> are you sure that's the best way to do it?
13:36 < kanzure> not by the technique being used?
13:36 < any44613385> kanzure, i read a report of autopsies that said some people are missing as many as 17 facial muscle groups, and couldn't make fine expressions anyhow
13:37 < kanzure> yeah it's a common issue- look at people next time they smile
13:37 < draz|lab> "what it detects" is like, dna, enzyme, etc, but no, this is better, because say you want a qualitative way to detect protein, you don't care what method it uses, unless you only have specific ones availible, and if so, you'd be able to find which one you have
13:37 < kanzure> you'll see that many people can't control one side of their smile
13:37 < draz|lab> detects is the wrong word
13:38 < draz|lab> oh shit
13:38 < any44613385> what wasn't documented is whetehr or not those who lacked the muscles had aspergers, and that may be a kenesthetic feedback situation as to why they could not see that in other people, because they themselves could not make those expressions
13:38 < draz|lab> you meant other stuff too
13:38 < kanzure> some lab techniques do not involve detection, draz|lab 
13:38 < draz|lab> like isolating enzymes and all that
13:38 < draz|lab> yeah
13:38 < kanzure> yes
13:38 < draz|lab> man, I'm working off 4 hours sleep and a secondhand potsmoke headache
13:38 < draz|lab> gimme a minute
13:38 < kanzure> any44613385: I don't think the lack of facial muscles correlates to aspergers. I'm fairly certain it's a common occurence.
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13:39 < kanzure> gah, why can't I find my papers
13:39 < kanzure> this is bothersome
13:39 < draz|lab> DNA/RNA/Cell Culture/etc|technique used|
13:40 < draz|lab> I dunno, actually
13:40 < kanzure> no
13:40 < any44613385> kanzure, i see a cultural thing to "smile control", if you smile you are not serious, therefore to get a point across you must frown
13:40 < kanzure> yes it's a hard question
13:40 < draz|lab> I don't smile or frown consciously
13:41 < draz|lab> also I am hella bored
13:41 < draz|lab> waiting for my gel to set
13:41 < any44613385> i have watched people switch back and forth in telling a joke between smiling and frowning, it's really odd, they want to smile, but to get the audience to listen, they frown
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13:42 < kanzure> it's also called being good at telling a joke
13:42 < kanzure> if you start cracking up before the joke gets out, it's less effective
13:43 < any44613385> yeas, but the switching back and forth is unnerving and distracting
13:43 < ybit> timschmidt__: weird, i had a dream last night that you came to my house and needed help in coding some app and then your two kids (i don't even know if you have kids) stomped in wearing camouflage and started destroying my room 
13:43 < any44613385> i have no kids
13:44 < strages> draz|lab: electrophoresis?
13:44 < ybit> maybe the dream's a sign of spending too much time on irc :)
13:45 < ybit> any44613385 meet strages, strages meet any44613385
13:45 < any44613385> ?
13:45 < ybit> local alabamians
13:46 < any44613385> i wass about to say
13:46 < strages> hi any44613385
13:46 < any44613385> hi strages
13:46 < ybit> any44613385, you're ~2 hours away from huntsville, correct?
13:46 -!- any44613385 is now known as katsmeow
13:46 < katsmeow> and 30 min from Bham
13:46 < strages> phenix city?
13:47 < katsmeow> no, 15 min outside Pell City
13:47 < strages> ah ok
13:48 < katsmeow> you are up near ybit
13:48 < strages> I am
13:48 < ybit> strages is in huntsville
13:48 < strages> I live in west huntsville currently
13:49 < ybit> i have several family members in that area
13:49 < ybit> the Englands
13:49 < strages> Chris England?
13:49 < strages> 25 or 26?
13:50 < ybit> hrm, never heard of the guy
13:50 < strages> nevermind then
13:50 < ybit> probably related though
13:50 < strages> went to highschool with him
13:50 < strages> in Athens
13:50 < ybit> ah, no. huntsville, don't know anyone in the family in athens
13:50 < strages> ok
13:52 < ybit> anyway, katsmeow, strages is organizing a hackerspace convention that is set to take place in september, and you should be there :)
13:52 < ybit> strages is part of #makerslocal 
13:53 < katsmeow> i don't think so, i want out of Alabama, and generally out of the usa, and to that end all my time and money is going towards the big boat
13:53 < ybit> :)
13:53 < ybit> katsmeow: where to?
13:53 < strages> seasteading?
13:53 < katsmeow> i don't care where to, as long as i can hoist sail and anchor and relocate
13:53 < ybit> you sound a lot like Phreedom
13:54 < ybit> he wants his own hovercraft
13:54 < katsmeow> tell him to get tomaking it
13:54 < ybit> give him ~15 years
13:55 < katsmeow> company in Louisiana makes and sells hovercraft kits that will sustain 10ft in horizontal travel
13:55 < ybit> i don't doubt that he's going to have it built
13:55 < katsmeow> company in Fla makes flying boats that will sustain 60ft, but will not hover
13:55 < ybit> he had a sweet plan for a RV if i can find it...
13:56 < ybit> katsmeow: link maybe?
13:56 < strages> katsmeow: flying boats?
13:56 < strages> you got a link to that company?
13:56 < ybit> that's what i'm wanting to see, never heard of them
13:56 < ybit> oh i see
13:57 < ybit> just google for it strages 
13:57 < ybit> and preferablly, use www2.sandbox.google.com like katsmeow found yesterday
13:57  * katsmeow checks Tiggr's data
13:57 < ybit> hrm, it doesn't give images like google.com does
13:57 < katsmeow> it's beta
13:57 < ybit> though it is 3x faster as mention previously
13:59 < ybit> anyway, when you get your boat katsmeow, come visit me in a coruna, spain one day
14:00 < katsmeow> why coruna?
14:00 < ybit> great weather, spain, spanish, europe
14:00 < katsmeow> ah
14:01 < katsmeow> i'd hate to have a passport issue with them and never get outa prison
14:01 < katsmeow> political rules can ruin anything
14:02 < ybit> middle-east coast of south america is the safest geographical location on this planet from what i've found, no tornadoes, hurricanes, and little to no earthquakes
14:02 < katsmeow> cusswords, i have *got* to merge these dbs
14:02 < ybit> which dbs?
14:02 < katsmeow> mass dowloads into the hand-edited one
14:02 < ybit> it is appealing that ~50km away from the coast, you are essentially your own nation-state
14:02 < ybit> ?
14:03 < ybit> link?
14:03 < katsmeow> i have /kb/boats/ , but no link back to mirroring an entire site
14:04 < katsmeow> none online
14:04 < katsmeow> it's over 500gig
14:04 < katsmeow> afk, brb
14:05 < ybit> http://www.youtube.com/watch?v=KzxuEOxYSLE&NR=1&feature=fvwp
14:05 < ybit> car-boat challenge..
14:08 < katsmeow> bak
14:09  * ybit wants to see a vid of http://cache.gizmodo.com/assets/resources/2007/10/FlyingBoatGI.jpg
14:10  * katsmeow wants a walkabout tour of the Alinghi
14:10 < katsmeow> ybit, that url you gave looks like the hover boat  i was thinking of
14:10 < katsmeow> it's slso sold with enclosed cockput, and 6 passenger
14:12 < fenn> whatever broke in lego is not broken in 56b35589 (you have to delete "from threads import Thread" in skdb.py) to test: import skdb; skdb.load_package('lego').load_data()
14:12 < katsmeow> if you find their site, they have video
14:13 < strages> when I say flying boat I mean like a Catalina or something
14:13 < strages> something I can live in
14:14 < katsmeow> "normal" hovercraft : http://www.neoterichovercraft.com/
14:14 < katsmeow> Catalina / PBY would use a lot of fuel and maintenance time
14:14 < katsmeow> and require faa certs
14:14 < strages> aye
14:16 < draz|lab> ahhahahaha
14:16 < draz|lab> my lab is on cnn
14:21 < katsmeow> http://www.hovercraft.com/content/index.php
14:21 < katsmeow> page has movies
14:28 < draz|lab> http://www.cnn.com/2009/HEALTH/07/14/heart.stem.cells/index.html
14:32 -!- katsmeow is now known as katsmeow-afk
14:34 < kanzure> http://xkcd.com/149/
14:34 < kanzure> vid: http://www.boingboing.net/2009/02/27/sudo-make-me-a-sandw.html
14:37 < katsmeow-afk> strages , it may be interesting that a trimaran with two 15ft x 30ft airtight boxes tween the hulls has 129,600 square inches of horizontal surface space, so 1 psi in those boxes would lift a 60ton boat, with the added advantage that 4 of the box sides are the hulls
14:37 < katsmeow-afk> or it may not be interesting
14:37 < katsmeow-afk> downside is at one psi, over water, the water surface will be depressed  a foot
14:39 < strages> neat
14:39 < katsmeow-afk> but the boat could still "fly" up onto sand bars, over low islands, or unbeach itself
14:39 < katsmeow-afk> and 60 tons is more boat than you are likely to build
14:39 < katsmeow-afk> once out of the water on air cushion, speed really builds
14:40 < katsmeow-afk> some large hydrofoil sailboats have hit 50mph and towed multiple skiers
14:42 < katsmeow-afk> i think it would be mind-blowing to see two old ww2 uboats apparently tied up to a floating dock, suddenly hop up to sitting atop the water, and take off at 200mph
14:44 < katsmeow-afk> they could do it with a 90ft x 300ft total "dock" area, given 1000ton uboats
14:44 < katsmeow-afk> 300ft isn't a problem, given ww2 uboats are ~300ft long
14:46 < katsmeow-afk> speaking of such, someone did a trial of a boat that resembled a catamaran, but the bottoms of the two hulls were hollow, so the boyancy was adjustable from 9ft draft to 2ft draft
14:47 < katsmeow-afk> at 2ft, the space tween the hulls grabbed enough air when in forward motion, the boat tried to fly, but wasn't designed for it
14:48 < katsmeow-afk> but it made good speed, because the bottoms of the two hulls was esentially air once inflated, so friction was zero
14:48 < katsmeow-afk> bbl
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15:05 < ybit> what's with yet another link to sudo make me a sandwich..?
15:06 < ybit> katsmeow-afk: meh, those hovercraft are small
15:07 < ybit> i was thinking something more like http://en.wikipedia.org/wiki/Mountbatten_class_hovercraft or http://en.wikipedia.org/wiki/Zubr_class_LCAC
15:08 < ybit> so, draz|lab, you're in chicago?
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15:09 < draz|lab> ybit: no, the lee lab
15:09 < ybit> kanzure, what's smari been doing lately? 
15:09 < draz|lab> ybit: buffalo
15:09 < ybit> i saw
15:09 < ybit> think i remember this coming up once too
15:19 < kanzure> ybit: trying to stop iceland from exploding
15:20 < bkero> kanzure: Do you have any idea how big NCBI is?
15:26 < genehacker> hovercraft?
15:26 < genehacker> how can one prevent iceland from exploding...
15:52 < ybit> by employing Brain and keeping Pinky away from him
15:53 < kanzure> bkero: no. many many terabtes.
15:53 < kanzure> terabytes
15:54 < bkero> At least it's in the right order of magnitude.
15:56 < kanzure> todo: subclass SetTranslation in Transform in skdb/geom/geom.py
16:01 < genehacker> yuck artifically created scarcity
16:51 < ybit> bkero: why are you asking, that would be a lot to copy. but if you could get a few labs to consider contributing space, you could have some type of distributed mirror maybe
16:51 < ybit> it's never bad to back-up after all
16:51  * ybit wonders what their back-up solution is there
16:52 < bkero> ybit: I happen to have a lab with a lot of space.
16:56 < ybit> bkero: maybe so, but enough for that...?
16:57 < bkero> I still need to know how many Terabytes it is
16:58 < ybit> email them?
16:59 < genehacker> ybit bkero has something like 200 TB of tape drive
16:59 < genehacker> isn't that right bkero?
17:00 < bkero> There's a stack of LTO-4 tapes here that will hold 1.6T each if that's what you're referring to
17:12 < genehacker> but we could use a second copy of NCBI
17:13 < bkero> This copy will be on I2 :)
17:13 < bkero> Which means gigabit to all universities!
17:14 < kanzure> bkero: would you be willing to back me up?
17:15 < bkero> kanzure: back you up?
17:15 < genehacker> in case of fire, drought, zombie apocalypse, swineflu pandemic, or nuclear holocaust
17:15 < kanzure> my data
17:15 < bkero> How much is there?
17:16 < kanzure> 700~ GB
17:16 < kanzure> not including movies
17:16 < kanzure> not including music
17:17 < bkero> Maybe
17:17 < bkero> Do you have iperf installed?
17:17 < genehacker> there's a /movies/?
17:17 < kanzure> genehacker: no
17:17 < kanzure> bkero: no
17:17 < bkero> kanzure: apt-get it real quick, it's very small
17:17 < genehacker> ok
17:17 < kanzure> bkero: ok
17:18 < bkero> kanzure: iperf -c ponderosa.osuosl.org
17:18 < kanzure> 89 Mbits/sec
17:18 < bkero> Not bad speed
17:19 < kanzure> fenn: do you have a reference for the "colder => better" ?
17:20 < fenn> no
17:20 < fenn> i remember reading somewhere that cold climates were good for thinking
17:20 < fenn> i think it was "guns, germs, and steel"
17:21 < kanzure> jared diamond
17:21  * kanzure wonders if he should have read that by now
17:21 < fenn> and it's well known that you can't think straight when overheating
17:21 < kanzure> it's one of those books you read by osmosis just by being around people who have read it
17:21 < fenn> so apply some linear wishful thinking...
17:21 < kanzure> you mean eliezer-thinking?
17:21 < fenn> i didnt actually read it
17:21 < genehacker> ah yes guns germs and steel is an interesting book
17:22 < fenn> really more like interpolation than extrapolation
17:22 < genehacker> had to know stuff about it for one of my classes in high school
17:22 < CIA-38> skdb: kanzure * r 140a67a2d68e /geom/geom.py: convert from assert to raise
17:22 < kanzure> genehacker: one of your classes required you to read it?
17:22 < kanzure> was this high school or the fake high school?
17:23 < kanzure> is stormfront.org the white supremacy forum?
17:24 < kanzure> nevermind. there was a thread there suggesting something about having to plan more in colder climates in evolutionary history, but then I realized that a white supremacy forum might not be the best place to read that
17:25 < fenn> historically people haven't been living in one place for very long anyway
17:25 < kanzure> right
17:25 < fenn> what's a couple thousand years wrt evolution
17:26 < kanzure> and even if they were, they would quickly mate with some other groups that weren't local
17:31 < genehacker> no we didn't read it
17:31 < genehacker> we watched a movie about it
17:31 < genehacker> real highschool
17:32 < genehacker> not the fake-highschool-college-highschool
17:33 < kanzure> there was a movie?
17:35 < genehacker> I think there was something like a TV documentary thing
17:36 < fenn> http://www.pbs.org/gunsgermssteel/
17:36 < genehacker> yeah I think it's that one
17:37 < genehacker> nothing about cold climates
17:37 < genehacker> as far as I can recall
17:38 < genehacker> his main premise is that domesticated plants and animals can move more easily accross same latitudes than different latitudes
17:40 < fenn> you'd expect there to be more about the link between heat and not being able to think straight
17:41 < fenn> :%s/foo\(.*\)/\1/
17:41 < fenn> foobar -> bar
17:43 < kanzure> I'm trying to do this:
17:44 < kanzure> :%s/\([0-9].\)*/\1/
17:44 < kanzure> doesn't seem to work
17:47 < kanzure> ok fixed
17:47 < CIA-38> brain: kanzure master * r3511ba2 / allenbraininstitute/entrez_geneid_list_human-cortices.txt : list of genes in the human cortices according to the Allen Brain Institute - http://bit.ly/2okLV
17:48 < kanzure> does anyone have a entrez gene id -> entrez gene name script?
17:48 < draz|lab> kanzure: if you're using biopython it's really easy
17:48 < draz|lab> it'sz something like:
17:49 < draz|lab> something = entrez.fetch(db=nucleotide,id=blah) ; something2 = entrez.read(something)
17:49 < draz|lab> it's very similar to that
17:51 < genehacker> well this one company is marketing a brain cooler for people whose brains overheat
17:51 < genehacker> or something like that
17:52 < draz|lab> I think my brain overheated today
17:52 < draz|lab> but that was fromt oo much coffee, too hot a building, and not enough sleep
17:52 -!- draz|lab is now known as drazak
17:54 < genehacker> there's a reference to heat making you not think straight in Macbeth
18:00 < genehacker> hey I can use qcad in linux right?
18:00 < genehacker> sudo apt-get qcad correct?
18:00 < kanzure> drazak: got it
18:01 < kanzure> er, got it many minutes ago :p
18:01 < kanzure> ut anyway, it's working now
18:01 < kanzure> I was thinking of maybe using a wet towel around the head
18:01 < genehacker> are you over clocking yourself?
18:02 < genehacker> well the sharper image(or what's left of them anyway)
18:02 < genehacker> used to sell a device you place around your neck to cool you down
18:03 < kanzure> no, I don't want to overclock myself 
18:03 < kanzure> there's just something weird about how I'm always sweating
18:03 < kanzure> it's really not conducive to work
18:04 < genehacker> the idea is that since you get a lot of bloodflow through your neck you can cool yourself down
18:04 < genehacker> any turn up the airconditioning
18:04 < fenn> "overclocking considered harmful" http://www.logarithmic.net/pfh/overclocking
18:05 < kanzure> wasn't there something similar on supermemo.com ?
18:06 < kanzure> fenn: is the connection slow for you?
18:08 < kanzure> wtf
18:09 < kanzure> the gene with entrez id 376475 does not seem to have a gene symbol 
18:09 < kanzure> but it seems to have the name "XXYorf1-related protein"
18:09 < kanzure> sorry, "CXYorf1-related protein"
18:10 < drazak> there's a bunch like  that
18:11 < kanzure> orly?
18:12 < CIA-38> brain: kanzure master * raa2e7bc / scripts/annotations.py : added annotations.py - figure out entrez gene name and symbols from entrez identification numbers - http://bit.ly/eerLy
18:12 < CIA-38> brain: kanzure master * r1739c01 / scripts/annotations.py : minor alterations to the gene name retrieval script - http://bit.ly/13vahA
18:12 < CIA-38> brain: kanzure master * r7d9181a / allenbraininstitute/brain_genes.yaml : added a list of genes appearing in the human brain according to the Allen Brain Institute, in yaml - http://bit.ly/2vH23
18:24 < ybit> brain is...
18:24 < ybit> at adl?
18:24 < ybit> or only github
18:26 < kanzure> github
18:31 < drazak> kanzure: yeah
18:31 < drazak> kanzure: a particular geneid will be tagged if you search for like, vegf, but it'll be the whole chromosome
18:33 < CIA-38> brain: kanzure master * ra6de58b / (3 files): find longest brain gene name - http://bit.ly/O2Szh
18:33 < CIA-38> brain: kanzure master * r1f5dbab / allenbraininstitute/brain_genes.yaml : fix brain_genes.yaml - http://bit.ly/13gUI4
18:33 < CIA-38> brain: kanzure master * re1e7e74 / allenbraininstitute/gene_names_by_len : the human brain gene with the longest name is aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III) - http://bit.ly/Flgz1
18:34 -!- kanzure changed the topic of #hplusroadmap to: aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)
18:45 < ybit> vegetarians are always cold, become vegetarian if you are looking to overclock your system ;)
18:47 < kanzure> gah, I'm not looking to overclock
18:47 < kanzure> I'm not normal .. my body is too hot most of the time (maybe)
18:47 < kanzure> or I have some sort of weird sweating condition
18:48 < kanzure> or I have an aversion to heat
18:48 < kanzure> I'm really not sure what it could be.
18:48  * kanzure needs to design a few experiments
18:57 < genehacker> http://brodylab.eng.uci.edu/~jpbrody/reynolds/lowpurcell.html
18:59 < genehacker> interestin article about low reynolds number propulsion
19:02 < CIA-38> brain: kanzure master * r1732b44 / (3 files in 2 dirs): added mouse brain genes, also found brain genes by length - http://bit.ly/1E7IF3
19:11 < kanzure> hm need to find a way to organize this information by organelle
19:11 < genehacker> blast pump broke on my heat exchanger
19:11 < kanzure> for instance, synaptogyrin is involved in vesicles, not necessarily any other part of a neuron
19:13 < kanzure> huh, the mouse brain only has DNA polymerase N?
19:13 < kanzure> "Unusual for an A-family DNA polymerase, POLN is a low fidelity enzyme incorporating T opposite template G with a frequency of 0.45 and G opposite template T with a frequency of 0.021. The frequency of misincorporation of T opposite template G is higher than any other known DNA polymerase."
19:21 < CIA-38> brain: kanzure master * re930f6f / scripts/receptors.sh : added a small script to quickly find some receptor-related genes in the mouse brain gene list - http://bit.ly/bIhOD
19:26 < CIA-38> brain: kanzure master * rcce5a12 / scripts/filter.sh : simple grep wrapper script - http://bit.ly/14QbMq
19:38 < genehacker> testing my personal cooling system
19:39 < genehacker> cannot discern if it is workign
19:43 < genehacker> it works, but not too well
19:49 < genehacker> oh yeah it works
19:51 < drazak> lol
19:52 < drazak> we have like a billion frezers at the lab
19:52 < drazak> I could just stick my head in one for 30secs
19:55 < genehacker> do you live in texas where it's hot outside?
19:56 < drazak> no
19:56 < drazak> it was 91 and 87% humidity here
19:56 < genehacker> oh that's even worse
19:56 < drazak> yeah
19:56 < drazak> it's nasty here
19:57 < genehacker> I need more heat transfer though
19:57 < drazak> and the freezers make the lab hot
19:57 < genehacker> vinyl tubing doesn't work that well at transferin heat to ice
19:57 < genehacker> heh damn thermodynamics
19:58 < genehacker> ideally we could harness all the energy in heat so that coolers generate electricity as opposed to using it
20:00 < genehacker> that's odd
20:00 < genehacker> why's my battery pack heating up?
20:03 < kanzure> does anyone have a photograph of a myostatin-inhibited silverback gorilla?
20:12 < genehacker> myostatin inhibited silverback gorilla?
20:12 < kanzure> ""Gumilid Lantod was alone in the jungle catching bats on Mindoro Island in the Philippines when a 23ft (7m) python bit him on the foot and squeezed him to death.  Then the monster swallowed the 154lb (60kg) man.  Friends later found the snake and slit it open, finding the father of six already half digested.""
20:12 < genehacker> is this something that happened naturally?
20:14 < kanzure> apparently
20:14 < genehacker> cool
20:18 < genehacker> are battery pack supposed to get hot?
20:18 < drazak> yes
20:18 < genehacker> hot enough to nearly burn?
20:18 < genehacker> do you know why?
20:20 < drazak> do you know the chemistry behind batteries?
20:20 < drazak> or stuff about electricity?
20:20 < drazak> resistence=heat
20:20 < drazak> drawing current=heat
20:21 < genehacker> ok understood
20:21 < genehacker> then I need to move my batteries...
20:24 < katsmeow-afk> why didn't Gumilid Lantod convert the python into steaks before the snake got to his arms?
20:24 < katsmeow-afk> as the snake had a mouthful of his foot, surely he could locate the snake's head and remove it
20:27 < genehacker> with what?
20:28 < katsmeow-afk> his machete
20:35 < kanzure> what might happen if you started slowly replacing the genes that encode the megaptera brain?
20:40 < genehacker> with what genes?
20:40 < genehacker> what are you trying to do with whale brains?
20:41 < genehacker> make a giant biocomputer?
20:41 < kanzure> "rs34516635, a SNP in the IGF1R gene, claimed to be of significance based on a study of centenarian Ashkenazi females"
20:44 < kanzure> heh Melanie Swan's snp data: http://www.snpedia.com/index.php/User:MelanieSwan
21:06 -!- genehacker [n=noko@pool-173-57-41-223.dllstx.fios.verizon.net] has quit []
21:15 -!- genehacker [n=chatzill@pool-173-57-41-223.dllstx.fios.verizon.net] has joined #hplusroadmap
21:19 -!- splicer [n=patrik@h55n1c1o261.bredband.skanova.com] has joined #hplusroadmap
21:22 < genehacker> fenn you run qcad correct
21:22 < genehacker> ?
21:25 < ybit> genehacker: what do you need to know?
21:26 < genehacker> how to install qcad community edition on linux
21:26 < genehacker> apparently I have to compile it from source
21:27 < ybit> genehacker: what's wrong with apt-get install qcad?
21:28 < genehacker> oh let me try that
21:29 < genehacker> wow
21:29 < ybit> next time you are curious if something is in the ubuntu repo, try this from the cli: apt-cache search <whatever_keyword>
21:29 < ybit> apt-cache search qcad
21:29 < ybit> for instance
21:29 < genehacker> thank you ybit
21:29 < ybit> apt-cache search bio
21:29 < ybit> etc
21:29 < genehacker> I think I love linux now
21:29 < ybit> np
21:29 < ybit> welcome to the family
21:30 < ybit> it only gets better
21:33 < genehacker> you know any good irc clients?
21:34 < ybit> genehacker: irssi
21:34 < ybit> you'll really like screen + irssi
21:34 < ybit> otherwise, konversation is n00b friendly
21:34 < ybit> some like xchat
21:34 < ybit> elites prefer screen + irssi or screen + weechat
21:35 < ybit> screen allows you to restart your X server and resume your shell sessions without losing any data
21:36 < ybit> i.e. you could restart your X server and when you resumed your irc client, you wouldn't lose any of the chat conversation
21:36 < ybit> also, if you were to ssh tunnel into your computer from some other computer you could view the screen shells from there too
21:36 < ybit> by just doing screen -d -r <screen #>
21:37 < ybit> true elites no weechat is where it's @ though ;)
21:37  * ybit has recently become fond of it
21:37 < ybit> it's highly extensible
21:40 < ybit> the command line (cli for short) will become your best friend just to let you know
21:40 < ybit> it allows you to do things much quicker than clickity clicking away
21:42 < ybit> you will eventually move into the text editing wars as well, vim or emacs (screw the rest)
21:42 < ybit> the shell wars were never big, but zsh rules the roost imho
21:42 < genehacker> what's this git thing everyone talks about
21:43 < ybit> it's a version control system for files
21:43 < ybit> apt-cache search git
21:43 < ybit> oh right.. so since you are new.. man pages and google will help a lot
21:43 < ybit> when you download software type in 'man <software' into your cli prompt
21:44 < ybit> man git
21:44 < ybit> man man
21:44 < ybit> man vim
21:44 < ybit> man emacs
21:44 < ybit> etc
21:44 < ybit> it will give you an overview of the software, its commands, and related man pages
21:45 < ybit> i'm sure there are several 'new to linux?' type how-tos out there as well
21:45 < ybit> say you want to clone a repo, you just do 'git clone <repoaddress>'
21:47 < ybit> you'll be using git status, git add <file(s)>, git commit -a -m "<comment>" and git push often before long
21:48 < ybit> your command line is a scripting language itself
21:48 < ybit> bash, zsh, etc.
21:49 < ybit> echo "mplayer -playlist /var/www/audio/playlists/alarm1.m3u" | at now + 9 hours && sleep 20m && mplayer -playlist /var/www/audio/playlists/alarm2.m3u && sleep 3m && mplayer /var/www/audio/playlists/alarm3.m3u
21:49 < ybit> that's a bad example of code, but it shows what can be done
21:49 < ybit> notice the | symbol?
21:50 < ybit> that's called piping
21:50 < ybit> you can pipe output to other programs
21:50 < ybit> in this case, i was able to pipe the output from the program 'echo' to the program 'at'
21:51 < ybit> the double ampersand (&&) means to perform a command after another has been completed
21:52 < ybit> the semi-colon is similar
21:52 < ybit> the double ampersands wait for a program to exit successfully before continuing
21:52 < ybit> the semi-colon ";" executes the command regardless if the previous program exited succesffully
21:53 < ybit> another example...
21:53 < ybit> for file in * ; do cp $file $file.bak; done
21:53 < ybit> this makes a simple backup of all files in a directory
21:53 < ybit> also... (and you really should be thankful i'm saving you time ;)
21:53 < ybit> ...aliases..
21:53 < ybit> they become helpful the more you use a shell
21:54 < ybit> you can make your own commands (called aliases) by editing you shell's config file
21:54 < ybit> for bash, and since you are using ubuntu, you are by default using bash, the config file is /home/genehacker/.bashrc
21:55 < ybit> you would do something like vim ~/.bashrc or emacs ~/.bashrc
21:55 < ybit> nano ~/.bashrc
21:55 < ybit> nano is alright if you are new to text editing using a cli
21:55 < genehacker> ok
21:55 < ybit> apt-get install vim emacs nano
21:55 < ybit> either or all doesn't matter
21:56 < ybit> so.. to create your own command.. you will put this in your config...
21:56 < ybit> alias grep='grep -i -r'
21:56 < ybit> alias mv='mv -i'
21:56 < ybit> alias "hci"='runhaskell Setup clean && runhaskell Setup configure --prefix=$HOME --user && runhaskell Setup build && runhaskell Setup install'
21:56 < ybit> those are a few i have in mine
21:57 < ybit> you can have aliases for different ssh sessions as well
21:58 < ybit> for kicks, you can do "sweeet"="echo 'this is so cool!'"
21:59 < ybit> save the file and exit
21:59 < ybit> and from the cli type..   source ~/.bashrc
21:59 < ybit> then type your alias/new command
21:59 < ybit> </mini_linux_101_lecture>
22:01 < ybit> the alias is sweeet (just in case you were wondering)
22:05 < ybit> and lastly /join #linux and /join #ubuntu from whatever irc client you decide to use, that will be a big help for you
22:10 < kanzure> ybit: it's not apt-cache search git; apt-cache search git-core .. on ubuntu and debian repos, it's git-core, not git (for some stupid reason)
22:10 < ybit> something fun to show complete n00bs is to show them 'apt-get install <awesome_looking_3d_game>' openarena tremulous sauerbraten etc
22:10 < ybit> apt-cache search git will show git-core
22:10 < ybit> it's keyword search
22:11 < kanzure> sure
22:11 < ybit> anyway, and then ask them if they know of any other operating system that by default allows them to freely download such games
22:11 < ybit> always brings a smile to their faces
22:11 < kanzure> have you tried bzflag?
22:11 < ybit> (after showing the game in action of course)
22:12 < ybit> yeah
22:12 < kanzure> how is it?
22:12 < ybit> been a long time, i didn't like the controls, seemed really slow compared to openarena
22:12 < ybit> which is my addiction..
22:12 < ybit> however.. since this fresh install of gentoo, i've kept myself from playing games
22:12 < ybit> i have more of a mind game going with myself now
22:12 < kanzure> I only play tetris. do you have any recommendations? I don't do FPSes.
22:13 < ybit> 'how many tasks can i complete in a day' is one objective of this game
22:13 < kanzure> the problem with todo lists and me is that I inevitably begin spending four or five hours a day obsessively updating the todo list
22:13 < ybit> er.. well... what do you want?
22:13 < ybit> artisitic intepretations of 8bit games? because i have several 8 bit game recommendations
22:13 < kanzure> sure
22:13 < ybit> if you want rts, spring is the way to go
22:14 < ybit> gles is more traditional
22:14 < ybit> btw, genehacker, you'll probably like battle (of|for) wesnoth
22:14 < ybit> apt-cache search wesnoth
22:14 < kanzure> yeah I played wesnoth for a while
22:14 < kanzure> then I broke down and got starcraft
22:14 < ybit> games # ls
22:14 < ybit> 8bit_killer              MondrianProvoked_1.1.exe  aether      gabaaba.exe             mr_heart_loves_you_very_much.zip  papermoon-gamma-public
22:14 < kanzure> er, wait
22:14 < ybit> Between_v5_UnixSource    Passage_v3_UnixSource     battlecode  games i've yet to play  n_v1linux                         pingpong.exe
22:14 < kanzure> it's not wesnoth that I am thinking of
22:14 < ybit> Disco Space Invader.zip  WorldOfGoo.tar.bz2        bgm.dll     judith.tar.gz           openarena-0.8.1                   sunset_runner.exe
22:15 < ybit> Don't Look Back.exe      Wubly_final_.zip          bloody.zip  mod-x                   owlcountry-win.zip
22:15 < kanzure> what's the warcraft-like rts that I'm thinking of?
22:15 < kanzure> heh World of Goo. is that supergoo?
22:15 < kanzure> there used to be this app called supergoo, and I spent way too many hours with it
22:15 < ybit> papermoon-gamma and passage are two neat games
22:16 < kanzure> alex4 is worth checking out
22:16 < kanzure> even if you're trying to stop playing games
22:16 < kanzure> it's rather short
22:16 < ybit> no, it's a playstation2|3 (i think) or maybe it was a pc game that was ported to linux
22:16 < ybit> you'll have to torrent it
22:16 < kanzure> can't seem to torrent properly any more
22:17 < ybit> there was some action-adventure game that i had...
22:17 < kanzure> any time I try any port number, every thing is shaped
22:17 < ybit> 256_seconds.zip        DoomedPlanet.zip  Pazzon.zip  bloody_zombies.zip                   fireflies-osx.zip           shitgame.zip
22:17 < ybit> 4mins33secs.zip        Execution.zip     Torque.zip  dive.zip                             flow_04142006.zip           stdbits.zip
22:17 < ybit> BlottoBrace_Final.rar  Frozzd.zip        arcade.zip  downloads\TheDepthsToWhichISink.zip  papermoon-gamma-public.zip
22:17 < ybit> those are games i never got around to playing
22:18 < ybit> genehacker: there are also several decent 3d mmorpg games
22:19 < genehacker> world of goo for linux?
22:20 < genehacker> I don't play rpgs
22:20  * ybit became a puzzle addict before moving onto math and logic problems, before finally and lastly moving onto coding problems
22:20 < ybit> now if i can find some links...
22:22 < katsmeow-afk> vectorTD
22:22 < ybit> genehacker, you'll also like these programs gimp inkscape blender and a bunch of other programs from the ubuntustudio repo
22:23 < genehacker> I don't use blender
22:23 < genehacker> have no use
22:26 < ybit> http://www.pythonchallenge.com/ http://www.spoj.pl/ http://projecteuler.net/ http://battlecode.mit.edu/2009/ http://domino.research.ibm.com/Comm/wwwr_ponder.nsf/pages/index.html 
22:26 < ybit> are all fun
22:26 < ybit> if you have time to spare
22:27 < ybit> so are the numb3rs genius challenges
22:32 < ybit> i ended up creating my 'game of life' though and have been creating rules with it. it's a way of ensuring productivity
22:33 < ybit> it's fun and productive, can't beat it
22:34 < ybit> fifo_dir                = /tmp
22:34 < ybit> socket_dir              = /tmp
22:34 < ybit> con_path               = $HOME/.local/share/uzbl/uzbl.png
22:37 < ybit> whoops that was supposed to go to someone having problems in #uzbl
22:44 -!- mason-l [n=x@202-89-188-136.static.dsl.amnet.net.au] has joined #hplusroadmap
22:44 < ybit> mason-l: welcome to 'where all the cool kids hang'
22:44 < ybit> http://adl.serveftp.org/papers may be of interest
22:45 < ybit> fenn and kanzure have been putting a lot of work into this git repo: http://adl.serftp.org/skdb.git
22:45 < ybit> also on github, check out http://github.com/kanzure
22:47 < ybit> mason-l: relevant mailing list: groups.google.com/group/diytranshumanist
22:53 < ybit> wasn't andrew hessel in australia...?
22:57 < ybit> he had some word on curing cancer iirc
22:57 < ybit> s/word/work
23:16 < genehacker> time to see if I can't see perseids
23:31 < ybit> don't forget a helment genehacker ;)
23:31 < ybit> mason-l is helping to form a hackerspace in perth, western australia if anyone is interested. i'm guessing most everyone is sleeping
23:46 < genehacker> we need to set up a hackerspace system
23:46 < ybit> go on..
23:47 < genehacker> so hackers all over the world can know where hackerspace are and collaborate with them
23:47 < genehacker> whenever they happen to be in the area
23:47 < genehacker> sorta like how masonic lodges used to be
23:47 < ybit> genehacker: #hackerspaces might be interested in discussing this when people are actually around and not sleeping
23:47 < strages> hackerspaces.org
23:48 < genehacker> also isn't there some sort of algorithm for approximated a circle of radius r with n line segments?
23:49 < genehacker> *approximating