2009-08-12.log

--- Day changed Wed Aug 12 2009
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genehackerwhat01:18
genehacker's giy01:18
genehackerwhat is git?01:18
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timschmidt__git is a version control application03:12
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CIA-38skdb: kanzure * r b23f03b7ba40 /doc/todo/TODO: more todo added09:35
CIA-38skdb: kanzure * r 21302447f47a /pymates/pymates.py: prototypes for some possibly useful methods in pymates09:35
CIA-38skdb: kanzure * r 9c22864c8f59 /doc/proposals/biology-protocol-ontology.yaml: fixed some lines in the biology protocol ontology proposal09:35
CIA-38skdb: kanzure * r a6aa23665497 /pymates/rapid-test.py: modified pymates rapid-test a while ago, committing09:35
CIA-38skdb: kanzure * r 3e21023750c4 /taxonomy.yaml: added biology protocol ontology to skdb/taxonomy.yaml, see the proposal dir for a possibly more useful file09:35
CIA-38skdb: kanzure * r ca1f21fb92ea /pymates/tests.py: cleaned up pymates unit tests (in pymates/tests.py)09:35
CIA-38skdb: kanzure * r 54aa32554049 /clients/skdb-get.py: preliminary skdb-get.py prototype- does not do anything yet09:35
CIA-38skdb: kanzure * r 3e74f3444f27 / (5 files in 2 dirs): Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb09:35
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kanzuretools and reagents according to Nature Protocols: http://adl.serveftp.org/papers/tools-and-reagents--nature-protocols.html09:42
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CIA-38skdb: fenn * r 4916aa82c290 /core/interface.py: documentation10:02
CIA-38skdb: fenn * r 3330ea4c92ef /geom/geom.py: python property stuff.. this probably doesn't work at all10:02
CIA-38skdb: fenn * r 88b6a3a43976 /packages/lego/grammar.yaml: attempt to quantify lego interface functionality10:02
CIA-38skdb: fenn * r b15a3afb8c04 /unittests/test_geom.py: half of a unit test10:02
fennfoo.IsEqual(gp_Pnt(0,0,0), Precision().Confusion()) == 110:06
fennwhere foo = gp_Pnt(0,0,0)10:06
kanzuretuition paid :/10:13
kanzurefenn: http://adl.serveftp.org/papers/repositoryData.png10:30
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kanzurefenn: http://www.civfanatics.com/images/civ3/tech%20tree/c3c_ancient.jpg11:38
kanzureor, rather11:38
kanzurehttp://www.civfanatics.com/images/civ3/tech%20tree/c3c_industrial.jpg11:38
kanzureor perhaps even better:11:38
kanzurehttp://www.civfanatics.com/images/civ3/tech%20tree/c3c_modern.jpg11:38
kanzure(the last two links are the better ones)11:38
kanzurehttp://home.comcast.net/~pmm1/games/civ3_tech_tree_rev100.gif11:39
ybithttp://cloud.github.com/downloads/yoshiki/yaml-mode/yaml-mode-0.0.4.tar.gz11:45
ybit^_^11:45
ybitthere's a mode for everything11:46
ybithttp://yaml-mode.clouder.jp/11:46
kanzurehttp://adl.serveftp.org/lab/techtrees/11:46
ybithttp://github.com/yoshiki/yaml-mode/tree/master11:46
kanzuremany of these are completely stupid however, so be careful with those images11:47
fennuh oh11:56
CIA-38skdb: fenn * r 746d7b3f90e3 /doc/dependency-tree.svg: drool12:06
CIA-38skdb: fenn * r f7e301782985 / (4 files in 4 dirs): Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb12:06
draz|labkanzure: who is johnathon cline?12:10
kanzurejonathan is an odd guy who lives in the attic of the molecular biology building across the street from where I am atm12:16
ybitwhy was the dependency-tree.svg removed?12:23
kanzureremoved?12:25
ybit fenn * r 746d7b3f90e3 /doc/dependency-tree.svg12:26
ybitthe r stands for removed iirc12:26
kanzurer stands for revision12:27
kanzurefenn made the r go to the left because you can't copy r3840180187204hdfoahfd but you can copy r 304108r4afoljdaf814812:28
kanzureuser interface crap re: irc clients :/12:28
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* ybit wonders why it's not in the repo browser on github12:30
ybithttp://github.com/kanzure/skdb/tree/01df6b3bb73e08b2a5fc4f0302721b5424f10479/doc12:30
kanzuresorry, let me push12:31
kanzureok have fun12:32
kanzurebut you should also consider using http://adl.serveftp.org/git/gitweb.cgi12:32
ybitso ..cia is following adl's git repo?12:32
kanzureyes12:33
ybitguess i should change the origin then12:33
ybitgit remote -v  12:33
ybitorigingit://github.com/kanzure/skdb.git12:33
kanzuregit remote add origin 12:34
kanzuregit remote rm some_old_name_goes_here12:34
ybitthe adl remote name ..git or http://?12:35
kanzureer12:35
kanzurefor your situation, do this:12:35
kanzuregit remote rm origin; 12:35
kanzuregit remote add origin http://adl.serveftp.org/skdb.git/12:35
kanzureor, alternatively, since you have ssh:12:35
ybitso it's http12:36
kanzuregit remote add origin ssh://ybit@adl.serveftp.org/var/www/skdb.git/12:36
ybitah, good point since i will have to do that later anyway12:37
* 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 projects12:41
ybitwith yaml-mode, it's just as easy to fold as it is in org-mode12:42
kanzureybit: maybe you could just start editing trans-tech.yaml instead?12:44
kanzuresince that already exists and such12:44
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ybitif you don't mind me adding the diyhplus hackerspace organizing part12:45
kanzurenot really12:46
CIA-38skdb: 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.py12:46
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ybitalright then, trans-tech.yaml it is12:46
kanzurehttp://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
kanzureYou 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."13:02
bkeroWhat is Richard Stallman's position at this GNU/Death camp?13:03
kanzurefunny how people like to hate on RMS as if he's crazy13:08
* kanzure fully expects splicer to come in here now and tell me how crazy RMS is (and by extension, /me)13:09
* bkero doesn't hate RMS.13:18
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bkeroNothing wrong with GNU13:18
kanzureexcept how people don't understand that project13:22
ybitkanzure: :P13:23
ybit13:05  * kanzure fully expects splicer to come in here now and tell me how crazy RMS is (and by extension, /me)13:23
draz|labkanzure: does he know anything?13:23
draz|labwell uhm, RMS is crazy13:24
* ybit barks like an insane loon at draz|lab 13:27
ybitdraz|lab: i know he created the biopunk forum, can't recall if he knows much bio though13:27
ybithe's highly defensive of mac & co13:28
draz|lab... awesome13:28
ybit</sarcasm> i'm assuming13:29
ybitspeak of mac&co believing in gnu death camps, kanzure, did he ever put a link to the git repo on diybio.org?13:30
kanzureno13:32
stragesgnu death camps?13:32
strageswtf?13:32
kanzurestrages: it was a quote from slashdot13:32
ybithi strages 13:32
draz|labah yes13:32
kanzurestrages: http://news.slashdot.org/comments.pl?sid=1333265&cid=2903471513:32
draz|labgnu death camps13:33
strageshey ybit13:33
draz|labkanzure: so does jcline know anything?13:33
kanzuredoes anyone know anyone at the Chinese WTA?13:33
kanzuredraz|lab: yes13:33
kanzuredraz|lab: one week he decided to read all of the microfluidic EWOD papers and subsequently build a device13:33
draz|labnot bad13:33
any44613385While 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
kanzurehe seems to have a background in EE and bio at the same time13:34
draz|labapparently I'm the only one in this lab that could do westerns properly the first time13:34
draz|labhmph13:34
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
kanzuredraz|lab: I need an ontology or way of organizing a few thousand biology lab protocols13:34
any44613385this smells like a commonality to aspergers, in some yet-unknown fashion13:35
draz|labkanzure: do a tree, like you would for taxonomy, start with qualitative or quantitative, then what it detects, then accuracy13:35
kanzureany44613385: there was a study once that I read that pinpointed the region responsible for facial issues in aspergers13:35
kanzuredraz|lab: "what it detects" ?13:36
kanzureare you sure that's the best way to do it?13:36
kanzurenot by the technique being used?13:36
any44613385kanzure, 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 anyhow13:36
kanzureyeah it's a common issue- look at people next time they smile13:37
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 have13:37
kanzureyou'll see that many people can't control one side of their smile13:37
draz|labdetects is the wrong word13:37
draz|laboh shit13:38
any44613385what 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 expressions13:38
draz|labyou meant other stuff too13:38
kanzuresome lab techniques do not involve detection, draz|lab 13:38
draz|lablike isolating enzymes and all that13:38
draz|labyeah13:38
kanzureyes13:38
draz|labman, I'm working off 4 hours sleep and a secondhand potsmoke headache13:38
draz|labgimme a minute13:38
kanzureany44613385: I don't think the lack of facial muscles correlates to aspergers. I'm fairly certain it's a common occurence.13:38
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kanzuregah, why can't I find my papers13:39
kanzurethis is bothersome13:39
draz|labDNA/RNA/Cell Culture/etc|technique used|13:39
draz|labI dunno, actually13:40
kanzureno13:40
any44613385kanzure, i see a cultural thing to "smile control", if you smile you are not serious, therefore to get a point across you must frown13:40
kanzureyes it's a hard question13:40
draz|labI don't smile or frown consciously13:40
draz|labalso I am hella bored13:41
draz|labwaiting for my gel to set13:41
any44613385i 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 frown13:41
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kanzureit's also called being good at telling a joke13:42
kanzureif you start cracking up before the joke gets out, it's less effective13:42
any44613385yeas, but the switching back and forth is unnerving and distracting13:43
ybittimschmidt__: 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
any44613385i have no kids13:43
stragesdraz|lab: electrophoresis?13:44
ybitmaybe the dream's a sign of spending too much time on irc :)13:44
ybitany44613385 meet strages, strages meet any4461338513:45
any44613385?13:45
ybitlocal alabamians13:45
any44613385i wass about to say13:46
strageshi any4461338513:46
any44613385hi strages13:46
ybitany44613385, you're ~2 hours away from huntsville, correct?13:46
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katsmeowand 30 min from Bham13:46
stragesphenix city?13:46
katsmeowno, 15 min outside Pell City13:47
stragesah ok13:47
katsmeowyou are up near ybit13:48
stragesI am13:48
ybitstrages is in huntsville13:48
stragesI live in west huntsville currently13:48
ybiti have several family members in that area13:49
ybitthe Englands13:49
stragesChris England?13:49
strages25 or 26?13:49
ybithrm, never heard of the guy13:50
stragesnevermind then13:50
ybitprobably related though13:50
strageswent to highschool with him13:50
stragesin Athens13:50
ybitah, no. huntsville, don't know anyone in the family in athens13:50
stragesok13:50
ybitanyway, katsmeow, strages is organizing a hackerspace convention that is set to take place in september, and you should be there :)13:52
ybitstrages is part of #makerslocal 13:52
katsmeowi 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 boat13:53
ybit:)13:53
ybitkatsmeow: where to?13:53
stragesseasteading?13:53
katsmeowi don't care where to, as long as i can hoist sail and anchor and relocate13:53
ybityou sound a lot like Phreedom13:53
ybithe wants his own hovercraft13:54
katsmeowtell him to get tomaking it13:54
ybitgive him ~15 years13:54
katsmeowcompany in Louisiana makes and sells hovercraft kits that will sustain 10ft in horizontal travel13:55
ybiti don't doubt that he's going to have it built13:55
katsmeowcompany in Fla makes flying boats that will sustain 60ft, but will not hover13:55
ybithe had a sweet plan for a RV if i can find it...13:55
ybitkatsmeow: link maybe?13:56
strageskatsmeow: flying boats?13:56
stragesyou got a link to that company?13:56
ybitthat's what i'm wanting to see, never heard of them13:56
ybitoh i see13:56
ybitjust google for it strages 13:57
ybitand preferablly, use www2.sandbox.google.com like katsmeow found yesterday13:57
* katsmeow checks Tiggr's data13:57
ybithrm, it doesn't give images like google.com does13:57
katsmeowit's beta13:57
ybitthough it is 3x faster as mention previously13:57
ybitanyway, when you get your boat katsmeow, come visit me in a coruna, spain one day13:59
katsmeowwhy coruna?14:00
ybitgreat weather, spain, spanish, europe14:00
katsmeowah14:00
katsmeowi'd hate to have a passport issue with them and never get outa prison14:01
katsmeowpolitical rules can ruin anything14:01
ybitmiddle-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 earthquakes14:02
katsmeowcusswords, i have *got* to merge these dbs14:02
ybitwhich dbs?14:02
katsmeowmass dowloads into the hand-edited one14:02
ybitit is appealing that ~50km away from the coast, you are essentially your own nation-state14:02
ybit?14:02
ybitlink?14:03
katsmeowi have /kb/boats/ , but no link back to mirroring an entire site14:03
katsmeownone online14:04
katsmeowit's over 500gig14:04
katsmeowafk, brb14:04
ybithttp://www.youtube.com/watch?v=KzxuEOxYSLE&NR=1&feature=fvwp14:05
ybitcar-boat challenge..14:05
katsmeowbak14:08
* ybit wants to see a vid of http://cache.gizmodo.com/assets/resources/2007/10/FlyingBoatGI.jpg14:09
* katsmeow wants a walkabout tour of the Alinghi14:10
katsmeowybit, that url you gave looks like the hover boat  i was thinking of14:10
katsmeowit's slso sold with enclosed cockput, and 6 passenger14:10
fennwhatever 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
katsmeowif you find their site, they have video14:12
strageswhen I say flying boat I mean like a Catalina or something14:13
stragessomething I can live in14:13
katsmeow"normal" hovercraft : http://www.neoterichovercraft.com/14:14
katsmeowCatalina / PBY would use a lot of fuel and maintenance time14:14
katsmeowand require faa certs14:14
stragesaye14:14
draz|labahhahahaha14:16
draz|labmy lab is on cnn14:16
katsmeowhttp://www.hovercraft.com/content/index.php14:21
katsmeowpage has movies14:21
draz|labhttp://www.cnn.com/2009/HEALTH/07/14/heart.stem.cells/index.html14:28
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kanzurehttp://xkcd.com/149/14:34
kanzurevid: http://www.boingboing.net/2009/02/27/sudo-make-me-a-sandw.html14:34
katsmeow-afkstrages , 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 hulls14:37
katsmeow-afkor it may not be interesting14:37
katsmeow-afkdownside is at one psi, over water, the water surface will be depressed  a foot14:37
stragesneat14:39
katsmeow-afkbut the boat could still "fly" up onto sand bars, over low islands, or unbeach itself14:39
katsmeow-afkand 60 tons is more boat than you are likely to build14:39
katsmeow-afkonce out of the water on air cushion, speed really builds14:39
katsmeow-afksome large hydrofoil sailboats have hit 50mph and towed multiple skiers14:40
katsmeow-afki 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 200mph14:42
katsmeow-afkthey could do it with a 90ft x 300ft total "dock" area, given 1000ton uboats14:44
katsmeow-afk300ft isn't a problem, given ww2 uboats are ~300ft long14:44
katsmeow-afkspeaking 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 draft14:46
katsmeow-afkat 2ft, the space tween the hulls grabbed enough air when in forward motion, the boat tried to fly, but wasn't designed for it14:47
katsmeow-afkbut it made good speed, because the bottoms of the two hulls was esentially air once inflated, so friction was zero14:48
katsmeow-afkbbl14:48
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ybitwhat's with yet another link to sudo make me a sandwich..?15:05
ybitkatsmeow-afk: meh, those hovercraft are small15:06
ybiti was thinking something more like http://en.wikipedia.org/wiki/Mountbatten_class_hovercraft or http://en.wikipedia.org/wiki/Zubr_class_LCAC15:07
ybitso, draz|lab, you're in chicago?15:08
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draz|labybit: no, the lee lab15:09
ybitkanzure, what's smari been doing lately? 15:09
draz|labybit: buffalo15:09
ybiti saw15:09
ybitthink i remember this coming up once too15:09
kanzureybit: trying to stop iceland from exploding15:19
bkerokanzure: Do you have any idea how big NCBI is?15:20
genehackerhovercraft?15:26
genehackerhow can one prevent iceland from exploding...15:26
ybitby employing Brain and keeping Pinky away from him15:52
kanzurebkero: no. many many terabtes.15:53
kanzureterabytes15:53
bkeroAt least it's in the right order of magnitude.15:54
kanzuretodo: subclass SetTranslation in Transform in skdb/geom/geom.py15:56
genehackeryuck artifically created scarcity16:01
ybitbkero: 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 maybe16:51
ybitit's never bad to back-up after all16:51
* ybit wonders what their back-up solution is there16:51
bkeroybit: I happen to have a lab with a lot of space.16:52
ybitbkero: maybe so, but enough for that...?16:56
bkeroI still need to know how many Terabytes it is16:57
ybitemail them?16:58
genehackerybit bkero has something like 200 TB of tape drive16:59
genehackerisn't that right bkero?16:59
bkeroThere's a stack of LTO-4 tapes here that will hold 1.6T each if that's what you're referring to17:00
genehackerbut we could use a second copy of NCBI17:12
bkeroThis copy will be on I2 :)17:13
bkeroWhich means gigabit to all universities!17:13
kanzurebkero: would you be willing to back me up?17:14
bkerokanzure: back you up?17:15
genehackerin case of fire, drought, zombie apocalypse, swineflu pandemic, or nuclear holocaust17:15
kanzuremy data17:15
bkeroHow much is there?17:15
kanzure700~ GB17:16
kanzurenot including movies17:16
kanzurenot including music17:16
bkeroMaybe17:17
bkeroDo you have iperf installed?17:17
genehackerthere's a /movies/?17:17
kanzuregenehacker: no17:17
kanzurebkero: no17:17
bkerokanzure: apt-get it real quick, it's very small17:17
genehackerok17:17
kanzurebkero: ok17:17
bkerokanzure: iperf -c ponderosa.osuosl.org17:18
kanzure89 Mbits/sec17:18
bkeroNot bad speed17:18
kanzurefenn: do you have a reference for the "colder => better" ?17:19
fennno17:20
fenni remember reading somewhere that cold climates were good for thinking17:20
fenni think it was "guns, germs, and steel"17:20
kanzurejared diamond17:21
* kanzure wonders if he should have read that by now17:21
fennand it's well known that you can't think straight when overheating17:21
kanzureit's one of those books you read by osmosis just by being around people who have read it17:21
fennso apply some linear wishful thinking...17:21
kanzureyou mean eliezer-thinking?17:21
fenni didnt actually read it17:21
genehackerah yes guns germs and steel is an interesting book17:21
fennreally more like interpolation than extrapolation17:22
genehackerhad to know stuff about it for one of my classes in high school17:22
CIA-38skdb: kanzure * r 140a67a2d68e /geom/geom.py: convert from assert to raise17:22
kanzuregenehacker: one of your classes required you to read it?17:22
kanzurewas this high school or the fake high school?17:22
kanzureis stormfront.org the white supremacy forum?17:23
kanzurenevermind. 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 that17:24
fennhistorically people haven't been living in one place for very long anyway17:25
kanzureright17:25
fennwhat's a couple thousand years wrt evolution17:25
kanzureand even if they were, they would quickly mate with some other groups that weren't local17:26
genehackerno we didn't read it17:31
genehackerwe watched a movie about it17:31
genehackerreal highschool17:31
genehackernot the fake-highschool-college-highschool17:32
kanzurethere was a movie?17:33
genehackerI think there was something like a TV documentary thing17:35
fennhttp://www.pbs.org/gunsgermssteel/17:36
genehackeryeah I think it's that one17:36
genehackernothing about cold climates17:37
genehackeras far as I can recall17:37
genehackerhis main premise is that domesticated plants and animals can move more easily accross same latitudes than different latitudes17:38
fennyou'd expect there to be more about the link between heat and not being able to think straight17:40
fenn:%s/foo\(.*\)/\1/17:41
fennfoobar -> bar17:41
kanzureI'm trying to do this:17:43
kanzure:%s/\([0-9].\)*/\1/17:44
kanzuredoesn't seem to work17:44
kanzureok fixed17:47
CIA-38brain: 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/2okLV17:47
kanzuredoes anyone have a entrez gene id -> entrez gene name script?17:48
draz|labkanzure: if you're using biopython it's really easy17:48
draz|labit'sz something like:17:48
draz|labsomething = entrez.fetch(db=nucleotide,id=blah) ; something2 = entrez.read(something)17:49
draz|labit's very similar to that17:49
genehackerwell this one company is marketing a brain cooler for people whose brains overheat17:51
genehackeror something like that17:51
draz|labI think my brain overheated today17:52
draz|labbut that was fromt oo much coffee, too hot a building, and not enough sleep17:52
-!- draz|lab is now known as drazak17:52
genehackerthere's a reference to heat making you not think straight in Macbeth17:54
genehackerhey I can use qcad in linux right?18:00
genehackersudo apt-get qcad correct?18:00
kanzuredrazak: got it18:00
kanzureer, got it many minutes ago :p18:01
kanzureut anyway, it's working now18:01
kanzureI was thinking of maybe using a wet towel around the head18:01
genehackerare you over clocking yourself?18:01
genehackerwell the sharper image(or what's left of them anyway)18:02
genehackerused to sell a device you place around your neck to cool you down18:02
kanzureno, I don't want to overclock myself 18:03
kanzurethere's just something weird about how I'm always sweating18:03
kanzureit's really not conducive to work18:03
genehackerthe idea is that since you get a lot of bloodflow through your neck you can cool yourself down18:04
genehackerany turn up the airconditioning18:04
fenn"overclocking considered harmful" http://www.logarithmic.net/pfh/overclocking18:04
kanzurewasn't there something similar on supermemo.com ?18:05
kanzurefenn: is the connection slow for you?18:06
kanzurewtf18:08
kanzurethe gene with entrez id 376475 does not seem to have a gene symbol 18:09
kanzurebut it seems to have the name "XXYorf1-related protein"18:09
kanzuresorry, "CXYorf1-related protein"18:09
drazakthere's a bunch like  that18:10
kanzureorly?18:11
CIA-38brain: kanzure master * raa2e7bc / scripts/annotations.py : added annotations.py - figure out entrez gene name and symbols from entrez identification numbers - http://bit.ly/eerLy18:12
CIA-38brain: kanzure master * r1739c01 / scripts/annotations.py : minor alterations to the gene name retrieval script - http://bit.ly/13vahA18:12
CIA-38brain: 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/2vH2318:12
ybitbrain is...18:24
ybitat adl?18:24
ybitor only github18:24
kanzuregithub18:26
drazakkanzure: yeah18:31
drazakkanzure: a particular geneid will be tagged if you search for like, vegf, but it'll be the whole chromosome18:31
CIA-38brain: kanzure master * ra6de58b / (3 files): find longest brain gene name - http://bit.ly/O2Szh18:33
CIA-38brain: kanzure master * r1f5dbab / allenbraininstitute/brain_genes.yaml : fix brain_genes.yaml - http://bit.ly/13gUI418:33
CIA-38brain: 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/Flgz118:33
-!- 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)18:34
ybitvegetarians are always cold, become vegetarian if you are looking to overclock your system ;)18:45
kanzuregah, I'm not looking to overclock18:47
kanzureI'm not normal .. my body is too hot most of the time (maybe)18:47
kanzureor I have some sort of weird sweating condition18:47
kanzureor I have an aversion to heat18:48
kanzureI'm really not sure what it could be.18:48
* kanzure needs to design a few experiments18:48
genehackerhttp://brodylab.eng.uci.edu/~jpbrody/reynolds/lowpurcell.html18:57
genehackerinterestin article about low reynolds number propulsion18:59
CIA-38brain: kanzure master * r1732b44 / (3 files in 2 dirs): added mouse brain genes, also found brain genes by length - http://bit.ly/1E7IF319:02
kanzurehm need to find a way to organize this information by organelle19:11
genehackerblast pump broke on my heat exchanger19:11
kanzurefor instance, synaptogyrin is involved in vesicles, not necessarily any other part of a neuron19:11
kanzurehuh, 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."19:13
CIA-38brain: 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/bIhOD19:21
CIA-38brain: kanzure master * rcce5a12 / scripts/filter.sh : simple grep wrapper script - http://bit.ly/14QbMq19:26
genehackertesting my personal cooling system19:38
genehackercannot discern if it is workign19:39
genehackerit works, but not too well19:43
genehackeroh yeah it works19:49
drazaklol19:51
drazakwe have like a billion frezers at the lab19:52
drazakI could just stick my head in one for 30secs19:52
genehackerdo you live in texas where it's hot outside?19:55
drazakno19:56
drazakit was 91 and 87% humidity here19:56
genehackeroh that's even worse19:56
drazakyeah19:56
drazakit's nasty here19:56
genehackerI need more heat transfer though19:57
drazakand the freezers make the lab hot19:57
genehackervinyl tubing doesn't work that well at transferin heat to ice19:57
genehackerheh damn thermodynamics19:57
genehackerideally we could harness all the energy in heat so that coolers generate electricity as opposed to using it19:58
genehackerthat's odd20:00
genehackerwhy's my battery pack heating up?20:00
kanzuredoes anyone have a photograph of a myostatin-inhibited silverback gorilla?20:03
genehackermyostatin 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
genehackeris this something that happened naturally?20:12
kanzureapparently20:14
genehackercool20:14
genehackerare battery pack supposed to get hot?20:18
drazakyes20:18
genehackerhot enough to nearly burn?20:18
genehackerdo you know why?20:18
drazakdo you know the chemistry behind batteries?20:20
drazakor stuff about electricity?20:20
drazakresistence=heat20:20
drazakdrawing current=heat20:20
genehackerok understood20:21
genehackerthen I need to move my batteries...20:21
katsmeow-afkwhy didn't Gumilid Lantod convert the python into steaks before the snake got to his arms?20:24
katsmeow-afkas the snake had a mouthful of his foot, surely he could locate the snake's head and remove it20:24
genehackerwith what?20:27
katsmeow-afkhis machete20:28
kanzurewhat might happen if you started slowly replacing the genes that encode the megaptera brain?20:35
genehackerwith what genes?20:40
genehackerwhat are you trying to do with whale brains?20:40
genehackermake 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"20:41
kanzureheh Melanie Swan's snp data: http://www.snpedia.com/index.php/User:MelanieSwan20:44
-!- genehacker [n=noko@pool-173-57-41-223.dllstx.fios.verizon.net] has quit []21:06
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-!- splicer [n=patrik@h55n1c1o261.bredband.skanova.com] has joined #hplusroadmap21:19
genehackerfenn you run qcad correct21:22
genehacker?21:22
ybitgenehacker: what do you need to know?21:25
genehackerhow to install qcad community edition on linux21:26
genehackerapparently I have to compile it from source21:26
ybitgenehacker: what's wrong with apt-get install qcad?21:27
genehackeroh let me try that21:28
genehackerwow21:29
ybitnext time you are curious if something is in the ubuntu repo, try this from the cli: apt-cache search <whatever_keyword>21:29
ybitapt-cache search qcad21:29
ybitfor instance21:29
genehackerthank you ybit21:29
ybitapt-cache search bio21:29
ybitetc21:29
genehackerI think I love linux now21:29
ybitnp21:29
ybitwelcome to the family21:29
ybitit only gets better21:30
genehackeryou know any good irc clients?21:33
ybitgenehacker: irssi21:34
ybityou'll really like screen + irssi21:34
ybitotherwise, konversation is n00b friendly21:34
ybitsome like xchat21:34
ybitelites prefer screen + irssi or screen + weechat21:34
ybitscreen allows you to restart your X server and resume your shell sessions without losing any data21:35
ybiti.e. you could restart your X server and when you resumed your irc client, you wouldn't lose any of the chat conversation21:36
ybitalso, if you were to ssh tunnel into your computer from some other computer you could view the screen shells from there too21:36
ybitby just doing screen -d -r <screen #>21:36
ybittrue elites no weechat is where it's @ though ;)21:37
* ybit has recently become fond of it21:37
ybitit's highly extensible21:37
ybitthe command line (cli for short) will become your best friend just to let you know21:40
ybitit allows you to do things much quicker than clickity clicking away21:40
ybityou will eventually move into the text editing wars as well, vim or emacs (screw the rest)21:42
ybitthe shell wars were never big, but zsh rules the roost imho21:42
genehackerwhat's this git thing everyone talks about21:42
ybitit's a version control system for files21:43
ybitapt-cache search git21:43
ybitoh right.. so since you are new.. man pages and google will help a lot21:43
ybitwhen you download software type in 'man <software' into your cli prompt21:43
ybitman git21:44
ybitman man21:44
ybitman vim21:44
ybitman emacs21:44
ybitetc21:44
ybitit will give you an overview of the software, its commands, and related man pages21:44
ybiti'm sure there are several 'new to linux?' type how-tos out there as well21:45
ybitsay you want to clone a repo, you just do 'git clone <repoaddress>'21:45
ybityou'll be using git status, git add <file(s)>, git commit -a -m "<comment>" and git push often before long21:47
ybityour command line is a scripting language itself21:48
ybitbash, zsh, etc.21:48
ybitecho "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.m3u21:49
ybitthat's a bad example of code, but it shows what can be done21:49
ybitnotice the | symbol?21:49
ybitthat's called piping21:50
ybityou can pipe output to other programs21:50
ybitin this case, i was able to pipe the output from the program 'echo' to the program 'at'21:50
ybitthe double ampersand (&&) means to perform a command after another has been completed21:51
ybitthe semi-colon is similar21:52
ybitthe double ampersands wait for a program to exit successfully before continuing21:52
ybitthe semi-colon ";" executes the command regardless if the previous program exited succesffully21:52
ybitanother example...21:53
ybitfor file in * ; do cp $file $file.bak; done21:53
ybitthis makes a simple backup of all files in a directory21:53
ybitalso... (and you really should be thankful i'm saving you time ;)21:53
ybit...aliases..21:53
ybitthey become helpful the more you use a shell21:53
ybityou can make your own commands (called aliases) by editing you shell's config file21:54
ybitfor bash, and since you are using ubuntu, you are by default using bash, the config file is /home/genehacker/.bashrc21:54
ybityou would do something like vim ~/.bashrc or emacs ~/.bashrc21:55
ybitnano ~/.bashrc21:55
ybitnano is alright if you are new to text editing using a cli21:55
genehackerok21:55
ybitapt-get install vim emacs nano21:55
ybiteither or all doesn't matter21:55
ybitso.. to create your own command.. you will put this in your config...21:56
ybitalias grep='grep -i -r'21:56
ybitalias mv='mv -i'21:56
ybitalias "hci"='runhaskell Setup clean && runhaskell Setup configure --prefix=$HOME --user && runhaskell Setup build && runhaskell Setup install'21:56
ybitthose are a few i have in mine21:56
ybityou can have aliases for different ssh sessions as well21:57
ybitfor kicks, you can do "sweeet"="echo 'this is so cool!'"21:58
ybitsave the file and exit21:59
ybitand from the cli type..   source ~/.bashrc21:59
ybitthen type your alias/new command21:59
ybit</mini_linux_101_lecture>21:59
ybitthe alias is sweeet (just in case you were wondering)22:01
ybitand lastly /join #linux and /join #ubuntu from whatever irc client you decide to use, that will be a big help for you22:05
kanzureybit: 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
ybitsomething fun to show complete n00bs is to show them 'apt-get install <awesome_looking_3d_game>' openarena tremulous sauerbraten etc22:10
ybitapt-cache search git will show git-core22:10
ybitit's keyword search22:10
kanzuresure22:11
ybitanyway, and then ask them if they know of any other operating system that by default allows them to freely download such games22:11
ybitalways brings a smile to their faces22:11
kanzurehave you tried bzflag?22:11
ybit(after showing the game in action of course)22:11
ybityeah22:12
kanzurehow is it?22:12
ybitbeen a long time, i didn't like the controls, seemed really slow compared to openarena22:12
ybitwhich is my addiction..22:12
ybithowever.. since this fresh install of gentoo, i've kept myself from playing games22:12
ybiti have more of a mind game going with myself now22:12
kanzureI only play tetris. do you have any recommendations? I don't do FPSes.22:12
ybit'how many tasks can i complete in a day' is one objective of this game22:13
kanzurethe problem with todo lists and me is that I inevitably begin spending four or five hours a day obsessively updating the todo list22:13
ybiter.. well... what do you want?22:13
ybitartisitic intepretations of 8bit games? because i have several 8 bit game recommendations22:13
kanzuresure22:13
ybitif you want rts, spring is the way to go22:13
ybitgles is more traditional22:14
ybitbtw, genehacker, you'll probably like battle (of|for) wesnoth22:14
ybitapt-cache search wesnoth22:14
kanzureyeah I played wesnoth for a while22:14
kanzurethen I broke down and got starcraft22:14
ybitgames # ls22:14
ybit8bit_killer              MondrianProvoked_1.1.exe  aether      gabaaba.exe             mr_heart_loves_you_very_much.zip  papermoon-gamma-public22:14
kanzureer, wait22:14
ybitBetween_v5_UnixSource    Passage_v3_UnixSource     battlecode  games i've yet to play  n_v1linux                         pingpong.exe22:14
kanzureit's not wesnoth that I am thinking of22:14
ybitDisco Space Invader.zip  WorldOfGoo.tar.bz2        bgm.dll     judith.tar.gz           openarena-0.8.1                   sunset_runner.exe22:14
ybitDon't Look Back.exe      Wubly_final_.zip          bloody.zip  mod-x                   owlcountry-win.zip22:15
kanzurewhat's the warcraft-like rts that I'm thinking of?22:15
kanzureheh World of Goo. is that supergoo?22:15
kanzurethere used to be this app called supergoo, and I spent way too many hours with it22:15
ybitpapermoon-gamma and passage are two neat games22:15
kanzurealex4 is worth checking out22:16
kanzureeven if you're trying to stop playing games22:16
kanzureit's rather short22:16
ybitno, it's a playstation2|3 (i think) or maybe it was a pc game that was ported to linux22:16
ybityou'll have to torrent it22:16
kanzurecan't seem to torrent properly any more22:16
ybitthere was some action-adventure game that i had...22:17
kanzureany time I try any port number, every thing is shaped22:17
ybit256_seconds.zip        DoomedPlanet.zip  Pazzon.zip  bloody_zombies.zip                   fireflies-osx.zip           shitgame.zip22:17
ybit4mins33secs.zip        Execution.zip     Torque.zip  dive.zip                             flow_04142006.zip           stdbits.zip22:17
ybitBlottoBrace_Final.rar  Frozzd.zip        arcade.zip  downloads\TheDepthsToWhichISink.zip  papermoon-gamma-public.zip22:17
ybitthose are games i never got around to playing22:17
ybitgenehacker: there are also several decent 3d mmorpg games22:18
genehackerworld of goo for linux?22:19
genehackerI don't play rpgs22:20
* ybit became a puzzle addict before moving onto math and logic problems, before finally and lastly moving onto coding problems22:20
ybitnow if i can find some links...22:20
katsmeow-afkvectorTD22:22
ybitgenehacker, you'll also like these programs gimp inkscape blender and a bunch of other programs from the ubuntustudio repo22:22
genehackerI don't use blender22:23
genehackerhave no use22:23
ybithttp://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
ybitare all fun22:26
ybitif you have time to spare22:26
ybitso are the numb3rs genius challenges22:27
ybiti ended up creating my 'game of life' though and have been creating rules with it. it's a way of ensuring productivity22:32
ybitit's fun and productive, can't beat it22:33
ybitfifo_dir                = /tmp22:34
ybitsocket_dir              = /tmp22:34
ybitcon_path               = $HOME/.local/share/uzbl/uzbl.png22:34
ybitwhoops that was supposed to go to someone having problems in #uzbl22:37
-!- mason-l [n=x@202-89-188-136.static.dsl.amnet.net.au] has joined #hplusroadmap22:44
ybitmason-l: welcome to 'where all the cool kids hang'22:44
ybithttp://adl.serveftp.org/papers may be of interest22:44
ybitfenn and kanzure have been putting a lot of work into this git repo: http://adl.serftp.org/skdb.git22:45
ybitalso on github, check out http://github.com/kanzure22:45
ybitmason-l: relevant mailing list: groups.google.com/group/diytranshumanist22:47
ybitwasn't andrew hessel in australia...?22:53
ybithe had some word on curing cancer iirc22:57
ybits/word/work22:57
genehackertime to see if I can't see perseids23:16
ybitdon't forget a helment genehacker ;)23:31
ybitmason-l is helping to form a hackerspace in perth, western australia if anyone is interested. i'm guessing most everyone is sleeping23:31
genehackerwe need to set up a hackerspace system23:46
ybitgo on..23:46
genehackerso hackers all over the world can know where hackerspace are and collaborate with them23:47
genehackerwhenever they happen to be in the area23:47
genehackersorta like how masonic lodges used to be23:47
ybitgenehacker: #hackerspaces might be interested in discussing this when people are actually around and not sleeping23:47
strageshackerspaces.org23:47
genehackeralso isn't there some sort of algorithm for approximated a circle of radius r with n line segments?23:48
genehacker*approximating23:49

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