2009-07-31.log

--- Day changed Fri Jul 31 2009
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wrldpc2dear lazyweb:  please bless Patricia.  Whoever she might be.00:17
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Ian_Daniherhttp://www.sciencemadness.org/talk/viewthread.php?tid=1163801:01
Ian_DaniherX.x01:02
Ian_Daniherbad press for DIY bio work01:02
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genehackercool and practical are what I pick04:30
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kanzureIan_Daniher: Meredith is a good friend of ours in here.07:01
kanzureshe sometimes comes in and commits code etc.07:02
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kanzurefaboo07:22
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kanzurehttp://i622.photobucket.com/albums/tt308/goku152008/dragonball%20evolution/jhg.jpg07:40
kanzuregood times .. http://web.archive.org/web/20021205011038/animeu.hey.nu/index2.php07:41
kanzurehttp://web.archive.org/web/20020601133734/http://www.jpavg.com/~au/07:44
kanzurehttp://web.archive.org/web/20020924020150/animeu.hey.nu/index.php?a=multiverse&valid_user=&password=&color1=373637&color2=20202008:00
kanzurehahah08:01
kanzurehttp://web.archive.org/web/20020930222119/animeu.hey.nu/index.php?a=ranks&valid_user=&password=&color1=373637&color2=20202008:01
kanzureyeah that's definitely over 900008:01
kanzurefenn: paths.py seg faults on "random sweep". er, at least, it did the first time but not the second time.08:19
kanzure"prototype vehicle for the blind: 08:36
kanzure"prototype vehicle for the blind: How are they going to know when I flip them the bird? Do I have to make chirping noises?08:36
kanzuretemplate.yaml seems to have some issues for skdb/packages/legos/08:52
kanzureI'm not entirely sure how to specify "there could be any number of interfaces, but they are all of either type Peg or type Hole"08:52
kanzurebecause previously in skdb/packages/screw/template.yaml, we just said "they all have only these three interfaces. suck it."08:53
kanzurehttp://adl.serveftp.org/papers/Fundamental%20lego%20lengths.pdf09:08
kanzureoh I guess you can also see that on the web here: http://www.owlnet.rice.edu/~elec201/Book/legos.html09:09
kanzurehomemade lego pneumatic air muscle: http://www.stop4stuff.com/lego/technic/pneumatic/air-muscle/09:09
kanzure"Worn-out molds are encased in the foundations of buildings to prevent them from falling into competitors' hands." hahah09:12
kanzure600 pieces per second of manufacturing? jeebus09:13
kanzure"To put this in context, if all the Lego bricks ever produced were to be divided equally among a world population of six billion, each person would have 62 Lego bricks."09:13
kanzureer, does anyone have lego dimensions/specs?09:13
kanzurehttp://www.lugnet.com/~330/FAQ/Build/dimensions09:14
kanzure"The actual dimension (rather than the ratios) can be determined by carefully measuring a properly constructed “wall” of bricks. Vertical dimensions are prone to error caused by sloppy stacking, but long horizontal walls constructed from two or more layers of overlapping bricks are not prone to such error. A wall of this type built from Technic beams made in the late 1990’s shows that the stud pitch distance is 7.986 millimeters, plus or minus 2 microns, when the parts are at 25 degrees centigrade (77 degrees Farenheit). "09:14
kanzureheh they included the temperature09:14
kanzurelego minifig dimensions: http://snively.blogspot.com/2009/04/lego-minifig-dimensions.html09:23
kanzurethe uncertainty seems to be 0.01mm09:23
kanzurealthough fillets are guessed09:23
kanzureI have no idea if the thigh dimension (R3.54) is a radius or not, because the line goes across the part..09:24
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kanzuredoes anyone know how far away from the edge of a brick that pegs begin to start?09:54
kanzurestud diameter is 4.5mm, stud height is 1.7mm.. blah.09:56
kanzurelego earth: http://farm4.static.flickr.com/3596/3609309331_0255153126.jpg?v=0 heh10:00
kanzurewhich is from: http://weblogs.java.net/blog/kohsuke/archive/2009/06/afterjavaone_pr.html10:00
kanzureI guess I can assume that they are evenly spaced10:01
kanzureotherwise what's the point?10:01
kanzurespacing of stud centers: 8mm10:02
kanzureso stud center spacing - stud diameter = 3 mm from the edge of one peg to the edge of another peg/stud10:02
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kanzureoops. the spacing would be 3mm+2.5mm=5.5mm from the edge. so 0.5mm from the perimeter of a peg to the nearest edge of the brick?10:14
kanzurethat looks about right: http://ny-image0.etsy.com/il_430xN.69299132.jpg10:15
kanzureharkopen sucks10:27
fennhey shouldnt you be writing a yaml file instead of saying these dimensions into the channel?10:30
fennis that a tongue ring?10:31
fennno it would be too pointy10:31
* fenn wonders why people would want to poke holes in various body parts10:32
kanzureto let out all the hot air10:32
Phreedomfenn: because the hole they already have doesn't have a sufficient throughput? ;)10:32
CIA-43skdb: kanzure * ra9aa78d4814a /packages/legos/ (9 files): first go at a package for legos10:33
kanzureI don't know what to do with skdb/packages/legos/dimensions.yaml10:33
fenni wonder if the stud pitch is due to shrinkage when the brick cools in the mold10:35
fennwhy it's not exactly 8mm10:35
kanzurewhat is stud pitch?10:35
fennthe distance between studs10:35
kanzureoh10:35
kanzurespacing of stud centers: 8mm10:36
kanzurestud pitch: 7.985mm10:36
kanzureok, I should have guessed they were the same variable10:36
fenner, yeah. the distance between stud centers10:36
fenni guess i should actually go measure one10:36
kanzureplease do10:36
kanzuregetting measurements from across the web is totally suck10:36
kanzurepeople don't know how to figure out uncertainties10:36
fennwell, i dont know how to figure out uncertainties either10:37
kanzurewtf10:37
fennsupposedly a caliper is accurate to +- 0.001inch but how do i really know that?10:37
kanzureno, that's not how you do it10:37
fenneh?10:38
kanzurea guide for the estimation of uncertainty of dimensional calibration: http://www.a2la.org/guidance/est_mu_dimen.pdf10:38
fennyou want a statistical sampling of bricks?10:38
fenni'm so not reading that10:39
kanzureonce I was taught how to figure out the uncertainty of analog calipers, somehow involving the number of markings on one of the lengths of the device10:40
kanzurebut that's not a digital caliper10:40
kanzure"As a good rule of thumb, the uncertainty of a measuring device is 50% of the least count"10:41
kanzure"Recall that the least count is the smallest subdivision given on the measuring device."10:41
kanzureheh I like how diybio-boston is planning to have an "impromptu" meeting at igem 200910:44
kanzure"we hereby plan to have an unplanned meeting the week of.."10:44
CIA-43skdb: kanzure * r4498a52d2395 / (9 files in 4 dirs): make the legos package work, add a method to pymates, update todo10:55
kanzureoops, forgot to edit __init__.py10:55
kanzuregrr10:55
CIA-43skdb: kanzure * r714de8f3abbc /packages/legos/__init__.py: fixed __init__.py error because of interfaces being moved around10:56
kanzurecd skdb/packages/legos/ ; py.test test_legos.py #tests pass.10:57
kanzureof course, the tests are totally nonsense at the moment :)10:57
kanzurethis is all kind of pointless since you still can't interactively add legos together under pymates. wah.10:58
kanzuremaybe I'll write the CAD generator in legos.py?10:58
kanzureand then load up some bricks by using the package. mmm.10:58
kanzureslightly more awesome than just using pyldraw.. but the library of parts will be smaller.10:58
fennwell that was totally futile11:01
kanzureno legos?11:01
fennthe toolbox in j-lab is gone (no sign of calipers anywhere)11:01
kanzureon the third floor on the hallway opposite to the hallway with our water fountain, there is an office for Mr. Wood11:01
kanzurehe lends out digital calipers11:01
kanzureBilly Wood, I think11:02
fennwhy would that be more awesome than pyldraw?11:03
kanzurebecause it's homemade :)11:04
kanzureer.11:04
kanzurealso pyldraw is slow when using my stl exporters etc.11:04
fenndoes ldraw have interface information?11:04
kanzureno11:04
fennhow does it know where to move stuff11:04
kanzureit's all just rotations11:04
kanzureer, and offsets11:05
fennthat's still better than doing it from scratch11:05
kanzureyeah I think we can do something like "offset checking" as well for the legos package11:05
fennmeaning what exactly?11:05
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fennhe didn't die :)11:06
kanzuretito claims that he built a lab for his iGEM project at brown .. but when I asked him what he built, he just ran away to a meeting (just a few seconds ago)11:06
kanzureanyway,11:06
kanzure"offset checking" isn't what we should use I guess11:06
kanzureit's not really checking11:06
kanzurethe way that ldraw does things is that it seems to just say "ok put it at an offset of 8 pegs"11:06
kanzureI'll have to look at the file format more closely11:07
* ybit didn't die but some of his screen sessions did due to a power surge11:07
fenn.. and then check if there's an interface at 8 pegs?11:07
kanzuresomething like that :)11:07
kanzureyeah sure, that's a good idea11:07
* ybit refers to himself in third person often11:07
kanzureI guess this would be a "simplified assembly yaml format"11:07
kanzure(for representing a lego assembly thingy)11:07
fenni think assembly should just spit out the coordinates (unless its indeterminate, like plugging in cables or something)11:08
fenni guess we could do both11:08
fennlist the connections, and also the coordinates11:09
fennthat way if you lose or change some configuration you still have some data lying around11:09
fennshould i go find this mister wood?11:09
kanzurecall him billy, he's no "Mr."11:09
fennok11:09
kanzureer, he's not one to prefer "Mr."11:09
kanzureyeah he might be around11:10
kanzurein skdb/packages/legos/data.yaml, if you move around the interfaces, it's ok because they currently have a name attribute ('peg1', 'peg2')11:10
kanzurehowever, one idea I documented in there is just putting a "size" attribute11:10
kanzurethe size:2x2 attribute would tell the lego class to make a generic 2x2 brick or something11:11
kanzureand this would then spit out a number of interfaces,11:11
kanzureand each one having a name that goes in a certain order11:11
kanzuresuch that the top left peg is peg1, and the bottom right is the last peg, or something.11:11
kanzurein some cases lego pieces will not be able to be generated from simple information like "2x2" or "2x4" (since they aren't just a brick)11:11
kanzureso I'm not so sure about spitting out coordinates. I guess a "full dump" should also be an option, but not preferable unless you want to do some sort of long term storage.11:12
kanzureer all of it should be long term storage :p11:12
kanzurels -I=*.pyc is my friend11:14
fennnot there11:16
kanzurefooey11:16
fennhow about a new unit for 7.985mm11:17
kanzurewhat?11:17
kanzure7985 microns?11:17
fennum. for describing individual lego bricks11:17
kanzureFLU = fundamental lego unit11:18
fenn1 stud = 7.985mm11:18
kanzure"fundamental lego unit" gets 34 results on google11:18
kanzure"A Fundamental LEGO Unit (FLU) is equivalent to the length of a LEGO nub"11:18
fennso your brick would have dimensions height: 1.666FLU width: 2FLU length: 4FLU11:19
kanzure2x2 brick?11:19
fenn2x411:19
kanzure"your brick" ?11:19
fennhuh?11:19
kanzureyou said "your brick"11:19
fennjust an example brick11:19
kanzureok11:19
kanzureFLU doesn't look pretty11:20
fenn2x4 was the original brick11:20
kanzure'stud' at least gives you some indication of where the fuck it comes from11:20
fennhow bout just 'lego'?11:20
kanzurenamespace conflict with the tag?11:21
kanzuremight confuse people11:21
fennno11:21
fennlego is a unit11:21
kanzureoh?11:21
fenntag would be !lego or something11:21
kanzureok11:21
kanzuresure, lego is fine11:21
kanzureFLU = 5/16in11:22
fennbah11:22
kanzure?11:22
fennthere's no way some danish guy is going to measure things in inches11:22
kanzureheh it's ok I prefer metric anyway11:23
fennoops height is actually 1.2lego11:23
kanzureer, in which case are you going to use the "lego" unit anyway?11:23
kanzureit's not exactly clear to me11:24
fennstud pitch11:24
kanzurewhy is that so special?11:24
kanzureIt Just Is?11:24
fennbecause it's the basic dimension everything is based on?11:24
kanzureis it?11:25
fennyeah11:25
kanzuresome of these other dimensions seem to have weird coefficients if they are to be converted to lego units11:25
fennit's not brick width because the bricks have to be undersized to fit together11:25
kanzurehow did they come up with these dimension decisions anyway?11:26
kanzurestatistical probability of choking hazard?11:26
CIA-43skdb:  * rb61402513538 /supplemental_units.dat: added fundamental lego unit11:26
fenn8mm?11:27
kanzurewhat about it?11:27
fennthe original legos came with a toy wooden pickup truck11:27
fennit was probably totally arbitrary11:27
kanzureyeah let's not use nice round numbers11:28
kanzure:p11:28
fenn8mm is not round?11:28
kanzurenot sure 8mm is correct11:28
kanzurethe stud pitch measurement claims 7.985mm11:28
kanzureso that's +-.115 of error. kinda big.11:28
fennthere may be digital calipers in my toolbox11:29
fenn.015mm is not big11:29
kanzuregenehacker has some.. so if he shows up today with a utexas hostname, maybe you can get him to ride the elevator up and lend them11:29
kanzureer, .015mm yes sorry11:29
kanzureok, yeah, not big11:30
kanzurelet's not repeat what happened yesterday: divide&conquer..11:30
fennso that's why i'm skeptical it's actually the unit of measure11:30
fennwhat happened yesterday? i tried to use opencascade?11:30
kanzureno, we both wrote different make_arrow() methods :p11:31
kanzureand wasted time doing it11:31
kanzureso if you want to work on skdb/packages/legos/ that's fine, I sprinkled in notes everywhere indicating wtf should be done next11:31
kanzureI'm trying to figure out what I should be doing for now11:31
fennomfg those bastards11:32
fennhttp://en.wikipedia.org/wiki/Belville_(Lego)11:32
fenneven worse than bionicle11:32
kanzureoh maybe I'll make pymates' tests (tests.py, test_part.py, rapid-test.py) use data from the packages instead of data from skdb/pymates/models/11:32
kanzurehow do I do that? tests would have to "import skdb.packages.legos" .. but then the skdb codebase is dependent on the packages, which we want to eventually separate right?11:33
kanzurehahah Lego Ninja theme :)11:35
fennwow Lego Scala is even worse than Belville (can you believe it?)11:36
kanzurefenn: is it ok if pymates unit tests are dependent on packages?11:37
fennsure11:37
kanzurehm it seems pymates.py still has some unvariablized information left over.. yeah that should be fixed hehe.11:39
fennthis could be useful (set inventories) http://www.peeron.com/inv11:39
kanzurenot loading11:39
kanzurethere we go..11:39
kanzurehttp://www.peeron.com/inv/master.txt11:40
fennexample inventory http://www.peeron.com/inv/sets/21004-111:41
kanzureI think  we should not do lego its :p11:42
kanzure*kits11:42
kanzuresimply because of the legal implications11:42
kanzurelego group has been known to be much like the Empire of Star Wars11:42
kanzure*in Star Wars11:42
kanzure"Added to peeron.com on Thu, Jul 30, 2009." huh11:42
fennwell we have to do some kind of assembly or what's the point11:43
kanzureok ok11:43
kanzurewe just won't sell thee particular kits11:43
kanzure*these11:43
fenni dont really care if it's an official lego kit or not11:43
kanzureok great11:43
fennthe list of part names and so on is useful tho11:44
kanzureldraw has its own list btw11:44
kanzurebut anyway.11:44
fennwhat i havent been able to figure out is whether ldraw's part number are the same as lego company11:45
kanzuredid you try to figure it out?11:46
kanzurethe method would be: look at catalog number in ldraw, look at part on lego.com11:46
fennwell, find me a part on lego.com11:46
kanzurehttp://shop.lego.com/ByCatalog/onlinecat.aspx?c=3311:47
kanzureew its in flash11:47
fennsee i think lego.com only sells kits11:48
fenni'm pretty sure it's possible to order individual bricks11:48
kanzurehttp://lego.richfx.com/catalog_lego/january2009/11:48
fennhmm @ http://guide.lugnet.com/partsref/colors/11:54
fennwow these new technic kits hardly even have any bricks in them12:04
fennactually i think this kit doesn't have any bricks at all12:04
fennok it has 13 bricks12:09
fennand a bazillion other parts12:09
fennhttp://www.bong69.com/pages/parts-catalog.php12:11
drazakkanzure: how's it coming?12:12
fennpartscatalog is GPL12:14
fennstrange that he doesn't have a link for source code12:14
fennhmm12:16
fenn"Parts Catalog is written in Delphi 4.  So... if there is a Kylix programer out there that would like t12:16
fennport it to linux, Please let me know and I will send you the source code 12:16
fennmeh. i'm not that attached to it12:17
fennsomething about timesheets12:19
kanzuretimesheets?12:20
* drazak sits on kanzure 12:25
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kanzure"From the time being we also suggest you to remove your vitae from the Internet ( http://heybryan.org/resume/2008-09-21_resume.pdf )."12:46
kanzurethe email came from live.com ?12:46
kanzureReceived: from BLU123-W27 ([65.55.116.9]) by blu0-omc1-s26.blu0.hotmail.com with Microsoft SMTPSVC(6.0.3790.3959);12:47
kanzurefuck you ybit, why'd you have to add my email address to /papers12:49
drazakso apparently my research project is going to be the differentation of mscs into caridomyoblasts12:50
kanzure"sincerely, The organization."12:51
kanzurewho the hell writes emails like that12:51
kanzure"We are an organization preventing young people like you from being victim of the legal system. At your young age, you are not very careful with the content you put on the Internet. As you may know, the Internet access is international."12:51
kanzure"Recently, a paper was published on the creation of sperm-like cells (see Nature http://www.nature.com/news/2009/090729/full/news.2009.646.html ).12:51
kanzureHowever, this paper was retracted (Nature http://www.nature.com/news/2009/090730/full/news.2009.753.html ) by Graham C. Parker, Ph.D. from the journal Stem Cells and Development (Publisher: http://www.liebertonline.com/doi/pdfplus/10.1089/scd.2009.0063 , doi: 10.1089/scd.2009.006, pubmed:http://www.ncbi.nlm.nih.gov/pubmed/19583494 ). Presumably, the paper was not retracted because of its fraudulent content, but because of competitors in the USA unwilling to be spectators of such an amazing discovery."12:51
kanzure"We searched the web with the query string 'In Vitro Derivation of Human Sperm from Embryonic Stem Cells, type: pdf' on google and found that you are hosting the very retracted paper."12:51
kanzureWe suggest you to erase it (we are not the publisher) to avoid being the target of legal threats. These legal threats could come from the following bodies:12:52
kanzureNorth East England Stem Cell Institute in Newcastle;12:52
kanzureUniversity of Newcastle;12:52
kanzureBiology of Reproduction (journal);12:52
kanzureEmbryonic Stem Cells (journal);12:52
kanzureand possibly authors, funding agencies, etc.12:52
kanzureFrom the time being we also suggest you to remove your vitae from the Internet ( http://heybryan.org/resume/2008-09-21_resume.pdf ).12:52
kanzureWe wish you success in life.12:52
kanzuresincerely,12:52
kanzureThe organization.12:52
kanzurep.s.: we did not notify any other bodies, but chances are that others will also search the web for the exact same thing.12:52
kanzurep.s.2: please confirm the reception of this mail.12:52
kanzurewho sends that kind of email from a hotmail account?12:53
kanzurethe paper in question:12:54
kanzurehttp://adl.serveftp.org/papers/In%20vitro%20derivation%20of%20human%20sperm%20from%20embryonic%20stem%20cells.pdf12:54
drazakkanzure: I would change your robots.txt so that they can't search papers12:57
fennwhy was the paper retracted?12:57
kanzuresee sperm_from_esc.zip12:59
fenn"because of competitors in the USA unwilling to be spectators of such an amazing discovery."13:00
fennwtf is that supposed to mean?13:00
fennplagiarism?13:01
kanzure"The journal's editor-in-chief Graham Parker says he took the radical step on 27 July because two paragraphs in the introduction of the paper, entitled 'In Vitro Derivation of Human Sperm from Embryonic Stem Cells',1 had been plagiarised from a 2007 review published in another journal, Biology of Reproduction.2"13:01
kanzurewhat the email said hardly says that13:01
kanzureplagiarism != "unwilling to be spectators of such an amazing discovery"13:01
fennthat's a stupid reason to retract a paper13:02
fenni mean its not like they didnt do the science13:02
kanzure"Although the text of the article modestly refers to these as "sperm-like cells" with "tail-like structures", its title, and the press release which accompanied its publication, refer baldly to human sperm."13:02
kanzure"Nayernia declined to comment to Nature, but an official statement from the university says that the paper's original first author, Jae Ho Lee, a postdoc who has since left the university, was responsible for the plagiarism and has apologized to the authors. "No question has been raised about the science conducted or the conclusions of the research," according to the statement. "The name of Dr Lee has been removed from the first authorship," the statement continues. "The paper will now be submitted to another peer-reviewed academic journal.""13:02
kanzure"The statement also says that the "correct version of the manuscript, upon the request of the journal's editor, had been immediately submitted to the journal during the process of proof reading"."13:03
kanzure"The paper had been published online 'ahead of editing' to avoid undue delay, with proofreading happening after publication to correct textual or copy-editing errors, explains Parker. "But plagiarism can come to light at any point in the publishing process," he says. "Proofing isn't a magical stage that allows authors to correct any inappropriate acts.""13:03
fenndo these people not understand what 'publish' means?13:03
kanzureso if I had this paper in my personal (private) reading collection, and it was "retracted", am I supposed to delete it?13:07
kanzureis that how "retraction" works?13:07
kanzurehow does google find 14k results for site:adl.serveftp.org ?13:09
fenni believe you were supposed to download  the DRM version which checks back with the copyright police to make sure everything is locked up good13:09
fennthat does seem a bit high13:09
ybitwhy would they want your resume removed?13:11
ybitthat's stupid13:11
fennso bad guys can't figure out who own the site13:11
kanzureto me these people seem like the "bad guys" ("The organization")13:12
kanzurenot much of an organization if they have to use hotmail13:12
ybitum.. whois?13:12
fennit all sounds quite odd13:12
fennNature would just send you a cease and desist notice13:12
kanzureas if the retraction wasn't odd enough13:12
-!- Traveler11 [i=fn-javac@dhcp-146-6-214-5.icmb.utexas.edu] has joined #hplusroadmap13:16
kanzurehello Traveler11 13:16
kanzureicmb.utexas.edu?13:16
Traveler11who am i13:16
kanzurejonathan13:16
Traveler11oh13:16
kanzureis that you jonathan?13:16
Traveler11why I'm traveller11?13:16
ybitkanzure: do you want me to change the email to go an alias?13:17
kanzureyou can change your name by typing /nick (something)13:17
ybit+to13:17
Traveler11yeah i'm in the lab heading out to lunch13:17
kanzureybit: I think the file should be deleted13:17
kanzureTraveler11: sorry, I'm not on campus today.. fenn is though.13:17
ybitalright13:17
-!- Traveler11 is now known as nickyourself13:17
ybitdone13:17
kanzurefenn: you around?13:18
-!- nickyourself is now known as jonathancline13:19
jonathanclinespam me.13:19
ybitwell if it isn't the laser printer microfluidics guy himself13:19
kanzure*what the fuck*13:19
kanzure"The organization" sent me a follow up email13:19
ybitjonathancline: i meant to email you the other day13:19
ybitlol, please paste kanzure 13:20
fennyar13:20
kanzureWe are the organization,13:20
kanzureOur mission is to watch over the Internet. We alert kids like you whose behavior is wild on the bold Internet.13:20
kanzureOur funds come from Zeal, and we are powered by the great Lavos. Each week, we download the Internet on an USB hard disk of infinite volume. Then, our team of monkeys and donkeys randomly analyzes with great caution the content of the Internet (on the USB hard disk, of course). We are using state-of-the-art computer software on a cutting-edge installation of Microsoft Windows 7 to dig out the data.13:20
kanzureOur sister organizations include notably http://www.4chan.org/ and http://www.reddit.com/ and http://icanhascheezburger.com/.13:20
kanzureYou can get a picture of our most imminent members here: http://icanhascheezburger.files.wordpress.com/2009/07/funny-pictures-cats-have-a-spaz-attack.jpg13:20
kanzureThey are in charge of supervising the monkeys and the donkeys. These lol cats were selected in regard to their superior genetic landscape.13:20
kanzureWe hope this short description of our organization fulfilled your burning desire to learn about us.13:20
kanzureThe organization.13:20
fennpwnt13:20
kanzure*what the fuck*13:20
jonathanclineforward to fox mulder13:20
jonathanclinefenn, lunch?13:21
CIA-43skdb: kanzure * rbf82aa43d591 /packages/screw/screw.py: some changes to the screw package13:21
fennjonathancline: please input geospatiotemporal coordinates13:21
jonathanclinebtw ellington reaffirmed his goals in a lab meeting today, he wants to refocus on big things like.. augmentation13:22
kanzureneat13:22
kanzurehow goes autogene? or whatever the hell it's called13:22
kanzurelevy's eternal project13:22
jonathanclinefenn: i'm in mbb now, so anything is a couple blocks walk is ok13:23
jonathanclinehe mentioned genomid13:23
fennyou like that mediterranean place on 24th right? shall i meet you there or at mbb?13:24
jonathanclinea plasmid but for an entire genome insertion13:24
ybitjonathancline: i meant to send you an email, but it seems it was just saved as a draft. jonathancline, did you and treadwell ever get further along with the circuit printing inkjet printer idea?13:24
kanzurenot sure how "entire genome insertion" would fare with plasma membranes .. which are not entirely "replicated" per-se.13:24
* ybit didn't sleep much, so excuse the redundancy13:24
jonathanclineybit:  never heard from him, I am ready to order an ink tho13:25
fennkanzure rosalie wants timesheets today :\13:25
kanzurefenn: what the fuck?13:25
jonathanclineybit: i should send him some q's13:25
kanzurejonathancline: be sure to ask fenn about our latest skdb/legos foray13:25
kanzurefenn: guess I'll call rosalie and see what's up13:25
jonathanclinefenn: sounds good for persian.  i'll meet u there13:26
kanzurefenn: I can be there at 3 PM. is that ok?13:26
kanzureor will rosalie not accept timesheets?13:27
fenni think you should ask her13:27
fenni can fill in some numbers and other scribbly marks *hint*13:27
jonathanclinemy lab pc has been spidering "nature biotechnology" in the backgrund.. for 9 days straight13:28
kanzurejonathancline: have you seen 'pyscholar' yet?13:28
kanzureit's my python-based wrappers for zotero13:28
kanzureso that you can use it outside of firefox13:28
kanzurehttp://github.com/kanzure/pyscholar13:29
jonathanclineos/x rocks for viewing pdfs, just scroll thru with the quickview turned on13:29
kanzurenot quite ready for production however13:29
kanzurefenn: she doesn't have a phone number13:29
fennheh13:29
fennemail then?13:29
jonathanclineI need to try the pdf filename script.  if it works it's the bomb13:29
ybit $ whois 65.55.116.913:30
ybitOrgName:    Microsoft Corp 13:30
ybitcould this be 'the organization'?13:30
kanzureybit: no that's just hotmail's server13:30
ybitlol13:30
kanzurejonathancline: people suck at naming pdf files :(13:31
kanzureok, time for me to go grab some lunch13:31
kanzureand then back to playing with legos13:31
kanzuregod I love this job13:31
jonathanclinewhere can i find "cone pt socket set screw 2x4" near downtown13:31
jonathancline"0914"13:32
fennETC machine shop?13:32
fennso jonathancline see you there at 1:45 or so?13:33
jonathanclinei'll bring the screw, maybe we go thre after feeding13:33
jonathanclinei'm leaving now13:33
jonathancline10 mins yeah13:33
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-!- ybit is now known as ybit213:52
-!- ybit2 is now known as ybit313:53
-!- ybit3 is now known as heath13:53
kanzureyou're cloning?13:53
heathsweet13:53
heathi knew it13:53
heathi had used heath a very very long time ago13:54
heathforgot what email i used to register, and had to wait for my inactivity to expire the username13:54
kanzureybit is better13:54
heathoh yeah, that's what i was doing, reclaiming my domain name13:54
* heath agrees13:54
-!- heath is now known as ybit14:02
ybit-_- http://co.de wasn't purchased. something about registrars not allowing for just two characters14:05
ybitand i have to be from germany to purchase this?..14:07
ybitwtf14:07
ybitthe reasons were the contact address has to be from germany and i didn't give a fax # o.O14:08
ybit"The .DE TLD is only open to German citizens and companies, or to people that can justify an administrative contact in Germany. Please note that the DNS need to be properly installed (Zonecheck verification) for the domain to be active."14:09
splicera bit like .us then14:17
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kanzurehello Phreedom 15:03
Phreedomhi :)15:05
kanzuredoes anyone know about BIL:PIL? does Todd run PIL?15:08
kanzure"A chance encounter with Marle at the fair begins a series of adventures and uncovers a pre-millennial evil. In 12000 B.C., when confronting the evil Lavos in the Ocean Palace of the Kingdom of Zeal, Crono dies sacrificing himself to save his friends"15:10
kanzure"Lavos, who awakens and ravages the world in A.D. 1999, is an extraterrestrial parasitic creature that harvests DNA and the Earth's energy for its own growth."15:12
CIA-43skdb: kanzure * r97ca7fc4621b /pymates/ (pymates.py tests.py): fix pymates/tests.py error re: OCC.Display in pymates.py15:24
fennthe availability matrix on the right is pretty cool" http://www.peeron.com/inv/parts/6636px3?ignorepat=y15:34
drazakkanzure: should I upload a bunch of papers on myocardin?15:38
kanzuredrazak: justr put them in a folder of their own :)15:45
drazakk15:45
drazakI'll upload them later tonight, when I'm at home15:46
drazakI emailed them to myself :P15:46
fenncolor availability matrix for a 2x2 brick http://www.peeron.com/inv/colortable/3003?ip=015:47
drazakkanzure: is there a way to make google scholar search for reviews and not just all papers?15:49
kanzureno15:53
kanzuredrazak: try searching "Annual Reviews"16:05
kanzureit's a particular journal just for reviews16:05
kanzurehttp://www.annualreviews.org/16:13
kanzureoptical projection tomography looks sexy16:24
drazakkanzure: I meant so that I can have pyscholar return only reviews :P16:27
kanzureat the moment pyscholar does not search annualreviews.org16:29
drazakkanzure: I thought pyscholar search google scholar and then went out from there16:31
kanzureat the moment it only grabs google scholar results16:39
kanzureyou could do a for loop on the results I guess16:39
kanzureand check for those that have string[:-3] == "pdf" or something16:39
kanzureand then wget those particular files16:39
drazakooh16:40
drazakdoes it bring back the link that will download a pdf from google scholar?16:41
drazakI can write a bashscript that parses for those links then wgets them16:41
kanzuredrazak: yes, it collects the pdf links16:43
kanzurebut you don't need to do a bash script :)16:43
kanzurejust add it in to the python script16:43
drazakI have nfc how to write python :P16:43
* drazak not programmer16:43
kanzureokay, go ahead and write your bash script16:44
kanzurehm where's that article about morphological variation due to predatory evolutionary pressures?16:45
drazakhow do I initiate pyscholar and how do I get it to read my search query file?16:46
kanzureum16:51
drazakor do I just pass it a string16:51
kanzureyou pass it a string16:51
kanzurepyscholar/other-code/16:51
kanzurepython pyscholar.py "my query goes here"16:51
drazakcool, thanks16:51
drazakthen just | to a file?16:52
drazakor >16:52
kanzure>16:52
drazakyeah, I was correcing myself16:52
drazakdrazak@dhcp-84-253:~/pyscholar/other-code$ python pyscholar.py mesenchymal stem cell differentiation myocardin16:56
drazak[]16:56
drazakkanzure: ^16:56
drazakdoesn't work with quotes around it either16:56
kanzuretry ./pyscholar "query here"16:58
kanzureoh fooey16:58
kanzureyeah I'm not sure why it's not working16:59
drazakyeah, no go16:59
kanzureI'm going to blame fenn16:59
drazakfenn: make it work17:01
drazakhe's probably at lunch still17:01
* fenn grunts17:01
kanzureyeah!17:01
* drazak mashes fenn with rocks17:02
kanzurenot really sure why pyscholar has decided to stop working17:03
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drazakthis sucks :(17:05
drazakthe only time I want to use pyscholar, it's broken17:11
kanzureyeah it's still in development17:12
fenni'm not sure it ever actually worked17:12
kanzureand I have a massive headache right now so I'm not thinking straight17:12
drazak:(17:12
* drazak offers kanzure acetiminophen17:12
kanzureI'm wondering why pymates/tests.py and pymates/test_part.py exists..17:13
kanzureI guess test_part.py doesn't call up wxSampleGui17:19
kanzureand tests.py does17:19
fennlooks like you should just copy test_part.py into tests.py17:19
kanzureI think it would be nice to keep some tests in a file that do not call wxSampleGui17:20
kanzurewxSamplesgui17:20
drazakfenn: any idea why pyscholar is broken?17:20
kanzureoh wait17:24
kanzureyou can try "import gsearch" and then "gsearch(q='hello')" from the python interpreter17:25
kanzurecd /home/bryan/code/pyscholar/other-code/17:25
kanzurepython17:25
kanzureimport gsearch17:25
kanzuregsearch.gsearch(q="some query goes here")17:25
kanzureand see if that works17:25
drazak>>> import gsearch17:26
drazakTraceback (most recent call last):17:26
drazak  File "<stdin>", line 1, in <module>17:26
drazak  File "gsearch.py", line 2, in <module>17:26
drazak    from lxml import etree as et17:26
drazakImportError: No module named lxml17:26
kanzurewell that's only because I'm an idiot17:26
* kanzure installs something on the server17:27
kanzuresudo apt-get install python-lxml17:27
drazakwrong window17:27
kanzurepasswordgoeshere17:27
kanzurecrap17:27
drazak:P17:27
drazaknow i know your password17:27
drazakdon't worry17:27
kanzureok try now17:27
drazakI won't tell anyone other than this channel17:27
kanzureit should have shown up as '********'17:27
drazakperfect17:28
drazakit showed up as "passwordgoeshere"17:28
kanzureall I see is "************"17:28
kanzureyou must have copied my ***'s and pasted them17:28
drazak>>> gsearch(q='stuff')17:30
drazakTraceback (most recent call last): File "<stdin>", line 1, in <module>17:30
drazakTypeError: 'module' object is not callable17:30
kanzuregsearch.gsearch(q='stuff')17:31
kanzureok I fixed the problem17:32
drazak>>> gsearch.gsearch(q='hello')17:32
drazak<Element html at b751693c>17:32
kanzureyou should go back to /home/bryan/code/pyscholar/other-code/17:32
kanzurethen do: python pyscholar.py "myquery goes here"17:32
kanzurehm the journal_href seems to be wrong for some reason17:33
kanzurehave they already changed Google Scholar's output? wtf17:33
drazaklo17:33
drazakl17:33
kanzureoh crap.. they probably show me something different since I am logged in when I use google scholar17:33
kanzureand adl.serveftp.org isn't logging in17:33
kanzureso, I should use wget'd pages as examples, not stuff I get from my firefox sessions17:34
kanzuremy fault :(17:34
kanzuredrazak: it's unlikely that I'm going to be motivated enough to get this fixed in the next few hours17:34
drazakok17:34
CIA-43pyscholar: kanzure master * r74815ad / other-code/pyscholar.py : fixed pyscholar for drazak - http://bit.ly/5tVK317:39
CIA-43pyscholar: kanzure master * rbb618e7 / doc/proposals/common-scrapers.txt : the data cleanup fileformat should probably be regular expressions - http://bit.ly/19drPU17:39
drazakthanks kanzure 17:39
kanzureer this is not the fix that you're thinking of17:39
kanzurethat was pushed to adl a few minutes ago when you last tried it17:39
drazakah17:39
kanzureit's just now being pushed to github17:39
kanzuresorry, false alarm17:39
drazak:P17:40
drazakkanzure: I kinda figured17:40
fennd'eaux: The name is misleading, because PCRE is Perl-compatible only if you consider a subset of PCRE's settings and a subset of Perl's regular expression facilities.17:40
drazakanyway, I have 13 papers to read17:40
drazakso by sunday fix it!17:40
kanzuresounds fun17:40
kanzuretake notes17:41
drazakI do17:42
kanzurefenn: eventually, it would be nice to use your manufacturing process shape generator code to say "here are the constraints of a lego brick part, now have fun" and just see what sort of weird models it comes up with that fit within the lego standard17:47
fennyes it would be nice if i could get anything to work at all17:49
kanzurehttp://www.youtube.com/watch?v=0rt620ztAf417:57
CIA-43skdb: kanzure * r6c495d9e6c56 /pymates/test_part.py: formatting issues with test_part.py, also added in some lego brick tests (they pass)18:10
genehackerugh19:12
genehackerguess what?19:12
genehackerapparently SLS isn't as accurate as it's cracked up to be19:13
kanzurego figure19:13
genehackerwhen you print big parts, things start to get distorted19:14
genehackertrying to find pic related19:14
genehackeranyway you would happen to know anything about making python scripts that generate parametrized parts?19:16
kanzuresure that's what pythonOCC is for19:16
genehackerso I want to make my rotary rolamite thing parametrizable19:18
genehackerhow do I do that?19:18
genehackeralso got (most of) a book on microfluidics, do you want it19:20
genehackerand how can I transfer it to you securely19:21
kanzureprobably by usb19:21
kanzureor over ssh19:21
kanzureeither way19:21
kanzuressh is secure enough19:21
kanzureyou make a parametric rotary rolamite by using breps found from the OCC documentation19:21
kanzureif you want I guess I can show you sometime19:22
genehackerI'm in dallas19:22
kanzureokay, then you'll just have to install python19:22
-!- strages [n=strages@c-68-62-216-5.hsd1.al.comcast.net] has quit [Read error: 113 (No route to host)]19:23
kanzurelook at the bottom of teh page here:19:23
kanzurehttp://adl.serveftp.org/dokuwiki/pythonocc19:23
kanzuredo step #2 and #3 tonight19:23
genehackerthink I'll switch to the good partition for that19:24
kanzuresounds good19:36
kanzurehttp://gbamedia.gamespy.com/gba/image/article/601/601745/lego-star-wars-the-video-game-20050405031317222.jpg 19:50
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kanzurehttp://www.acorscadden.com/wp-content/uploads/2009/01/tarp-30198.jpg20:32
kanzureAdmiral Ackbar had a cereal brand for a while, IIRC20:32
genehackerreally?20:35
kanzurepy.test takes 2.4 seconds to run skdb/pymates/tests.py20:44
kanzurejust running python takes 0.551s to run skdb/pymates/tests.py20:44
kanzurefrom skdb.pymates import Part, Interface, Mate; from skdb.packages.legos import Lego; brick1 = Lego("2x2 brick #1", num_pegs=4, num_holes=1); brick2 = Lego("2x2 brick #2", num_pegs=4, num_holes=1); brick1.options(brick2); brick1+brick2;20:58
kanzurebahaha20:58
* fenn plays with Actual Legos21:00
kanzurevirtual legos are better21:00
kanzuremanufactured right here in the US of A21:00
fennmemalloc()'ed on our virtual server somewhere in cyberspace21:01
kanzureCloud Computing21:02
kanzureew cloud computing for legos21:02
kanzurewhen I say (brick1+brick2)[0].apply(), I want to see it applied on my screen, damn it21:03
fenner.. what does that mean?21:04
fennthe first compatible interface between 1 and 2?21:04
kanzurewell you should do print (brick1+brick2) to see21:04
kanzurewell the "first" isn't necessarily going to be the same if the code changes or something21:04
kanzurefor some reason part names aren't being properly used in Hole and Peg objects21:05
fennhole.part.name doesnt work?21:05
kanzureright21:05
kanzurehole.part == None :(21:05
-!- xp_prg [n=xp_prg3@99.2.31.217] has quit ["This computer has gone to sleep"]21:05
kanzurelemme push21:05
CIA-43skdb: kanzure * r629abbc472a7 / (5 files in 2 dirs): improved smoothness of running all of this from the interpreter21:06
kanzurebrick1.name works21:11
kanzureer, not that would make hole.part.name or hole.part work21:12
kanzurefenn: http://adl.serveftp.org/lab/legos/21:23
drazakkanzure: any more fixed?21:24
kanzuredrazak: rawr 21:24
kanzureno21:24
drazakok21:24
kanzurebeen busy playing with fenn's legos (psychicly)21:24
drazaklol21:24
drazakrawr fixit!21:26
kanzurefenn: cd ~/code/skdb/packages/; python -i "import legos.legos" 21:33
CIA-43skdb: kanzure * rd9d72640f146 /doc/DEVELOP: some notes for developers on setting up your PYTHONPATH21:35
CIA-43skdb: kanzure * r82ed377e4d10 /doc/pythonOCC: added pythonOCC installation notes (why wasn't this in here?)21:43
CIA-43skdb: fenn * r19085b6d972c /packages/ (16 files in 2 dirs): rename to lego mostly21:45
CIA-43skdb: fenn * r343e54d3d640 /doc/DEVELOP: Merge branch 'master' of adl.serveftp.org:/var/www/skdb21:45
CIA-43skdb: fenn * r06490e5fba62 /doc/DEVELOP: meddling21:45
CIA-43skdb: fenn * r287e9cfa024b /doc/ (DEVELOP hacking): i hate caps21:45
CIA-43skdb: fenn * r925091d0868e /doc/pythonOCC: Merge branch 'master' of adl.serveftp.org:/var/www/skdb21:45
fennwhy do you have to do export CASROOT?21:51
kanzurethat may be for OCC21:52
kanzureor it may be necessary for running swig21:53
CIA-43skdb: fenn * rd766b95f9987 /doc/pythonOCC: more meddling21:58
CIA-43skdb: fenn * r56c27f25f665 /doc/ (compile_pythonOCC pythonOCC): rename21:58
kanzuretabnamespace conflict with comp*21:59
kanzure:p21:59
CIA-43skdb: fenn * rffe795883039 /doc/ (12 files in 2 dirs): tab namespace conflict comp*22:00
fennit belonged there anyway22:00
kanzuremust rot my brain22:02
ybitwell today didn't go as planned22:33
ybitwhen i came home this morning, i'm guessing the computer had experienced a power surge because it had rebooted. so i took the opportunity to install xmonad.. have spent the entire today configuring it.. i _finally_ have it the way i want it22:34
ybitreplaced the konversation with weechat and kopete with bitlbee-otr22:35
ybitnow, back to configuring postfix, dovecot, and offlineimap...22:35
-!- katsmeow-afk is now known as un-afk23:00
fennhow the fuck did this get so tangled23:09
kanzure?23:10
ybitso my goal is to start working on djangit by august 1023:12
kanzuresad23:12
kanzureorgs-mode has put you into metamode, it seems23:12
ybitwhy is that?23:12
ybitbah23:12
ybiti'm just being realistic23:13
drazakso23:15
drazakwho can tell me about the extracellular structure of the heart?23:15
drazakkanzure: could I use adl an ssh/socks proxy23:19
ybitadl as a proxy would be much quicker than -X23:24
ybiter, ssh -X23:25
drazakexactly23:26
kanzureyou shouldn't have to use -X unless you're not sure what you're doing23:34
drazaknot saying to use -X23:37
drazakkanzure: I'm saying to use ssh -L23:40
kanzureI'm not familiar with -L.23:41
drazakit lets you use the server as a socks proxy over ssh23:41
kanzurejust forwards from a local port to a remote port?23:42
kanzureer, bridging?23:42
drazakkindof23:43
drazakhttp://www.bitvise.com/port-forwarding23:43
drazakanyway, it' just like me using adl as a socks proxy, but it doesn't leave an open proxy port thing23:45
kanzurei am currently braindead and am wondering if there is server configuration that I will need to do to make this work23:46
drazaknope23:47
drazakshould work right away unless you disapbled it23:47
kanzuredunno, I might secretly be a crazy security nazi sysadmin23:48
drazakName Address: dhcp-84-36.me.utexas.edu 23:50
kanzurehm?23:52
drazakthat's what my host is shwoing up as when using firefox :P23:56
genehackerkanzure, reprap prize23:58
genehackerhttp://dev.forums.reprap.org/read.php?1,2567123:58
fennyou know, semantics always goes to hell when people start using nouns to describe a state23:58
fennit's the origin of all those terrible philosophical arguments like "what is death?"23:59

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