2009-04-26.log

--- Day changed Sun Apr 26 2009
kanzurehttp://www.scipy.org/Cookbook/CoupledSpringMassSystem00:23
kanzureI like how something that is supposed to be a mass system doesn't have a variable explicitly defined as mass.00:24
drazakwell00:25
drazakI think diybio needs a list of things they should figure out00:25
kanzurein what sense?00:25
drazaklike00:25
drazak"how to make a home made sequencer"00:25
drazak"how to make a home make xyz"00:25
kanzureyeah?00:25
drazak"how not to get infected by the shit you're working with"00:26
drazak"how not to contaminate what you're working with"00:26
kanzureso, do you want to add these questions to the FAQ?00:26
drazaksome other time00:26
drazakI have a lot of projects right now00:26
kanzurehttp://openwetware.org/wiki/DIYbio/FAQ00:26
drazakI need a way to get this densitometer a bit sooner than it's coming to me00:26
kanzureit takes a minute to edit the page.00:26
kanzureperhaps less if your fingers aren't retardedly slow00:26
* drazak has nfc how to edit wikis00:26
kanzureneat.00:26
drazakyeah00:27
kanzureI can respect that.00:27
drazakI mean00:27
drazakI know how to get into the edit page00:27
drazakbut I know nothing about wiki markup00:27
drazakand the person that could help me, usually, is having a bootycall00:27
kanzuredrazak: Most people copy what they see.00:27
drazakyeah, I could do that00:28
drazakbut there needs to be lists of procedures, with even stupid things00:28
kanzureprotocol-online.org ?00:28
drazakyou can't assume anyone took lab practices in their junior year of college00:28
drazakso it has to be like00:28
drazak'change tips on pippeter, or change pippeters" etc00:28
kanzureAs it is now, the issue is that nobody wants to spend forever retyping protocol-online.org.00:30
drazakyeah00:31
drazakI know00:31
kanzure-Overand: What is #outhouse?00:46
fennybit: what's this about metasequoia?00:54
kanzure-fenn: have you tried apt-get install units-filter ?00:56
kanzure- ~$ echo 1.5e3 nN.m.s^-1 | units-filter00:56
kanzure-              1.5e-6   2   1  -3   0   0   0   000:56
kanzure-              which means : 1.5e-6 (SI unit) m^2.kg.s^-300:56
fennno, but why would i want that?00:57
kanzure-still reading the man pages.00:57
kanzure-does equivalencies00:57
fennso does units and pq00:57
ybitgenehacker ^ 00:57
kanzure-then why is this here.00:57
kanzure-multiple tools for the same job, but still00:57
ybitfenn: i don't know, haven't looked at it, genehacker mentioned it00:58
genehackerwhat?00:58
ybitgenehacker: [00:53] <fenn> ybit: what's this about metasequoia?00:58
genehackermetasequia is an ok 3d modelling program00:58
genehackerthat's about it00:58
genehackerno big deal really00:58
fenni see.. nevermind then00:58
fenni hate it when people refer to 'SI' as 'International System'00:59
fennunits-filter looks pretty weaksauce01:00
kanzure-I'm trying to figure out how to get octave+units or sympy+units or something without killing myself with rewriting libraries01:01
fenni guarantee there's already something for octave01:01
kanzure-I think numpy + pq might do the trick01:01
kanzure-oh? I was reading the octave manual and saw nothing01:01
fennno reason to bother with python if you're working with octave01:01
kanzure-where else should I look?01:01
fenni dont know.. aren't there craploads of plugin/libraries for octave?01:02
fennor can you use matlab add-ons?01:02
* kanzure- checks the wiki01:02
kanzure-http://wiki.octave.org/wiki.pl?Octave_Wiki01:02
fenni remember maxima had a units plugin01:03
kanzure-there's one for physical constants01:03
fennhttp://www.my-tool.com/mathematics/maximaphp/doc/maxima_71.html01:03
kanzure-thank you01:04
fennfrom sympy.physics.units import m, s01:04
kanzure-er? really?01:05
fenn(x * m/s).integrate((x, 1*s, 5*s))01:05
kanzure-google says yes. hrm.01:05
fenndid you even do a basic search yet?01:05
kanzure-yes, but I was focusing on scipy and numpy and octave01:05
kanzure-not maxima and sympy01:06
genehackerunit conversion?01:08
kanzure-hrm: from sympy.physics.units import units01:08
genehackerjust use google01:08
kanzure-dir(units)01:08
genehackerhahhahahaha01:08
genehackerI got some spam01:08
genehackerjust say ######### to ###########01:09
genehackercan even be cubic millimeters to weird american equivalent01:09
fenngood god, why does sympy want to install all that crap01:14
genehackerunit conversions?01:16
genehackerI have the code from solidworks that does that01:16
fennit recommends ipython, which pulls in all sorts of crap.. so --no-install-recommends prevents that from being installed01:16
kanzure-what are you passing that arg to01:17
fennapt-get install01:17
fennfrom sympy.physics.units import units won't work01:17
kanzure-worked for me.01:18
fennmaybe you mean import sympy.physics.units as units01:18
kanzure-es01:18
kanzure-yes01:18
kanzure-"centiliters" appears in the dir(units) list01:19
kanzure-I think they are missing the point01:19
fennyes, that's rather silly01:19
kanzure-micron and microns are two different units01:19
kanzure-hah01:19
kanzure-what's the point of this?01:19
fennso they dont have to do string parsing01:19
kanzure-units.microns eq units.micron01:20
kanzure-er, ==01:20
fennTrue01:21
fennpython equivalent of 'eq' is 'is'01:22
fenni think01:22
kanzure-hrm. doesn't seem to work with sympy.01:32
kanzure-er, sorry. I'm using quantites as pq now.01:32
kanzure-x = Symbol("x"). blah = x * pq.J <-- does not work.01:32
kanzure-and yet this does: t = sympy.var('t') \n q = 5 * t * pq.J02:18
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splicercentiliters is often used for food.. like a coke can is 33cl.04:14
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kanzureany idea on resolving class conflicts when making a new class that has both Symbol and pq.Quantity as parents?10:02
kanzureI get a vague error instead of a specific list of what conflicts.10:02
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kanzureCooling of a Particle by Coupling to its Own Reflection12:06
kanzurehttp://arxiv.org/abs/0904.305912:06
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kanzurehttp://cnczone.com/modules.php?name=Sections&op=viewarticle&id=26 tool change script. but I'm not sure what the interpreter is.12:33
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kanzure-http://pdf.textfiles.com/zines/GBPPR/16:42
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kanzure-fenn: Would you be kind enough to poke les if he's been home in the last ~24 hours and if you also happen to know if he's checked his email? He hasn't subscribed to "atxfab".16:51
genehackerI have17:02
genehackerbtw what do you need to lasercut for the mechmate?17:02
genehackeris it metal?17:03
kanzure-yes17:03
kanzure-Treadwell and I went over to the shop the other day, and les reminded me that the mechmate needs to have two things fixed before things can proceed with it.17:04
kanzure-(1) Motor mounts need to be fabricated. He claims to have the CAD files already.17:04
kanzure-(2) Welding error needs to be fixed.17:04
kanzure-once you get #1 done, you throw all of the wires together and the pcb boards and motors and controllers and install emc17:04
kanzure-or possibly kitware, but I'd prefer going with emc17:04
kanzure-so I asked him to send over the motor mount file thingies, so we can check out what the prices might be on ponoko17:05
kanzure-and if they suck, we could always check out what it would cost to make here at the university17:05
kanzure-genehacker: Ultimately once all of that starts working, I'd like to write the software to make it so that people can order stuff to be in the job queue for the CNC router. And I know it's a pipe dream, but a way to automatically load/unload work pieces and stack piles would be really, really sweet. For engraved pieces, it's easy, but for amorphous stuff..17:07
kanzure-blah, that probably hit the cutoff point17:07
kanzure-summary: giant-ass linkage to move stuff off of the router17:07
genehackerwell 17:08
genehackeryou saw that paper on mating trajectory calculation?\17:08
kanzure-yes, but I don't want to have to build an arm17:08
genehackerI for one would like a bunch of automatic warehouse robots17:09
kanzure-if you have an arm then ytf do you only have a 2-axis CNC router17:09
genehackerto take stuff of the CNC and put it into boxes17:09
kanzure-but you might as well use it for multi-axis stuff.17:10
kanzure-anyway, my experience with the desktop CNC machines (like the Fireball) is that people say they catch on fire often17:10
kanzure-I hope this thing doesn't require human supervision at all times17:10
genehackerhahahahaha17:10
genehackerFireball no doubt17:10
genehackerpossibly do all the work in a co2 atmosphere17:11
kanzure-er, I don't think that's going to be likely17:11
kanzure-not even an inflatable co2 atmosphere17:11
kanzure-because that's still going to take up too much room17:11
kanzure-maybe not. nevermind.17:11
genehackerautomatic fire extinguisher perhaps?17:11
genehackerI was thinking an open air tub17:12
kanzure-fire extinguisher robot :p17:12
kanzure-"DANGER! DANGER!"17:12
genehackerbecause CO2 is heavier than air17:12
genehackerthey do exist17:12
kanzure-then why do we have firefighters17:12
genehackersome people put a webcam on their repraps17:12
kanzure-and if you say 'rescuers', then I'll just retort with calling them fire-rescuer-people.17:12
genehackerbecause the firefigthing robots usually only put out candles17:12
kanzure-the one thing that most people are capable of doing? Sounds redundant.17:13
kanzure-Anyway.17:13
kanzure-do you want to rent half a room with me?17:13
kanzure-at the shop.17:14
genehackerhttp://robotics.youngester.com/2008/08/fighting-fire-with-robots.html17:15
genehackerhuh?17:15
kanzure-My latest apartment is about a mile away, so I'll be there more often. Will probably get Jonathan Cline to dump some diybio stuff there too. Treadwell claims he wants to bring his makerbot, lathe, and chemistry stuff.17:15
kanzure-well we're renting out specific storage room thingies17:15
genehackerhow much and how far away?17:15
genehackerfrom the campus?17:15
kanzure-well it's at Congress and Ben White, so it's about 5 mi from campus17:15
genehackerno17:15
kanzure-heh17:15
genehackerI have an 8:00 am class17:15
kanzure-when?17:15
genehackerAT 8 am in the morning17:16
kanzure-summer?17:16
genehackeryeah17:16
kanzure-is that a good idea?17:16
genehackerChemistry stuff17:16
genehackeronly class available17:16
genehackerhmmm...17:16
genehackerhey do you know if we have an air compressor?17:16
kanzure-but you still want to see it, right?17:16
kanzure-yes, there is an air compressor17:16
genehackerVERY YES17:17
genehackeranyway one simple fire fighting robot we could make could shoot baking soda17:17
genehackerRecently I've been thinking about making a robot that shoots water at smokers...17:17
kanzure-it would be nice to get a PE-engineer on the scene to kick up the "engineering" feeling of it all17:18
genehackera burning cigarrete is easy to identify in infrared17:18
genehackerPE?17:18
genehackerpetro?17:18
kanzure-it's the exam that engineers go through to get "certified" in engineering17:18
kanzure-and it's mostly what guys who run job shops have, or something17:19
genehackeroh17:19
kanzure-or it's the type of people that they hire17:19
genehackerok17:19
genehackerI could take that exam17:19
kanzure-I haven't. I hear it's basically your mechanical engineering thermo, fluids, mechanics, statics, dynamics, etc.17:20
genehackerI wonder, how do all these japanese robot makers make the huge shiny plastic injection molded parts?17:20
genehackerok17:20
kanzure-how big?17:20
genehackerhttp://hackedgadgets.com/wp-content/_robot_fire_fighter.jpg17:20
genehackerthat big17:20
genehackerlook at those joints17:20
genehackerthey probably have harmonic drives17:21
genehackercheap? NO17:21
genehackerwe need cheaper robots17:21
kanzure-Actually, I would be happy with knowing how to make very expensive robots- rather than the cheap little pieces of crap that I used to make.17:23
kanzure-i.e., where do you go to figure out what to buy to make it expensive and to make it work too :p17:23
genehackerI don't know17:24
genehackerbut really17:24
genehackercheap robots are  better17:24
genehackera bunch of cheap robots are better than one big expensive one17:25
genehackeras the big expensive one could break17:25
genehackerif a couple cheap ones break you're ok17:25
genehackerI'm a big fan of Rodney Brooks robotics philosophy17:29
genehackerhmmmm...17:31
genehackernow how could we get a thermal camera17:31
kanzure-don't some consumer cameras have a thermal mode?17:31
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kanzure-consumer video cameras17:31
kanzure-er, camcorders.17:31
genehackernot a very good one17:33
genehackersure you can see some ir like the IR from LEDs17:34
genehackerfound a paper awhile back on making a low res thermal camera17:36
genehackerfor not that much17:36
kanzure-can you cite it?17:36
genehackerhold on17:38
genehackercite?17:38
genehackerI'll send it to ya17:38
genehackerhttp://amasci.com/amateur/elehob.html17:39
genehackerin here under projects17:39
genehackerFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---17:40
genehackerit isn't there17:40
kanzure-try the internet archive17:40
genehackerhttp://users.bestweb.net/~hobbs/footprints/fpspie11.pdf17:40
kanzure-http://web.archive.org/web/*/http://amasci.com/amateur/elehob.html17:40
kanzure-ok, got it17:41
fenngenehacker: those huge plastic pieces are probably vacuum formed, which anyone can do in a kitchen with a shopvac and an oven17:41
genehackerah17:41
genehackerof course17:41
fenni happen to think it's highly gay17:41
genehackerno17:42
fennbut whatever floats your boat17:42
genehackerthat's not it17:42
fennseriously, what's with the uniforms?17:42
fennlooks like char aznable17:42
genehackerit's japanese TV17:42
kanzure-$10 thermal imager thingy: http://web.archive.org/web/20070612054034/http://users.bestweb.net/~hobbs/footprints/fpspie11.pdf17:42
genehackerfenn that's exactly the point17:43
genehackershe's supposed to look like that17:44
genehackerI haven't seen any gundam animes so I wouldn't know17:44
genehackerSAVED17:44
fennso where do you get ferroelectric PVDF film?17:45
* kanzure- was just wondering the same17:45
genehackerebay17:45
kanzure-relying on ebay just doesn't sound like a smart plan..17:45
kanzure-but I might be clueless, so whatever17:46
genehackerI PVDF eh?17:46
genehackerI think I know where to get that17:46
fenni was hoping it was something like a PIR sensor diode, a pinhole, and some x/y scanning mechanism17:46
kanzure-PIR?17:46
fennbut that would be too easy i guess17:46
fennpassive infrared17:46
kanzure-oh.17:47
kanzure-well that would be useful17:47
kanzure-would that require crazy condenser optics?17:47
kanzure-er, sorry, magnification optics17:47
fennif you want17:47
fenni dont know how sensitive those things are17:47
genehackerhttp://en.wikipedia.org/wiki/Polyvinylidene_fluoride17:47
genehackerhmmm...17:47
genehackermaybe17:47
kanzure-fenn: poke les?17:47
fenngenehacker: it has to be charged, not just any pvdf film17:48
fennkanzure-: he's asleep17:48
kanzure-okay.17:48
fenndon't spazz out because someone didnt sign up right away17:48
kanzure-well it's just kind of pointless for you and me to be talking to each other on a mailing list when we could be doing it in here :p17:49
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kanzureGoogle Scholar Citation Explorer19:31
kanzurehttp://compbio.cs.uic.edu/~mayank/software/slh/index.html19:31
kanzure"show all common citations for a subset of documents you select"19:34
kanzureer, I think he means to say "show papers that cite those papers". I think.19:34
kanzureThe most cited paper ever- that I can find- is one that is cited 10,000 times re: pdb (the bioinformatics db) published in 2002.19:59
kanzureaccording to Google Scholar.19:59
kanzurenow, it occurs to me that Google Scholar is indexing my PDF collection19:59
kanzureit also occurs to me that PDFs are mostly generated by latex templates20:00
kanzureIn principle, I should be able to make myself the most cited individual-- according to Google Scholar-- ever.20:00
kanzurethe question is, what should the paper be about?20:00
spliceryou would write a paper and add a citation to it in all your pdf:s?20:05
kanzure-No, I'd just generate a few hundred thousand papers or something and reference it.20:19
kanzure-ooh20:19
kanzure-i'll make it self-referential20:19
kanzure-the paper will be about writing the paper20:19
kanzure- or doing the hack.20:20
splicerit's called bombing?20:28
splicerI've heard of companies who have been blacklisted by google for doing SEO that google didn't like. 20:32
kanzure-"google bombing" is not commonly done with google scholar20:32
splicerFor a company it can be a bit like falling off the face of the earth20:32
splicer...until now ; )20:32
splicerthe swedish riaa and mpaa equivalents homepages here were down today. It seems the reason was that some people wanted to show that they could... 20:37
splicerthey said... riaa is going down at two... and it did.20:38
drazakwhat is google scholar anyway20:44
kanzure http://scholar.google.com/20:44
kanzuresearch engine for scholarly bullshit20:44
drazakoh cool20:44
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kanzure-genehacker: I'm reading through some of my old notes. Here's something on piezoelectric self-replicating machines. http://heybryan.org/pipermail/hplusroadmap/2008-March/000423.html21:33
genehackerhmmm?21:33
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kanzure-woah, I totally forgot about this21:38
kanzure-http://heybryan.org/pipermail/hplusroadmap/2008-June/000580.html21:38
kanzure-"Mammalian cells can produce tiny magnetic nuggets after the  21:39
kanzure-introduction of a single gene from bacteria, scientists have found.  21:39
kanzure-The gene MagA could become a valuable tool for tracking cells'  21:39
kanzure-movement through the body via magnetic resonance imaging (MRI), says  :21:39
kanzure-"21:39
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kanzure-argument as to why a singularity can't happen in a box in the middle of outer space: http://heybryan.org/pipermail/hplusroadmap/2008-June/000599.html21:40
kanzure-bacteria producing 'brain proteins' naturally: http://heybryan.org/pipermail/hplusroadmap/2008-June/000638.html21:43
kanzure-CNC machining in free fall http://heybryan.org/pipermail/hplusroadmap/2008-May/000473.html21:45
kanzure-ooh, here's the original diybio announcement: http://heybryan.org/pipermail/hplusroadmap/2008-April/000425.html21:48
kanzure-oh. That's right. I was working on the 2D phenotype/SNP map for brain map stuff, informed by gene expression regulatory studies or something from humancortex.alleninstitute.org22:34
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kanzure-"I am program, programmer and that which is programmed."22:36
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genehackerWOAH23:11
genehackerMAGNETIC CELLS23:11
kanzure-:)23:23
kanzure-"things bryan has forgotten over the years"23:23
genehackeryou didn't forget it23:25
genehackerit was just in your external memory23:25
genehackerwait CNC milling in freefall?23:26
genehackerread about milling on the moon23:26
genehackerit's harder than it looks23:26
genehackeryou have to damp vibration23:27
kanzure-genehacker: search for "MRI reporter gene"23:28
kanzure-apparently there are others23:28
genehackerWOAH23:28
kanzure-you could couple it to gene regulation I think23:28
kanzure-and then you have a dynamic way of MRI'ing gene regulation in vivo23:28
kanzure-might be useful for teh brain23:29
kanzure-ooh23:29
genehackerhttp://www.waterjets.org/index.php?option=com_content&task=view&id=116&Itemid=3123:30
genehackercould I get more info about cnc milling in freefall?23:30
kanzure-did you read the link I gave above?23:31
kanzure-because that's all I have23:31
genehackerthat's not much23:32
kanzure-odd. my server clock is wrong - it thinks it's back in 2008.23:32
genehackerI wonder if nasa has done any studies on it23:32
genehackermaybe it is FOR YOU23:32
kanzure-"can you manufacture a new turbojet engine in freefall in time to install it and stop an airplane from crashing into the ground"23:33
kanzure-hehe23:33
fennreminds me of indiana jones' inflatable life-raft makeshift parachute23:34
genehackerhahaha23:34
genehackerwhere's that23:34
genehackerI don't think so23:34
kanzure-it's a new extreme sport23:34
kanzure-you're thrown from the highest possible point in the atmosphere- maybe extreme orbital diving-23:35
kanzure-and your job is to construct a mechanism to land safely using only the tools that you have available23:35
genehackermaybe a ramjet...23:35
genehackerI don't think so23:35
fenni'll take a parachute as one of my tools23:35
genehackeryou'd blackout23:35
fennit's a 'survival backpack'23:35
kanzure-eh, but you won't get too many points for parachutes23:36
genehackeryou know what would be cool?23:36
genehackera blimp at the edge of space23:36
fennon jupiter23:36
genehackernah23:36
genehackerhere on earth23:36
kanzure-IN M31! YEAH!23:36
kanzure-is there a biobrick for these MRI reporter genes yet?23:36
genehackerwhat are you gonna see on jupiter? clouds?23:36
genehackerI bet not23:37
genehackerwell then, let's form an iGEM team23:37
kanzure-things to make into biobricks: (1) ComB gene system thingy, (2) MRI reporter genes, (3) voltage-mediated dyes, ..23:37
kanzure-why? it costs so much..23:37
genehackerwhy does it costs so much?23:37
fenn"because"23:38
kanzure-because people who attend igem are made of money23:38
genehackerthen let's make a tree that grows money23:38
fennhow about pot oranges23:38
genehackerhow about a DNA synthesizer first23:39
fennhow about anything at all23:41
kanzure-heh.23:42
genehackerok23:42
* kanzure- has been reminding himself how much he hates XUL/CSS/HTML/JS work.23:42
genehackerwhen summer comes and I don't have as much work23:42
fennyay a new mailing list!23:46
kanzure-another one?23:46
fennno23:46
kanzure-oh, your email23:46
kanzure-ok, if it needs to be drill pressed then let's just use the machine shop services here on campus23:46
kanzure-I'll even gift wrap them and hand deliver them..23:47
fennwill you include the cookie you so rudely stole from me?23:47
kanzure-check the envelope.23:47
genehackerkanzure you can use the machine shop23:49
genehackeri can;t23:49
kanzure-you still haven't got training?23:49
kanzure-you were only banned for three weeks or something23:49
genehackera month23:49
fennbanned from taking training classes?23:50
genehackernow all the classes are when I have class :(23:50
kanzure-fenn: yep.23:50
fennhow do you manage that?23:51
kanzure-he didn't wear jeans and he arrived late23:51
genehackerhad a test23:52
fennsounds a bit harsh23:52
kanzure-the machine shops tend to feel like that here23:52
genehackerthey don't want to get sued23:52
fennwhat are jeans supposed to do?23:53
fennstop a big block of metal from crushing your foot?23:53
fennreally now23:53
genehacker???23:54
kanzure-hrm, I wonder if you could use MagA like you can GFP for tagging different specific proteins23:57
fennno23:57
kanzure-what's the GFP tagging mechanism?23:58
fennthe protein is stuck to the target and it glows23:58
kanzure-whereas you can't stick a magnetic protein to something?23:58
fennmagA creates some kind of magnetic nugget23:58
kanzure-oh, it creates the nugget?23:58
kanzure-er, nevermind.23:58
kanzure-I meant to ask, "it catalyzes the creation of the nugget?"23:58
kanzure-which makes sense, since iron isn't incorporated into amino acids23:58
fennand it's membrane located23:59

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