2009-02-02.log

--- Day changed Mon Feb 02 2009
genehackeryeah00:00
genehackerlet me check00:00
kanzurethe unptnt guy (Dave) and I are doing lunch00:00
genehackeryeah sure00:00
genehacker12-100:00
genehackerlunch where?00:01
kanzuresomewhere within walking distance00:01
genehackerok00:01
kanzurealright, great00:03
kanzurewait, what? isn't that my lab meeting time?00:14
kanzurehm, 10 to 12:30. no way that undergrad is going to fill up that time.00:14
genehackerlab meeting for?00:16
kanzureADL00:16
genehackerof course00:16
kanzuregenehacker: what is noodlehouse?00:27
genehackerI don't know00:27
kanzure2602 Guadalupe 00:28
kanzureokay, two blocks up from where I am, past dean keeton00:28
genehackerHmmm... I'll have to check how long it takes em to get down there00:29
kanzurefive minutes.00:30
genehackerfrom my other class00:30
kanzure3_http://www.hektor.ch/ ?00:31
kanzure3_ex: http://www.hektor.ch/Work/Hektor+Meets+Dexter+Sinister/DSC_0337.jpg00:32
kanzure3_seems to be a weird whiteboard bot00:32
genehackerholy cow00:32
genehackerhow they get the control that good00:33
genehacker*did00:33
kanzureguess we find out Wednesday at noon00:33
genehackerthat's who's coming?00:33
kanzureno00:33
kanzurebut the guy is doing a kit for a 'whiteboard bot'00:34
kanzurethe guy (Dave) is doing http://unptnt.com/ 00:34
kanzuredo you remember him from dorkbot?00:34
genehackeryeah00:34
Utopiahhttp://www.onlinedocumentaries4u.com/2009/02/homo-futurus.html03:18
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wrldpchttp://www.hektor.ch/Work/Hektor+Meets+Dexter+Sinister/DSC_0337.jpg05:56
fenntechshop has way more stuff than their website lets on07:27
fenni bet nobody even knows what all is there07:27
fennperhaps i should add this as a separate entry http://techshopdurham.com/equipment07:32
fennoh that's a wishlist nm07:33
kanzure3_"The London Ultrasound Centre in the UK offers the ability to take a 3D scan of your offspring - before birth - and produce a 3D print of the child."08:59
kanzure3_"You might think you can't seriously print an entire boat with current 3D printing tech, but Robotboat thinks otherwise. Their ingenious plan: print miniature robotically controlled boats! 09:00
kanzure3_Robotboat is a startup company intending on producing "advanced robotic boats for the global oceanographic surveillance market". They intend on using 3D printing to rapidly produce unique hull and sail shapes."09:00
kanzure3_http://robotboat.blogspot.com/09:00
kanzure3_"Recently we developed some more sophisticated manufacturing techniques for the boat. The most exciting of these is the use of 3D printing to make the hulls and sails. This new manufacturing technique allows us to also "print in" the major elements of the control actuators (sail and rudder). The values of this are lower manufacturing costs and better performance."09:00
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kanzure3_"Marshall Brain added you as a friend on Facebook.."09:26
kanzure3_wtf?09:26
fennheh09:29
fenntell me when edge.org sends you an invitation :P09:29
fennplease promise you wont publish marc fawzi in the abundance journal09:30
kanzureI know I know I know09:30
kanzureI told Joseph that we all know Marc is a troll, and he seems to be ok about being cautious09:30
kanzureSamantha Atkins went running to the cosmic-engineers list saying "they are focusing too much on silly economics too early"09:30
fennwaaah09:31
kanzureand if edge.org ever sends me an invitation, I'll just proxy Eric Hunting.09:31
fenni like robotboat's design09:32
kanzurehm, we might be getting abundancestudies.org09:47
fennhmm @ making a stick-on version of these: http://customwheel.com/custom_wheels/product_info.php/products_id/168709:52
fenn$12k is a bit much for most people i bet09:53
kanzure3_where in the hell are they pulling *that* price from?09:53
fennand the hole in the middl is sorta pointless09:53
kanzure3_"26x10 Package with tires ($16,050.00"09:53
fenncould do parasitic power by placing a magnet on a stick next to the wheel, which has coils that pass by the magnet09:58
fenn$10 laptop: http://business.timesonline.co.uk/tol/business/industry_sectors/technology/article5639463.ece10:05
fennwith an 80 character e-ink display it would be totally doable10:06
fennsegment display instead of pixels10:07
kanzure3_"Pipe Viewer or pv for short. Pipe viewer is a terminal-based tool for monitoring the progress of data through a pipeline. It can be inserted into any normal pipeline between two processes to give a visual indication of how quickly data is passing through, how long it has taken, how near to completion it is, and an estimate of how long it will be until completion."10:53
kanzure3_http://www.catonmat.net/blog/unix-utilities-pipe-viewer/10:53
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kanzureoh wait. Eric works for a publishing company.11:41
fennMost software today is very much like an Egyptian pyramid with millions of bricks piled on top of each other, with no structural integrity, but just done by brute force and thousands of slaves.11:47
kanzure3_yay vern11:52
kanzure3_I researched and wrote about this very topic, starting with an idea I touched on for the "Appetizer" column in the August 2007 issue of SERVO magazine. The article was entitled "Recovering our Technical Literacy" and in it I first mentioned a concept I called "Habitat For Hobbies":11:52
kanzure3_http://www.notepad.org/RecoveringOurTechnicalLiteracy.pdf11:52
kanzure3_The idea was that all hobbies need a place to "live". For the electronics hobbyist, this "habitat" is the workbench. This lead to a two-part series of articles published in Nuts and Volts magazine. The first was published in June of 2008:11:52
kanzure3_http://www.notepad.org/HabitatForHobbies-PT1.pdf11:52
kanzure3_This article introduced the concept, went over some details and closed with a challenge. I asked users to submit their ideas for all the equipment needed to transform an empty table into a electronic hobbyist workbench -- BUT -- the kicker was to do it all for $100 or less!. I got lots of great responses that I detailed in my September 2008 column:11:52
kanzure3_http://www.notepad.org/HabitatForHobbies-PT2.pdf11:52
kanzure3_I then posted the winning proposals and all the additional entries on the Nuts and Volts online forum here:11:52
kanzure3_http://forum.servomagazine.com/viewtopic.php?f=1&t=837011:52
kanzure3_This topic actually received a nice comment from none other than the11:52
kanzure3_famous Forrest M. Mims III himself!11:52
kanzure3_http://forum.servomagazine.com/viewtopic.php?f=1&t=8370#p6116911:53
kanzure3_http://www.notepad.org/wbc/1st-Place-AndrewAyers.pdf "Early in the process of selecting items, I decided to base my purchasing decisions toward the goal of stocking an entry-11:55
kanzure3_level robotics and industrial automation workbench11:55
kanzure3_"11:55
kanzure3_http://lists.puremagic.com/pipermail/robotgroup/2009-February/011649.html12:01
fennthe second place entry is much more realistic (jess lewis)12:13
fennsubstituting the individual components in 1st place entry for the grab bags though12:14
fenngrab bags are always crap that nobody wants12:14
kanzureI keep pushing the whitespace in the PDF where there should be a "buy" button next to these kits/lists, but nothing's happening :(12:17
kanzureguess I should file a bug report12:17
fennbug!12:17
fennmore like feature request :)12:17
fennits too bad "starter kits" always suck so hard12:18
kanzurewhat's up with those anyway?12:18
kanzurewe've all had them - from crap radioshack stuff, to other starter kits and many still being sold today12:18
kanzurebut they are never really all that high quality or interesting overall12:18
fennthis is kinda neat (and the other kits they sell) W0QQitemZ110343747884QQihZ001QQcategoryZ4663QQssPageNameZWDVWQQrdZ1QQcmdZViewItem12:23
fennoops12:23
fennhttp://search.ebay.com/11034374788412:23
fennneeds some red led's too though..12:24
kanzure3_was there anything wrong with PikPack?12:25
kanzure3_the standard.12:25
fennand capacitors12:25
* fenn looks12:25
fennwhat is pikpack?12:25
kanzure3_pinpack12:25
kanzure3_http://archives.si2.org/si2_publications/pinpak12:25
kanzure3_http://archives.si2.org/si2_publications/12:25
fennoh12:25
kanzure3_sample: http://archives.si2.org/si2_publications/pinpak/SampleInstances/KM736.xml12:26
fennum.. nobody uses it?12:26
kanzure3_:p other than that though?12:26
fennthe only thing i remember is wishing that they could convey the whole datasheet in xml12:27
kanzure3_that's what pinpack seems to be for.12:28
fennno its just pin names/functions and package shape 12:28
fennwhich is good enough for EDA so i'm not complaining12:29
kanzure3_thought I saw voltage info per each pin12:29
kanzure3_<pin id= num= dir= pol= type=data name=12:30
kanzure3_so the pdf for that example (the datasheet) is http://archives.si2.org/si2_publications/pinpak/Parts/Samsung_KM736V687A/KM736V687A.pdf12:31
kanzure3_on pg 5 there's "absolute maximum ratings" and "operating conditions" - this needs to be encoded in pinpack.12:32
fennhuh that ebay guy is in austin12:32
fenn"typical" values would be a lot more helpful than absolute maximums12:35
fennbut you might as well do all if any12:36
fennall those timing diagrams at the end are the important bit12:37
kanzureum, if I take the standard deviation of a dataset, and the standard deviation is higher than the average *and* it's higher than any of the other values, have I done something wrong?12:38
fennno12:39
fennstandard deviation is the spread in the data12:39
fennso if you have +5 and -5 you'll get standard deviation of .. about 7 i guess12:40
kanzure3_"Just wondering, because the biotech cooperative I am building is going live soon.  The lawyers are doing their thing, got a web development group making pages, and have been pulling together a board.  It should integrate with iGEM/DIY well, but if there was some more concrete way for you to be involved, I would like to facilitate that."12:41
fennin my example it would be 512:42
fennnot 712:42
fennlawyers? biotech cooperative?12:43
kanzure3_Andrew Hessel's "one-to-one battles with cancer" open source biology thingy12:44
kanzure3_http://pinkarmy.org/ "PinkArmy is the working name of an open source biology project based in Canada that is taking aim at breast cancer therapeutic development. The goal of the project is to create personalized medicines that are safe, effective, and affordable. We expect to be fully active in 2008. For more information, please email: info@pinkarmy.org"12:44
fennpeople are dying, we need some lawyers, quick!12:46
kanzurehe's fairly serious about all this12:46
kanzurehe has some big funding from the breast cancer societies12:46
kanzurehe wants to get at least one person "through the pipeline"12:46
fennas in, productive and actually doing something?12:46
kanzure*nod*12:46
kanzurehe's also willing to pick up and move to another country that would be happy to have a first class biotech startup12:47
kanzure(he's already in Canada, but traveling abouts)12:47
* fenn suggests somewhere with a decent climate12:47
kanzureturns out Andrew was looking into a position back at Ellington's lab, "Bryan! You should go talk to Dr. Ellington back in Austin!" ".. uh, I'm already employed with him."12:48
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kanzureso in the last 24 hours: became an editor(?) of a journal of abundance, met a possible angel investor, might have been stalked by the CIA (?), and may or may not have an interesting way of killing cancer13:00
kanzureok, neat. this is starting to feel like a college anime story.13:00
* kanzure has to get down to turn in a timeslip to get paycheck..13:00
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kanzure3_http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Nucleic-Acid-Purification-and-Analysis/Nucleic-Acid-Gel-Electrophoresis/nucleic_acid_gel_electrophoresis/DNA-Band-Extraction.html16:37
kanzure3_What's that about? It looks like it's a mechanical doo-hickey to cut out a slice from a gel, but it says "recover your DNA without purification" (i.e., without spinning down your gel)16:37
kanzure3_". To extract your DNA band of interest without gel purification, simply load your sample into the top row and electrophorese until your band moves into the second row of wells. Then use a pipette to easily remove your purified DNA band."16:37
kanzure3_hm, a video is there.16:38
kanzure3_oh, they want you to make a second row for pipetting the results at the end16:39
kanzure3_but that means that it's assuming that all of your dna will arrive there at the same time16:39
bkeroand you need to electrophorese until you get to the well16:42
bkeroYou might need to run the gel longer/shorter. :/16:43
kanzure3_hrm.16:43
kanzure3_well, there's probably a few tricks you can do to have it alert you for each band or something16:43
kanzure3_but another idea might be to have it multi-channeled so that it's already in separate slices of gel16:43
kanzure3_and these slices get different voltages or whatever16:43
kanzure3_so that you can kick it up near the end if you're getting bored of waiting for bad results that you still need to have16:44
bkerolol16:44
kanzure3_little timer going "ding" for when it hits the right spot heh'16:44
* bkero thought voltage variations would pollute the result.16:44
kanzure3_if you know the if that DNA slice sucks already..16:44
kanzure3_*if you know that that gel slice sucks already..16:45
bkeroBut you're still adding entropy to an otherwise shitty run16:45
kanzure3_ok, screw you. I have a better idea,16:45
bkeroHeh16:45
kanzure3_automatic pipetting arm that will grab it when it hits the open hole16:45
kanzure3_rawr16:45
bkeroYou trying to automate gel runs?16:45
kanzure3_No, that link comes from the diybio list.16:46
kanzure3_Somebody suggested it for the open hardware gel box designs16:46
kanzure3_(I guess the comb would be part of the design)16:46
kanzure3_too bad you can't just make tiny grooves at the bottom of the gel plate for the dna to run off into16:46
kanzure3_and then a timer to record when it happened in comparison (to get the information) - although this doesn't work for those gels which need to be running for a longer time16:47
kanzure3_blah.16:47
bkeroNot a bad idea.16:48
kanzure3_No, it needs to remain running - it's logarithmic anyway.16:48
kanzure3_so the longer it runs, the more accurate the distances between the DNA runs.16:48
kanzure3_so if you just have a time log, you're only extracting what it was showing up to that point in terms of "average speed", which isn't necessarily what the final average speed was going to be16:49
bkeroIt'd be nice to hook up a microcontroller and do some polling as the DNA crawled across the gel.16:49
kanzure3_DNAlogger with an arduinio :p16:50
kanzure3_*arduino16:50
kanzure3_no more visual analysis of results *heaven*16:50
bkeroI was thinking something with slightly higher resolution.  Say, a webcam with python and some image analysis software.16:50
kanzure3_webcam with the right photo filter to see the stain.16:51
kanzure3_(if not visual spectrum nasty ethidium bromide)16:51
genehackerdifferent colored LEDs16:51
bkeroWith basically any stains and the right color agar, you should be able to dither it to 2-bit very easily.16:51
kanzure3_genehacker: Hm?16:51
kanzure3_bkero: What? 16:51
kanzure3_shadows?16:51
genehackerLEDs16:51
kanzure3_genehacker: Why different colors?16:52
genehackermake it flouresce16:52
kanzure3_oh.16:52
kanzure3_you just mean for added lighting?16:52
bkerokanzure3_: Give it an overhead diffused light, and it should get rid of shadows16:52
kanzure3_bkero: No, I was wondering if you meant to use shadows. But you said stains, so nevermind- I'm guessing you mean a colored stain.16:52
kanzure3_was hoping you meant without a stain :)16:52
kanzure3_because we currently don't have a cheap "diy stain" that doesn't suck16:52
bkeroYea16:53
kanzure3_one's patented and super secret, the other is deadly, etc.16:53
bkeroYou might be able to do it with shadow16:53
bkeroHow does one see gel runs without a stain? :/16:53
kanzure3_magic? :(16:53
bkerolol16:53
* bkero would really like some way to turn the lines into variable resistors16:53
bkeroIf there were some way to do an inert metallic stain, you'd be able to do that, but I'm very doubtful there is.16:54
kanzure3_well, if you slice the strip in two, each of equal size, one should have a greater resistance to the other on average16:55
kanzure3_but unfortunately this is not a good method because the natural resistance is going to vary too greatly methinks,16:55
kanzure3_or it's not going to be specific enough to figure out in which half the DNA presently is.16:55
bkeroagar is going to provide complete resistance16:55
kanzure3_okie, nevermind.16:56
kanzure3_guess that's how it works anyway16:56
kanzure3_silly me.16:56
bkeroWhat if you did a stain afterwards that only bonded to the dna and not the agar?16:57
kanzure3_afterwards?16:57
kanzure3_you need to be able to find the dna.16:57
bkeroAfter electrophoresing16:57
kanzure3_how do you know where the dna is?16:57
kanzure3_oh.16:58
bkeroYou don't know how far it's gone towards the other side16:58
bkeroBut you know it went in a straight line(hopefully)16:58
bkeroSo if you made an incision in the gel, could you add something to stain it afterwards?16:58
kanzure3_heh, I just had one of those moments where all of those months talking with molecular biologists flashed before me17:03
kanzure3_make a gel where the dna travels down, and behind it there's a fatty layer that contains some chemicals that easily degrade (chemically react) with the gel, something like an emulsion system17:03
kanzure3_and this reaction would be visible as obvious damage to the gel17:04
kanzure3_and your dna would be in front of it, or something.17:04
kanzure3_emulsions require lots of special chemicals though, methinks. Not going to be easier than staining.17:05
splicerIn optical microscopes they have a way of making the refraction index visible... The way light bends differently through different non opaque media...17:09
splicermaybe that could be used to separate DNA 17:10
kanzurespecial fresnel lense perhaps..17:10
kanzuresomething that could be printed out would be fun.17:11
kanzure(as a mask)17:11
splicerif you connected it to a camera you could steer the dna into a cup if you want 17:11
splicerusing current to seer it17:11
kanzuresteer, oh?17:11
spliceryeah17:12
kanzurehow many directions are you thinking?17:12
splicer417:12
splicerah17:12
splicerwell17:12
splicer(better dismatle my lego build)17:13
kanzuresay, wait a second17:14
kanzureif you have wells at the bottom, could you make it so that when the dna hits, the resistance changes?17:15
kanzureso, the idea here would be that there's a sensor at the bottom well17:15
kanzurewhen the dna drains into it, you get your timestamp (or really, an interval)17:15
splicerwhy is that better than using the refraction index and a cam?.. seems simpler17:16
kanzure3_could you describe the index to me?17:18
kanzure3_uh, the method17:19
kanzure3_sorry17:19
splicer(it would be possible to steer it in 4 directions, using only one of the 2 channels at a time)17:19
kanzure3_polarized light microscopy maybe?17:19
splicerit's something else.. I think it has to do with that they change the pase on different colors... w817:20
kanzure3_phase?17:20
splicer(phase)17:20
kanzure3_hm.17:20
kanzure3_"The use of local increments of refractive index in polyacrylamide gels for measuring protein concentrations in zones during electrophoresis is briefly"17:21
kanzure3_http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=116417717:21
kanzure3_Real-Time Monitoring of Polyacrylamide Gel Electrophoresis by Schlieren Optics17:22
kanzure3_http://jb.oxfordjournals.org/cgi/content/abstract/102/4/68117:22
kanzure3_oh, is just for proteins17:22
kanzure3_". A band containing as little as 0.3 µg of a protein could be detected."17:22
splicerhttp://en.wikipedia.org/wiki/Phase_contrast_microscope17:23
kanzureZernike plates. hrm.17:27
kanzure3_"Perl zone distance calculator for making binary (radial) zone plate diffractive lenses17:27
kanzure3_Fresnel zone plate diffractive lenses are mostly used for xray frequencies, which was how I came upon them, but I think with a high quality commercial printer and transparent film anyone could make one for visible light. They simply consist of alternately transparent and opaque zones whose radii are proportional to the square root of the natural numbers.17:27
kanzure3_My perl script takes the options: -help, -foc, -freq, and -zones. If any or all are left out the defaults are -freq: 560nm (~daylight), -foc: 200 millimeters, -zones: 13 zones.17:27
kanzure3_./zoneplate.pl -freq 560 -foc 200 -zones 1317:27
kanzure3_This would calculate the width of a zone for a zoneplate at 560nm, with a focal length of 200 millimeters, and 13 alternating zones (counting the middle SOLID as 1)."17:27
kanzurebut we need a Zernike zone plate generator17:28
kanzurecan it be done by just a transparent film on top of a lense?17:28
kanzureor does it require actual glass and optics equipment?17:28
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PeerInfinitythe hplusroadmap wiki has now been mirrored on the Cosmic Engineers wiki18:35
PeerInfinityhttp://cosmeng.org/publicwiki/index.php/Hplusroadmap_Wiki18:35
genehackerwhoa20:18
genehackerI think the internet is broken20:19
genehackeris it?20:19
PeerInfinitythe internet is working okay from here...20:27
genehackerIE works20:27
genehackerbut firefox doesn't20:27
genehackerood20:28
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kanzureHi all.22:00
kanzureAny new thoughts on the do-it-yourself zernicke lense?22:00
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kanzure3_"You can't create open hardware with closed EDA tools"22:14
kanzure3_http://wiblocks.luciani.org/remix/index.html22:14
kanzure3_http://groups.google.com/group/wiblocks22:15
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* PeerInfinity returns from being afk...22:26
PeerInfinityhi kanzure, hi outlawpoet :)22:26
AlonzoTGom22:27
* PeerInfinity repeats:22:27
PeerInfinitythe hplusroadmap wiki has now been mirrored on the Cosmic Engineers wiki22:27
PeerInfinityhttp://cosmeng.org/publicwiki/index.php/Hplusroadmap_Wiki22:27
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genehackerhttp://www.drudgereport.com/22:59
genehackerand now t begins22:59
genehackerand now it begins23:00
genehacker*23:00
genehackerWARNING PEOPLE WHO CLICK THE ABOVE LINK ARE STRONGLY ENCOURAGED TO READ ONLY THE LINE OTHER THE PICTURE23:01
outlawpoet_drudge report is such an aggressively ugly website23:01
genehackerOTHER INFORMATION ON THAT PAGE IS LIKELY TO BE POLITICS23:01
genehackeryet it's so sucessful23:01
kanzureWhy'd I have to abort that fetus of my clone? I could really use a clone right about now.23:04
genehackerBecause you ran out of nutrient solution23:06
kanzureBloody bitch was eating too much.23:06
genehackerheh23:08
genehackerthat's one reason for teh algal bioreactor23:08
genehackercheap growth media23:08
kanzureAlgae still needs to eat. A few of my friends have been worrying that the nutrient intake will explode with the growth of the algae, and thereby diverting natural resources from the environment.23:09
kanzureGood growth media cheap does not make.23:09
kanzure(Well, it does on at least one variable.)23:10
genehackerso?23:10
kanzureJust means that the amount of time is linear, without stratified development in resource harvesting tech to keep up with growth rates. That's all.23:13
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genehackerIf we could only feed it rocks23:21
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kanzure3_Some spam just made its way into my inbox. "I intend sell my kidney for personal reasons plz contact me" to debian-isp.23:58
kanzure3_Wonder what sort of scheme *that* is?23:58

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