--- Day changed Thu Feb 19 2009
00:18 < samrose> yep, got a slow response from http://heybryan.org/mediawiki/index.php/Skdb
00:22 < kanzure> it's entirely possible that I'm currently splitting the account/connection. erm, it's hard to explain how this is working. 
00:22 < kanzure> (or it might not be)
00:22 < kanzure> it might be getting confused as to which MAC address to submit packets to, since it's supposed to be one MAC address per account, and one of my internet accounts is inactive at the moment (apparently)
00:22 < kanzure> anyway.
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08:09 < kanzure> Hey davidnunez.
08:16 < davidnunez> morning
08:54 < kanzure> http://www.doviak.net/debian/debian_install_guide.pdf the illustrated guide to installing debian
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11:30 < kanzure> samrose: hey
11:30 < kanzure> samrose: Nathan and I are going to have a phone call sometime later today, to synchronize each other on things
11:30 < kanzure> I was wondering if you met him when he was visiting Factor E Farm.
11:31 < samrose> kanzure, I would love to join you. I will be in meetings all day today at MacArhtur Foundation Grantee Gathering, so I can't (unless I am msireading that you were offering for me to join :-)  )
11:33 < kanzure> well, you misread, but you correctly predicted that Nathan and I would like the Factor E Farm guys, OSE, and such, and the Austin Fab Lab people to have a phone conference or something at some point
11:58 < kanzure> http://www.dellsocialinnovationcompetition.com/apex/ideaView?id=087800000005GA5AAM The Farmery
11:59 < kanzure> " The Farmery will be created with stacked shipping containers so that each container can be pre-manufactured and stacked to reduce production costs. Each container will have a 4 foot wide greenhouse attached to each long side. The crops will be grown hydroponically in vertical sacks holding the growing substrate that hang from rails inside the greenhouses that allow the crops to be rotated easily. Inside the container, specialty mushrooms will be grown. The bottom container will serve as the retail site for the food grown at the Farmery. The nutrients for the crops at the Farmery will come from composting local food wastes, so there is a constant cycle of turning the communities wastes into food."
11:59 < kanzure> http://www.dellsocialinnovationcompetition.com/apex/ideaView?id=087800000005GA5AAM
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14:05 < fenn> what are the conveyor belts for? just put a clear wall on the shipping containers and be done with it
14:06 < fenn> 'if it ain't broke don't fix it"
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15:03 < kanzure_bio> fenn: so it turns out the machine shop doesn't know how to convert the model to gcode (or doesn't have 'mastercam' or something).
15:03 < kanzure_bio> score another point for "design for machinability" .. or not.
15:04  * kanzure_bio compiles openfoam in the background
15:20 < fenn> i think there are packages on opennovation.org
15:56 < kanzure_bio> blah
15:57 < kanzure_bio> the response on the diybio list to the dopamine synthesis pathways is awesome
15:57 < kanzure_bio> I immediately got two IMs from Andrew Hessel, and one from Tito
15:57 < kanzure_bio> as soon as it hit the mailing list.
16:51 < kanzure> http://heybryan.org/~bbishop/docs/Step-and-scan%20maskless%20lithography%20for%20ultra%20large%20scale%20DNA%20chips.pdf
16:51 < kanzure> A maskless photolithography test bed was constructed to examine the requirements for stepper-based synthesis of Ultra Large Scale DNA chips (ULS-DNA chips). The test bed is based on a microscope optical layout with a 5 × reduction imaging lens and micro/nano controlled staging at the image plane. Spatial light modulation is enabled by a Digital Micromirror Device (Texas Instruments DMD 0.7XGA) and the positioning system is composed of a piezoelectric nano-positioner (nPoint Inc., Madison, WI) mounted on a high precision linear-motor stage (Newport Corp., Irvine, CA). With this test bed we examined the requirements of overlay and alignment in a stepper-based DNA microarray synthesis system. We demonstrated multi-field chip synthesis with a spot size of 3.15 μm at the 5 × reduction. All tests were verified by standard hybridization, and fluorescence microscopy. In addition to our demonstration of step-and-scan lithography for DNA chip synthesis, we drafted and modeled an imaging optic for a production scale tool capable of synthesizing DNA chips containing up to 20 million pixels.
16:51 < kanzure> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V0W-4RMNYCM-5&_user=108429&_coverDate=06%2F30%2F2008&_rdoc=1&_fmt=full&_orig=search&_cdi=5657&_sort=d&_docanchor=&view=c&_acct=C000059713&_version=1&_urlVersion=0&_userid=108429&md5=5c61a528aecd8d80e044e5e0978ed957#fig1
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17:27 < xp_prg> where do I get adp1 and rdp?
17:33 < kanzure> did you see the adp1 page on heybryan.org?
17:33 < kanzure> http://heybryan.org/docs/Acinetobacter_instead_of_ecoli.html
17:33 < xp_prg> on
17:34 < xp_prg> sweet where do I get that man?
17:39 < xp_prg> hello?
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17:45 < xp_prg> kanzure are you ignoring me?
17:48 < kanzure> no
17:49 < kanzure> I was buying food. give me a break.
17:49 < kanzure> you get it from a bacteria collection at some university
17:49 < kanzure> look it up in the diybio mailing list archives
17:49 < kanzure> http://groups.google.com/group/diybio
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18:18 < kanzure> http://en.wikipedia.org/w/index.php?title=Natasha_Vita-More&diff=271954921&oldid=268703404
18:18 < kanzure> so..
18:27 < kanzure> hm, I have old #sl4 logs from 2002 now.
18:35 < PeerInfinity> ooh, where did you get them from?
18:39 < kanzure> Michael Anissimov
18:45 < PeerInfinity> nice :)
19:07 < kanzure> fenn: I'd eventually like to hear your opinion on dave
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19:10 < kanzure> Hey Locke.
19:10 < Locke> Hello
19:10 < kanzure> Hey notTraveler.
19:11 < notTraveler> hi, I'm just testing out the java IRC applet
19:11 < notTraveler> http://cosmeng.org/chat/
19:11 < kanzure> Ah.
19:12 < kanzure> http://heybryan.org/SSH2/ has a java SSH client that could be used to run irssi on a remote server
19:12 < Locke> And I'm pretty much bound to the java IRC applet, not an IRC user naturally.
19:12 < Locke> Another OCE member here.
19:12 < kanzure> Hi there.
19:12 < PeerInfinity> :)
19:12 < kanzure> Did either of you see the "how to synthesize dopamine in a cell" post I made today?
19:13 < PeerInfinity> ooh, you already figured out how to change your text color?
19:13 < Locke> ...it's a single click, Peer.
19:13 < notTraveler> ah, so it is :)
19:14 < Locke> No, may I have a link?
19:22 < PeerInfinity> hmm, the hplusroadmap archives only go up to July 2008:  http://heybryan.org/pipermail/hplusroadmap/
19:25 < kanzure> sorry, my bad
19:25 < kanzure> just had a chat with Natasha on the phone
19:25 < kanzure> no, it was on the diybio list
19:26 < kanzure> hrm, finding a link
19:26 < kanzure> http://groups.google.com/group/diybio
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19:27 < PeerInfinity> thanks for the link :)
19:28  * PeerInfinity looks at Locke's quit message and says in a cute bunny voice "I didn't do it..."
19:37 < kanzure> http://heybryan.org/~bbishop/docs/diybio.png
19:41 < PeerInfinity> nice graph :)
19:43 < bkero> kanzure: what's it a graph of?
19:43 < kanzure> diybio :)
19:43 < kanzure> I posted it a few moments ago
19:43 < kanzure> On Thu, Feb 19, 2009 at 7:09 PM, Nick Taylor wrote:
19:43 < kanzure> > This list is great btw. Every day a couple of things turn up that make me go
19:43 < kanzure> > "holy crap!"
19:43 < kanzure> so I replied with http://heybryan.org/~bbishop/docs/diybio.png
19:50 < PeerInfinity> LOL!
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20:20 < kanzure> hey gene.
20:21 < gene> lolwut
20:21 < kanzure> did you see the email I sent to diybio with the graph?
20:21 < kanzure> On Thu, Feb 19, 2009 at 7:09 PM, Nick Taylor wrote:
20:21 < kanzure> > This list is great btw. Every day a couple of things turn up that make me go
20:21 < kanzure> > "holy crap!"
20:21 < kanzure> so I replied with http://heybryan.org/~bbishop/docs/diybio.png
20:21 < gene> heh
20:22 < gene> I need to post the moore's law graph
20:26 < kanzure> refresh that image
20:26 < kanzure> I originally had a parabola, but an exponential seems better
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21:03 < kanzure> phone call with Nathan. Need to call Marcin up eventually.
21:04 < gene> huh
21:04 < gene> some of my posts to diybio didn't show up
21:04 < gene> google blox?
21:04 < kanzure> which posts in particular?
21:05 < kanzure> the group front page kind of hides them
21:05 < kanzure> but they got through to me
21:05 < kanzure> I got a few of them today, were there more?
21:05 < gene> on the $25
21:05  * kanzure looks over http://www.genome.ad.jp/dbget-bin/get_linkdb?-t+alldb+rn:R00345
21:05 < gene> thermocycler
21:05 < kanzure> yeah, it got through
21:05 < gene> after josh
21:06 < kanzure> "
21:06 < kanzure> "
21:06 < kanzure> I'm willing to bet we could make an illuminator using a tanning bed
21:06 < kanzure> light or a UV disinfector.
21:06 < kanzure> UV disinfector 185-365 nm, $139.99, but I think one might be able to
21:06 < kanzure> find a cheaper one:
21:06 < gene> wait a second
21:06 < kanzure> "
21:06 < gene> nope
21:06 < gene> not it
21:06 < kanzure> oh, after josh?
21:06 < kanzure> hrm
21:06 < gene> so reply to author means only they can see it
21:06 < gene> ohhh
21:06 < kanzure> hahah
21:06 < gene> shit
21:06 < kanzure> yeah :/
21:07 < gene> Now I have to repost
21:08 < kanzure> blah, 2 hours remaining on the genes.tar.gz download from KEGG
21:11 < gene> holy shit though easy bake thermocycler
21:12 < kanzure> heh
21:13 < gene> we should make one at the fablab
21:13 < gene> BTW since the fab lab has a vacuum pump
21:13 < kanzure> btw, sybr stains are like iodine drops added to the dna before you run your gel (IIRC)
21:14 < gene> JUST IODINE!
21:14 < gene> is it just iodine?
21:14 < kanzure> no
21:14 < gene> fuck
21:14 < kanzure> it's something else
21:14 < kanzure> sorry
21:14 < kanzure> I wonder if the patent is out yet
21:14 < kanzure> you could go look it up I guess
21:15 < gene> if it was just iodine, we could do gels for dirt cheap
21:15 < gene> none of that ethidium bromide crap
21:15 < kanzure> or better yet, go look up the company that produces sybr gold,
21:15 < kanzure> and then go look up when it was released (as a product)
21:15 < gene> invitrogen
21:15 < kanzure> then go look up who they hired a few years earlier
21:15 < gene> google it
21:15 < kanzure> and go read their theses
21:15 < kanzure> and that will tell you what they were working on ;-)
21:15 < kanzure> heh
21:15 < gene> hahahahahahahahahahahahahahahahahahah
21:16 < gene> since the fab lab has a vacuum pump
21:16 < kanzure> btw, I have a call with carolina biological tomorrow
21:16 < gene> there's something I'd like to try
21:16 < kanzure> yeah?
21:16 < gene> I want to make a room temperature quasi-superconductor
21:16 < gene> carolina biological?
21:17 < kanzure> it's like invitrogen except a smaller company I guess
21:17 < gene> http://arxiv.org/abs/0805.0230
21:17 < gene> yeah I know them
21:17 < gene> what are you calling them for
21:18 < kanzure> I want them to see if they'd like to hook up their API to my XML biology protocols
21:18 < gene> carolina is pretty diy biology friendly
21:18 < kanzure> so that we can automatically buy parts for kits for diybio
21:18 < kanzure> yeah
21:18 < kanzure> so that's why I'm calling
21:18 < kanzure> I'm talking with their ecommerce director
21:19 < gene> you know there is a diybio meetup in San Francisco
21:19 < kanzure> yes
21:20 < gene> if they follow my suggestions
21:20 < kanzure> did you see the diybio map?
21:20 < gene> they might be able to get us some GFP and e.coli fairly cheaply
21:20 < gene> you can clone the tubes of GFP gene right?
21:21 < gene> same with lab grade e.coli too?
21:23 < kanzure> "Microwave improved Escherichia coli transformation"
21:24 < kanzure> "We found that giving calcium chloride competent cells a 1 min microwave pulse at the lowest power setting (180 W), instead of the classic 1–2 min 42°C heat-shock step, increases the transformation efficiency around threefold (3.3 ± 0.5). Moreover, when both treatments were given in a 2-min 42°C − 5 min on ice − 1 min microwave pluse sequence, an additional improvement of 1.6 was obtained, resulting in an overall increase in efficiency of approximately 5.3-fold compared to classical heat shock."
21:24 < kanzure> http://www3.interscience.wiley.com/journal/119400964/abstract?CRETRY=1&SRETRY=0
21:24 < kanzure> "Significance and Impact of the Study: This method might be useful to those laboratories that cannot afford an electroporation apparatus."
21:26 < gene> hahahahahaha
21:26 < gene> nice
21:26 < gene> post it in diybio
21:32 < kanzure> okay.
21:37 < kanzure> http://astrometry.net/
21:38 < kanzure> http://astrometry.net/gallery.html
21:38 < kanzure> wonder if it's cross-referenced with respect to a star catalog
21:38 < kanzure> one of the freaky awesome things to do would be to make it so that you could click the dots in the images, and find all other photos on flickr with those exact stars
21:38 < kanzure> which would be one of those "holy shit these people are too spooky smart"
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22:41 < kanzure> http://www.youtube.com/watch?v=v_p4t1Buv-I Amazing AeroGarden
22:41 < kanzure> "The AeroGarden is the world's first indoor gardening appliance. Grow fresh herbs, produce, salad greens, flowers and more indoors, with no dirt, weeds or mess."
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