--- Log opened Fri Apr 15 00:00:10 2011
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00:17 < Utopiah> http://www.datacenterknowledge.com/archives/2011/04/14/will-open-compute-alter-the-data-center-market/ on using open designs in the industry
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10:59 < ybit> http://www.ted.com/talks/marcin_jakubowski.html
11:00 < kanzure> ah finally
11:00 < ybit> yeah
11:06 < kanzure> so why does he keep marginalizing skdb, again?
11:06 < kanzure> fenn: did you gay him out or something and that's why he doesn't like it?
11:26 < ybit> the title sounds an awfully lot like the 2009 h+ from you two :)
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11:54 < kanzure> Juul: hmm you're at LBL?
11:56 < Juul> kanzure, yeah, I'm at the BIOFAB which is located at JBEI, which is an external LBL facility
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11:57 < kanzure> ah i didn't know
11:57 < kanzure> why are you at biofab, is it sb5 already?
11:58 < Juul> nah, I'm doing my master's thesis at the biofab
11:58 < Juul> been here since november
11:58 < Juul> working on increasing modularity of expression-controlling DNA/RNA sub-sequences
11:59 < Juul> specifically predictable translation-initiation
12:01 < kanzure> so.. new promoters?
12:01 < kanzure> or just "translation factors"?
12:04 < Juul> we already have a small library of characterised promoters, and the interaction between promoters and the mRNA 5' UTR seems to be fairly minimal. The big problem has been secondary structure that forms between the coding sequence and the 5' UTR of the mRNA, which makes it difficult to predict translation rate of the mRNA
12:06 < kanzure> my experience with secondary structures has been with DNA, not mRNA, so i have no idea if it gets the same sort of loops or what
12:06 < Juul> it does
12:06 < Juul> a 5' UTR that's optimized to give a high translation can be disrupted by mRNA secondary structure, if the coding sequence interacts strongly with the 5' UTR
12:07 < kanzure> so wait, are you testing this with in vitro ribozymes
12:07 < Juul> we're basically just measuring changes in GFP expression when the 5' UTR or beginning of the CDS changes, and everything else is kept unchanged
12:08 < kanzure> gfp expression.. in vivo?
12:08 < Juul> yeah, in E. coli
12:08 < kanzure> er, that seems like an awkward logn route to take?
12:08 < kanzure> *awkwardly long route
12:08 < Juul> the goal of the BIOFAB right now is to make it possible to forward design expression level in E. coli
12:09 < kanzure> iirc there are protein translation kits that you can use
12:09 < kanzure> i suppose the environments are sufficiently different that it warrants using ecoli from the outset
12:09 < Juul> exactly
12:10 < Juul> in vitro would give some clues, but there is so much more going on in E. coli that we couldn't trust our conclusions from the in vitro experiments to apply in E. coli
12:10 < kanzure> well, presumably secondary structures in mRNA would still occur inside vs. outside
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12:19 < Juul> true, but factors like ribosome turnaround could be significantly different
12:25 < ybit> will someone please hax0r into their account and changed the address and heading to read "not an open source cnc" http://opensourcecnc.blogspot.com/
12:25 < ybit> s/changed/change
12:27 < kanzure> Juul: i guess. i've seen studies where they opted to make mRNA in vitro, then inject the molecules into a single cell to examine production efficiency
12:29 < Juul> kanzure, interesting
12:29 < Juul> we're keeping it fairly simple, ordering oligos, assembling using golden gate, transforming cells and running the cells through a flow cytometer to check GFP expression.
12:35 < kanzure> i've only done a handful of cell cultures before.. people are lazy and have always told me to avoid doing cell cultures if i can,
12:35 < kanzure> and that it's an awful experience and takes forever for anything to ever work,
12:35 < kanzure> but that's probably just them being lazy :) so if it the growth period doesn't make you go mad i say go for it
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12:58 < Juul> kanzure, hehe, luckily i'm not doing the wet lab work right now
13:10 < kanzure> ah.
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14:00 < kanzure> haha
14:00 < kanzure> http://www.amazon.com/Manga-Guide-Molecular-Biology/dp/1593272022
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15:05 < kanzure> http://foresight.org/reunion/
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15:06 < kanzure> haha wow it costs money?
15:06 < kanzure> just show up.. jeesh
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15:31 < delinquentme> umm anyone happen to know of some companies who offer high quality plastic extrusions?
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15:40 < kanzure> another excerpt from the book.. http://www.boingboing.net/2011/04/15/biopunk02.html
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16:01 < fenn> where did all those cad models for OSE come from?
16:01 < kanzure> the gnomes.
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16:15 < fenn> "drew endy's lab's "holy grail" was to create a DNA-based eight-bit information storage system." wtf, a 4-bit DNA-based information storage system isn't good enough?
16:19 < fenn> actually DNA is a 2-bit system, sorry
16:20 < fenn> why would boingboing decide to publish the spooky hoo-rah chapter of biopunk? or is the whole book like that?
16:29 < kanzure> the book is basically "let's write a few paragaphs about everyone in bryan's meetlog.txt file"
16:30 < kanzure> marcus is a news reporter and was probably expected to write at least a little spooky fearmongering
16:31 < kanzure> also, that's not much of a holy grail for a lab
16:32 < kanzure> these things are supposed to be nearly impossible, damnit
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17:26 < Lukas__> Hello
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18:28 < fenn> anyone know of duygu kuzum? maybe going to "nanoelectronic synaptic devices" talk tomorrow
18:31 < kanzure> NANOELECTRONIC!
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19:39 < Juul> what is gitduino?
19:40 < kanzure> basically github + thingiverse
19:41 < Juul> skdb?
19:41 < Juul> is it related to
19:41 < kanzure> http://gnusha.org/skdb/
19:41 < kanzure> sort of.
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19:41 < kanzure> projects on gitduino don't have to follow the skdb format but it would be nice :)
19:43 < Juul> ah
19:43 < Juul> we'
19:43 < Juul> oops. we're thinking about a git-based synthetic biology library
19:43 < kanzure> for dna?
19:44 < Juul> yeah, and possibly measurement data
19:44 < kanzure> or that biobrick definition language
19:44 < Juul> probably SBOL
19:44 < kanzure> there was some wsdl-specific language (not SBOL or SBML) on partsregistry.org a while back
19:44 < Juul> hm
19:45 < kanzure> meh probably lost by now
19:47 < kanzure> maybe it's in the link log
19:47 < kanzure> http://gnusha.org/logs/meta/hplusroadmap-2011-01-30-links.url.txt
19:48 < kanzure> aha
19:48 < kanzure> http://partsregistry.org/das/parts/features/?segment=BBa_R0050:0,500000
19:52 < kanzure> i have a backup of that data somewhere if you want it. it seems to not exist any more
19:52 < QuantumG> yeah, seems to redirect forever
19:58 < kanzure> haha http://code.google.com/p/android/issues/detail?id=2384
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20:59 < kanzure> http://hardware.slashdot.org/comments.pl?sid=2086242&cid=35835880
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22:53 < JayDugger> Good evening, everyone.
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--- Log closed Sat Apr 16 00:00:10 2011