--- Log opened Fri Jul 13 00:00:07 2012
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03:27 < kanzure> jrayhawk: don't leave me :(
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07:50 < JayDugger> Get back to sleep, kanzure.
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08:41 < nmz787> howdy
08:42 < nmz787> Mokbortolan_: I'm in your neck of the woods... and don't have plans while the girl is interviewing til 5pm
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09:57 < kanzure> nmz787: go bug joe or his brother steve
10:00 < nmz787> lol
10:01 < nmz787> I pinged him in here
10:01 < nmz787> dunno their info otherwise
10:01 < klafka> hey
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10:03 < kanzure> nmz787: ok i'll send over some data
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10:06 < kanzure> nmz787: emailed
10:10 < nmz787> cool
10:10 < nmz787> gonna go to bank now to take care of something, will bug them after :D
10:11 < nmz787> ttyl peeps
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11:27 < rdb> ow.  this is the first time that a microcontroller violently came loose from my breadboard and made a pretty deep cut in my finger
11:28 < rdb> it's supposed to zap my brain, not cut me
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11:37 < kanzure> http://beautifulmind.io/ claims to do "real-time collaborative mind mapping"
11:39 < kanzure> http://beautifulmind.io/1269-kanzure
11:41 < rdb> that sounds interesting
11:41 < kanzure> i usually hate mindmaps, but i know Utopiah likes them or something
11:41 < rdb> my connection gets lost all the time, apparently
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12:12 < Sanky> reminds me of, uhh
12:13 < archels> kanzure: That one seems particularly terrible.
12:16 < Sanky> I don't even know how the thing I used was named
12:16 < Sanky> all I remember is it was in java
12:16 < Sanky> anyway
12:16 < Sanky> workflowy rules
12:18 < kanzure> what does workflowy do?
12:19 < Sanky> it's a brainstorming tool/todo list of sorts
12:19 < Sanky> it's extremely simple
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12:29 < kanzure> http://blogs.plos.org/neuroanthropology/2012/07/09/roid-age-steroids-in-sport-and-the-paradox-of-pharmacological-puritanism/
12:29 < kanzure> "timeline of performance enhancing drugs in sports" http://sportsanddrugs.procon.org/view.resource.php?resourceID=002366
12:30 < kanzure> "His blood sample was sent to U.C.L.A.'s Olympic Analytical Laboratory, which is accredited by the World Anti-Doping Agency, and scientists there detected H.G.H. in it."
12:30 < kanzure> hahah there's an olympic analytical lab :\
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12:34 < Mariu> is Gregory Stock still working in U.C.L.A. ?
12:35 < kanzure> i think he's working at http://signumbio.com/
12:35 < rdb> I just put together what's probably the safest DIY tDCS device around.
12:35 < kanzure> or at least.. he was
12:35 < Mariu> oh nice
12:35 < rdb> now to find some sponges and fashion some electrodes
12:39 < Adrian_> kanzure: u didnt  know?
12:40 < Adrian_> there are a few of these labs
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12:40 < kanzure> i know about analytics labs, just not one that is explicitly "olympic"
12:40 -!- AdrianG_ is now known as AdrianG
12:41 < AdrianG> i think its just a name
12:41 < AdrianG> there are a few labs under contract with WADA
12:41 < AdrianG> ive heard gene therapy is the hottest doping right now.
12:51 < kanzure> heard from who
12:52 < kanzure> i'm totally willing to make gene doping products if you can show me someone interested in paying me cash
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13:03 < AdrianG> kanzure: rumors
13:10 < AdrianG> kanzure: what can you make
13:11 < kanzure> that depends on what my motivations are
13:11 < kanzure> right now i don't actively synthesize anything
13:11 < AdrianG> what can you synthesize
13:11 < AdrianG> that would be useful in sports
13:11 < kanzure> there are many low-hanging fruit projects for sports doping
13:11 < kanzure> http://diyhpl.us/wiki/germline-genetic-modifications/
13:11 < kanzure> uh, i don't know why i named that germline-anything
13:14 < AdrianG> yes, but can you make anything that can be used tomorrow in a real person
13:15 < kanzure> tomorrow? gee that's a fast deadline
13:15 < kanzure> i don't even know what you want me to synthesize yet
13:16 < AdrianG> im asking what can you do
13:16 < AdrianG> well, tomorrow is flexible
13:16 < kanzure> i have some modest lab skills, if that's what you're asking.
13:16 < AdrianG> london olympics are in two weeks, you know
13:17 < kanzure> wouldn't you want to spend more than 2 weeks checking out a drug, if you're an athlete that has to be sure he's at best performance at the event?
13:17 < kanzure> i doubt that athletes start doping at a last minute :P
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13:18 < kanzure> aw :(
13:18 < kanzure> maybe he's angry that i'm not already synthesizing something
13:19 < Steel2> Sanky: mindmeister
13:19 < Steel2> ?
13:20 < Sanky> what's that?
13:20 < Sanky> oh, no
13:20 < Sanky> something else, meh
13:20 < Steel2> I like mindmeister
13:20 < Sanky> I'll try to remember it
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13:28 < yashterdam> kanz you named it germline- because you forked it from my thing
13:28 < kanzure> hrmmm
13:28 < kanzure> this makes sense
13:31 < yashterdam> anyway gotta go, that's what I get for checking the logs before sleep
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13:31 < kanzure> i feel that yash is misappropriating his time in amsterdamn by sleeping
13:31 < kanzure> :P
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13:40 < AdrianG> kanzure: im just saying we are too late for these olympics
13:41 < archels> kanzure: what is this "gene doping"
13:42 < kanzure> archels: a popular example is siRNA doping
13:42 < kanzure> well, wait. no. there are many forms of small-molecule RNA doping, but i don't think siRNA is one of them. hrmm..
13:42 < archels> okay, that's roughly what I expected
13:43 < kanzure> i also think people count adenoviral and lentiviral methods as gene doping
13:43 < archels> injecting silencing RNAs?
13:43 < AdrianG> possibly
13:44 < kanzure> my /gene-therapy folder is so pathetic
13:44 < kanzure> http://diyhpl.us/~bryan/papers2/gene-therapy
13:44 < kanzure> only 20 articles? geeze.
13:44 < AdrianG> :<
13:44 < archels> indicative of the state of affairs
13:44 < kanzure> that i am bad at finding good articles, yes
13:45 < kanzure> but there's lots of stuff published
13:45 < kanzure> (i was just observing that i seem to be slacking on that front)
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13:45 < archels> anything worthwhile, besides messing with silencing RNA a bit?
13:48 < kanzure> i'm not in the right brain state right now to produce that knowledge from my brain :P
13:49 < kanzure> i'm in javascript-and-anti-feminism-mode and very confused
13:49 < archels> haha, o-kay
13:49 < archels> like I said I doubt the problem is you; I think the problem is the state of affairs in the field
13:49 < archels> we're just not there yet
13:50 < kanzure> there have been tons of clinical trials for all sorts of interesting methods
13:50 < kanzure> and lab studies of others; like just naked dna injection is pretty neat
13:50 < archels> yes, but you can't really pull that off in vivo can you
13:50 < archels> it's the delivery mechanism that's the crux
13:51 < kanzure> naked dna injection was through rat tails
13:51 < kanzure> how's that not in vivo :P
13:51 < kanzure> retrograde renal vein injection http://diyhpl.us/~bryan/papers2/bio/Kidney-targeted%20naked%20DNA%20transfer%20by%20retrograde%20renal%20vein%20injection%20in%20rats.pdf
13:52 < kanzure> although admittedly that's a limited method because kidneys
13:52 < archels> clicking
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13:54 < yashterdam> gah fine
13:54 < kanzure> damn straight, boy
13:55 < yashterdam> anyway yeah gene therapy's mostly stilted since that fucking kid died
13:55 < yashterdam> hmm wait no it's stulted
13:57 < archels> kanzure: I'm not following this, so the "naked DNA" plasmid is injected into the bloodstream, and then how does it find its way into the cell nuclei exactly?
13:57 < kanzure> i don't think you need to get into the nuclei to get copied around entirely
13:57 < yashterdam> occasionally cells have holes in them, or there's the transient overpressure from the injection
13:58 < yashterdam> you do need to get into the nucleus, but in an actively dividing cell that's not a large barrier
13:58 < kanzure> i think even ecoli is naturally competent and takes up DNA (at very very low rates)
13:58 < archels> ah the paper they refer to has 'electroporation' in the title
13:58 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Genetic%20transformation%20in%20freshwater%20-%20Escherichia%20coli%20is%20able%20to%20develop%20natural%20competence.pdf
13:58 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Natural%20plasmid%20transformation%20in%20ecoli.pdf
13:59 < archels> but e-coli sounds like in vitro
14:00 < kanzure> oh, it's definitely not human-related, sorry
14:00 < archels> although I guess the results they describe are impressive, so they must be managing it somehow
14:00 < kanzure> but since we were talking about per-cell dna uptake, i thought to mention it
14:00 < archels> if they actually use electroporation in vivo, that's pretty nasty though
14:00 < yashterdam> hey at least it's in a limb and not the brain
14:01 < kanzure> did you read the article about optical electroporation? http://diyhpl.us/~bryan/papers2/neuro/Subretinal%20injection%20and%20electroporation%20into%20adult%20mouse%20eyes.pdf
14:01 < kanzure> i guess that's not optical electroporation
14:01 < kanzure> electroocularporation
14:01 < kanzure> erm.. no that can still mean "shine lasers on to things to make them porate"
14:01 < yashterdam> ehhh eyes are a prime candidate for viral vectors, much as I dislike viral vectors
14:02 < archels> 13MB and still going
14:02 < archels> 26
14:03 < kanzure> i apologize for how terrible science is.
14:03 < archels> woo pretty pictures
14:05 < archels> okay, so in conclusion, it seems that this intravenous DNA plasmid injection still relies on some variant of electroporation.
14:06 < yashterdam> you can get measurable transfection just injecting in mice, less so in larger mammals
14:08 < archels> you probably need to inject unholy amounts of DNA for that, even
14:08 < yashterdam> so what, dna is cheap
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14:08 < kanzure> it's the one thing that we're really good at making
14:08 < kanzure> s/making/copying
14:09 < yashterdam> yeah writing is expensive, copying much less so
14:10 < archels> can't be good for the animal
14:10 < kanzure> oh yay me
14:10 < kanzure> http://diyhpl.us/wiki/natural-competence
14:11 < archels> okay, I'm off, nice chat
14:12 < yashterdam> ok cool because I am too
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14:12 < gnusha> diyhpluswiki.git: 914096b move germline-genetic-modifications to genetic-modifications
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14:34 < kanzure> is there a javascript deobfuscation tool that can rename variables for me?
14:34 < kanzure> like if i want to rename "a" or something?
14:34 < kanzure> it's hard to do search-and-replace on single-letter variable names
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14:43 < rdb> kanzure, um, use \b with sed around the letter to include word boundaries?
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14:44 < rdb> like sed -i'' 's/\ba\b/somename/g' somefile.js ?
14:44 < kanzure> what does \b include though
14:44 < rdb> nothing, just indicates word boundary
14:44 < kanzure> what counts as a word boundary? parentheses? periods? whitespace?
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14:45 < rdb> [A-Za-z0-9_] are included in the word
14:45 < rdb> which means that it'll work for most variable names out there
14:45 < kanzure> well okay then.
14:45 < kanzure> thanks.
14:45 < rdb> or more fun!   for i in "abcdefghij..z"; do sed -i "s/\b$i\b/$(random /usr/share/dict/words)/g" somefile.js; done
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14:45 < rdb> replaces every single-letter variable name with a random english word
14:45 < kanzure> yeah, i wanted to avoid writing regular expressions with [A-Za-z0-9_], but \b looks reasonable
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14:48 < kanzure> oh, i guess the one exception to this that i am okay with is i, j, and k iterators in for loops
14:48 < kanzure> hrmm
14:50 < rdb> anyway, good luck, my brain is pretty much dead right now so I'll just head to bed
14:51 < kanzure> good night
14:51 < kanzure> thanks for the regex wizardry
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15:18 < kanzure> "nventory for Composable Elements (ICE) is being developed by the Joint Bio Energy Institute (JBEI) as an open source Registry software for biological parts. It is a web application software that can be used by laboratories to track and search their constructs."
15:18 < kanzure> http://public-registry.jbei.org/
15:18 < kanzure> http://code.google.com/p/gd-ice/
15:19 < kanzure> oh boy.. soap api :(
15:20 < AdrianG> kanzure: do you ever experience information overload
15:21 < kanzure> no
15:21 < kanzure> at the moment i'm writing some code in another window and i get bored waiting for the buffers to finish typing
15:21 < kanzure> and it's javascript, so i feel terrible about it too
15:22 < kanzure> also i think juul or nmz787 possibly contributed to that project; hard to tell
15:27 < AdrianG> how do you organize information
15:31 < kanzure> hyperlinks, git repositories, software i write
15:31 < kanzure> AdrianG: example: http://quantifiedself.com/2011/08/bryan-bishop-on-meetlog/
15:33 < kanzure> http://diyhpl.us/cgit
15:36 < AdrianG> sometimes I suspect you are just a very convincing bot.
15:36 < kanzure> http://heybryan.org/mac.html
15:36 < AdrianG> not because of that
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15:37 < kanzure> rdb: apparently it is \< and \> in vim
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15:59 < AdrianG> kanzure: r u a student
16:00 < kanzure> no
16:10 < AdrianG> wat u do for a living
16:10 < AdrianG> besides irc chatting
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16:25 < brownies> he types very quickly
16:31 < kanzure> AdrianG: http://diyhpl.us/~bryan/resume.pdf
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20:10 < kanzure> jrayhawk: why did you get kicked offline
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20:16 < Juul> allo
20:16 < kanzure> Juul: hi
20:16 < Juul> :)
20:16  * Juul is at HOPE
20:16 < Juul> I was talking to some of the makerbot employees earlier
20:17 < Juul> they say they've talked about NURBS, but nothing has been planned
20:17 < Juul> I didn't realize they had two-material printing
20:18 < Juul> and when I found out I expected them to use the second material for dissolvable support
20:18 < Juul> but they don't have a dissolvable support material yet
20:18 < Juul> I wonder how difficult that will prove
20:18 < Juul> to have something that can be fed in as a somewhat bendable wire
20:18 < Juul> which is dissolvable without nasty chemicals
20:18 < Juul> and has a melting point at leas above that of PLA
20:19 < kanzure> reprap has all sorts of printing materials, including stuff for pcb printing and tissue printing
20:20 < kanzure> makerbot extruders are only somewhat behind (but it's the same compatability anyway, so it's not much of a difference)
20:20 < Juul> do any of the cheap/home-use printers have dissolvable support yet?
20:21 < kanzure> i can't recall at the moment.. #reprap will know
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20:47 < kanzure> biocurious class survey http://www.surveymonkey.com/s/W2CZJCB
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23:33 < joshcryer> http://www.kurzweilai.net/hp-memristors-will-reinvent-computer-memory-by-2014
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--- Log closed Sat Jul 14 00:00:08 2012