--- Day changed Wed Apr 22 2009
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00:17 < kanzure-> Prefrontal norepinephrine determines attribution of 'high' motivational salience
00:17 < kanzure-> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2516177
00:26 < katsmeow> now all i need is a prefrontal drip to give me a psychopathology relavant to getting up in the morning?
00:27 < katsmeow> i wonder if a tilting bed might be safer and cheaper
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00:57 < kanzure-> "generation of acoustic waves in neural tissue"
01:03 < kanzure-> "
01:03 < kanzure-> "
01:03 < kanzure-> Laser-induced photoacoustic injury of skin: effect of inertial confinement
01:03 < kanzure-> well that's somewhat close
01:04 < kanzure-> except it's skin instead of neurons
01:06 < kanzure-> "We believe this extensive bone damage, following 193 nm irradiation, to be a result of photoacoustic waves propagating in the bone following each pulse"
01:06 < kanzure-> "Pressure waves, which are generated by intense laser radiation, can permeabilize
01:06 < kanzure-> the stratum corneum (SC) as well as the cell membrane"
01:14 < kanzure-> hm. infrared stimulation of auditory neurons.
01:14  * kanzure- sees sounds, or something
01:15 < kanzure-> at first I was thinking of trying to use the laser micropump methods of a highly focused LED to generate some intense ultrasound cavitation bubble shockwave thingy
01:15 < kanzure-> but I guess infrared lasers produce neuronal effects without photomechanical pressure waves
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03:29 < fenn> neurophone was based on pressure waves induced by electric fields (piezo effect maybe?)
03:29 < fenn> except deaf people with broken auditory neurons could hear it even
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07:42 < kanzure> fenn: I still find that hard to believe. shouldn't they have heard at least static first until they could figure out how to descramble the signal?
07:43 < kanzure> also, that "neuroenhancing drugs" article was right-on. I think "Alex" is codename for "Bryan"
08:19 < faceface> kanzure: is that the recent drugs for sci article?
08:23 < kanzure-> no, it's the one from the newyorker
08:23 < kanzure-> "The underground world of neuroenhancing drugs"
08:23 < kanzure-> it was posted to postbiota.org's "tt" mailing list
08:23 < kanzure-> (transhumantech)
08:27 < kanzure> http://heybryan.org/~bbishop/docs/neuroenhancing.html
08:30 < faceface> ty
08:30 < faceface> someone recently mentioned a letter to a journal saying scientists should be allowed to take these 
08:31 < kanzure> huh the article mentions ImmInst
08:38 < wrldpc> http://www.filedropper.com/themitpress-structureandinterpretationofcomputerprogramswizardbook19962nded
08:46 < kanzure-> a list of recent emails sent to papers@postbiota.org
08:46 < kanzure-> "Single cell transfection using plasmid decorated AFM probes"
08:46 < kanzure-> "Genetically encoded fluorescent sensors of membrane potential"
08:47 < kanzure-> "Light-activation of gene function in mammalian cells via ribozymes"
08:47 < kanzure-> "Application of infrared light to in vivo neural stimulation"
08:47 < kanzure-> anyone pick up on a trend yet?
08:49 < kanzure-> btw, for the light-activation article- if you have a regulatory network, you could ideally encode it such that there are three promoters or something
08:49 < kanzure-> and these three promoters respond to different wavelengths of light
08:49 < kanzure-> so that you can get 3D targeting within the brain
08:49 < kanzure-> the region that would activate would be the one where the three beams intersect and there's sufficient stimulation
08:59 < kanzure-> oh uh another one is
08:59 < kanzure-> "Remote control of neuronal activity with a light-gated glutamate receptor"
08:59 < kanzure-> "Remote excitation of neuronal circuits using low-intensity, low-frequency ultrasound"
08:59 < kanzure-> "Prefrontal norepinephrine levels determines attribution of high motivational salience"
09:00 < kanzure-> "Gene silencing in mammalian cells with light-activated antisense agents"
09:12 < kanzure-> for links to those papers, see the twitter feed http://twitter.com/kanzure
09:27 < katsmeow-afk> Cost of Peer Review Exceeds the Cost of Giving Every Researcher a Grant
09:27 < katsmeow-afk> Scott Leslie passed this along. "We show that the $40,000 (Canadian) cost of preparation for a grant application and rejection by peer review in 2007 exceeded that of giving every qualified investigator a direct baseline discovery grant of $30,000 (average grant).
09:27 < katsmeow-afk> This means the Canadian Federal Government could institute direct grants for 100% of qualified applicants for the same money." Ironically, this report is published in a subscription-locked peer-reviewed paper, the total cost of which is entangled in the mechanisms for selecting which papers are good enough to publish.
09:28 < katsmeow-afk> Pot, meet kettle. A.J. Cann, Science of the Invisible, April 21, 2009  http://scienceoftheinvisible.blogspot.com/2009/04/cost-of-peer-review-exceeds-cost-of.html
09:28 < katsmeow-afk> related at http://www.downes.ca/news/OLDaily.htm
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09:34 < kanzure-> hah
09:34 < kanzure-> katsmeow-afk: awesome :)
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09:57 < kanzure-> anybody know of any lifetime studies of receptors in dendrites? i.e., are they replaced or do they stay put?
09:57 < kanzure-> if they are replaced- or, you know what, nevermind
09:58 < kanzure-> if you couple GFP to the expression of AMPA receptors, then you will have a readout of synaptic plasticity
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09:58 < kanzure-> at least from when you got that modified gene inserted into your neurons
09:59 < kanzure-> which probably isn't all too interesting- it's the underlying (original) plasticity that took place that might be more interesting or more usable in some perverse sense of the word "usable"
10:04 < kanzure-> Henry Markram and friends were doing some study about recombinant neurotransmitter receptor genes or something- that allows for the wide range of receptor recognition sites- 
10:04 < kanzure-> but now I don't remember if there have been studies that visualize the location of individual receptors or anything
10:10 < kanzure-> yay somebody has done this
10:10 < kanzure-> awesome
10:11 < kanzure> awesomeness: http://heybryan.org/books/papers/Functional%20expression%20of%20distinct%20NMDA%20channel%20subunits%20tagged%20with%20green%20fluorescent%20protein%20in%20hippocampal%20neurons%20in%20culture.pdf
10:28 < katsmeow-afk> New 167-processor Chip Is Super-fast, Ultra Energy-efficient
10:28 < katsmeow-afk> April 21, 2009
10:28 < katsmeow-afk> Maximum clock speed for the 167-processor AsAP is 1.2 gigahertz (GHz), but at slower speeds its energy efficiency soars. Twelve chips working together could perform more than half-a-trillion operations per second (.52 Tera-ops/sec) while using less power than a 7-watt light bulb.
10:28 < katsmeow-afk> more at http://www.news.ucdavis.edu/search/news_detail.lasso?id=9082
10:29 < katsmeow-afk> my concern is that the address/data buss if effectively 167 times slower (for each cpu) than a single cpu chip
10:30 < myelinzar> which data bus are we talking about? the one onboard the cpu?
10:30 < myelinzar> if it's a motherboard issue, just design a new mobo
10:31 < katsmeow-afk> if every cpu accesses the buss at the same time, the buss speed as seen by the last cpu is 6 MEGAhertz
10:31 < katsmeow-afk> the one to system mobo ram and i/o
10:32 < katsmeow-afk> 6 Mhz is slower than the 1990 8 bit ISA buss on pcs
10:33 < katsmeow-afk> likewise, if they all had files on a harddrive to access, the drive access times will be horrendously bad,, leading some to make up huge drive banks
10:34 < katsmeow-afk> 8ms latency, not counting cache problems, time 167 accesses, is 1.336 seconds access time
10:34 < katsmeow-afk> that's *forever* on a 1.2ghz cpu
10:35 < katsmeow-afk> it might as well be a propellor chip
10:35 < katsmeow-afk> is there a solution to this problem?
10:35 < katsmeow-afk> piggyback a terabyte of sram right on the cpu chip?
10:38 < katsmeow-afk> unless,,,, they mean the max clock is 1.2ghz,, or 7.2mhz per cpu?
10:41 < myelinzar> decisions, decisions. go to lab meeting, or stay on the phone with the WSJ.
10:45 < myelinzar> added some images: http://heybryan.org/books/papers/?C=M;O=D
10:48 < katsmeow-afk> what is the purpose of "C=M;O=D" ?
10:52 < myelinzar> O=D or O=A means descending or ascending
10:52 < myelinzar> C=M for some reason means sort by date modified
10:52 < myelinzar> I wonder if I could make pinkarmy as a co-op opportunity for me
10:53 < myelinzar> that's super win-win
10:53 < katsmeow-afk> oh,, i have seen such vars in urls before, and the page returned for diferent vars settings have been identical, regardless of the vars, their values, or their ordering
10:54 < myelinzar> really?
10:54 < myelinzar> try clicking the links at the top of the page
10:54  * katsmeow-afk nods,, it's a pain in datamining the internet, making multiple fetches for the same data
10:55 < katsmeow-afk> umm,,, i am speaking of other sites, not the url you gave just a min ago
10:55 < katsmeow-afk> i have not visited that url, so am not talking about it
10:55 < myelinzar> the images are very purty
10:55 < myelinzar> http://heybryan.org/books/papers/Functional%20expression%20of%20distinct%20NMDA%20channel%20subunits%20tagged%20with%20green%20fluorescent%20protein%20in%20hippocampal%20neurons%20in%20culture.5.png
10:55 < katsmeow-afk> i am speaking of historical ,, err,, history, of sites with those sorts of vars appended to the url
10:57 < katsmeow-afk> glad i am not on dialup now, that's a 420k byte pic!
10:58 < myelinzar> and if you didn't see this yesterday, you're just a bad person: http://heybryan.org/books/papers/brainbow/brainbow2.jpg
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11:34 < myelinzar> http://packages.python.org/quantities/
11:38 < faceface> now I remember why I stopped hanging out in here... its too interesting!
11:38 < faceface> kanzure: receptors in neurones should be turned over rapidly
11:38 < faceface> the half life for most proteins is 'quite low'
11:38 < myelinzar> can you cite a paper that shows the half life of a receptor protein?
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12:06 < myelinzar> faceface: please?
12:07 < faceface> myelinzar: please what?
12:07 < faceface> oh sorry
12:07 < faceface> good question
12:13 < faceface> one thing this article neglects (http://scienceoftheinvisible.blogspot.com/2009/04/cost-of-peer-review-exceeds-cost-of.html) is that peer review happens all the time. People don't want to seem dumb, so its another reason to free up grant funding.
12:14 < faceface> myelinzar: this looks related : http://www3.interscience.wiley.com/journal/119706577/abstract?CRETRY=1&SRETRY=0 
12:14 < faceface> PROTEIN TURNOVER IN CELL-ENRICHED FRACTIONS FROM RABBIT BRAIN
12:15 < faceface> The rate of incorporation of tritiated leucine and the turnover rates of protein during 10 days was studied in the bulkprepared cell fractions. The rate of incorporation into the nerve cell fraction was approximately three times greater than in the glia fraction.
12:15 < faceface> but there seems to be a lot of literature out there
12:15 < myelinzar> how is it then that there is a relatively stable concentration of receptors then?
12:15 < faceface> http://en.wikipedia.org/wiki/Protein_turnover
12:16 < faceface> myelinzar: regulatory processes ;-)
12:16 < myelinzar> see, the way that synaptic plasticity works is that NMDA stimulation coupled with AMPA stimulation causes the incorporation of further AMPA receptors
12:16 < faceface> degredateion is highly regulated
12:16 < faceface> ing?
12:16 < myelinzar> but if the AMPA receptors are being "refreshed", then how is the incorporation of new receptors regulated so as to not over-express or under-express the receptors ?
12:16 < faceface> oh... I thought that was a question
12:16 < faceface> myelinzar: is this during brain maturation or during old age?
12:17 < myelinzar> during any time 
12:17 < faceface> i.e. child -> adult or adult -> death?
12:17 < faceface> oh
12:17 < myelinzar> that's how synaptic plasticity regularly works
12:17 < faceface> I see
12:17 < myelinzar> but if the proteins are refreshed, how are the levels maintained properly?
12:17 < myelinzar> since the levels are specific to synaptic plasticity / learning
12:17 < faceface> well, cellular regulation of expression and protein degredation is a big field
12:18 < faceface> there are several mechanisms of regulation that are more or less independent
12:18 < myelinzar> but how would it know how many proteins to express? there would have to be some internal regulation feedback amplifier circuit or something
12:18 < faceface> I don't want to fob you off with a vague answer, but teh real answer is that it is not simple
12:18 < myelinzar> that would have a range of possible exprssion values or something
12:18 < myelinzar> hrm
12:18 < faceface> yes exactly
12:18 < faceface> some very highly expressed proteins are present in the genome many times for example
12:19 < faceface> others have 'efficient' promoters
12:19 < faceface> others have 'efficient' rna 
12:19 < faceface> others have rna degredation
12:19 < faceface> others have protein degredation
12:19 < faceface> any of these steps can (and do) have regulatory pathways related to them
12:20 < faceface> (often more than one)
12:20 < faceface> the basics are well known, well understood, and in some cases well characterized
12:20 < faceface> but new pathways of gene regulation are being discovered all the time.
12:21 < myelinzar> I'm sure people have studied the regulatory networks of synaptic plasticity already
12:21 < faceface> one way to get round this complexity (IMHO) is to somehow develop models that rely on teh 'cyberneic principle', matching up to reality and augmented with what we know, but allowed to fit w.r.t. what we don't know.
12:21 < faceface> perhaps
12:21 < faceface> http://en.wikipedia.org/wiki/Protein_turnover
12:22 < faceface> http://scholar.google.co.uk/scholar?q=protein+expression+regulation+neuronal+plasticity&hl=en&client=firefox-a&rls=org.mozilla:en-GB:official&um=1&ie=UTF-8&oi=scholart
12:22 < faceface> Characterization of a novel protein regulated during the critical period for song learning in the zebra finch.
12:22 < faceface> http://www.ncbi.nlm.nih.gov/pubmed/7646890
12:22 < myelinzar> btw I'm working on a firefox plugin for using Google Scholar
12:22 < faceface> agh
12:22 < faceface> sorry
12:22 < myelinzar> the idea is to help make search more effective while using google scholar
12:22 < faceface> so many 'literature management solutions' out there...
12:23 < myelinzar> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T0V-470V3B2-D&_user=108429&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059713&_version=1&_urlVersion=0&_userid=108429&md5=183b3abb9a02ef050d9e56d7b9d206ed
12:23 < myelinzar> well it's not literature management per-se
12:23 < myelinzar> I've been using zotero and mendeley
12:23 < myelinzar> but the idea is that it should help you with the searching
12:23 < myelinzar> for instance, sometimes I type in the same damn query again
12:23 < faceface> myelinzar: I would realy really like that to work, but at the end of the day I don't have time to read as many papers as I'd like to read.
12:23 < myelinzar> because I don't remember how I changed my keywords
12:23 < faceface> right
12:24 < myelinzar> so a way to automatically change the keywords or something is what I'm working on, because I don't like having to manually do 20 different queries with 20 different possibilities because Google's search query parser sucks now
12:24 < faceface> your link killed my browser ;-)
12:24 < myelinzar> the idea is to just find the good papers
12:24 < myelinzar> ouch
12:24 < faceface> right
12:24 < faceface> myelinzar: don't worry, it dies all the time
12:25 < faceface> need to re install desktop I fear
12:25 < faceface> gl
12:25 < faceface> l8r
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13:25 < myelinzar> Photoinactivation of Native AMPA Receptors Reveals Their Real-Time Trafficking
13:25 < myelinzar> Fast cycling of surface AMPA receptors with receptors from internal stores does occur but exclusively at extrasynaptic somatic sites. 
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13:26 < myelinzar> "The cycling of synaptic AMPA receptors only occurs on a much longer timescale with complete exchange requiring at least 16 hr. "
13:26 < myelinzar> "This cycling is not dependent on protein synthesis or action potential driven network activity."
13:28 < myelinzar> aha. GluR1, GluR2L, GLuR4.
13:37 < myelinzar> if this wasn't so awesome it'd be sick
13:37 < myelinzar> http://heybryan.org/books/papers/Real-Time%20Imaging%20of%20Discrete%20Exocytic%20Events%20Mediating%20Surface%20Delivery%20of%20AMPA%20Receptors.pdf
13:37 < myelinzar> real-time imaging of the addition of a receptor
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14:42 < kanzure-> anyone not subscribed is foolish: http://postbiota.org/mailman/private/papers/2009-April/thread.html
14:42 < kanzure-> here's the index of threads that you can't see:
14:42 < kanzure-> http://heybryan.org/books/papers/threads.html
14:42 < kanzure-> most of those papers are in that directory anyway of course
14:44 < ybit> hey brayn, what are you doing for brl-cad for gsoc?
14:45 < ybit> bryan*
14:46 < ybit> http://tech.slashdot.org/comments.pl?sid=1206403&cid=27661197 :: which of these
14:46 < kanzure-> I'm doing nothing :(
14:46 < ybit> that's a surprise
14:47 < kanzure-> um
14:47 < kanzure-> wait. maybe I'm doing one of those.
14:47 < kanzure-> I'm certainly not getting paid by them, that's for sure
14:47 < kanzure-> but I did talk with them extensively about the web repository and constraints stuff
14:47 < kanzure-> I think someone else is doing the constraints stuff this time around again
14:47 < kanzure-> but I'm not sure about the web repository
14:47 < kanzure-> ybit: have you subscribed to the papers mailing list yet?
14:48 < kanzure-> you really should. those papers really are fun/awesome/delicious.
14:48 < ybit> for brl-cad?
14:48 < kanzure-> (you wouldn't know this, but earlier today I sent off a proposal to ADL about SKDB related stuff)
14:48 < ybit> do you have a link?...
14:48 < kanzure-> yeah so what I was thinking was that I'd do some BRLCAD stuff
14:48 < kanzure-> and it would just so happen to be what i'm being paid for in ADL anyway
14:48 < kanzure-> hehe
14:48 < kanzure-> ybit: http://heybryan.org/books/papers/thread.html
14:49 < kanzure-> that has a link on the page
14:49 < kanzure-> or at least it should.
14:49 < kanzure-> anyway, as it turns out, I'm not GSoC for BRLCAD this year, so whatever- I'm still doing the similar work so I might as well contribute it to their code base or something, I'm not bitter. :)
14:50 < ybit> i didn't submit again this year, decided to wait
14:50 < kanzure-> I didn't submit either (that's why I wasn't accepted)
14:50 < ybit> :P
14:52 < ybit> this list does have some interesting papers, thanks
14:52 < kanzure-> it's a mailing list. :p subscribe
14:52 < ybit> wonder why eugen doesn't have a link to it from his homepage
14:52 < kanzure-> Eugen Leitl ("superstar transhumanist" as others describe him) and I decided to throw it together since we both read lots of interesting papers
14:52 < kanzure-> eugen doesn't link much from his home page
14:53 < kanzure-> for instance, nobody knows about http://eugen.leitl.org/
14:53 < ybit> how did you find it?
14:53 < kanzure-> I asked him to make it
14:53 < kanzure-> oh
14:53 < kanzure-> well, eugen.leitl.org was found by reading papers
14:53 < kanzure-> you know how google scholar sometimes links to PDFs?
14:53 < kanzure-> for some reason it indexed his collection
14:53 < kanzure-> so sometimes when you're reading a paper that he also read, you see that he has it on his server
14:53 < kanzure-> and it's the one that google scholar recommends or links to :p
14:54 < kanzure-> for instance: 
14:54 < kanzure-> http://heybryan.org/shots/2008-03-23_autoscholar.png
14:54 < ybit> aha
14:54 < ybit> i've seen that photo
14:55 < ybit> i actually know about eugen.leitl.org because of it :)
14:59 < kanzure-> hrm. so I wonder.. 
14:59 < kanzure-> what was that paper about reprogramming fibroblasts into a stem cell? didn't we recently have one about reprogramming any cell into a stem cell, and if so which paper was that?
15:00 < kanzure-> because if we used light-activated oligonucleotides, infected a system with them, and then selectively targeted a group of cells (with some lasers), then we would be able to tell a part of the human body to "reboot" itself into being a stem cell or something
15:03 < kanzure-> there was a recent one about using miRNAs to reprogram any stem cell into an embryonic stem cell, but that's not the same thing
15:03 < kanzure-> although it might be sufficient for Aubrey's cause :p
16:45 < kanzure> " A fly expressing the UAS-P2X2 transgene under the control of the shakB-GAL4 driver in the TTMn-PSI-DLMns group of neurons in the thoracic ganglion responds to a 150 ms laser pulse with wing flapping."
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17:23 < kanzure> hrm
17:23 < kanzure> I have a guy here from diybio talking to me about in vivo dna sequencing and in vivo dna synthesis
17:24 < xp_prg> where is this?
17:24 < kanzure> elsewhere
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19:09 < kanzure-> http://heybryan.org/books/papers/Low-cost,%20rapid-prototyping%20of%20digital%20microfluidics%20devices.pdf
19:09 < kanzure-> low-cost rapid prototyping of digital microfluidics devices
19:09 < kanzure-> via ferric chloride for etching of copper via sharpie masks
19:09 < kanzure-> to make electrodes for electrowetting
19:09 < kanzure-> so that you can do splitting and recombining of droplets and various forms of actuation of teh droplets
19:11 < kanzure-> does anyone know how these electrowetting devices work? blah
19:16 < kanzure-> A scaling model for electrowetting-on-dielectric microfluidic actuators
19:17 < kanzure-> http://heybryan.org/books/papers/A%20scaling%20model%20for%20electrowetting-on-dielectric%20microfluidic%20actuators.pdf
19:17 < kanzure-> I guess that's how
19:24 < kanzure-> welp. that's fairly impressive.
19:27  * kanzure- drools all over the laptop
19:47 < fenn> "And what if I wanted to go make one, would I be shot by people busting down my door or something?" <- yep
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19:50 < kanzure-> fenn: thanks for the clarification.
20:26 < kanzure-> wonder if a bullet-proof vest would protect me.
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20:35 < fenn> no
20:41 < kanzure-> foo on you
20:41 < kanzure-> those last two papers I linked to are kinda worth reading 
20:44 < kanzure-> huh. example of a microfluidic actuator: a golden ladder.
20:47 < kanzure-> 460 nL water droplet actuated by 15 V
20:49 < kanzure-> ooh, hello
20:49 < kanzure-> Pyrosequencing of DNA using Electrowetting on Dielectrics
20:53 < kanzure-> "By means of a photoconductive layer deposited underneath the dielectric layer, the voltage drop over the dielectric layer can be controlled by light. High electric fields over parts of a droplet may therefore be defined by light irradiation of the substrate. By using moving light patterns, liquid droplets may be moved continuously over a substrate, and even cell sorting is accessible using very simple devices"
20:53 < kanzure-> opto-electrowetting
20:54 -!- genehacker [n=chatzill@wireless-128-62-98-46.public.utexas.edu] has joined #hplusroadmap
20:54 < kanzure-> genehacker: electrowetting
20:54 < genehacker> yeah heard of that before
20:55 < genehacker> what about it?
20:56 < kanzure-> we needed a method of actuating liquid droplets in the sharpie microfluidic system
20:56 < kanzure-> well, that's how.
20:56 < kanzure-> http://heybryan.org/books/papers/Low-cost,%20rapid-prototyping%20of%20digital%20microfluidics%20devices.pdf
21:00 < genehacker> it's teflon coated right?
21:00 < genehacker> so can it resist nasty stuff?
21:02 < kanzure-> something cheaper than teflon
21:03 < genehacker> what?
21:03 < genehacker> that stuff that they put around the edges of plastic stuff containers to prevent ants from escaping?
21:04 < kanzure-> I thought teflon was expensive?
21:05 < genehacker> it's not teflong
21:05 < fenn> kanzure-: i think the proposal is too broad, and campbell is likely to say the same
21:06 < kanzure-> fenn: he already wants to go ahead with it
21:06 < genehacker> huh?
21:06 < kanzure-> but I've been trying to split it up into more manageable chunks
21:06 < kanzure-> for example, saying a week spent playing around with physical quantities here and there :p
21:06 < kanzure-> or something
21:07 < fenn> pq is easy
21:07 < kanzure-> so that I'm not just sitting around acting like I'm doing work
21:07 < kanzure-> yes, I know
21:07 < kanzure-> but a timeline would be nice or something
21:07 < kanzure-> so that I could say "hey, give me another undergrad to work with" or something
21:07 < kanzure-> just because it's nice to have somebody to have yelling at me or something
21:07 < kanzure-> also because he might be willing to go for grants eventually .. i.e. copy and paste the text
21:07 < kanzure-> but I think it proves how poor of a writer I am
21:11 < genehacker> you could just take that spiffy engineering writing class
21:11 < kanzure-> I think I should take a class where for each word written,
21:11 < kanzure-> they shoot me
21:12 < genehacker> why?
21:12 < genehacker> well I do hate writing too
21:13 < genehacker> hmmmmmm....
21:14 < genehacker> now should I take that mechatronics class this summer
21:17 < kanzure-> yes
21:18 < genehacker> I'm thinking I want to do some research over the summer
21:19 < kanzure-> with who?
21:20 < kanzure-> genehacker: Campbell is hiring
21:20 < genehacker> Sata for sure
21:20 < kanzure-> oh
21:20 < genehacker> the the solid freeform fabrication people
21:20 < genehacker> too
21:20 < kanzure-> what do they research?
21:21 < genehacker> solid freeform fabrication
21:21 < kanzure-> http://heybryan.org/books/papers/electrowetting.html a bibliography of electrowetting papers
21:21 < genehacker> 3d printing
21:25 < genehacker> but it looks like I might get to learn a bit of microcontroller and control system stuff in that mechatronics class
21:28 < kanzure-> I don't have experience taking classes about programming microcontrollers,
21:28 < kanzure-> but if it is anything like my previous electronics classes,
21:28 < kanzure-> you'd learn more just buying an arduino kit and playing with it for a weekend
21:29 < fenn> and it'd be useful info, not totally outdated z80 crap
21:29 < kanzure-> plus you'd have an .. arduino
21:29 < kanzure-> *gasp*
21:29 < fenn> i'd suggets a solderless breadboard and some atmega's and attiny's, but then people wouldn't feel they were paying enough
21:30 < fenn> arduino is nice in that it has the USB port built in
21:31 < kanzure-> erm
21:31 < kanzure-> but with some atmega's you need to make yourself a flasher thingy
21:31 < kanzure-> I have had bad experiences associated with making those
21:31 < fenn> well, if you are into that sort of thing
21:31 < genehacker> I believe it's about control systems, programming, and mechanics
21:31 < kanzure-> maybe the situation has become better
21:31 < fenn> you dont *have* to make your own flasher
21:31 < kanzure-> I've seen presentations about control systems .. I don't understand what they are blabering about
21:31 < kanzure-> I mean, I understand control systems
21:31 < kanzure-> but it just sounds like a load of bullshit
21:32 < kanzure-> in particular I saw stuff over youtube
21:32 < fenn> it's a load of bullshit
21:32 < kanzure-> nobody actually knew about dynamic load optimization
21:32 < fenn> surprised?
21:32 < kanzure-> or anything like that
21:32 < kanzure-> well, yes
21:32 < kanzure-> because supposedly people should know how to optimize control systems
21:32 < kanzure-> no?:
21:32 < genehacker> inverted pendulum
21:32 < fenn> hm. i'd rather have a control system that optimizes itself
21:32  * kanzure- pokes fenn to optimize himself
21:32  * fenn twitches
21:32 < kanzure-> come on.. when's it going to optimize?
21:33 < genehacker> there are algorithms that do that
21:33 < genehacker> haven't you ever played around with simulated control systems?
21:34 < kanzure-> er, you mean, programming?
21:34 < kanzure-> I don't really see what the difference is supposed to be
21:34 < genehacker> yeah, but programming stuff with physics
21:34 < kanzure-> do they even know how to write a task manager?
21:34 < kanzure-> microkernels? blah.
21:34 < kanzure-> I shouldn't bother asking
21:35 < genehacker> IE making an accurate simulation of a harrier that you can fly around 
21:36 < kanzure-> why would that be a simulated control system
21:36 < kanzure-> that sounds like 3D modeling to me
21:37 < genehacker> I'm talking about that rigid chips thing I showed you
21:37 < fenn> kanzure ever play x-plane?
21:38 < kanzure-> no.
21:38 < kanzure-> a flight simulator?
21:38 < fenn> it's interesting in that it tries to be as realistic as possible for as wide a range of airplanes
21:38 < fenn> so you can model a lunar lander for example, and program its autopilot'
21:39 < kanzure-> can you do wacky nonlinear control systems?
21:39 < kanzure-> is it just a library plugin architecture?
21:39 < genehacker> it's interesting in that people are using it to design airplanes
21:39 < genehacker> in rigid chips you betcha
21:39 < kanzure-> why are you so obsessed with god damn closed source software
21:40 < genehacker> because it's so easy to use
21:40 < kanzure-> but you can't use it beyond what you see there
21:40 < genehacker> you can though
21:40 < kanzure-> not really
21:40 < genehacker> what do you want to do?
21:40 < genehacker> if you can write it in lua....
21:40 < kanzure-> make a modification and sell it without being shot in the ass
21:40 < kanzure-> no, it's nothing to do with lua
21:40 < kanzure-> lua is an open source project
21:40 < genehacker> hahahah
21:40 < kanzure-> rigidchips is not
21:41 < genehacker> rigidchips is free
21:41 < kanzure-> so what?
21:41 < genehacker> it's not opensource because whoever made it is too lazy to document it
21:42 < kanzure-> it has nothing to do with documentation
21:42 < kanzure-> although documentation is always nice of course
21:42 < genehacker> oh wait there is documentation
21:43 < genehacker> it's just all in japanese
21:43 < fenn> so what open source 3d physics simulators are out there?
21:43 < kanzure-> fenn: what's the typical argument to use here?
21:43 < kanzure-> OGRE, OPAL, etc.
21:43 < kanzure-> OPE, ..
21:43 < fenn> those are development libraries
21:43 < kanzure-> huh?
21:43 < fenn> i'm thinking something like crayon physics but 3d
21:43 < kanzure-> crayon physics?
21:44 < fenn> phun
21:44 < kanzure-> oh
21:44 < kanzure-> um, I guess nobody has implemented that yet
21:44 < genehacker> rigidchips is sorta like that
21:44 < kanzure-> they're all too busy obsessing over "free" software
21:44 < kanzure-> :p
21:44 < genehacker> it does suck for simulating real objects
21:45 < kanzure-> I don't even know how you would correctly do a phun-like interface but for 3d
21:45 < kanzure-> I guess you'd just do something scriptable
21:45 < fenn> the usual 3d primitives
21:45 < kanzure-> and have a few buttons
21:45 < kanzure-> what's wrong with the primitive methods in the libraries as it is
21:45 < fenn> nothing
21:45 < genehacker> blocks
21:45 < kanzure-> I don't think he gets it though
21:46 < fenn> i'm just saying don't fret because you can't draw a 3d shape with crayons (though there have been some efforts towards this in academia)
21:46 < kanzure-> this has been pointless, hasn't it?
21:46 < genehacker> actuator, jet, tire, laser, magnet
21:46 < fenn> yes it's pointless
21:46 < kanzure-> genehacker: do I sound like I'm speaking a foreign language?
21:46 < genehacker> no
21:47 < kanzure-> then what's so good about allegedly "free" versus free software per the usual definitions of free software?
21:47 < genehacker> if you're just simulating 3d primitives things get boring real fast
21:47 < kanzure-> that doesn't answer the question :(
21:48 < genehacker> it's fun and there isn't much of anything like it out there that isn't free
21:48 < kanzure-> but it's not even really 'free'
21:48 < kanzure-> it's kind of like the retarded brother of 'free'
21:48 < kanzure-> as in, "not quite all there"
21:49 < fenn> http://www-ui.is.s.u-tokyo.ac.jp/~takeo/teddy/teddy.htm  3d shape sketching with crayons
21:49 < kanzure-> while it would be nice to think that the civil engineers freely build bridges (and some do!), it's even more terrible to think that you don't need to become a civil engineer
21:50 < genehacker> http://www.youtube.com/watch?v=_Bv81U-ZbOs
21:50 < kanzure-> but once somebody builds a bridge-building-machine, you just need to be able to maintain *that* machine rather than the actual bridge
21:50 < kanzure-> same concept here ..
21:50 < kanzure-> but it doesn't seem to be getting through
21:50 < genehacker> not  rigidchips, but what rigidchips is based off of
21:50 < kanzure-> but if you had to modify rigidchips in a way that the lua extensions don't allow,
21:51 < kanzure-> then you need to start from scratch
21:51 < kanzure-> whereas you could have, all along, gone with software that has already done that ofr you
21:51 < kanzure-> and is truly 'free'
21:51 < genehacker> yeah good point I have wanted to modify rigid chips
21:52 < kanzure-> what's stopped you from using the open source physics simulator engines? 
21:52 < genehacker> umm
21:52 < genehacker> how do I use them to make something like this?
21:52 < genehacker> http://www.youtube.com/watch?v=iwnOj1OZmLU&feature=related
21:52 < kanzure-> well normally when programming you start off with the simple components
21:52 < kanzure-> and then you work your way up
21:53 < kanzure-> so something like that- well, I would start with trying to make the platform 
21:53 < kanzure-> r whatever that is
21:53 < genehacker> let me find the documentation for rigidchips
21:53 < kanzure-> then the vehicle, and then the HUD, etc.
21:53 < kanzure-> and then tying it in to the underlying engine
21:53 < kanzure-> the hard work is done: the engines are sitting over there waiting for you to use them
21:53 < kanzure-> I suggest reading their tutorials
21:54 < genehacker> yeah that's pretty much what rigidchips is
21:54 < genehacker> really
21:54 < kanzure-> http://artis.imag.fr/Membres/Xavier.Decoret/resources/ode/tutorial1.html
21:54 < genehacker> I've looked at the programming and from my computers garbled attempt to display japanese it looks like it just launches directx
21:55 < kanzure-> what?
21:55 < kanzure-> garbled text?
21:55 < kanzure-> what are you looking at in particular?
21:55 < fenn> rigidchips docs
21:56 < kanzure-> are you sure? he might be trying to read the .EXE file
21:56 < fenn> genehacker: you know it'd be fairly easy to create a rigidchips clone with ODE
21:56 < genehacker> maybe
21:58 < kanzure-> heh did you guys see the post to diybio today about some guy
21:58 < kanzure-> who claims he can publish 838430124814801  papers/day
21:58 < genehacker> I'm looking at a VBP file, an FRM file, and a VBW file
21:59 < genehacker> nah
21:59 < kanzure-> that's visual basic stuff
21:59 < genehacker> that's not it
21:59 < genehacker> looks like configuration stuff to me
21:59 < kanzure-> FRM is visual basic's file format for "form"
21:59 < kanzure-> it's probably BAS (basic)
21:59 < kanzure-> god why do I know this bullshit :(
21:59 < kanzure-> it's worse than glade even
22:00 < genehacker> its all in japanese too
22:00 < genehacker> is that what I'm looking for
22:00 < kanzure-> what *are* you looking for?
22:00 < genehacker> the stuff to modify it
22:01 < kanzure-> but it's not open source. the source code was not released with rigidchips.
22:01 < kanzure-> that's my point- you can't really modify it
22:01 < kanzure-> ((((secretly, there is, but it's very hard to read decompiled assembly shit))))
22:02 < genehacker> well I have no idea it could be
22:03 < genehacker> this folder called resources has all this stuff
22:03 < genehacker> no
22:03 < genehacker> it's called doc
22:03 < kanzure-> didn't you take a programming class?
22:04 < genehacker> yeah but I can't read this:
22:04 < kanzure-> read what?
22:05 < genehacker> l:0=‹U,1=^)
22:05 < genehacker> _WARP(ƒ`ƒbƒv”ԍ†,ˆÊ’ux,ˆÊ’uy,ˆÊ’uz)
22:05 < genehacker> 	--ƒ`ƒbƒv”ԍ†‚ðŠÜ‚ÞŒn‚ð‹­§“I‚Ɉʒuxyz‚Ɉړ®
22:05 < genehacker> _WARPOBJ(ƒIƒuƒWƒFƒNƒg”ԍ†,ˆÊ’ux,ˆÊ’uy,ˆÊ’uz)
22:05 < genehacker> 	--ƒIƒuƒWƒFƒNƒg‚ð‹­§“I‚Ɉʒuxyz‚Ɉړ®
22:05 < genehacker> _FORCE(ƒ`ƒbƒv”ԍ†,x,y,z)
22:05 < genehacker> 	--ƒ`ƒbƒv‚É—Í(x,y,z)‚ð‰Á‚¦‚é
22:05 < genehacker> _FORCEOBJ(ƒIƒuƒWƒFƒNƒg”ԍ†,x,y,z)
22:05 < genehacker> 	--ƒIƒuƒWƒFƒNƒg‚É—Í(x,y,z)‚ð‰Á‚¦‚é
22:05 < genehacker> _TORQUE(ƒ`ƒbƒv”ԍ†,xŽ²,yŽ²,zŽ²)
22:05 < genehacker> 	--ƒ`ƒbƒv‚Ƀgƒ‹ƒN(xŽ²,yŽ²,zŽ²)‚ð‰Á‚¦‚é
22:05 < genehacker> _TORQUEOBJ(ƒIƒuƒWƒFƒNƒg”ԍ†,xŽ²,yŽ²,zŽ²)
22:05 < genehacker> 	--ƒIƒuƒWƒFƒNƒg‚Ƀgƒ‹ƒN(xŽ²,yŽ²,zŽ²)‚ð‰Á‚¦‚é
22:05 < genehacker> _GETHIT(ƒ`ƒbƒv”ԍ†,ÚG•¨–¼)
22:05 < kanzure-> what file is that in
22:05 < genehacker> doc
22:05 < kanzure-> the full file name
22:05 < kanzure-> including extension
22:06 < genehacker> âVâiâèâIè+ÉöêOùùv1.5.txt
22:06 < kanzure-> huh?
22:07 < genehacker> that's the name of the file
22:07 < kanzure-> hrm. well. I thought you might have been reading a binary file.
22:07 < genehacker> it's not a binary
22:08 < genehacker> just download rigidchips
22:08 < kanzure-> uhm
22:08 < kanzure-> a binary is what you run ..
22:08 < kanzure-> erm.. that's why you download it ..
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22:08 < genehacker> steal a copy of directx and run it in wine
22:09 < genehacker> give me a code paste website
22:11 < genehacker> found one
22:11 < fenn> gene this is so stupid, please find something better to do
22:11 < genehacker> http://pbox.ca/u0mp
22:11 < genehacker> ok
22:12 < fenn> you could be halfway to a working physics demo with pyode by now
22:12 < kanzure-> heh it's true :)
22:15 < genehacker> you are probably right
22:15 < genehacker> http://www.eonet.ne.jp/~owhari/rc/reference/rc_rf_script.htm
22:15 < genehacker> here's the script documentation
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22:20 < genehacker> this is open http://code.google.com/p/openpanekit/
22:21 < kanzure-> so try it?
22:28 < genehacker> can ODE do lot's of objects?
22:28 -!- jm [n=jm@p57B9CC17.dip.t-dialin.net] has joined #hplusroadmap
22:28 < genehacker> and flexible objects?
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23:20 < kanzure-> heh droplet actuation by surface acoustic waves on a piezoelectric crystal
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23:27 < kanzure-> interesting, these guys were smart enough to model the dependencies between different unit operations on microfluidic biochip operations
23:28 < kanzure-> using "SystemC"? 
23:29 < kanzure-> okie..
23:29 < kanzure-> not sure why
23:29 < kanzure-> fenn: how would you package components for microfluidic systems, in the sense that it's not entirely obvious that something is only 2D? like a mask
23:30 < kanzure-> you could package an entirely separate device to do some simple operation, that's true,
23:30 < kanzure-> or you can integrate it on the same chip and i.e. paste the masks together
23:30 < kanzure-> but how would you distinguish a mask versus something taht should be 3D milled etc?
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23:33 < fenn> as a surface instead of a volume? i dont really see the problem
23:33 < fenn> just use the 2D class of wahtever your 3D model is done in
23:35 < genehacker> packaging
23:35 < genehacker> that's pretty hard
23:36 < genehacker> encase it in black epoxy?
23:36 < genehacker> nah
23:36 < kanzure-> that's not the issue though
23:36 < kanzure-> and I don't think fenn's answer made sense anyway :p
23:44 < genehacker> kanzure could you send me a list of things that gear optimizing program needs?
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23:49 < kanzure-> genehacker: input xyz torque, output xyz torque