2009-04-22.log

--- Day changed Wed Apr 22 2009
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kanzure-Prefrontal norepinephrine determines attribution of 'high' motivational salience00:17
kanzure-http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=251617700:17
katsmeownow all i need is a prefrontal drip to give me a psychopathology relavant to getting up in the morning?00:26
katsmeowi wonder if a tilting bed might be safer and cheaper00:27
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kanzure-"generation of acoustic waves in neural tissue"00:57
kanzure-"01:03
kanzure-"01:03
kanzure-Laser-induced photoacoustic injury of skin: effect of inertial confinement01:03
kanzure-well that's somewhat close01:03
kanzure-except it's skin instead of neurons01:04
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 permeabilize01:06
kanzure-the stratum corneum (SC) as well as the cell membrane"01:06
kanzure-hm. infrared stimulation of auditory neurons.01:14
* kanzure- sees sounds, or something01:14
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 thingy01:15
kanzure-but I guess infrared lasers produce neuronal effects without photomechanical pressure waves01:15
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fennneurophone was based on pressure waves induced by electric fields (piezo effect maybe?)03:29
fennexcept deaf people with broken auditory neurons could hear it even03:29
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kanzurefenn: 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?07:42
kanzurealso, that "neuroenhancing drugs" article was right-on. I think "Alex" is codename for "Bryan"07:43
facefacekanzure: is that the recent drugs for sci article?08:19
kanzure-no, it's the one from the newyorker08:23
kanzure-"The underground world of neuroenhancing drugs"08:23
kanzure-it was posted to postbiota.org's "tt" mailing list08:23
kanzure-(transhumantech)08:23
kanzurehttp://heybryan.org/~bbishop/docs/neuroenhancing.html08:27
facefacety08:30
facefacesomeone recently mentioned a letter to a journal saying scientists should be allowed to take these 08:30
kanzurehuh the article mentions ImmInst08:31
wrldpchttp://www.filedropper.com/themitpress-structureandinterpretationofcomputerprogramswizardbook19962nded08:38
kanzure-a list of recent emails sent to papers@postbiota.org08:46
kanzure-"Single cell transfection using plasmid decorated AFM probes"08:46
kanzure-"Genetically encoded fluorescent sensors of membrane potential"08:46
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?08:47
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 something08:49
kanzure-and these three promoters respond to different wavelengths of light08:49
kanzure-so that you can get 3D targeting within the brain08:49
kanzure-the region that would activate would be the one where the three beams intersect and there's sufficient stimulation08:49
kanzure-oh uh another one is08:59
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"08:59
kanzure-"Gene silencing in mammalian cells with light-activated antisense agents"09:00
kanzure-for links to those papers, see the twitter feed http://twitter.com/kanzure09:12
katsmeow-afkCost of Peer Review Exceeds the Cost of Giving Every Researcher a Grant09:27
katsmeow-afkScott 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-afkThis 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.09:27
katsmeow-afkPot, 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.html09:28
katsmeow-afkrelated at http://www.downes.ca/news/OLDaily.htm09:28
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kanzure-hah09:34
kanzure-katsmeow-afk: awesome :)09:34
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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, nevermind09:57
kanzure-if you couple GFP to the expression of AMPA receptors, then you will have a readout of synaptic plasticity09:58
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kanzure-at least from when you got that modified gene inserted into your neurons09:58
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"09:59
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 anything10:04
kanzure-yay somebody has done this10:10
kanzure-awesome10:10
kanzureawesomeness: http://heybryan.org/books/papers/Functional%20expression%20of%20distinct%20NMDA%20channel%20subunits%20tagged%20with%20green%20fluorescent%20protein%20in%20hippocampal%20neurons%20in%20culture.pdf10:11
katsmeow-afkNew 167-processor Chip Is Super-fast, Ultra Energy-efficient10:28
katsmeow-afkApril 21, 200910:28
katsmeow-afkMaximum 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-afkmore at http://www.news.ucdavis.edu/search/news_detail.lasso?id=908210:28
katsmeow-afkmy concern is that the address/data buss if effectively 167 times slower (for each cpu) than a single cpu chip10:29
myelinzarwhich data bus are we talking about? the one onboard the cpu?10:30
myelinzarif it's a motherboard issue, just design a new mobo10:30
katsmeow-afkif every cpu accesses the buss at the same time, the buss speed as seen by the last cpu is 6 MEGAhertz10:31
katsmeow-afkthe one to system mobo ram and i/o10:31
katsmeow-afk6 Mhz is slower than the 1990 8 bit ISA buss on pcs10:32
katsmeow-afklikewise, 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 banks10:33
katsmeow-afk8ms latency, not counting cache problems, time 167 accesses, is 1.336 seconds access time10:34
katsmeow-afkthat's *forever* on a 1.2ghz cpu10:34
katsmeow-afkit might as well be a propellor chip10:35
katsmeow-afkis there a solution to this problem?10:35
katsmeow-afkpiggyback a terabyte of sram right on the cpu chip?10:35
katsmeow-afkunless,,,, they mean the max clock is 1.2ghz,, or 7.2mhz per cpu?10:38
myelinzardecisions, decisions. go to lab meeting, or stay on the phone with the WSJ.10:41
myelinzaradded some images: http://heybryan.org/books/papers/?C=M;O=D10:45
katsmeow-afkwhat is the purpose of "C=M;O=D" ?10:48
myelinzarO=D or O=A means descending or ascending10:52
myelinzarC=M for some reason means sort by date modified10:52
myelinzarI wonder if I could make pinkarmy as a co-op opportunity for me10:52
myelinzarthat's super win-win10:53
katsmeow-afkoh,, 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 ordering10:53
myelinzarreally?10:54
myelinzartry clicking the links at the top of the page10:54
* katsmeow-afk nods,, it's a pain in datamining the internet, making multiple fetches for the same data10:54
katsmeow-afkumm,,, i am speaking of other sites, not the url you gave just a min ago10:55
katsmeow-afki have not visited that url, so am not talking about it10:55
myelinzarthe images are very purty10:55
myelinzarhttp://heybryan.org/books/papers/Functional%20expression%20of%20distinct%20NMDA%20channel%20subunits%20tagged%20with%20green%20fluorescent%20protein%20in%20hippocampal%20neurons%20in%20culture.5.png10:55
katsmeow-afki am speaking of historical ,, err,, history, of sites with those sorts of vars appended to the url10:55
katsmeow-afkglad i am not on dialup now, that's a 420k byte pic!10:57
myelinzarand if you didn't see this yesterday, you're just a bad person: http://heybryan.org/books/papers/brainbow/brainbow2.jpg10:58
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myelinzarhttp://packages.python.org/quantities/11:34
facefacenow I remember why I stopped hanging out in here... its too interesting!11:38
facefacekanzure: receptors in neurones should be turned over rapidly11:38
facefacethe half life for most proteins is 'quite low'11:38
myelinzarcan you cite a paper that shows the half life of a receptor protein?11:38
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myelinzarfaceface: please?12:06
facefacemyelinzar: please what?12:07
facefaceoh sorry12:07
facefacegood question12:07
facefaceone 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.12:13
facefacemyelinzar: this looks related : http://www3.interscience.wiley.com/journal/119706577/abstract?CRETRY=1&SRETRY=0 12:14
facefacePROTEIN TURNOVER IN CELL-ENRICHED FRACTIONS FROM RABBIT BRAIN12:14
facefaceThe 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
facefacebut there seems to be a lot of literature out there12:15
myelinzarhow is it then that there is a relatively stable concentration of receptors then?12:15
facefacehttp://en.wikipedia.org/wiki/Protein_turnover12:15
facefacemyelinzar: regulatory processes ;-)12:16
myelinzarsee, the way that synaptic plasticity works is that NMDA stimulation coupled with AMPA stimulation causes the incorporation of further AMPA receptors12:16
facefacedegredateion is highly regulated12:16
facefaceing?12:16
myelinzarbut 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
facefaceoh... I thought that was a question12:16
facefacemyelinzar: is this during brain maturation or during old age?12:16
myelinzarduring any time 12:17
facefacei.e. child -> adult or adult -> death?12:17
facefaceoh12:17
myelinzarthat's how synaptic plasticity regularly works12:17
facefaceI see12:17
myelinzarbut if the proteins are refreshed, how are the levels maintained properly?12:17
myelinzarsince the levels are specific to synaptic plasticity / learning12:17
facefacewell, cellular regulation of expression and protein degredation is a big field12:17
facefacethere are several mechanisms of regulation that are more or less independent12:18
myelinzarbut how would it know how many proteins to express? there would have to be some internal regulation feedback amplifier circuit or something12:18
facefaceI don't want to fob you off with a vague answer, but teh real answer is that it is not simple12:18
myelinzarthat would have a range of possible exprssion values or something12:18
myelinzarhrm12:18
facefaceyes exactly12:18
facefacesome very highly expressed proteins are present in the genome many times for example12:18
facefaceothers have 'efficient' promoters12:19
facefaceothers have 'efficient' rna 12:19
facefaceothers have rna degredation12:19
facefaceothers have protein degredation12:19
facefaceany of these steps can (and do) have regulatory pathways related to them12:19
faceface(often more than one)12:20
facefacethe basics are well known, well understood, and in some cases well characterized12:20
facefacebut new pathways of gene regulation are being discovered all the time.12:20
myelinzarI'm sure people have studied the regulatory networks of synaptic plasticity already12:21
facefaceone 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
facefaceperhaps12:21
facefacehttp://en.wikipedia.org/wiki/Protein_turnover12:21
facefacehttp://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=scholart12:22
facefaceCharacterization of a novel protein regulated during the critical period for song learning in the zebra finch.12:22
facefacehttp://www.ncbi.nlm.nih.gov/pubmed/764689012:22
myelinzarbtw I'm working on a firefox plugin for using Google Scholar12:22
facefaceagh12:22
facefacesorry12:22
myelinzarthe idea is to help make search more effective while using google scholar12:22
facefaceso many 'literature management solutions' out there...12:22
myelinzarhttp://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=183b3abb9a02ef050d9e56d7b9d206ed12:23
myelinzarwell it's not literature management per-se12:23
myelinzarI've been using zotero and mendeley12:23
myelinzarbut the idea is that it should help you with the searching12:23
myelinzarfor instance, sometimes I type in the same damn query again12:23
facefacemyelinzar: 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
myelinzarbecause I don't remember how I changed my keywords12:23
facefaceright12:23
myelinzarso 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 now12:24
facefaceyour link killed my browser ;-)12:24
myelinzarthe idea is to just find the good papers12:24
myelinzarouch12:24
facefaceright12:24
facefacemyelinzar: don't worry, it dies all the time12:24
facefaceneed to re install desktop I fear12:25
facefacegl12:25
facefacel8r12:25
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myelinzarPhotoinactivation of Native AMPA Receptors Reveals Their Real-Time Trafficking13:25
myelinzarFast cycling of surface AMPA receptors with receptors from internal stores does occur but exclusively at extrasynaptic somatic sites. 13:25
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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."13:26
myelinzaraha. GluR1, GluR2L, GLuR4.13:28
myelinzarif this wasn't so awesome it'd be sick13:37
myelinzarhttp://heybryan.org/books/papers/Real-Time%20Imaging%20of%20Discrete%20Exocytic%20Events%20Mediating%20Surface%20Delivery%20of%20AMPA%20Receptors.pdf13:37
myelinzarreal-time imaging of the addition of a receptor13:37
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kanzure-anyone not subscribed is foolish: http://postbiota.org/mailman/private/papers/2009-April/thread.html14:42
kanzure-here's the index of threads that you can't see:14:42
kanzure-http://heybryan.org/books/papers/threads.html14:42
kanzure-most of those papers are in that directory anyway of course14:42
ybithey brayn, what are you doing for brl-cad for gsoc?14:44
ybitbryan*14:45
ybithttp://tech.slashdot.org/comments.pl?sid=1206403&cid=27661197 :: which of these14:46
kanzure-I'm doing nothing :(14:46
ybitthat's a surprise14:46
kanzure-um14:47
kanzure-wait. maybe I'm doing one of those.14:47
kanzure-I'm certainly not getting paid by them, that's for sure14:47
kanzure-but I did talk with them extensively about the web repository and constraints stuff14:47
kanzure-I think someone else is doing the constraints stuff this time around again14:47
kanzure-but I'm not sure about the web repository14:47
kanzure-ybit: have you subscribed to the papers mailing list yet?14:47
kanzure-you really should. those papers really are fun/awesome/delicious.14:48
ybitfor 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
ybitdo you have a link?...14:48
kanzure-yeah so what I was thinking was that I'd do some BRLCAD stuff14:48
kanzure-and it would just so happen to be what i'm being paid for in ADL anyway14:48
kanzure-hehe14:48
kanzure-ybit: http://heybryan.org/books/papers/thread.html14:48
kanzure-that has a link on the page14:49
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. :)14:49
ybiti didn't submit again this year, decided to wait14:50
kanzure-I didn't submit either (that's why I wasn't accepted)14:50
ybit:P14:50
ybitthis list does have some interesting papers, thanks14:52
kanzure-it's a mailing list. :p subscribe14:52
ybitwonder why eugen doesn't have a link to it from his homepage14:52
kanzure-Eugen Leitl ("superstar transhumanist" as others describe him) and I decided to throw it together since we both read lots of interesting papers14:52
kanzure-eugen doesn't link much from his home page14:52
kanzure-for instance, nobody knows about http://eugen.leitl.org/14:53
ybithow did you find it?14:53
kanzure-I asked him to make it14:53
kanzure-oh14:53
kanzure-well, eugen.leitl.org was found by reading papers14:53
kanzure-you know how google scholar sometimes links to PDFs?14:53
kanzure-for some reason it indexed his collection14:53
kanzure-so sometimes when you're reading a paper that he also read, you see that he has it on his server14:53
kanzure-and it's the one that google scholar recommends or links to :p14:53
kanzure-for instance: 14:54
kanzure-http://heybryan.org/shots/2008-03-23_autoscholar.png14:54
ybitaha14:54
ybiti've seen that photo14:54
ybiti actually know about eugen.leitl.org because of it :)14:55
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?14:59
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 something15:00
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 thing15:03
kanzure-although it might be sufficient for Aubrey's cause :p15:03
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."16:45
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kanzurehrm17:23
kanzureI have a guy here from diybio talking to me about in vivo dna sequencing and in vivo dna synthesis17:23
xp_prgwhere is this?17:24
kanzureelsewhere17:24
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kanzure-http://heybryan.org/books/papers/Low-cost,%20rapid-prototyping%20of%20digital%20microfluidics%20devices.pdf19:09
kanzure-low-cost rapid prototyping of digital microfluidics devices19:09
kanzure-via ferric chloride for etching of copper via sharpie masks19:09
kanzure-to make electrodes for electrowetting19:09
kanzure-so that you can do splitting and recombining of droplets and various forms of actuation of teh droplets19:09
kanzure-does anyone know how these electrowetting devices work? blah19:11
kanzure-A scaling model for electrowetting-on-dielectric microfluidic actuators19:16
kanzure-http://heybryan.org/books/papers/A%20scaling%20model%20for%20electrowetting-on-dielectric%20microfluidic%20actuators.pdf19:17
kanzure-I guess that's how19:17
kanzure-welp. that's fairly impressive.19:24
* kanzure- drools all over the laptop19:27
fenn"And what if I wanted to go make one, would I be shot by people busting down my door or something?" <- yep19:47
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kanzure-fenn: thanks for the clarification.19:50
kanzure-wonder if a bullet-proof vest would protect me.20:26
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fennno20:35
kanzure-foo on you20:41
kanzure-those last two papers I linked to are kinda worth reading 20:41
kanzure-huh. example of a microfluidic actuator: a golden ladder.20:44
kanzure-460 nL water droplet actuated by 15 V20:47
kanzure-ooh, hello20:49
kanzure-Pyrosequencing of DNA using Electrowetting on Dielectrics20:49
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-electrowetting20:53
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kanzure-genehacker: electrowetting20:54
genehackeryeah heard of that before20:54
genehackerwhat about it?20:55
kanzure-we needed a method of actuating liquid droplets in the sharpie microfluidic system20:56
kanzure-well, that's how.20:56
kanzure-http://heybryan.org/books/papers/Low-cost,%20rapid-prototyping%20of%20digital%20microfluidics%20devices.pdf20:56
genehackerit's teflon coated right?21:00
genehackerso can it resist nasty stuff?21:00
kanzure-something cheaper than teflon21:02
genehackerwhat?21:03
genehackerthat stuff that they put around the edges of plastic stuff containers to prevent ants from escaping?21:03
kanzure-I thought teflon was expensive?21:04
genehackerit's not teflong21:05
fennkanzure-: i think the proposal is too broad, and campbell is likely to say the same21:05
kanzure-fenn: he already wants to go ahead with it21:06
genehackerhuh?21:06
kanzure-but I've been trying to split it up into more manageable chunks21:06
kanzure-for example, saying a week spent playing around with physical quantities here and there :p21:06
kanzure-or something21:06
fennpq is easy21:07
kanzure-so that I'm not just sitting around acting like I'm doing work21:07
kanzure-yes, I know21:07
kanzure-but a timeline would be nice or something21:07
kanzure-so that I could say "hey, give me another undergrad to work with" or something21:07
kanzure-just because it's nice to have somebody to have yelling at me or something21:07
kanzure-also because he might be willing to go for grants eventually .. i.e. copy and paste the text21:07
kanzure-but I think it proves how poor of a writer I am21:07
genehackeryou could just take that spiffy engineering writing class21:11
kanzure-I think I should take a class where for each word written,21:11
kanzure-they shoot me21:11
genehackerwhy?21:12
genehackerwell I do hate writing too21:12
genehackerhmmmmmm....21:13
genehackernow should I take that mechatronics class this summer21:14
kanzure-yes21:17
genehackerI'm thinking I want to do some research over the summer21:18
kanzure-with who?21:19
kanzure-genehacker: Campbell is hiring21:20
genehackerSata for sure21:20
kanzure-oh21:20
genehackerthe the solid freeform fabrication people21:20
genehackertoo21:20
kanzure-what do they research?21:20
genehackersolid freeform fabrication21:21
kanzure-http://heybryan.org/books/papers/electrowetting.html a bibliography of electrowetting papers21:21
genehacker3d printing21:21
genehackerbut it looks like I might get to learn a bit of microcontroller and control system stuff in that mechatronics class21:25
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 weekend21:28
fennand it'd be useful info, not totally outdated z80 crap21:29
kanzure-plus you'd have an .. arduino21:29
kanzure-*gasp*21:29
fenni'd suggets a solderless breadboard and some atmega's and attiny's, but then people wouldn't feel they were paying enough21:29
fennarduino is nice in that it has the USB port built in21:30
kanzure-erm21:31
kanzure-but with some atmega's you need to make yourself a flasher thingy21:31
kanzure-I have had bad experiences associated with making those21:31
fennwell, if you are into that sort of thing21:31
genehackerI believe it's about control systems, programming, and mechanics21:31
kanzure-maybe the situation has become better21:31
fennyou dont *have* to make your own flasher21:31
kanzure-I've seen presentations about control systems .. I don't understand what they are blabering about21:31
kanzure-I mean, I understand control systems21:31
kanzure-but it just sounds like a load of bullshit21:31
kanzure-in particular I saw stuff over youtube21:32
fennit's a load of bullshit21:32
kanzure-nobody actually knew about dynamic load optimization21:32
fennsurprised?21:32
kanzure-or anything like that21:32
kanzure-well, yes21:32
kanzure-because supposedly people should know how to optimize control systems21:32
kanzure-no?:21:32
genehackerinverted pendulum21:32
fennhm. i'd rather have a control system that optimizes itself21:32
* kanzure- pokes fenn to optimize himself21:32
* fenn twitches21:32
kanzure-come on.. when's it going to optimize?21:32
genehackerthere are algorithms that do that21:33
genehackerhaven't you ever played around with simulated control systems?21:33
kanzure-er, you mean, programming?21:34
kanzure-I don't really see what the difference is supposed to be21:34
genehackeryeah, but programming stuff with physics21:34
kanzure-do they even know how to write a task manager?21:34
kanzure-microkernels? blah.21:34
kanzure-I shouldn't bother asking21:34
genehackerIE making an accurate simulation of a harrier that you can fly around 21:35
kanzure-why would that be a simulated control system21:36
kanzure-that sounds like 3D modeling to me21:36
genehackerI'm talking about that rigid chips thing I showed you21:37
fennkanzure ever play x-plane?21:37
kanzure-no.21:38
kanzure-a flight simulator?21:38
fennit's interesting in that it tries to be as realistic as possible for as wide a range of airplanes21:38
fennso you can model a lunar lander for example, and program its autopilot'21:38
kanzure-can you do wacky nonlinear control systems?21:39
kanzure-is it just a library plugin architecture?21:39
genehackerit's interesting in that people are using it to design airplanes21:39
genehackerin rigid chips you betcha21:39
kanzure-why are you so obsessed with god damn closed source software21:39
genehackerbecause it's so easy to use21:40
kanzure-but you can't use it beyond what you see there21:40
genehackeryou can though21:40
kanzure-not really21:40
genehackerwhat do you want to do?21:40
genehackerif you can write it in lua....21:40
kanzure-make a modification and sell it without being shot in the ass21:40
kanzure-no, it's nothing to do with lua21:40
kanzure-lua is an open source project21:40
genehackerhahahah21:40
kanzure-rigidchips is not21:40
genehackerrigidchips is free21:41
kanzure-so what?21:41
genehackerit's not opensource because whoever made it is too lazy to document it21:41
kanzure-it has nothing to do with documentation21:42
kanzure-although documentation is always nice of course21:42
genehackeroh wait there is documentation21:42
genehackerit's just all in japanese21:43
fennso 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
fennthose are development libraries21:43
kanzure-huh?21:43
fenni'm thinking something like crayon physics but 3d21:43
kanzure-crayon physics?21:43
fennphun21:44
kanzure-oh21:44
kanzure-um, I guess nobody has implemented that yet21:44
genehackerrigidchips is sorta like that21:44
kanzure-they're all too busy obsessing over "free" software21:44
kanzure-:p21:44
genehackerit does suck for simulating real objects21:44
kanzure-I don't even know how you would correctly do a phun-like interface but for 3d21:45
kanzure-I guess you'd just do something scriptable21:45
fennthe usual 3d primitives21:45
kanzure-and have a few buttons21:45
kanzure-what's wrong with the primitive methods in the libraries as it is21:45
fennnothing21:45
genehackerblocks21:45
kanzure-I don't think he gets it though21:45
fenni'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
genehackeractuator, jet, tire, laser, magnet21:46
fennyes it's pointless21:46
kanzure-genehacker: do I sound like I'm speaking a foreign language?21:46
genehackerno21:46
kanzure-then what's so good about allegedly "free" versus free software per the usual definitions of free software?21:47
genehackerif you're just simulating 3d primitives things get boring real fast21:47
kanzure-that doesn't answer the question :(21:47
genehackerit's fun and there isn't much of anything like it out there that isn't free21:48
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"21:48
fennhttp://www-ui.is.s.u-tokyo.ac.jp/~takeo/teddy/teddy.htm  3d shape sketching with crayons21:49
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 engineer21:49
genehackerhttp://www.youtube.com/watch?v=_Bv81U-ZbOs21:50
kanzure-but once somebody builds a bridge-building-machine, you just need to be able to maintain *that* machine rather than the actual bridge21:50
kanzure-same concept here ..21:50
kanzure-but it doesn't seem to be getting through21:50
genehackernot  rigidchips, but what rigidchips is based off of21:50
kanzure-but if you had to modify rigidchips in a way that the lua extensions don't allow,21:50
kanzure-then you need to start from scratch21:51
kanzure-whereas you could have, all along, gone with software that has already done that ofr you21:51
kanzure-and is truly 'free'21:51
genehackeryeah good point I have wanted to modify rigid chips21:51
kanzure-what's stopped you from using the open source physics simulator engines? 21:52
genehackerumm21:52
genehackerhow do I use them to make something like this?21:52
genehackerhttp://www.youtube.com/watch?v=iwnOj1OZmLU&feature=related21:52
kanzure-well normally when programming you start off with the simple components21:52
kanzure-and then you work your way up21:52
kanzure-so something like that- well, I would start with trying to make the platform 21:53
kanzure-r whatever that is21:53
genehackerlet me find the documentation for rigidchips21:53
kanzure-then the vehicle, and then the HUD, etc.21:53
kanzure-and then tying it in to the underlying engine21:53
kanzure-the hard work is done: the engines are sitting over there waiting for you to use them21:53
kanzure-I suggest reading their tutorials21:53
genehackeryeah that's pretty much what rigidchips is21:54
genehackerreally21:54
kanzure-http://artis.imag.fr/Membres/Xavier.Decoret/resources/ode/tutorial1.html21:54
genehackerI've looked at the programming and from my computers garbled attempt to display japanese it looks like it just launches directx21:54
kanzure-what?21:55
kanzure-garbled text?21:55
kanzure-what are you looking at in particular?21:55
fennrigidchips docs21:55
kanzure-are you sure? he might be trying to read the .EXE file21:56
fenngenehacker: you know it'd be fairly easy to create a rigidchips clone with ODE21:56
genehackermaybe21:56
kanzure-heh did you guys see the post to diybio today about some guy21:58
kanzure-who claims he can publish 838430124814801  papers/day21:58
genehackerI'm looking at a VBP file, an FRM file, and a VBW file21:58
genehackernah21:59
kanzure-that's visual basic stuff21:59
genehackerthat's not it21:59
genehackerlooks like configuration stuff to me21:59
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 even21:59
genehackerits all in japanese too22:00
genehackeris that what I'm looking for22:00
kanzure-what *are* you looking for?22:00
genehackerthe stuff to modify it22:00
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 it22:01
kanzure-((((secretly, there is, but it's very hard to read decompiled assembly shit))))22:01
genehackerwell I have no idea it could be22:02
genehackerthis folder called resources has all this stuff22:03
genehackerno22:03
genehackerit's called doc22:03
kanzure-didn't you take a programming class?22:03
genehackeryeah but I can't read this:22:04
kanzure-read what?22:04
genehackerl: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‚¦‚é22:05
genehacker_FORCEOBJ(ƒIƒuƒWƒFƒNƒg”ԍ†,x,y,z)22:05
genehacker--ƒIƒuƒWƒFƒNƒg‚É—Í(x,y,z)‚ð‰Á‚¦‚é22:05
genehacker_TORQUE(ƒ`ƒbƒv”ԍ†,xŽ²,yŽ²,zŽ²)22:05
genehacker--ƒ`ƒbƒv‚Ƀgƒ‹ƒN(xŽ²,yŽ²,zŽ²)‚ð‰Á‚¦‚é22:05
genehacker_TORQUEOBJ(ƒIƒuƒWƒFƒNƒg”ԍ†,xŽ²,yŽ²,zŽ²)22:05
genehacker--ƒIƒuƒWƒFƒNƒg‚Ƀgƒ‹ƒN(xŽ²,yŽ²,zŽ²)‚ð‰Á‚¦‚é22:05
genehacker_GETHIT(ƒ`ƒbƒv”ԍ†,ÚG•¨–¼)22:05
kanzure-what file is that in22:05
genehackerdoc22:05
kanzure-the full file name22:05
kanzure-including extension22:05
genehackerâVâiâèâIè+ÉöêOùùv1.5.txt22:06
kanzure-huh?22:06
genehackerthat's the name of the file22:07
kanzure-hrm. well. I thought you might have been reading a binary file.22:07
genehackerit's not a binary22:07
genehackerjust download rigidchips22:08
kanzure-uhm22:08
kanzure-a binary is what you run ..22:08
kanzure-erm.. that's why you download it ..22:08
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genehackersteal a copy of directx and run it in wine22:08
genehackergive me a code paste website22:09
genehackerfound one22:11
fenngene this is so stupid, please find something better to do22:11
genehackerhttp://pbox.ca/u0mp22:11
genehackerok22:11
fennyou could be halfway to a working physics demo with pyode by now22:12
kanzure-heh it's true :)22:12
genehackeryou are probably right22:15
genehackerhttp://www.eonet.ne.jp/~owhari/rc/reference/rc_rf_script.htm22:15
genehackerhere's the script documentation22:15
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genehackerthis is open http://code.google.com/p/openpanekit/22:20
kanzure-so try it?22:21
genehackercan ODE do lot's of objects?22:28
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genehackerand flexible objects?22:28
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kanzure-heh droplet actuation by surface acoustic waves on a piezoelectric crystal23:20
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kanzure-interesting, these guys were smart enough to model the dependencies between different unit operations on microfluidic biochip operations23:27
kanzure-using "SystemC"? 23:28
kanzure-okie..23:29
kanzure-not sure why23:29
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 mask23:29
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 together23:30
kanzure-but how would you distinguish a mask versus something taht should be 3D milled etc?23:30
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fennas a surface instead of a volume? i dont really see the problem23:33
fennjust use the 2D class of wahtever your 3D model is done in23:33
genehackerpackaging23:35
genehackerthat's pretty hard23:35
genehackerencase it in black epoxy?23:36
genehackernah23:36
kanzure-that's not the issue though23:36
kanzure-and I don't think fenn's answer made sense anyway :p23:36
genehackerkanzure could you send me a list of things that gear optimizing program needs?23:44
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kanzure-genehacker: input xyz torque, output xyz torque23:49

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