2013-04-23.log

--- Log opened Tue Apr 23 00:00:05 2013
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kanzurei am having trouble remembering all of the tiny nodejs packages.01:24
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kanzurehm.. this looks thorough: https://github.com/hyperandroid/Automata01:44
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rigelso apparently phantomjs had selenium support built-in02:36
rigelbut then not so much, and ghost.py was suggested02:36
rigelpart of my problem, i guess, is that i am using the webdriver'd ff instance both for automation and for probing02:38
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kanzurerigel: phantomjs recently had a webdriver implemented, yes.03:07
kanzureghost.py isn't really similar, but yours truly has a few commits in that repo anyway.03:07
kanzurelots of folks like casperjs, but i've never wanted it.03:08
kanzurephantomjs has the webkit remote debugger enabled if you want to use that for development03:10
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nmz787_makoLime: nope, I usually use irssi04:01
* nmz787_ nmz78704:02
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makoLimenmz787, oh, so the "Page closed" quit message is... irssi refering to tabs as pages?04:22
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superkuhLame. NASA's STI Reports are still censored by the Dept. of Homeland Security but their RSS feed still updates with titles and summaries. Such a tease. The service has been censored for going on a month now.04:27
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nmz787makoLime: not sure what you're talking about04:32
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delinquentmele weh07:58
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kanzurebrownies: since you like glowing crap so much, http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit11:45
kanzurewho the hell pledged $10,000?11:46
kanzureit's at $15666 and they are spamming my inbox with crap like "WE ALREADY REACHED 20% OF OUR GOAL"11:47
ParahSailinah geez11:47
kanzureso.. i think they just pledged their own money in that.11:47
ParahSailindefinitely11:47
kanzurei really don't like omri ("mr. genome compiler").. it's not a compiler, stop lying to me.11:48
ParahSailinomri?11:48
kanzurealso, nobody likes adobe air/flash.11:48
kanzurethis is one of omri's projects11:48
ParahSailinman theres so much absolute trash11:48
ParahSailinand the sad thing is, there's not really much useful stuff that _can_ be done at the current level of technology11:49
kanzureomri also raised something like $500k for his "genome compiler".11:49
kanzurethere's a lot of useful things that could be done.. the vast majority of lab equipment has no open source equivalent.11:49
ParahSailinso no chance of weighing out the bad11:49
ParahSailinwhat would it take to marshall the resources to do that11:53
kanzurefirst thing is to figure out how to make the incentives align11:53
kanzurethere may or may not be a market for open source equipment. imagine that there's no market for it. even if there's no market, those devices are still worth having and using for our development activities. so the incentives are still tricky to figure out in that case.11:54
ParahSailini think pirated illumina would be a pretty killer app11:54
kanzurethe software?11:54
ParahSailinno, the machine11:54
kanzurewell, biocurious is theoretically doing a teardown of an illumina today or tomorrow or w/e.. hopefully they document enough of it that we can ship it off to china.11:55
kanzurei've asked them to also get a copy of any hard drives or ROMs on chips and shit, but they just looked at me confused. so it might not be a thorough teardown..11:55
ParahSailinthey really got a gaiix that they can completely tear down11:56
ParahSailini have such a hard time believing that11:56
ParahSailini might even bet money on that11:57
ParahSailinthe theory of illumina isnt that complicated, it might not even be that hard to reverse engineer12:05
ParahSailintricks are the flow cell surface preparation and the clustering wet chemistry12:06
ParahSailinwho knows, the patents might even cover how those work12:06
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kanzuremakerbot industries trying to patent obvious things http://forums.reprap.org/read.php?1,201914,20195413:14
ParahSailinwell, the legal definition of obvious is simple composition of things that are patented13:17
kanzureguess i better start filing for patents on socially networked transcranial brain things.13:18
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kanzurestupid glowplant is up to $20k :(13:26
kanzurepft "We will be printing our DNA with Cambrian Genomics who have developed a revolutionary laser printing system that massively reduces the cost of DNA synthesis."13:27
kanzure"Funds raised will also be used to support our work to develop an open policy framework for DIY Bio work involving recombinant DNA."13:27
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kanzurefuck those assholes. "open policy framework.." how about no?13:27
kanzure"The framework will include recommendations for what kinds of projects are safe for DIY Bio enthusiasts "13:27
kanzurewhat the hell is this shit :(13:27
kanzure"Genome Compiler is software, designed by Omri and his team, which allows a user to easily design genetic sequences and order them online.  The software includes a large database of genetic parts and a beautiful interface so you can easily combine them to create your desired results."13:28
kanzurethis is not a compiler. what a liar.13:28
ParahSailinwhat printing dna?13:29
ParahSailinlaser printing dna?13:29
kanzurefenn wrote some notes in the logs about what cambrian genomics is actually doing.. it's something like "let's use sequencing to reduce the cost of gene synthesis" or something.13:32
ParahSailini should just give up doing honest work and be a charlatan13:33
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ParahSailinthe upshot is that we won't have any more how-do-i-make-a-glowing-plant posts on diybio13:42
kanzureno they are going to increase :(13:43
ParahSailinkanzure: lets do a charlatan kickstarter to get money to divert towards a useful open hardware13:45
kanzurewell it seems that people only donate if they like the video and the rewards13:45
kanzureand the rewards seem to have to be actual products, which i don't really want to do. that's low margins and a lot of work..13:45
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kanzureParahSailin: how about you just tell me what you want to do and i just pay for it13:49
kanzureParahSailin: isn't that easier?13:49
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ParahSailinhm13:54
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makoLimenmz787, you sometimes use an IRC client that has "page closed" as its quit message. I wonder what that is.16:05
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ThomasEgimakoLime, a webchat client?16:13
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makoLimeThomasEgi, I'd presume so.16:16
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SphericalMouseSup?16:31
kanzurebusy being annoyed at omri16:31
kanzuretrying to pick projects to dump money into16:31
SphericalMouse?16:32
kanzurehow goes the teardown?16:32
SphericalMousehappens sunday16:32
kanzuredrats.16:32
SphericalMousefilled up in under a day16:32
kanzurephoto everything. get the ROMs off the chips.16:33
SphericalMousehave you done group teardowns before?16:33
kanzureno. i've done teardowns before on my own, though.16:33
SphericalMouseI'm just wondering how to best present it16:34
kanzureget one of those mirror-based overhead projectors to show the smaller parts on a wall16:35
SphericalMousethat would just cast a shadow16:35
SphericalMousemaybe having a camera guy linked into a projector16:35
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kanzureParahSail1n: ask SphericalMouse about your teardown woes17:09
SphericalMouse?17:11
kanzureSphericalMouse: give him a minute, geeze..17:11
SphericalMousejust saying im here is all17:12
kanzureokay17:12
ParahSail1nhey17:24
ParahSail1nyou have access to a ga2x?17:24
SphericalMousedepends, the ones at biocurious are just GAs17:26
SphericalMousemight have some 2xs at work17:26
SphericalMousewhat do you need?17:33
ParahSail1nyou were reverse engineering one?17:34
SphericalMouseno, we use them as test platforms17:35
ParahSail1nwhat does your work do?17:36
SphericalMousethough that would an amusing case of lost knowledge17:36
SphericalMousewe make DNA sequencers17:37
ParahSail1nillumina competitor?17:37
SphericalMousenot quite17:38
kanzurejust think of the benefits for your employer: if you can prove that illumina's software is wrong, that would be a net gain.17:40
kanzurehint: embedded stuff is usually wrong in a number of ways, unless it happens to be nasa..17:40
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SphericalMousedoes anyone use GAs any more anyways?17:42
ParahSail1ni think that the embedded stuff is not likely to be a problem with the illumina systems17:42
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ParahSail1nbecause all the embedded stuff has to do is transmit the images to the RTA software on the computer17:42
SphericalMousenot even that17:42
kanzurewell, i'd also be willing to take a stab at the software on the computer.17:43
kanzurewhich i do not have.17:43
ParahSail1nkanzure, i can give you a password to download casava and olb if you want17:43
kanzuresure. not right now. stuffing my face with food and acting like i can write javascript.17:43
ParahSail1ncasava's like 1.5 GB17:44
kanzurewhat's in it?17:44
ParahSail1ni forget if casava includes the rta software or if its just deindexing and miscellaneous stuff17:45
SphericalMousehttp://www.illumina.com/software/genome_analyzer_software.ilmn17:45
ParahSail1nthere's a shitty mapper included i think17:45
SphericalMousenot sure if it is much use without test images though17:46
kanzuremost of the time vendors put extra software on, or they make mistakes in the product and release other software online17:46
ParahSail1ni might have test images somewhere17:46
ParahSail1nhm, looks like illumina doesnt require login anymore http://support.illumina.com/documents/MyIllumina/6e422abb-dc36-4d09-b223-0eafef26ddc5/CASAVA_v1.8.2.tar17:47
kanzurei am also curious about their security.. do they have significant blocks against just dumping your own software onto the device, etc.17:47
SphericalMouseyou mean while connected to the computer?17:50
kanzurethat's also worth exploring i think17:51
kanzurewhat is their connection anyway?17:51
kanzureusb? has anyone sniffed it?17:51
SphericalMousethink its usb, but maybe usb to serial17:52
SphericalMousethe GA is elegant in its lack of pretense17:53
kanzureah yes... "elegant" http://med.fsu.edu/userImages/6-Illumina--HiSeq-2000.jpg17:54
SphericalMousethats a hiseq17:55
ParahSail1nhm the server at work must not be the one that is hooked up to the ga2x's17:55
kanzureactually i guess that doesn't look as bad as the bage boxes like the rest17:55
ParahSail1nso they give you a proprietary computer to hook up to the sequencer?17:55
SphericalMousejust a dell17:56
SphericalMouseat least for the GA17:56
ParahSail1ni guess the machine doesnt have to be that fast, because it does like one cycle every few hours17:57
nmz787howdy17:57
nmz787this might be useful for ROM dumping the illumina http://conference.hitb.org/hitbsecconf2013ams/materials/D1T1%20-%20Travis%20Goodspeed%20-%20Nifty%20Tricks%20and%20Sage%20Advice%20for%20Shellcode%20on%20Embedded%20Systems.pdf17:58
SphericalMousenot really true, needs to process large data files.17:58
ParahSail1nbut it has plenty of time to do that17:58
SphericalMousethe cycle time is the collection of those large files17:59
ParahSail1noh, really? the cycle time is compute bound?17:59
SphericalMousemodern systems are faster too17:59
SphericalMousenot really18:00
ParahSail1nthe cycle time is camera bound?18:00
SphericalMouseroughly18:00
ParahSail1ner, microscope18:00
ParahSail1nah18:00
SphericalMousethese vary between models and configurations18:01
nmz787SphericalMouse: have you seen the blu-ray drive sled stereolithography paper?18:03
SphericalMouseno18:03
nmz787they made <1micron features in SU-8 using unmodified blu-ray optics @ 2 mm distance18:03
ParahSail1nwow18:03
nmz787so the question i have is, can the drive spindle be moved about 1.5mm away from the lens in off-the-shelf drives (without removing the sled from the drive)18:04
nmz787if so, you could simply wire up the spindle motor, sled translation motor, and laser18:05
nmz787throw some polar coordinate software together18:05
SphericalMousewas the system in the paper 1d?18:06
nmz787they took the sled and put it on an XY stage18:06
nmz787and Z! then tested Z depths18:06
nmz787and found 2mm was best18:06
nmz787i guess with that thickness SU-8 at least18:07
SphericalMousemight have more to do with the focal plane of the laser than the su818:07
SphericalMousehow fast? was it?18:08
SphericalMouseI didn't work with these guys, but I sat near them https://str.llnl.gov/Mar12/spadaccini.html18:10
nmz787http://diyhpl.us/~bryan/papers2/paperbot/High%20resolution%2C%20low%20cost%20laser%20lithography%20using%20a%20Blu-ray%20optical%20head%20assembly.pdf18:10
nmz787did you know lars ullrich?18:10
nmz787wait18:11
nmz787no18:11
nmz787ulrich schaff18:11
SphericalMouseno18:11
nmz787who the hell is lars?18:11
nmz787hah18:11
nmz787drummer of metallica18:11
nmz787lol18:11
nmz787how about Greg Sommer?18:14
nmz787he's a microfluidics guy18:14
SphericalMouseno, looks like he was at sandia, not livermore18:16
nmz787ahh18:17
SphericalMousegot to go eat dinner, maybe back later18:17
nmz787see ya18:17
ParahSail1nillumina's profit margin is 70%18:17
SphericalMousethats a bit misleading.18:18
ParahSail1nseems it wouldnt be that hard to rip off their systems18:18
SphericalMouse~lols~18:18
ParahSail1ni wonder why BGI hasn't18:19
SphericalMousebecause chemistry is hard, and so is precision engineering. Why else buy complete genomics18:20
ParahSail1ni dont think it's _that_ hard18:21
SphericalMouseits not hard to do it poorly. bit why doesn't everyone use ion torrent systems?18:22
ParahSail1nion torrent is more expensive per data18:23
SphericalMousebut cheaper machines and faster runtimes18:24
ParahSail1nnormally people dont need data faster when its so expensive18:25
SphericalMousei'm not sure how the cheapest per data iontorrent runs stack up against the miseq costwise18:26
ParahSail1nseems like there's no reason to use miseq18:26
SphericalMousebetter data quality I guess18:27
ParahSail1nits about the same or worse than hiseq18:28
SphericalMouseyou dont always need tons of data18:28
ParahSail1ngoing to 150 cycles doesnt really get you anything useful18:28
SphericalMouse2x15018:28
ParahSail1nif you dont need tons of data, you can outsource it to someone who will run a fraction of a lnae18:28
SphericalMousethe hiseq is mostly 2x10018:29
SphericalMouseyeah, I keep asking why not move to an all factory model.18:29
SphericalMousenot sure what the average turnaround time is in a genome factory18:30
SphericalMousea few weeks maybe?18:30
kanzurefor synthesis? up to a couple months.18:30
SphericalMousesequencing18:30
ParahSail1nturnaround time is a few days longer than the machine's run time at ucdavis18:30
ParahSail1nand its <3k per lane18:30
SphericalMouseI wa spart of a project that tried to use davis a year ago, and it seemed like it was hard to get approval to get in at the time18:32
SphericalMousemaybe it was 2 years at this point. probably out of date, I guess18:33
ParahSail1ni guess there might be situations where faster data off ion torrent or proton one could be worth it18:35
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SphericalMouseworkflow is important18:45
SphericalMousei've heard complaints about the ~28 hour miseq runtime since you cant do a run a day18:45
SphericalMousenmz787, what do you want to do with a direct write system?18:46
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delinquentmehey does anyone in here know how information is encoded along the magnetic strip of a master card?18:53
delinquentmespecifically how much of the magnetics strip do I need to destroy so that any information is sufficiently difficult to retrieve?18:54
ParahSail1nintention is to destroy?19:01
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delinquentmeParahSail1n, correct19:03
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delinquentmeso for example ... if the information is encoded across the entire strip ... if I cut it in half theres not much chance to reconstruct half the information19:04
ParahSail1nscrape it off?19:04
delinquentmenot bad@19:13
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delinquentmeJuul, whats going on man!!19:36
delinquentmequestionmarks.19:36
Juul:)19:37
Juuli'm chillin' at sudo19:37
delinquentmeI'm sitting here sucking on coffee drawing venn diagrams19:37
Juuldrawing venn diagrams with coffee mug stains?19:37
rigelsee, THIS is what i'm fucking talking about19:37
delinquentmewondering if theres a quicker way than the normal step-wise education process to get thing into my brain19:37
delinquentmeHA!19:37
rigeli implemented this class in python using selenium webdriver19:37
delinquentmenot bad!19:37
rigeland now i can just swap out for https://github.com/detro/ghostdriver19:38
rigeli knew there was a reason i made myself do it that way19:38
rigelalso dongs19:39
rigellul19:39
Juulwhat's the reason for the standard -80 C freezers?19:40
Juulwho concluded that -80 was the right temperature?19:40
rigelnow all i need is to integrate https://github.com/murilobr/amf.js into my toolchain somehow19:41
delinquentmeJuul, maybe engineering ?19:44
Juuldelinquentme, possibly19:46
Juuli'm looking into building a small low-cost -80 freezer for diybio19:47
Juuli'm not going to blindly design for -80 though19:47
rigeldry ice?19:48
rigelyeah, dry ice19:48
delinquentmeoh wow19:48
rigeljust like food freezers are targeted at 28-30f19:49
delinquentmehow do commercial ones get that low?19:49
rigelin a pinch, you can load it up with dry ice to keep a -80c freezer cool19:49
delinquentmeI'd assume the PSU and the heat exchanger are the expensive parts19:49
delinquentmerigel, I dont think Juul is trying to fix a one off19:49
delinquentmeI think hes after building something that can be replicated19:49
rigeli was making comments about design19:49
Juulrigel, you're saying they designed them based on the approximate temperature of dry ice19:50
Juulcould be19:50
rigeland why -80c was likely chosen19:50
delinquentmeohhh19:50
Juulit's about 78 if i remember19:50
rigelyeah -78c19:50
rigelso, a couple degrees cooler than that19:50
rigeldry ice is easily available19:50
JuulI'll have to see if there is some research on different temperatures19:50
Juulno reason to spend more money on a -80 capable pump if -40 is fine19:51
rigelhow will you stabilize -40 if something breaks down19:51
rigeli think that's part of the issue19:51
rigeldesign for failure19:52
rigelat -40 what are your options, -80, which is a substantial temperature difference, or 0, which is a substantial temperature difference19:52
Juuldo you think there will be damage to cells by varying between -40 and -80?19:53
Juuli guess that's likely19:53
rigelfor storage you want stable temperature19:53
Juulok, good point19:53
rigelif you have to store things at -40, get a failure, and then dump a bunch of dry ice on them in the interim19:54
rigelthen you either let them thaw back to -40 or you keep them at -8019:54
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Juulthanks for the logic19:57
Juuli'm gonna bike home and cook some dinner19:57
Juullater19:57
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ParahSail1ni think you can get -80s pretty cheap on auction20:12
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delinquentmebest options for getting a static address to forward to a dynamically assigned IP?21:01
klafkahey delinquentme how are you liking it out here21:29
klafkaor are you in eugene now21:29
klafkaall up in oregon21:29
delinquentmeklafka, hahah nah dude im here right now in the mission kicking ass21:31
delinquentmeloving the shit out of lIFEEE21:31
delinquentmealso got a bike!21:31
klafkaah awesome21:31
klafkayeah you need one there :P21:31
klafkai got done with a psychedelic conference this weekend21:32
klafkahey kanzure do you remember a ferrouswheel ?21:32
kanzureyes i remember ferrouswheel21:34
kanzurejoel pitt21:34
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kanzurerigel: what do you need amf for?21:36
kanzureflash serialization?21:36
klafkai met his partner at the maps conference21:37
klafkait was really weird how it happened21:37
abetuskany recommendations for things to check out in Boston while I'm there?21:41
kanzurebosslab21:42
kanzureavery louie21:43
kanzurealec resnick.. he's probably at sprouts.21:43
kanzurethis guy http://edboyden.org/21:43
klafkayeah omg21:43
klafkacan you just like go up to his lab and be like 'hay guys sup'21:43
kanzureprobably21:43
kanzurethere's a lot of fablab people at mit so there's probably at least one or two different events going on21:44
kanzurei think jason bobe (diybio) still lives in boston? who knows. george church's group would be fun to visit.21:45
klafkawhat are they doing these days21:47
kanzuregeorge church is busy finding the next 200 companies to play co-founder at21:48
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abetuskI feel weird about just dropping in without anything specifically to talk about21:49
kanzureusually the protocol is to send an email in advance21:49
abetuskyeah, I should have planned better21:49
kanzureask about any presentations, or if someone could give you a tour if they're into that, etc.21:49
kanzureturns out people love blabbing about their projects.21:49
kanzurealso if you have particular lab expertise that you think they would benefit from, you should offer to do a presentation or whatever.21:50
kanzurealthough usually it is very obvious if they want that.21:50
kanzurethis one time, paul rothemund was in town21:51
kanzureand i swear at least two grad students were assigned to tracking him down and getting him to show up to do presentations21:51
klafkaoh kanzure that's a great idea21:54
abetuskok, thanks kanzure.  I'll try and send some emails out when I'm there and see if they can squeeze me in before I leave21:54
juri_kanzure: if you're looking for some reverse engineering.. we should talk more. as a 'found engineer', i build most of the things I own out of whatever others throw away. that involves a lot of reverse engineering. i've also helped random strangers build thousands of PCs over the last few years (again, out of what others throw away). do you have something small you'd like dox'd, and re-engineered?22:40
kanzurejuri_: how about the rest of http://github.com/openyou/emokit 's protocol23:03
juri_um, why would i bother?23:04
juri_(one second, getting a URL)23:04
kanzurehuh? you just asked for interesting things to reverse engineer?23:04
kanzuremy answer seems reasonable.23:04
juri_http://mirage335.dyndns.org/wiki/BiosignalAmplifier23:05
juri_I;ve been working with the developer of that. ---^23:05
kanzurewhat about it?23:05
kanzureok.23:05
juri_so, why would i work on reverse engineering the proprietary one, when there's an open attempt to do the same task?23:05
kanzurethe reason that emokit is interesting is because there's a consumer headset that people are buying.23:06
juri_want one of mirage's kits? that can be aranged.23:06
kanzurebecause why would i use that kit when i can just use openeeg? fuck.23:06
kanzurethere might be a reasonable answer to that question23:08
juri_However, as of 2012-03-14, the already well published Common-Mode Shield Driver and AC Coupling Feedback seem not to have been implemented.23:08
juri_so, mirage's kit is less noisy. i've been meaning to work on his cabling (esata instead of sata), but haven't found the time.23:09
kanzurei'm not sure if modulareeg is part of openeeg, if that's what you mean23:09
kanzureoh wait modulareeg is23:09
juri_yes, it is.23:09
kanzureyes yes i corrected myself yeesh23:09
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juri_no fair. i've been working so hard to get one over on you.. ;P23:10
kanzureshouldn't be that hard.23:10
juri_'kanzure, you are the WRONG one! WRONG-o-WRONG-o-WRONG!' i've even got a dance made up.23:10
kanzurealright23:11
juri_still, in this case, i think my effort is better spent improving the open alternatives.23:11
kanzurethe open alternatives to modulareeg?23:11
juri_no, either modulareeg or mirage's toy.23:11
juri_either way, the one you want reverse engineered.. is there a reason to use it over a modularEEG/biosignalamp?23:12
kanzureno, it's terrible and i hate it23:12
kanzurebut that was partly why i started reversing the protocol23:12
kanzurein general, this hatred extends to all eeg. i'm not sure if an eeg project being open source is enough to get me excited these days. :( they just end up fairly disappointing..23:12
* juri_ nods.23:13
kanzure"64 channels, but we can only train 3 actions. have fun, dinkwad."23:13
juri_agreed. my input to mirage's work has been just some advice, and some 3d printer work/parts.23:13
juri_so, again, i can't directly bio-hack.. but if you need something fixed, printed, or a printer fixed, i'm here. ;)23:14
juri_also, i'd need one of the items in question in my hands, to do a deep reverse engineer.. unless its protocol level stuff, like you pointed to. i just think that we should let the users of the closed gear suffer with the gear.23:15
kanzurei may or may not have some anonymously contributed header files that i've been working from23:16
juri_fun. :)23:16
kanzurei don't have the device anymore either.23:17
juri_oh wow, i pointed you at the wrong link.23:17
juri_http://mirage335.dyndns.org/wiki/Mirage335BiosignalAmp23:18
juri_so, you don't have one.. so whom would we be helping by reversing the protocol then? a company's customerbase, which does not include either of us?23:34
rigelkanzure: ustream uses it to obfuscate their direct video URLs23:45
--- Log closed Wed Apr 24 00:00:06 2013

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