--- Log opened Thu Mar 07 00:00:20 2013 | ||
@kanzure | archels: he claims work/kids. | 00:00 |
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archels | ##hplusroadmap is a bit of both--perfect, not? :) | 00:01 |
@kanzure | yeah i don't see his problem :p | 00:01 |
@kanzure | but i meant, he claimed his own work/his own kids were demanding his attention heh | 00:02 |
archels | jrayhawk, fenn: alright, thanks for your replies on calcium | 00:03 |
* archels wonders if this "refurbishing" of multielectrode arrays is a feasible option | 00:04 | |
@kanzure | what part of them requires refurbishing? | 00:05 |
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archels | the contact points degrade due to chemical/redox reactions | 00:07 |
archels | mostly oxidation I suppose; I'm by no means an expert on this | 00:07 |
@kanzure | and labs throw them out? | 00:07 |
archels | The electrodes are embedded in a carrier material, usually glass. Standard tracks made of titanium | 00:08 |
archels | (Ti) or indium tin oxide (ITO) are electrically isolated with silicon nitride (SiN). Standard contact | 00:08 |
archels | pads are made of titanium nitride (TiN) or indium tin oxide (ITO). ITO contact pads and tracks | 00:08 |
archels | are transparent, for a perfect view of the specimen under the microscope. | 00:08 |
archels | yes | 00:08 |
archels | I might be able to score a few for eleitl, not sure if that will be at all useful for him | 00:08 |
archels | can't imagine refurbished ones to hold up for very much longer | 00:09 |
@kanzure | he says he is leaving for work | 00:11 |
@kanzure | so he wont be on i guess | 00:11 |
archels | I'll ask my labmate when I see him again on Monday | 00:12 |
archels | oh, now I remember the brainwave I had about this just before I went to sleep | 00:13 |
archels | what could potentially be interesting for a low-cost version, is to simply get it made as a printed circuit board (flexboard) | 00:14 |
archels | the smallest pitch on those should be about 100 um | 00:14 |
archels | I guess I should just type all of this up and reply to that thread on diybio... | 00:15 |
@kanzure | agreed, i'm not going to play messenger for you heh | 00:15 |
archels | where do you chat with him outside of IRC? | 00:16 |
@kanzure | jabber | 00:17 |
@kanzure | he uses the gmail xmpp server as eleitl@gmail.com | 00:18 |
@kanzure | archels: so are you definitely going to be doing work for hbp? | 00:19 |
archels | err, I'm going to be working for the dude who heads the HBP in The Netherlands | 00:21 |
archels | but the content of the project is rather ill-defined at this point | 00:22 |
archels | (not the HBP; my project :) ) | 00:22 |
archels | I'm hoping I can spend some time building hierarchical artificial neural networks | 00:23 |
@kanzure | paperbot: http://www.jneurosci.org/content/33/7/3131.short | 00:25 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Patch-Clamp%20Recordings%20from%20Lateral%20Line%20Neuromast%20Hair%20Cells%20of%20the%20Living%20Zebrafish.pdf | 00:25 |
archels | Your post has been sent for review and will appear after it has been approved. | 00:37 |
archels | kanzure: is this a Google Groups thing or a DIYbio-group thing? | 00:37 |
@kanzure | unfortunately google groups does not provide reasonable spam controls, so the only practical option is for a moderator to choose to moderate first-time posts | 00:38 |
archels | fair enough | 00:38 |
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eleitl | moin moin | 01:10 |
eleitl | is archels in da house? | 01:11 |
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@kanzure | archels: ping | 01:16 |
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eleitl | hi kanzure | 01:16 |
eleitl | I'll idle here for about 35 min, after which I'll be off to a meeting | 01:16 |
archels | oh hey eleitl | 01:27 |
archels | not sure whether my message on diybio got through yet? | 01:27 |
archels | looks like a negative. kanzure, I kinda tacitly assumed you were a moderator for the diybio group :) | 01:28 |
eleitl | Hi archels | 01:28 |
eleitl | kanzure dropped me a couple lines from you | 01:29 |
eleitl | what kind of MEAs are you working with? | 01:29 |
eleitl | notice that my current plans are very, very modest: just record 2-4 channels, in a qualitative test | 01:30 |
eleitl | the experimental assembly has to survive cycling from RT to -150 and then back | 01:30 |
@kanzure | archels: i am not a diybio moderator | 01:31 |
@kanzure | archels: the diybio moderators are always on the verge of banning me, i think | 01:31 |
archels | hah | 01:31 |
archels | eleitl: what are the rough dimensions of these ganglions? | 01:31 |
archels | about a millimeter? | 01:31 |
eleitl | the whole assembly is ~1 cm across | 01:31 |
eleitl | size bar is 1 mm | 01:32 |
eleitl | http://upload.wikimedia.org/wikipedia/commons/5/58/Lymnaea_stagnalis_central_ring_ganglia.jpg | 01:32 |
archels | ah, alright. Conveniently large indeed. | 01:32 |
eleitl | yeah, that's one of the reasons why the snail is so great | 01:32 |
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eleitl | same complexity of aplysia, but conveniently concentrated in a manageable volume | 01:33 |
eleitl | plus, unlike Aplysia, it's probably going to deal with chilling injury a lot better | 01:33 |
archels | Hmm, would it be an option to obtain the thinnest needles you can find, coat everything but the very tip with isolating material, and maybe make a little holder so you can make a 3x3 array? | 01:34 |
archels | fixation might be a problem with that approach | 01:34 |
archels | http://en.wikipedia.org/wiki/Needle_gauge_comparison_chart | 01:35 |
eleitl | I was thinking about that. I can use electrothinning e.g. on tungsten wire or stainless, or platinum | 01:35 |
archels | goes down to 0.2mm outer diameter | 01:35 |
eleitl | I can electrothin down to submicron | 01:36 |
archels | ah | 01:36 |
eleitl | can you recommend a good recording rig? | 01:36 |
eleitl | I'm ready to solder something, if it can be done easily enough | 01:36 |
eleitl | something which can run on a 9 V battery, and then pass on to USB A/D | 01:37 |
eleitl | I don't need to record more than 1 kHz, right? | 01:37 |
archels | hehe. From my experience, these scientific data capture devices are ridiculously overpriced. | 01:37 |
eleitl | my point precisely | 01:37 |
archels | you could quite possible use the OpenEEG frontend, or something similar. | 01:37 |
@kanzure | there was an open source hardware recording rig that was released | 01:37 |
eleitl | kanzure, in which context? | 01:37 |
@kanzure | http://code.google.com/p/neurorighter/ | 01:38 |
archels | 1 kHz is cutting it very close if you want to see spikes | 01:38 |
@kanzure | "Data Acquisition System for Multi-electrode Recordings" | 01:38 |
@kanzure | "NeuroRighter is an open-source electrophysiology platform for conducting closed-loop, multichannel neural recording and stimulation experiments." | 01:38 |
eleitl | http://openeeg.sourceforge.net/doc/hw/ | 01:38 |
eleitl | https://code.google.com/p/neurorighter/ ? | 01:38 |
@kanzure | yes | 01:38 |
@kanzure | i just linked to that :P | 01:38 |
eleitl | thanks | 01:38 |
eleitl | that looks doable | 01:39 |
@kanzure | pcbs: https://sites.google.com/site/neurorighter/download-neurorighter-pcbs | 01:39 |
@kanzure | https://sites.google.com/site/neurorighter/download-neurorighter-pcbs/NeuroRighter_PCBs_InVitro.zip?attredirects=0&d=1 | 01:40 |
eleitl | for just recording qualitative activity (did it survive vitrification?) something much simpler will do | 01:40 |
@kanzure | https://sites.google.com/site/neurorighter/download-neurorighter-pcbs/NeuroRighter_PCBs_InVivo.zip?attredirects=0&d=1 | 01:40 |
@kanzure | paperbot: http://iopscience.iop.org/1741-2552/1/1/006 | 01:40 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/A%20versatile%20all-channel%20stimulator%20for%20electrode%20arrays%2C%20with%20real-time%20control.pdf | 01:40 |
@kanzure | that's their paper for describing this system. | 01:40 |
eleitl | thank you, you both are very helpful | 01:41 |
archels | . o O {Does L. stagnalis even have spiking neurons?} | 01:41 |
eleitl | as far as I know, it does | 01:42 |
eleitl | unlike C. elegans | 01:42 |
archels | interesting | 01:42 |
eleitl | it's the system suggested by Peter Passaro, of the Foundation Volunteers | 01:42 |
eleitl | he worked with it a lot, and he will likely work with it again | 01:42 |
eleitl | if the openworm guys deliver, this will be a good next target | 01:44 |
eleitl | these are big neurons, so connectome should be feasible | 01:44 |
eleitl | archels, two questions: | 01:45 |
eleitl | is this a tolerable dissection microscope: http://www.amazon.de/Bresser-Researcher-20x-80x-Mikroskop-Vergrößerung/dp/B0017J1UC0/ | 01:45 |
eleitl | is this a tolerabe experimental microscope for the snail: http://www.amazon.de/Bresser-Science-Mikroskop-100x-400x-Vergr%C3%B6%C3%9Ferung/dp/B001CIW4IK/ | 01:46 |
eleitl | of course LED illumination strictly, no halogens | 01:46 |
archels | sorry dude, I'm not really an experimentalist. couldn't tell one way or the other without doing a bunch of reading up myself | 01:47 |
@kanzure | nmz787: maybe you have some opinions about which microscope? | 01:47 |
eleitl | thanks, gotta run to the meeting. will check the scroll later for info. | 01:48 |
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@kanzure | On Thu, Mar 7, 2013 at 4:02 AM, nah sivar <nahsivar@gmail.com> wrote: | 02:06 |
@kanzure | > Hi Kanzure, | 02:06 |
@kanzure | > | 02:06 |
@kanzure | > I came across your repository of ez-proxy urls on github. Could you tell me | 02:06 |
@kanzure | > the usefulness of it ? Have gone a full round from finding many posted | 02:06 |
@kanzure | > ezproxy hacks (username/password leaks etc.,) | 02:06 |
@kanzure | > to plugins etc., for facilitating journal access (if one has proper | 02:07 |
@kanzure | > credentials). Would be glad to know the motivation behind the urls file and | 02:07 |
@kanzure | > any source that would enable one to use ém ! | 02:07 |
@kanzure | hmmm. | 02:07 |
@kanzure | Dear Nahsivar, I am part of a secret cabal of ezproxy users that... ? | 02:07 |
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archels | "The goal of this handout is to help you avoid taking notes during the lecture." | 03:58 |
archels | that's... doing it wrong. | 03:59 |
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eleitl | archels, what do you think about http://www.multichannelsystems.com/products/stimulus-generators | 04:55 |
eleitl | Peter was the reviewer on the open hardware paper actually | 04:55 |
eleitl | A versatile all-channel stimulator for electrode arrays, with real-time control one. | 04:56 |
archels | eleitl: What's the pricing on those? | 05:24 |
eleitl | Peter recommended them to me. I've sent a request to sales. | 05:25 |
eleitl | 8-channel should do plenty. | 05:25 |
eleitl | "May be easier to just buy one of these if you have the money and want to avoid the custom dev time though... | 05:26 |
eleitl | Even though they only have 8 channel stim, they provide a fast switching amplifier that can be programmed to stim any number of channels, i.e. up to the 256 MEA channels you can get on their more expensive hardware. | 05:26 |
eleitl | From previous experience though, hold off on making any decisions on stimulation until you get your recording platform established." | 05:26 |
eleitl | BTW from your previous message, avoid the MED64 system as I've heard of lots of quality problems with their equipment | 05:27 |
eleitl | " | 05:27 |
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archels | yes, it's always going to be a tradeoff between time and money | 05:34 |
archels | you could always get a generic USB digital-to-analog converter and make your own differential output stage | 05:35 |
archels | that contains a limited amount of effort and potential for bugs | 05:35 |
archels | also http://www.circuitsathome.com/mcu/usb/usb-isolator and a 9V battery :) | 05:37 |
archels | it will be el-cheapo in that it is a voltage-controlled source with no current feedback | 05:40 |
eleitl | that sound ideal for starters | 05:42 |
eleitl | do you think this circuit might do: http://backyardbrains.com/products/spikerbox ? | 05:47 |
eleitl | http://backyardbrains.com/products/files/SpikerBox.v.1.3c.Annotated.Schematics.pdf | 05:47 |
eleitl | it seems enough for a qualitative test of survivability during vitrification | 05:50 |
eleitl | it seems just 99 USD and a smartphone to record | 05:53 |
eleitl | these look pricey: http://www.multichannelsystems.com/products/usb-mea256-systems | 05:55 |
archels | hehe it's funny how audio gear has specs that are such a lot better than those data acquisition/stimulation systems | 05:57 |
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archels | stuff like 24 bit/96 kHz | 05:57 |
eleitl | yeah, why not use it. The SpikeBox even is in PLOS http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030837 | 05:58 |
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eleitl | that looks quite good: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030837 | 06:02 |
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eleitl | wow, that thing is comparable to a SRS560 | 06:04 |
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eleitl | quite a bit cheaper though https://orders.thinksrs.com/OnlineOrders2003/html/AddToCart.asp?EPrdGroup=SR560 | 06:05 |
ThomasEgi | archels, the soundcard input for connecting it to the device eleitl linked? | 06:05 |
* eleitl will use smartphones | 06:05 | |
eleitl | cheap enough, one amplifier, one smartphone per channel | 06:05 |
eleitl | record directly to flash | 06:05 |
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eleitl | hope it melts outside soon, got to catch some snails | 06:06 |
eleitl | we've got an aquarium recently, so I can observe the critters for a while | 06:07 |
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archels | ThomasEgi: I was thinking along those lines. Maybe with a phonograph or microphone preamplifier. | 06:08 |
archels | < eleitl> hope it melts outside soon, got to catch some snails | 06:08 |
archels | lol | 06:08 |
eleitl | we have L. stagnalis in our garden pond | 06:09 |
eleitl | plus the bright red snail, trumpet something | 06:09 |
ThomasEgi | archels, just a a small warning. unless you shield the crap out of your circuit with massive metal and high quality wires, there's no need for a 24bit adc. 16bit will do just fine. | 06:10 |
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eleitl | Most neurons of the L. stagnalis CNS are large in size (diameter: up to ~100 μm), thus allowing electrophysiological dissection of neuronal networks that has yielded profound insights in the working mechanisms of neuronal networks controlling relatively simple behaviors such as feeding [1,2], respiration [3,4], locomotion [5], and reproduction [6,7]. | 06:13 |
eleitl | That sounds great. | 06:13 |
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eleitl | 12 GBytes, browser unresponsive. I'm so tired of your shit, browser. | 06:21 |
ThomasEgi | lynx | 06:21 |
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eleitl | oh, great. all instances of chrome are now fucked. | 06:24 |
eleitl | "close all windows" doesn't work, because windows can't deal with focus follows mouse | 06:26 |
eleitl | "Its only a couple electrodes, but should be enough to get some basic recording experience. Should probably try and make some small cross section flat circle electrodes to stick on the end of those leads, preferably platinum coated. | 06:30 |
eleitl | Snails are definitely good for that equipment - some of the potentials coming out of the buccal ganglia are huge, so you shouldn't have any problem there if you position it correctly. Essentially you will just need to align the ganglia correctly and then use gentle pressure (I used a thin glass coverslip on the opposite side of the ganglia) to make sure you get good contact to the electrode." | 06:30 |
ThomasEgi | eleitl, that spikebox has room for improvements, the circuit is almost fine, could use a few blocking capacitors near the op-amps tho. the bigger problem is, there's no shielding case. this circuit should go into an all metallic box. with a coax cable to the electrodes, | 06:30 |
eleitl | Sounds good, ThomasEgi. | 06:31 |
eleitl | This is for preliminary experiments anyway. | 06:31 |
nsh | so's your face. | 06:36 |
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eleitl | hi eudoxia | 07:12 |
eudoxia | hi eleitl | 07:14 |
eleitl | how's things? | 07:16 |
eudoxia | oh, just fine, how about you? | 07:17 |
eleitl | busy. happy, since we've got a little funding. | 07:18 |
eudoxia | i heard you're making a MEA for the snail upload? | 07:18 |
eleitl | eventually, right now a few SpikerBox kits would do | 07:18 |
eudoxia | is that like EEG for small brains? | 07:19 |
eudoxia | oh the backyard brains thing hahahaha | 07:19 |
eleitl | yeah, it's a 99 USD kit which has a rather good preamp, and you can use a smartphone audio input for recording | 07:19 |
eudoxia | and make RC insects | 07:20 |
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eleitl | see http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030837 for a paper describing the kit | 07:20 |
eudoxia | i was going to paperbot it but then i noticed | 07:22 |
eleitl | I need to see whether the vitrification will kill the ganglia, or not | 07:22 |
eleitl | so just a couple channels would do | 07:23 |
eleitl | first step would be chilling the prep, then rewarming, then chilling, and diffusion-perfusion, then flush out then rewarming, then the whole enchilada | 07:23 |
eleitl | chances are, M22 alone will kill the thing. then, maybe not. | 07:24 |
eleitl | they say cortical slices survive it and vitrification fine | 07:24 |
eudoxia | i thought you were using CI-VM-1? | 07:40 |
eudoxia | (derp xchat didn't mark me as being away) | 07:40 |
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eleitl | we've made some VM-1 for internal use | 07:56 |
eleitl | it's interesting because it vitrifies so very robustly | 07:57 |
eleitl | we're going to study is as well, because CI uses it | 07:57 |
eleitl | it doesn't work for full-body, and nobody does yet quite know what it does to the brain | 07:58 |
eudoxia | what do you mean it doesn't work for full body? i thought they only vitrified heads to cut costs | 07:58 |
eleitl | CI doesn't do head-only | 07:59 |
eleitl | they perfuse whole body, but they do ligate some vessels afaik | 07:59 |
eudoxia | i know | 07:59 |
eleitl | I'm really clueless about their protocol | 07:59 |
eudoxia | but only the brain is vitrified, i think Darwin said that | 07:59 |
eleitl | yeah, whole body would give you massive edema | 08:00 |
eleitl | so you can't do VM-1, and CI is doing effectively neuro, but stores everything | 08:00 |
eleitl | doesn't really make sense, other than for PR reasons | 08:00 |
eudoxia | that's what i meant | 08:00 |
eleitl | so, VM-1 might or might be useful. | 08:01 |
eleitl | A good comparison would be VM-1 vs. M22 on the same system. | 08:01 |
eleitl | If VM-1 is significantly more toxic, there's an incentive not to use it | 08:02 |
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eudoxia | CI always had what i thought was an almost visceral fear of neuro, which makes me wonder | 08:02 |
eudoxia | if they are storing Margaret Bradshaw and Jerry White in the dewar with the dead cats | 08:02 |
eleitl | a lot of former CI principals were not very rational | 08:02 |
eleitl | I don't know who's running CI at the moment, and I don't really care | 08:03 |
eleitl | from a remote point of view both are patient storage abstractions | 08:03 |
eleitl | oh, and it seems active shutdown is legal in Switzerland | 08:03 |
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eudoxia | yes they are but i doubt they care much about the pet dewar or think neuros are recoverable | 08:11 |
eudoxia | which might lead to irresponsible behaviour on their part | 08:12 |
eleitl | I think I will only be happy if we have our own storage | 08:12 |
eleitl | if it happens, it will be in Switzerland. | 08:12 |
eudoxia | i assumed active shutdown meant euthanasia but i'm not sure | 08:14 |
eleitl | euthanasia is correct, but it's not "good death" since you're not killing your patients | 08:15 |
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eleitl | you're using a usual prediction scale, and perfuse life patients to not have a peri-arrest phase | 08:15 |
eleitl | ethically problemathic as fuck, so forget you ever read it | 08:16 |
eudoxia | beginning the process while they are still alive? | 08:16 |
eleitl | yes, when the prediction scale indicate they're going down soon | 08:16 |
eleitl | or, if a patient insists the time is now. which is even more problematic. | 08:17 |
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eleitl | it is a serious complication, which I wish wasn't necessary | 08:18 |
eudoxia | pumping living humans full of cytotoxic chemicals might be bad PR, yes | 08:19 |
eleitl | indeedly | 08:19 |
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eleitl | there's additonal angle: in Germany, death pronouncement criteria are extremely conservative | 08:24 |
eleitl | as a cryonicist, you don't want to die on German soil | 08:24 |
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eudoxia | conservative? as in they won't pronounce you dead after hours of ischemia? | 08:28 |
eleitl | yes, or longer | 08:29 |
eleitl | lividity, rigor mortis, petechia, the whole shebang | 08:29 |
eleitl | these are the signs by which they make sure that you are dead, for sure | 08:30 |
eleitl | http://upload.wikimedia.org/wikipedia/commons/3/3e/%D0%9F%D1%8F%D1%82%D0%BD%D0%B0_%D1%82%D1%80%D1%83%D0%BF%D0%BD%D1%8B%D0%B5.jpg <-- do not looks good, this patient | 08:32 |
eleitl | but, CI wouldn't give a shit | 08:32 |
eudoxia | most doctors would just poke you in the foot and get over it | 08:33 |
eleitl | in much of the world, yes | 08:33 |
eleitl | in Germany, no | 08:33 |
yashgaroth | can't they just do an EEG | 08:33 |
eleitl | vee must make shure he is tot! | 08:33 |
eleitl | EEG is flat after 20-30 sec of stopped blood flow, so it's no good | 08:34 |
eudoxia | people have woken up from long periods of electrocerebral silence | 08:34 |
yashgaroth | hmm, didn't know that | 08:34 |
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eleitl | there are many causes when the brain is electrically silent | 08:34 |
rigel | eudoxia: {{citation needed}} | 08:35 |
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eleitl | e.g. in deep hypothermia these lacunes can be many hours long | 08:35 |
eleitl | rigel: I've seen it quite a few times in person. | 08:35 |
eleitl | {{this article may contain original research}} | 08:35 |
rigel | the plural of anecdote is not data | 08:35 |
eleitl | ;[ | 08:35 |
eleitl | ;p | 08:36 |
rigel | how do you know the probes were placed correctly | 08:36 |
eleitl | rigel, ask your medical student | 08:36 |
eleitl | it's basic knowledge | 08:36 |
rigel | there are any number of possible explanations, including that you are correct | 08:36 |
eleitl | rigel, is your google broken today? | 08:36 |
rigel | why would you use google to research that? | 08:37 |
eleitl | because it will give you the reply in seconds, without you having to lift the chair | 08:37 |
eudoxia | http://www.ncbi.nlm.nih.gov/pubmed/20568022 | 08:37 |
eudoxia | [haven't read the abstract] | 08:38 |
rigel | eleitl: i was commenting more on the use of google versus something more canonical, like pubmed | 08:38 |
rigel | eudoxia: case reports mean fuckall | 08:39 |
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eudoxia | lol google took me to pubmed | 08:39 |
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eleitl | google (scholar) index everything, and it ranks things, so you will get you the answer quicker | 08:39 |
* eleitl is surprised he has to explain that | 08:39 | |
eleitl | in other news, the sky has clouds! | 08:39 |
rigel | quicker? | 08:40 |
eleitl | {{weather satellite feed missing}} | 08:40 |
rigel | more cluttered with irrelevant stuff is my experience | 08:40 |
rigel | does google use MeSH terms? | 08:40 |
rigel | DIDNT THINK SO | 08:40 |
eleitl | time to sushi | 08:50 |
eleitl | byes, see you later | 08:53 |
eudoxia | bai | 08:53 |
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nmz787 | kanzure: so should I look into using phonegap to make this uploader, or just use native android? | 09:15 |
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@kanzure | nmz787: phonegap will work fine for file uploads, because you can always offload the file uploading to native android things if necessary. | 09:52 |
nmz787 | all i really care about is multi-image selectrion | 09:52 |
nmz787 | can I just pass each file to the webkit browser, once they're selected? | 09:53 |
nmz787 | since the webpage already has an uploader | 09:53 |
@kanzure | probably, but if you can't, then you can make a plugin for phonegap that can be given the files | 09:58 |
@kanzure | eleitl: humanity+ is closing :rainbows: | 09:59 |
eudoxia | it is? | 09:59 |
eudoxia | [citation needed] | 10:00 |
@kanzure | straight from central command. | 10:00 |
eudoxia | that might be bullshit but i believe it | 10:00 |
eudoxia | any reason why? | 10:02 |
@kanzure | because it's useless, broken, terrible and awful? | 10:04 |
eudoxia | but i didn't think they realized that | 10:04 |
yashgaroth | they've managed to overcome that for years | 10:04 |
@kanzure | ughhh "NeoHumanitas is a recently launched Swiss Think Tank that promotes critical discussion and reflection about some socio-ethical issues concerning the use of emerging and future technologies on human beings" | 10:06 |
nsh | (definitely an illuminati front) | 10:07 |
@kanzure | http://blogs.nature.com/news/2013/02/award-mints-millionaire-biologists.html | 10:07 |
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@kanzure | "The inaugural awards, however, went to a bumper crop: 11 pioneers who will help to select winners in subsequent years. This year’s winners include those working in genomics (David Botstein and Eric Lander), cancer (Lew Cantley, Hans Clevers, Napoleone Ferrara, Charles Sawyers, Bert Vogelstein and Robert Weinberg), telomeres (Titia de Lange), stem cells (Shinya Yamanaka) and neurobiology (Cori Bargmann). " | 10:08 |
@kanzure | zuckerberg got around to awarding yamanaka before the nobel prize committee did.. not a big surprise i guess. | 10:08 |
@kanzure | oh wait no, he got the 2012 nobel prize | 10:08 |
@kanzure | "Yamanaka received the Wolf Prize in Medicine in 2011 with Rudolf Jaenisch;[6] the Millennium Technology Prize in 2012 together with Linus Torvalds." | 10:09 |
@kanzure | so.... he's rolling with linus. | 10:09 |
@kanzure | who the hell is ethan kurzweil | 10:12 |
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nmz787 | paperbot: http://link.springer.com/article/10.1007%2FBF02830159?LI=true | 10:51 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/6aa77bdb491c654dcd7be4299d7130fd.txt | 10:51 |
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@kanzure | hmm i'm not sure who is responsible for this document | 11:37 |
@kanzure | but it looks like a spreadsheet that is trying to do an open hardware specification thing | 11:38 |
@kanzure | https://docs.google.com/spreadsheet/ccc?key=0AkNG-lv1ELQvdHViNEdtVHp4dHRWOU8tcDNSbXROY3c&usp=sharing#gid=2 | 11:38 |
@kanzure | http://www.opensourcewarehouse.org/problem-statement/ | 11:38 |
@kanzure | "There’s no simple way to remix and mashup hardware. We propose a modular approach to open source hardware documentation that would facilitate remix, mashup and branching" | 11:38 |
@kanzure | i don't see their actual proposal. vaporware? | 11:38 |
@kanzure | "entity relationship diagram" https://docs.google.com/drawings/d/1ZNT1_rhLgRAqDk_8qyQ3eRGgANCs7-HV5oA37o10M44/edit | 11:39 |
@kanzure | oh god that is disgusting | 11:39 |
@kanzure | "Due to practical matters, the number of participants will be limited, so please let us know by March 18 if you would like to join us." | 11:40 |
@kanzure | "New York City, April 26-28" | 11:40 |
@kanzure | hmmm. | 11:40 |
@kanzure | i am not convinced by any of this. the fact that they think an "entity relationship diagram" is useful is very telling. | 11:42 |
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nsh | it could just mean they went to college, and stupidly took notes, kanzure. there wouldn't be many people left to hold out hope for if we dismiss everyone that went to college. | 11:50 |
@kanzure | "entity relationship diagram" is not a packaging format | 11:51 |
@kanzure | i don't care if you went to college or not. that will win no favor with me. | 11:51 |
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@kanzure | isn't it usually bad when a standards body is formed before a standard is actually proposed? they don't seem to be aware of my own proposals, or any of the others. | 11:54 |
nmz787 | hmm | 11:54 |
nmz787 | i dunno | 11:54 |
nmz787 | DIYbio was formed as a 'body' before we talked about standards | 11:54 |
@kanzure | what standards | 11:54 |
eudoxia | on that note, kanzure, wouldn't it help the development of skdb to move away from CAD and make the program basically just a package manager? leave the "send these files to the reprap/CNC mill" part to build scripts in a scripts.yaml file | 11:54 |
@kanzure | eudoxia: i'd be happy to look at any proof of concept | 11:55 |
eudoxia | okay | 11:55 |
nmz787 | does skdb exist at all? | 11:55 |
@kanzure | there is source code and packages | 11:55 |
nmz787 | in code? | 11:55 |
nmz787 | ahh | 11:55 |
@kanzure | and cad integration with pythonocc | 11:55 |
nmz787 | what file formats can you shove into it? | 11:55 |
@kanzure | you make a git repository and add some yaml files | 11:56 |
eudoxia | it's more abstract than that | 11:56 |
@kanzure | then you point to the files in the yaml | 11:56 |
eudoxia | the package is a git repo that can have anything you want + metadata.yaml + package.yaml, IIRC | 11:56 |
eudoxia | and in package.yaml there might be a section like: "cad: ['cad/main.dwg','cad/screw.dwg']" | 11:57 |
eudoxia | please don't kill me for using dwg i don't know anything else | 11:57 |
@kanzure | that doesn't sound right | 11:57 |
@kanzure | http://gnusha.org/skdb/package_spec.html | 11:58 |
@kanzure | anyway, the two big problems we encountered were that one, nobody wanted to review the specification or suggest reasonable alternatives (except for smari, except he went off and made tangiblebit and then stopped that; he had an allergic reaction to python which was not helpful) | 11:58 |
@kanzure | second, was the cad integration issues. | 11:58 |
eudoxia | thanks kanz now i'm gonna get droned for visiting riseup.net | 11:59 |
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@kanzure | https://github.com/OpenDesign-WorkingGroup/Open-Design-Definition | 12:11 |
@kanzure | http://lists.okfn.org/mailman/listinfo/opendesign | 12:11 |
@kanzure | http://lists.okfn.org/pipermail/opendesign/ | 12:11 |
@kanzure | http://groups.google.com/group/openmanufacturing/t/7912e33497324301 | 12:17 |
@kanzure | http://groups.google.com/group/openmanufacturing/t/d12235679cb57cb7 | 12:17 |
@kanzure | http://groups.google.com/group/openmanufacturing/t/fc222ad4b6affc3d | 12:17 |
@kanzure | http://groups.google.com/group/openmanufacturing/t/78aea87f8629a4f5 | 12:17 |
@kanzure | just some discussion about open source hardware things from the people who organized open source hardware summit | 12:18 |
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@kanzure | paperbot: http://www.frontiersin.org/Neural_Circuits/10.3389/fncir.2012.00098/full | 12:59 |
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paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Closed-Loop%2C%20Multichannel%20Experimentation%20Using%20the%20Open-Source%20NeuroRighter%20Electrophysiology%20Platform.pdf | 12:59 |
@kanzure | "NeuroRighter allows 64 channels of stimulation and recording for around US $10,000, along with the ability to integrate with other software and hardware." | 13:01 |
@kanzure | that's.. a bit much? | 13:01 |
@kanzure | i wonder if that's the chinese pcb production cost | 13:03 |
@kanzure | in fact, if these systems are usually that expensive, then it sounds like a chinese-cheap version would be in high demand? | 13:04 |
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@kanzure | heh stimitless.com | 13:06 |
nmz787 | damn, I guess my feedback time is 3 years | 13:13 |
nmz787 | i just responded to a 3 year old diybio thread, i finally did the experiment yesterday | 13:13 |
nmz787 | does that mean i'm an inertial, kanzure ? | 13:13 |
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@kanzure | nmz787: it means you are a time traveler | 13:22 |
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@kanzure | "SciPy John Hunter Excellence in Plotting Contest"... excellence in plotting.. revenge? | 13:25 |
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@kanzure | plur: welcome back | 13:34 |
@kanzure | oh wait. barriers. | 13:35 |
@kanzure | i see. | 13:35 |
plur | owo | 13:35 |
plur | we make this confusing | 13:35 |
plur | as complexity has been stripped from many other areas of our lives | 13:36 |
plur | but thanks | 13:36 |
@kanzure | um, what? | 13:36 |
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@kanzure | On Thu, Mar 7, 2013 at 4:39 PM, Javier Serrano <Javier.Serrano@cern.ch> wrote: | 15:00 |
@kanzure | > On 03/07/2013 11:25 PM, Bryan Bishop wrote: | 15:00 |
@kanzure | >> On Thu, Mar 7, 2013 at 3:58 PM, Javier Serrano <Javier.Serrano@cern.ch> wrote: | 15:00 |
@kanzure | >>> What we are focusing our OSHW effort on these days is design tools. We | 15:00 |
@kanzure | >>> are contributing to Icarus Verilog and Kicad [1]. I think this is the | 15:00 |
@kanzure | >> | 15:00 |
@kanzure | >> I am curious, does that mean CERN has someone specifically allocated | 15:00 |
@kanzure | >> to verilog and kicad? That would be really exciting news. | 15:00 |
@kanzure | > | 15:00 |
@kanzure | > So far we have only contributed by asking companies to do development. | 15:00 |
@kanzure | > You can grep the iverilog and Kicad sources for CERN copyright notices | 15:00 |
@kanzure | > to see where we have contributed. And this year we had the opportunity | 15:00 |
@kanzure | > to bring a student using CERN's technical student program. He has only | 15:00 |
@kanzure | > been with us for a week, and he's planned to work full time on Kicad | 15:00 |
@kanzure | > this year. | 15:00 |
@kanzure | neat. | 15:00 |
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@kanzure | one of the members of tc184-sc4 dropped an ISO 10303 bombshell in that conversation: http://groups.google.com/group/openmanufacturing/msg/99362921bbe76222 | 15:11 |
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superkuh | paperbot: http://apl.aip.org/resource/1/applab/v102/i8/p082601_s1 | 16:21 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Macroscale%20refrigeration%20by%20nanoscale%20electron%20transport.pdf | 16:21 |
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@kanzure | "At Tuesday's open house a few of you saw my latest project, a raster image to SVG conversion app I wrote to make designs to etch with the laser cutter. I got a lot of questions about it, so I decided to send it out to the list." | 18:48 |
@kanzure | http://svg.hipokrit.com/ | 18:48 |
@kanzure | http://svg.hipokrit.com/handler.py/display?img=ATX_Hackerspace_logo.svg | 18:48 |
@kanzure | http://svg.hipokrit.com/handler.py/fullsize?img=grumpcat.svg | 18:48 |
@kanzure | https://github.com/mattprintz/derasterizer | 18:48 |
@kanzure | "Converts a raster image to a SVG image by converting blocks of pixels to an SVG circle with a radius based upon the average pixel values of the block." | 18:49 |
@kanzure | well that's not really taking advantage of svg objects is it.. but i guess it works for cases where you don't need exact shapes. | 18:50 |
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@kanzure | seems to work alright with qr codes.. for whatever that's worth. http://svg.hipokrit.com/handler.py/fullsize?img=download.svg | 19:07 |
nsh | reminds me of a 'fun' evolutionary algorithm that reduced/replicated an image to/with a series of overlapping translucent blobs | 19:13 |
nsh | possibly circles, i forget the details | 19:13 |
@kanzure | trivial details like circles and squares are for toddlers! damn them all. | 19:13 |
@kanzure | this makes laser etching a qr code on to things more practical though. | 19:13 |
nsh | once you've squared one circle, they're all largely the same | 19:13 |
@kanzure | instead of engraving a name into the back of your laptop, you can engrave a qr code with details like your email address, a url, phone numbers, etc. | 19:14 |
@kanzure | nsh: amen | 19:14 |
@kanzure | you could probably also place/pick colonies to a qr code pattern (for whatever that's worth, again) | 19:14 |
nsh | i was just thinking about a crop-circle kinda thing | 19:15 |
nsh | but with colouring agents | 19:15 |
@kanzure | wait, i think vector cutting a qr code on a laser cutter takes longer than cutting the actual data you want to communicate (maybe) | 19:18 |
nsh | .g entropy of QR codes | 19:18 |
yoleaux | https://bitcointalk.org/index.php?topic=117054.10;wap2 | 19:18 |
nsh | lolk | 19:18 |
@kanzure | i get lots of results for 'entropy cryogenics' which does not sound like an outfit i'd want to store any bodies with | 19:19 |
nsh | hah | 19:20 |
nsh | "We're preserve you in the strictest thermodynamic sense." | 19:20 |
nsh | *We'll | 19:20 |
nsh | one of my results (from startpage.com) is entitled "I am Anna Skryabina: What is entropy and how to fight with it?" | 19:21 |
@kanzure | i think it is better with We're | 19:21 |
nsh | agreed | 19:21 |
* nsh kinda wants to join battle with Anna Skryabina against the forces of entropy | 19:22 | |
nsh | she seems the resolute kind, able and determined, but with an intuitive, almost mystical aspect | 19:22 |
nmz787 | i fight entropy everyday | 19:22 |
nmz787 | sometimes I tire of it | 19:22 |
nmz787 | why would someone want to take a raster to SVG anyway? | 19:23 |
@kanzure | laser cutting | 19:23 |
nsh | i mostly flirt with entropy in the hopes that in a moment of weakness we will someday copulate | 19:23 |
nmz787 | using an algorithm like that anyway | 19:23 |
@kanzure | mostly images | 19:23 |
@kanzure | probably photos | 19:23 |
@kanzure | "laser etch a photo of your anus to the back of your laptop!" or whatever the hell the trend is | 19:23 |
@kanzure | "QR_STENCILER, a free, fully-automated utility which converts QR codes into vector-based stencil patterns suitable for laser-cutting." | 19:25 |
JayDugger | Tool-marking? | 19:25 |
@kanzure | i see. i guess that's more efficient anyway... just directly generate the qr code with vector lines/edges in the first place. that would be much faster than cutting circles. | 19:26 |
JayDugger | QR-codes aren't human readable. | 19:26 |
JayDugger | (Ignore me. Below the two cups to consciousness threshold.) | 19:26 |
@kanzure | "As Fred Trotter has pointed out, QR codes contain stencil islands in unpredictable configurations. QR_STENCILER automatically detects and bridges these islands, using thin lines that are minimally disruptive to the highly robust QR algorithm. It does so through the use of two basic image processing techniques: connected component labeling (sometimes called blob detection) and 8-connected chain coding (sometimes called contour tracing)." | 19:27 |
@kanzure | welp nevermind. that's going to be way more efficient. | 19:27 |
nmz787 | kanzure: you could be raking in $$$ http://en.wikipedia.org/wiki/Pwn2Own | 19:27 |
nmz787 | geohot made $70k by pwning Adobe Reader | 19:28 |
nmz787 | today | 19:28 |
nmz787 | "And I'm 70k richer, Adobe Reader 0-day landed first try, on a cute little slim acer which I now own. Wouldn't have been able to do it without my 410, 411, and PPP skills. Cost of tuition justified." | 19:28 |
@kanzure | is that because adobe paid out the $70k? | 19:29 |
@kanzure | oh i see. you can only exploit things on the target laptop. | 19:30 |
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@kanzure | "Web browsers Google Chrome, Internet Explorer and Firefox along with Windows 8 and Java have been exploited.[50]" that seems like cheating since java has had a number of vulnerabilities for the past few months. | 19:33 |
@kanzure | very well known vulnerabilities, i might add. | 19:34 |
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nmz787 | http://phys.org/news/2013-03-russia-bacteria-antarctic-lake.html | 19:36 |
nmz787 | kanzure: google sponsored it this year | 19:37 |
nmz787 | kanzure: with the requirement all exploits be fully divulged (at least to google) | 19:37 |
nmz787 | (not sure) | 19:37 |
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@kanzure | nice overview of the mpeg patent pool and vp8 http://news.ycombinator.com/item?id=5341850 | 20:17 |
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@kanzure | paperbot: http://www.springerlink.com/content/l467218g107h8013/ | 20:33 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/64f4f85846d33a20dfd117b4dd21fef0.txt | 20:33 |
ParahSail1n | thats cool http://privat.bahnhof.se/wb907234/killuav.htm | 20:36 |
ParahSail1n | paperbot: http://privat.bahnhof.se/wb907234/killuav.htm | 20:37 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/2b6a92b18c3987b21078f982a8f33164.txt | 20:37 |
@kanzure | it would be pretty costly to replace all of the radio communication equipment that is deployed | 20:41 |
@kanzure | so that will remain a vulnerability for quite a while i think | 20:42 |
ParahSail1n | yeah, it sucks having to launch new satellites to fix hardware vulns | 20:43 |
@kanzure | i've always wondered who gets to do satellite pen testing | 20:44 |
ParahSail1n | i knew a guy who did some high security clearance work on the gps constellation, something about the guidance software | 20:46 |
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nmz787 | hey some EE help here | 21:33 |
nmz787 | i have two relays | 21:33 |
nmz787 | I want to one , when triggered, to also send power to the other relay | 21:34 |
nmz787 | relay's output | 21:34 |
nmz787 | (it's a heater and a fan, that used to be connected to the same switch) | 21:35 |
nmz787 | (i want the heater circuit to ALWAYS turn on the fan, but the fan be switchable on it's own too) | 21:35 |
nmz787 | so I was thinking I could add a diode | 21:35 |
nmz787 | so the output of relay 0 would power relay 1's output, but relay 1 wouldn't power relay 0's output when it was switched | 21:36 |
nmz787 | but how big of a diode do I need | 21:36 |
nmz787 | ? | 21:36 |
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