--- Log opened Thu Mar 07 00:00:20 2013
00:00 <@kanzure> archels: he claims work/kids.
00:01 < archels> ##hplusroadmap is a bit of both--perfect, not? :)
00:01 <@kanzure> yeah i don't see his problem :p
00:02 <@kanzure> but i meant, he claimed his own work/his own kids were demanding his attention heh
00:03 < archels> jrayhawk, fenn: alright, thanks for your replies on calcium
00:04  * archels wonders if this "refurbishing" of multielectrode arrays is a feasible option
00:05 <@kanzure> what part of them requires refurbishing?
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00:07 < 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?
00:08 < 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
00:09 < archels> can't imagine refurbished ones to hold up for very much longer
00:11 <@kanzure> he says he is leaving for work
00:11 <@kanzure> so he wont be on i guess
00:12 < archels> I'll ask my labmate when I see him again on Monday
00:13 < archels> oh, now I remember the brainwave I had about this just before I went to sleep
00:14 < 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
00:15 < 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
00:16 < archels> where do you chat with him outside of IRC?
00:17 <@kanzure> jabber
00:18 <@kanzure> he uses the gmail xmpp server as eleitl@gmail.com
00:19 <@kanzure> archels: so are you definitely going to be doing work for hbp?
00:21 < archels> err, I'm going to be working for the dude who heads the HBP in The Netherlands
00:22 < archels> but the content of the project is rather ill-defined at this point
00:22 < archels> (not the HBP; my project :) )
00:23 < archels> I'm hoping I can spend some time building hierarchical artificial neural networks
00:25 <@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
00:37 < 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?
00:38 <@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
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01:10 < eleitl> moin moin
01:11 < eleitl> is archels in da house?
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01:16 <@kanzure> archels: ping
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01:16 < eleitl> hi kanzure
01:16 < eleitl> I'll idle here for about 35 min, after which I'll be off to a meeting
01:27 < archels> oh hey eleitl
01:27 < archels> not sure whether my message on diybio got through yet?
01:28 < archels> looks like a negative. kanzure, I kinda tacitly assumed you were a moderator for the diybio group :)
01:28 < eleitl> Hi archels
01:29 < eleitl> kanzure dropped me a couple lines from you
01:29 < eleitl> what kind of MEAs are you working with?
01:30 < 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
01:31 <@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
01:32 < 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
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01:33 < 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
01:34 < 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
01:35 < 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
01:36 < 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
01:37 < 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?
01:38 <@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
01:39 < eleitl> that looks doable
01:39 <@kanzure> pcbs: https://sites.google.com/site/neurorighter/download-neurorighter-pcbs
01:40 <@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.
01:41 < eleitl> thank you, you both are very helpful
01:41 < archels> . o O {Does L. stagnalis even have spiking neurons?}
01:42 < 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
01:44 < 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
01:45 < 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/
01:46 < 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
01:47 < 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?
01:48 < eleitl> thanks, gotta run to the meeting. will check the scroll later for info.
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02:06 <@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.,)
02:07 <@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... ?
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03:58 < archels> "The goal of this handout is to help you avoid taking notes during the lecture."
03:59 < archels> that's... doing it wrong.
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04:55 < 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
04:56 < eleitl> A versatile all-channel stimulator for electrode arrays, with real-time control one.
05:24 < archels> eleitl: What's the pricing on those?
05:25 < eleitl> Peter recommended them to me. I've sent a request to sales.
05:25 < eleitl> 8-channel should do plenty.
05:26 < 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."
05:27 < 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> "
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05:34 < archels> yes, it's always going to be a tradeoff between time and money
05:35 < 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
05:37 < archels> also http://www.circuitsathome.com/mcu/usb/usb-isolator and a 9V battery :)
05:40 < archels> it will be el-cheapo in that it is a voltage-controlled source with no current feedback
05:42 < eleitl> that sound ideal for starters
05:47 < 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
05:50 < eleitl> it seems enough for a qualitative test of survivability during vitrification
05:53 < eleitl> it seems just 99 USD and a smartphone to record
05:55 < eleitl> these look pricey: http://www.multichannelsystems.com/products/usb-mea256-systems
05:57 < archels> hehe it's funny how audio gear has specs that are such a lot better than those data acquisition/stimulation systems
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05:57 < archels> stuff like 24 bit/96 kHz
05:58 < eleitl> yeah, why not use it. The SpikeBox even is in PLOS http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030837
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06:02 < eleitl> that looks quite good: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030837
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06:04 < eleitl> wow, that thing is comparable to a SRS560
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06:05 < 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
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06:06 < eleitl> hope it melts outside soon, got to catch some snails
06:07 < eleitl> we've got an aquarium recently, so I can observe the critters for a while
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06:08 < 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
06:09 < eleitl> we have L. stagnalis in our garden pond
06:09 < eleitl> plus the bright red snail, trumpet something
06:10 < 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.
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06:13 < 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.
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06:21 < eleitl> 12 GBytes, browser unresponsive. I'm so tired of your shit, browser.
06:21 < ThomasEgi> lynx
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06:24 < eleitl> oh, great. all instances of chrome are now fucked.
06:26 < eleitl> "close all windows" doesn't work, because windows can't deal with focus follows mouse
06:30 < 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,
06:31 < eleitl> Sounds good, ThomasEgi.
06:31 < eleitl> This is for preliminary experiments anyway.
06:36 < nsh> so's your face.
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07:12 < eleitl> hi eudoxia
07:14 < eudoxia> hi eleitl
07:16 < eleitl> how's things?
07:17 < eudoxia> oh, just fine, how about you?
07:18 < 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
07:19 < 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
07:20 < eudoxia> and make RC insects
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07:20 < eleitl> see http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030837 for a paper describing the kit
07:22 < 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
07:23 < 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
07:24 < eleitl> chances are, M22 alone will kill the thing. then, maybe not.
07:24 < eleitl> they say cortical slices survive it and vitrification fine
07:40 < eudoxia> i thought you were using CI-VM-1?
07:40 < eudoxia> (derp xchat didn't mark me as being away)
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07:56 < eleitl> we've made some VM-1 for internal use
07:57 < 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
07:58 < 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
07:59 < 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
08:00 < 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
08:01 < 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.
08:02 < eleitl> If VM-1 is significantly more toxic, there's an incentive not to use it
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08:02 < 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
08:03 < 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
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08:11 < eudoxia> yes they are but i doubt they care much about the pet dewar or think neuros are recoverable
08:12 < 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.
08:14 < eudoxia> i assumed active shutdown meant euthanasia but i'm not sure
08:15 < eleitl> euthanasia is correct, but it's not "good death" since you're not killing your patients
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08:15 < eleitl> you're using a usual prediction scale, and perfuse life patients to not have a peri-arrest phase
08:16 < 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
08:17 < eleitl> or, if a patient insists the time is now. which is even more problematic.
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08:18 < eleitl> it is a serious complication, which I wish wasn't necessary
08:19 < eudoxia> pumping living humans full of cytotoxic chemicals might be bad PR, yes
08:19 < eleitl> indeedly
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08:24 < 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
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08:28 < eudoxia> conservative? as in they won't pronounce you dead after hours of ischemia?
08:29 < eleitl> yes, or longer
08:29 < eleitl> lividity, rigor mortis, petechia, the whole shebang
08:30 < eleitl> these are the signs by which they make sure that you are dead, for sure
08:32 < 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
08:33 < 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!
08:34 < 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
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08:34 < eleitl> there are many causes when the brain is electrically silent
08:35 < rigel> eudoxia: {{citation needed}}
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08:35 < 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> ;[
08:36 < 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?
08:37 < 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
08:38 < 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
08:39 < rigel> eudoxia: case reports mean fuckall
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08:39 < eudoxia> lol google took me to pubmed
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08:39 < 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!
08:40 < 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
08:50 < eleitl> time to sushi
08:53 < eleitl> byes, see you later
08:53 < eudoxia> bai
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09:15 < nmz787> kanzure: so should I look into using phonegap to make this uploader, or just use native android?
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09:52 <@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
09:53 < 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
09:58 <@kanzure> probably, but if you can't, then you can make a plugin for phonegap that can be given the files
09:59 <@kanzure> eleitl: humanity+ is closing :rainbows:
09:59 < eudoxia> it is?
10:00 < eudoxia> [citation needed]
10:00 <@kanzure> straight from central command.
10:00 < eudoxia> that might be bullshit but i believe it
10:02 < eudoxia> any reason why?
10:04 <@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
10:06 <@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"
10:07 < nsh> (definitely an illuminati front)
10:07 <@kanzure> http://blogs.nature.com/news/2013/02/award-mints-millionaire-biologists.html
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10:08 <@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
10:09 <@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.
10:12 <@kanzure> who the hell is ethan kurzweil
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10:51 < 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
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11:37 <@kanzure> hmm i'm not sure who is responsible for this document
11:38 <@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?
11:39 <@kanzure> "entity relationship diagram" https://docs.google.com/drawings/d/1ZNT1_rhLgRAqDk_8qyQ3eRGgANCs7-HV5oA37o10M44/edit
11:39 <@kanzure> oh god that is disgusting
11:40 <@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.
11:42 <@kanzure> i am not convinced by any of this. the fact that they think an "entity relationship diagram" is useful is very telling.
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11:50 < 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.
11:51 <@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.
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11:54 <@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
11:55 <@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?
11:56 <@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
11:57 < 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
11:58 <@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.
11:59 < eudoxia> thanks kanz now i'm gonna get droned for visiting riseup.net
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12:11 <@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/
12:17 <@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
12:18 <@kanzure> just some discussion about open source hardware things from the people who organized open source hardware summit
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12:59 <@kanzure> paperbot: http://www.frontiersin.org/Neural_Circuits/10.3389/fncir.2012.00098/full
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12:59 < 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
13:01 <@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?
13:03 <@kanzure> i wonder if that's the chinese pcb production cost
13:04 <@kanzure> in fact, if these systems are usually that expensive, then it sounds like a chinese-cheap version would be in high demand?
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13:06 <@kanzure> heh stimitless.com
13:13 < 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 ?
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13:22 <@kanzure> nmz787: it means you are a time traveler
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13:25 <@kanzure> "SciPy John Hunter Excellence in Plotting Contest"... excellence in plotting.. revenge?
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13:34 <@kanzure> plur: welcome back
13:35 <@kanzure> oh wait. barriers.
13:35 <@kanzure> i see.
13:35 < plur> owo
13:35 < plur> we make this confusing
13:36 < plur> as complexity has been stripped from many other areas of our lives
13:36 < plur> but thanks
13:36 <@kanzure> um, what?
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15:00 <@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.
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15:11 <@kanzure> one of the members of tc184-sc4 dropped an ISO 10303 bombshell in that conversation: http://groups.google.com/group/openmanufacturing/msg/99362921bbe76222
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16:21 < 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
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18:48 <@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
18:49 <@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."
18:50 <@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.
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19:07 <@kanzure> seems to work alright with qr codes.. for whatever that's worth. http://svg.hipokrit.com/handler.py/fullsize?img=download.svg
19:13 < 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
19:14 <@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)
19:15 < nsh> i was just thinking about a crop-circle kinda thing
19:15 < nsh> but with colouring agents
19:18 <@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
19:19 <@kanzure> i get lots of results for 'entropy cryogenics' which does not sound like an outfit i'd want to store any bodies with
19:20 < nsh> hah
19:20 < nsh> "We're preserve you in the strictest thermodynamic sense."
19:20 < nsh> *We'll
19:21 < 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
19:22  * 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
19:23 < 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
19:25 <@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?
19:26 <@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.)
19:27 <@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
19:28 < 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."
19:29 <@kanzure> is that because adobe paid out the $70k?
19:30 <@kanzure> oh i see. you can only exploit things on the target laptop.
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19:33 <@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.
19:34 <@kanzure> very well known vulnerabilities, i might add.
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19:36 < nmz787> http://phys.org/news/2013-03-russia-bacteria-antarctic-lake.html
19:37 < 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)
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20:17 <@kanzure> nice overview of the mpeg patent pool and vp8 http://news.ycombinator.com/item?id=5341850
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20:33 <@kanzure> paperbot: http://www.springerlink.com/content/l467218g107h8013/
20:33 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/64f4f85846d33a20dfd117b4dd21fef0.txt
20:36 < ParahSail1n> thats cool http://privat.bahnhof.se/wb907234/killuav.htm
20:37 < 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
20:41 <@kanzure> it would be pretty costly to replace all of the radio communication equipment that is deployed
20:42 <@kanzure> so that will remain a vulnerability for quite a while i think
20:43 < ParahSail1n> yeah, it sucks having to launch new satellites to fix hardware vulns
20:44 <@kanzure> i've always wondered who gets to do satellite pen testing
20:46 < ParahSail1n> i knew a guy who did some high security clearance work on the gps constellation, something about the guidance software
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21:33 < nmz787> hey some EE help here
21:33 < nmz787> i have two relays
21:34 < nmz787> I want to one , when triggered, to also send power to the other relay
21:34 < nmz787> relay's output
21:35 < 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
21:36 < 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> ?
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--- Log closed Fri Mar 08 00:00:21 2013