--- Log opened Mon Sep 09 00:00:20 2013
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01:05 < Lemminkainen> paperbot http://jasn.asnjournals.org/content/early/2013/06/11/ASN.2012121143.abstract
01:07 < paperbot> http://libgen.org/scimag/get.php?doi=10.1681%2FASN.2012121143
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05:45 < archels> paperbot: http://www.sciencedirect.com/science/article/pii/S0079612305490111
05:45 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Drivers%20and%20modulators%20from%20push-pull%20and%20balanced%20synaptic%20input.txt
05:45 < archels> paperbot: http://www.sciencedirect.com/science/article/pii/S0079612305490111/pdfft?md5=4e9f202f1b5597532ebec1c9ed0d6bc1&pid=1-s2.0-S0079612305490111-main.pdf
05:45 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Drivers%20and%20modulators%20from%20push-pull%20and%20balanced%20synaptic%20input.txt
05:52 < juri_> ok, whos going to print me a new left forearm? my carpel tunnel issues have persisted. :/
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08:23 < kanzure> hehe the cypherpunks and cryptology lists are exploding
08:25 < chris_99> i'm curious if there are m(any) implementations of McEliece/Lattice based crypto
08:48 < kanzure> "In a perspective of in vivo applications, our approach is to address the problem of fine spinal cord interfacing first in vitro, where a whole neonatal rat spinal cord is isolated. This isolated network indeed contains all the circuitry required to generate locomotor rhythms, which can be revealed for example by pharmacological application of neuromodulators. Such preparation further offers an easy access to spinal networks for thorough ...
08:49 < kanzure> ... exploration and identification of optimal intraspinal sites for high-density microelectrode array recording and stimulation to restore functional activity after a lesion. The goal of the project is thus to successfully hybridize this living preparation with artificial networks in order to restore functoinal hindlimb locomotor-like activity in a transected spinal cord using an artificial bridge over the lesion. .. This ANN will be ...
08:49 < kanzure> ... controlled by neural activity above the lesion and will control intraspinal electrical microstimulation below the lesion."
08:49 < kanzure> *functional
08:49 < kanzure> "256-channel high-density NeuroPXI system" does that mean only 256 electrodes?
08:50 < archels> yes, it does, although you can measure the spiking activity of more than 256 neurons with 256 electrodes
08:52 < kanzure> tell me cool things about recent microelectrode arrays
08:53 < archels> it's a flat array, even, so no depth recordings
08:53 < archels> there isn't anything cool to say about microelectrode neural interfaces, it's a dead-end street
08:54 < kanzure> do you mean dead-end because nobody is bothering, or dead-end because of some reality-imposing constraint?
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08:55 < archels> the latter; biology and electronics simply aren't very compatible
08:55 < archels> breakthroughs and actually workable neural interfaces are going to be based on optics
08:55 < kanzure> why have i never seen a million-electrode microelectrode array?
08:56 < archels> that would be due to technical (process) constraints that could conceivably be overcome
08:56 < archels> but I wouldn't put my money on it
08:56 < archels> CMOS arrays have put us in the tens-of-thousands range, but they're flat
08:58 < kanzure> i haven't seen any research with 10k microelectrodes on an array for neuro things
08:58 < kanzure> i think i've seen at most 1k..
08:58 < kanzure> most usually 64-256
08:59 < kanzure> and whatever the utah array is
08:59 < archels> e.g. http://www.qbic.riken.jp/freyiru/cmosmea.html
08:59 < ThomasEgi> i think utah was 8x8 or so so 64 iirc
08:59 < kanzure> 8x8 gah
09:00 < kanzure> M. Ballini, J. Müller, P. Livi, Y. Chen, U. Frey, A. Shadmani, I. L. Jones, W. Gong, M. Fiscella, M. Radivojevic, D. Bakkum, A. Stettler, F. Heer, and A. Hierlemann, “A 1024-Channel CMOS Microelectrode-Array System with 26’400 Electrodes for Recording and Stimulation of Electro-active Cells In-vitro,” in Symposium on VLSI Circuits, Kyoto, Japan, 2013, pp. 54–55.
09:00 < archels> 256x256 is also out there
09:00 < kanzure> 26400 is better
09:01 < archels> 256^2 > 26400
09:01 < ThomasEgi> is it flat too? or build like the utah array?
09:01 < archels> anyway, this is the general range we are in now, but all of this is surface recording only
09:01 < archels> flat, yes
09:01 < kanzure> "High-resolution MEA with 11,011 electrodes and 126 readout channels" http://www.qbic.riken.jp/freyiru/img/research/CMOS-MEA-thumb.png
09:03 < gradstudentbot> Oh yeah, I'll pay you once my stipend posts.
09:05 < ThomasEgi> hm well with an MEA shaped the utah one, and that many electrodes/channels it would be quite possible to tap into the neuron bundles branching off the spine.
09:06 < archels> yeah, that has been possible for a long time, but the density is still poor, and moreover it doesn't work well for chronic implants
09:06 < archels> sticking electrodes in neural tissue causes inflammation and a resulting encapsulation of the electrodes with glial cells
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09:06 < kanzure> my complaint about using fewer electrodes is that neurons have no particular reason to respond to broad stimulation like that. high-resolution stimulation seems more likely to be capable of selectively training neurons to do things.
09:07 < archels> optics. enough said
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09:07 < archels> (you know about halo/channelrhodopsins, right?)
09:07 < kanzure> what are you gonna do, have a thousand lasers on a chip?
09:07 < kanzure> unfortunately most neurons in existence do not have rhodopsins
09:07 < archels> shrug, laser scanning or DLP or a thousand other possibilities
09:07 < kanzure> dlp in an implant?
09:07 < archels> yeah, but that's just one virus infection away :)
09:07 < kanzure> just trying to understand
09:08 < kanzure> you want to put DLP on a chip next to a nerve?
09:08 < ThomasEgi> why not?
09:08 < archels> something like that, yes. Two-photon would be ideal.
09:08 < kanzure> because he might mean something else, that's why not
09:08 < archels> you can place it up to a few mm from the actual nerve.
09:08 < gradstudentbot> Hey, I got 100% yield! Oh wait, no.
09:09 < ThomasEgi> the distance might be short enough to allow focussing through the neurons.
09:09 < archels> and through the inevitable scar tissue
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09:11 < gradstudentbot> You know, I can just do consulting.
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09:16 < kanzure> i wonder if you could convince some bacteria to attach to neurons (let's assume the immune system isn't present in culture)
09:16 < kanzure> and that you can make them avoid e.g. glial cells
09:18 < archels> what function do you want them to perform?
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09:19 < kanzure> dunno, just selective attachment first
09:20 < kanzure> you can add payloads to them. like magnetically-responsive proteins. i'm not completely sure what i'd want to do with them just yet.
09:23 < ThomasEgi> hm. that sort of pops up magnetic core memory in my mind.
09:23 < archels> that reminds me of an experiment where they put a voltage sensitive protein in nanospheres, then injected them into a cell
09:23 < archels> worked pretty well for visualizing the microscopic arrangement of electric fields in a cell, but it was also fairly toxic
09:24 < archels> it's probably easier to get the selective attachment using viruses
09:31 < archels> actually, it's possible to record spiking activity from neurons optically without any exogenous indicators or dyes, but the optical changes are minute and probably impractical for neuronal interfacing
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09:46 < kanzure> haha datanitro is doing ipython things now https://datanitro.com/blog/2013/9/9/ipython_excel/
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11:05 < kanzure> http://jreinhardt.github.io/BOLTS/index.html
11:05 < kanzure> https://github.com/nophead/Mendel90
11:13 < nalkri> There's a cool fab thing on kickstarter at the momemnt(that isn't going to make it)
11:13 < kanzure> https://github.com/jreinhardt/BOLTS/blob/master/freecad_bolts.py
11:14 < nalkri> http://www.kickstarter.com/projects/327919589/the-microfactory-a-machine-shop-in-a-box
11:16 < kanzure> i think people have been conditioned to like FreeCAD just because of its name
11:17 < kanzure> it's really not that great. it's a UI layer on top of opencascade so at minimum it inherits all of the problems of opencascade...
11:17 < kanzure> https://groups.google.com/forum/#!topic/openmanufacturing/_WrkmhHnB1I
11:18 < kanzure> i wonder if libffi is capable of making sense of opencascade
11:18 < kanzure> or brlcad
11:18 < kanzure> oh actually, ctypes + brlcad probably works i bet
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11:26 < kanzure> jreinhardt: sup
11:26 < kanzure> oh hello
11:26 < jreinhardt> Hi
11:27 < kanzure> i am thinking about trying to use brlcad from python today via ctypes
11:27 < kanzure> yesterday i did some work with ctypes against vba-linux and had very useful results
11:27 < jreinhardt> I was just in the process of writing a reply to your second mail
11:27 < jreinhardt> this is cool
11:27 < kanzure> the brlcad swig bindings are broken as far as i can tell. and based on my swig experiences with opencascade i don't really care much for swig.
11:28 < jreinhardt> so if one can access brlcad from python than it should be relatively easy to get BOLTS for brlcad working
11:28 < jreinhardt> this is somehow my vision
11:28 < jreinhardt> having a shared base of data
11:29 < jreinhardt> that makes it easy for everyone to get a useful library of standard parts
11:29 < kanzure> skdb has a number of packages- they are git repositories with yaml specifications and cad files accessible through the skdb python lib
11:29 < jreinhardt> I have to look into skdb, but it looks like we had similar ideas
11:29 < jreinhardt> great minds think alike
11:29 < kanzure> i think including opencascade as a dependency was a mistake and i regret it
11:30 < kanzure> freecad is nice but the problem is that it's a UI on top of opencascade. and i've wasted too many 100s of hours trying to fix opencascade.
11:30 < kanzure> https://github.com/kanzure/oce is the "community edition" of opencascade
11:30 < jreinhardt> as I said, I have to look in detail in your stuff
11:30 < kanzure> sure, i'm just ranting
11:31 < jreinhardt> :)
11:31 < jreinhardt> I would like to stay on a much higher level
11:31 < kanzure> i should warn you that there's lots of broken skdb things
11:34 < jreinhardt> So are there many people using skdb?
11:35 < kanzure> three or four entire persons
11:36 < jreinhardt> better than three or four partial persons
11:36 < jreinhardt> that would be a mess
11:36 < kanzure> there's also some other projects that i have archived over the years that you might enjoy,
11:36 < kanzure> http://diyhpl.us/cgit/tangiblebit
11:37 < kanzure> https://github.com/kanzure/nanoengineer
11:37 < kanzure> some skdb packages http://diyhpl.us/cgit/screw/ http://diyhpl.us/cgit/threads/
11:37 < kanzure> tiny cad library that doesn't work http://diyhpl.us/cgit/lolcad/
11:37 < kanzure> skdb lego package http://diyhpl.us/cgit/lego/ (hey wait.. legos aren't open hardware.)
11:38 < kanzure> b-rep geometry kernel (uncertain licensing terms) http://diyhpl.us/cgit/esolid/
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12:16 < kanzure> ctypes wont work with brlcad because brlcad is C++. i forgot about this.
12:16 < kanzure> so a possibly better idea is to just write a cython wrapper http://docs.cython.org/src/userguide/wrapping_CPlusPlus.html
12:29 < nmz787> this is weird
12:29 < nmz787> http://cytocomp-bitstarter-mooc.herokuapp.com/
12:29 < nmz787> highest funded http://startupmooc.org/
12:29 < ParahSailin> do we have any lawyers?
12:29 < ThomasEgi> didn't the patent on lego run out like in 2011?
12:30 < ParahSailin> 1989
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13:50 < kanzure> On Mon, Sep 9, 2013 at 3:42 PM, Gregory Sizemore <gregory.sizemore@mail.sifter.org> wrote:
13:50 < kanzure> I have experienced this before Firefox implemented "load tabs on demand." I
13:50 < kanzure> keep 1-2k tabs open a lot of the time (1.5k) right now. I used to have to
13:51 < kanzure> "The aforementioned BarTab extension lightens Firefox’s memory load and prevents crashes by unloading tabs that you are currently not using but want to keep accessible. It can intercept when tabs are opened in the background or restored after a browser restart and will only load the content when the tab is actually visited"
13:51 < kanzure> oh it seems to just fetch the content again. damn.
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14:08 < ParahSailin> thousand tabs...
14:09 < kanzure> yeah, it's a lie, they aren't real tabs
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14:15 < kanzure> jreinhardt: brlcad libged is in c so python + ctypes will work there
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16:03 < kanzure> jrayhawk: any chance of bumping up the disk space on gnusha pretty please? i could also go on a deletion expedition if you insist..
16:06 < jrayhawk> done
16:07 < jrayhawk> also if you have stuff you think should be excluded from backups let me know
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16:09 < kanzure> jrayhawk: what sorta backups are we doing? some of this is worth excluding from "bury it under 400 feet of water" backups.
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16:43 < jrayhawk> stuff goes to tape for long-term storage
16:44 < kanzure> cool
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18:15 < kanzure> yashgaroth: sup
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18:16 < yashgaroth> yo
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18:32 < dkslkwdl> Hello
18:38 < kanzure> dkslkwdl: hi
18:38 < dkslkwdl> kanzure: are you an NE1 dev?
18:40 < kanzure> yes
18:41 < dkslkwdl> Is NE1 pretty much abandoned, or does it have a new website?
18:41 < kanzure> https://github.com/kanzure/nanoengineer
18:41 < kanzure> this is where development is happening (slowly)
18:41 < kanzure> i need more manpower
18:41 < kanzure> if you can give me 5-8 highly trained python people that would be wonderful
18:41 < kanzure> there's a lot of stuff that needs to be fixed
18:42 < dkslkwdl> You should try to get into touch with the person who runs the wiki. I used to edit it, but after a while no one else did and I just ended up deleting spam from spambots
18:42 < kanzure> i have a backup of the mediawiki wiki but i haven't deployed it yet
18:43 < kanzure> nobody has really bugged me about it
18:43 < dkslkwdl> Is NE1 made completely in python?
18:44 < kanzure> no, i think the nanohive stuff wasn't python
18:44 < kanzure> most of it is python. but the downside is that it's all depending on pyqt4 (a really really old version of pyqt4)
18:44 < kanzure> and i think that needs to be stripped out
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18:46 < kanzure> dkslkwdl: were you working for nanorex?
18:46 < eudoxia> dkslkwdl: you might want to get in touch with kirka, he did some NE-1 dev and was thinking about rolling his own NE clone. i talked to him briefly about that but he never replied so i'm guessing he's busy or in a coma or something
18:46 < dkslkwdl> kanzure: no, I just am really into nanotech
18:46 < dkslkwdl> I'm surprised development halted like it did, it is a really fancy program
18:48 < dkslkwdl> So what is this irc channel for? Just futurism? I found this on /r/nanotech
18:49 < eudoxia> transhumanist tech, open manufacturing stuff
18:49 < eudoxia> there's a strict ban on philosophy/futurism :)
18:49 < kanzure> dkslkwdl: we are not about futurism at all. we hate futurism.
18:49 < kanzure> dkslkwdl: we build things
18:50 < kanzure> dkslkwdl: nanorex folded in 2009 so development halted. i noticed in 2010 and rescued most of what you see of nanoengineer. the rest is the progress since then.
18:51 < dkslkwdl> Did Nanorex have any income? How did they sustain themselves?
18:51 < eudoxia> i'm curious about that too. kanzure?
18:52 < kanzure> mark was dumping large quantities of cash into nanorex (about $1M/year)
18:53 < kanzure> in 2009 he just wasn't seeing the traction he had hoped for so he called it quits
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18:56 < dkslkwdl> Was Nanohive not free? Or did he plan on making money some other way?
18:56 < kanzure> some other way
18:57 < kanzure> near the end they tried to do more dna origami integration so they got paul rothemund to oversee some stuff (dunno if he was paid, haven't asked)
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19:55 < kanzure> add2virtualenv is really really useful
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