2016-06-13.log

--- Log opened Mon Jun 13 00:00:29 2016
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archelsnmz787: AD should have some good chips for that01:17
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archelsthese new Joylent granola bars taste even stranger than Joylent itself06:16
archelstheir only redeeming factor is chocolate06:16
c0rw1nchocolate one is somewhat better than the banana one yes06:30
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chris_99random question, anyone know if thin latex is likely to be permeable to IR06:39
yoleaux05:39Z <nmz787> chris_99: hey do you know any good chips with a Programmable Gain Amplifier (PGA) for pre-ADC?06:39
yoleaux05:41Z <nmz787> chris_99: preferably something that can run micropython :/06:39
chris_99nmz787, i've used an ADC with a PGA06:39
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archelssomeone recommended me https://en.todoist.com/07:14
archelsmaybe this is right for me http://todotxt.com/07:15
kanzure.title https://cibolo.us/pipermail/open_electroporator/2016-June/000087.html07:15
yoleaux[Open_electroporator] Culture Shock, the open electroporator is a go07:15
chris_99i used to use todoist iirc07:16
archelsfrom "26 reasons not to use GTD":07:17
archels22. Panic focuses the mind07:17
archelsWe’ve already pointed out that most people naturally prioritize their work by waiting till the important stuff becomes urgent, then panicking and getting on with it. If GTD works, then you’ll lose the focus that panic can bring. And if it doesn’t, why do it?07:17
archelslol.07:17
maakuarchels: wtf 'our product brings your panic and stress' is a selling point?07:19
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maakuarchels: what OS do you use?07:19
archelsLinux/KDE07:25
archelsAndroid on my phone07:25
JayDuggerkanzure, do those methods of "certain overarching topic feeds" and the other one do anything other than reinforce past conversation history?07:35
JayDuggerI don't mean that as a rhetorical question, but seriously. I'd rather be at least a little surprised by what you (in the generic user sense) tell me, even if I suspect that the suggestions push me in a particular direction. I.e., "Oh, he suggested this to me because he thought it would do me good."07:36
kanzurewithout a specific and monitored method with a procedure written down, for all i know i might as well already be doing simple "reinforcement" based on previous topics, i don't know07:37
maakuarchels: then todoist is probably the best for you07:38
JayDuggerThat's fair.07:38
maakui used them for a short while, then went back to OmniFocus on OS X. nobody tops OF, but todoist comes closest07:39
JayDuggermaaku, does OF's location-based reminders work well enough to deserve using?07:40
JayDuggerI.e., the ad copy "Walk by a grocery store and your wrist will get a tap; pick up some milk and bread."07:40
maakuJayDugger: I haven't use them. (I have an Android phone, so I haven't used themobile version much)07:41
JayDuggerPity. I'd like a nice reliable prospective memory amplifer, and that sounds as if it might work.07:42
maakuI have it on my iPod touch though (which lacks location services), and just instilled the habit of looking at the list for the store I'm visiting, or the entire errands context if I have spare time on a commute07:42
maakuJayDugger: I have no reason to think it wouldn't work as advertised. I just don't have the hardware to test it.07:42
JayDuggerHmm...that should work, but it relies on remembering to cultivate the habit. I've had less success with that than I'd like.07:44
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maakuas I said if you have an iPhone the location-aware notifications probably just work as advertised. Omni is pretty good about this stuff.08:02
maakui just happen to have a Nexus, so no mobile interface for me.08:02
mz_o__808:23
mz_o__messed up my irssi command. my bad08:24
JayDuggerMy to-do list reminds me to do the housework. Thank you, maaku, and you too, kanzure.08:28
maakunp08:28
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andytoshii wonder if there are even NLP tools out there that can read irc and unweave conversation threads09:55
andytoshior better, packetize individual conversations09:56
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maakuandytoshi: Yes, if by that you mean "is there known technology that solves this problem"09:56
andytoshithat's half of what i mean09:56
maakuit'd take a lot of hard work and elbow greese to actually do so though09:57
andytoshithe other half is "is there stuff i can download that'll work with irc"09:57
maakuno09:57
maakuit's something I would like to see written09:57
kanzureif you write up the outline, i think a bunch of bored machine learning people would probably do it09:57
andytoshithere are bored machine learning people with spare cycles?09:59
maakulots09:59
maakusee r/machinelearning09:59
andytoshiwow10:00
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maakuandytoshi: I can give you an intuitive mathmatician's argument for how this works10:02
andytoshii'd like that10:02
maakuimagine a massive multi-dimensional space, where most dimensions are concepts10:03
maakue.g. the two vector space (Gender, Royal) where (male, 1) = King and (female, 1) = Queen, (male, 0) = man, etc.10:04
andytoshiyep, i gotcha. (i took a first-year AI survey course once :P)10:04
maakuok awesome makes this easier10:05
andytoshis/first/third/ actually, i had to learn a bunch of lisp and write a neural net in C10:05
maakuthen you add a few dimensions representing nicks, and one representing time10:05
andytoshi(to give an idea of where the prof was comingfrom)10:05
maakuthen you feed in the IRC log, and you start building up a point cloud in this space10:05
maaku(using standard NLP techniques to reduce sentences to thought vectors in this space, tools exist for this)10:06
andytoshigotcha so far10:06
andytoshiok cool, i was gonna ask about the granularity of points10:06
maakuthen you just need to separate this point cloud into groupings by region, tools also exist for this10:07
maakuand then you have the IRC log separated by topic10:07
andytoshikool, that makes sense in principle10:07
maakuand if you have two separate groupings separated only by time, then you know those are related, etc.10:07
andytoshibut for example « kool, that makes sense in principle » does not have any strong concepts associated to it (i think)10:07
kanzureandytoshi: that would require something like conversation structure parsing or something.10:08
andytoshiyou'd have a lot of "ok" and "yeah"s to deal with, i mean10:08
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maakuthat's where the elbow grease comes in .. you can't consider each line in isolation (as you point out), so you'd have to match these isolates based on the final grouping10:10
maakuand once you know the context of a single statement, that could in principle give you a better thought vector representation of it (because you'd resolve pronoun referents, etc), but this is wandering into open areas of research10:11
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andytoshii think you can probably get away with just grouping based on temporal proximity for fragments that aren't well-defined10:12
andytoshiand by concatenating adjacent things written by one person10:12
maakuyeah i suspect that would get you 90% there and work well enough for the whole thing to be useful in practice10:13
andytoshiyeah. an immediately useful thing would be for it to just text me when certain people are discussing certain things10:13
maakuplus it is rare that an IRC channel (at least the ones I frequent) have more than 1 serious conversation going on. it's mostly the overlap and topic transition that you need to detect.10:14
maakuandytoshi: right10:14
kanzurefor my conversation log stuff, i should just use a bloom filter over topics, and just send the bloom filter to each person10:14
andytoshiyeah, me too. but i often go to -wizards and there's like five lines of crypto squished between a bunch of stuff about bramc's work or proof of storage or smart contracts10:15
andytoshikanzure: i think to the extent that'd be useful it'd be too privacy invasive .. like if you'd update the bloom filter every day i'd have a pretty good idea of what you're talking about at all times10:18
kanzurei think you have a pretty good idea of what i'm talking about all the time /anyway/10:19
andytoshiotoh if you don't update it often i'll be like "oh, bryan talked about multisignatures with somebody, but that's probably the same conversation from last week"10:19
andytoshihehehe10:19
maakuandytoshi: preserving privacy of interests is sortof an anti-goal here10:25
andytoshithen i'm unsure the benefit of publishing a bloom filter instead of the actual contents (or metadata)10:26
andytoshii guess volume10:27
kanzuredesign is probably broken. i'm still lost re: figuring out relevant metrics and goals.10:27
andytoshikanzure: so, i can't keep up with IRC. not even hplus and wizards. nor can i keep up with my news emails (which are much more self-contained and probably a better candidate for prototyping anything)10:28
maakuandytoshi: i think he means is he needs a filter definition to decide what information gets transmitted to which people10:28
andytoshiall those things are 90% shit though10:28
maakuwhich a region definition in concept space would provide10:28
andytoshiif i could get at just the topics i care about (or ones related to things i care about) then i'd be fine10:28
maaku(which in practice would be created from a bunch of 'did you find this helpful?'yes/no responses)10:28
maakui hope this channel is less than 90% shit ;)10:29
andytoshilol, yes, this channel has a very high snr ratio. but still probably half of it is things i don't know enough about to grok10:30
andytoshihmm i'll bet there's canned software for doing email filtering. i tried doing this with spamassassin and it didn't work at alll10:30
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kanzure.title http://ropengov.github.io/r/2016/06/10/FOI/10:45
yoleauxScientific journal subscription costs in Finland 2010-2015: a preliminary analysis — rOpenGov10:45
nmz787_isooo, ethereum?10:45
kanzurewhat would you like to know10:49
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nmz787_iis ethereum 'good'? in y'alls opinion?11:03
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kanzurenot a good question11:04
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mag1c_Erbbyhello :)11:09
kanzuregreetings.11:09
mag1c_Erbbyim  thinking about doing some shit.. what do you recommend ? im new to all of this :)11:11
mag1c_Erbby?11:22
nmz787_imag1c_Erbby: what are you interests and skills?11:22
andytoshiare you interested in natural language processing and classification?11:22
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andytoshiguess not11:25
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juri_doing things is hard. can i just philosophize uselessly, write bad scifi starring cats i want to sleep with, and wait for nerds to do everything for me?12:39
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kanzurewhat hard things are you up to?12:46
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nmz787_ijuri_: met a guy few days ago that reminded me of you, he made an induction heater for melting metal12:50
nmz787_isomething about 100 Amp service just for that circuit12:51
nmz787_iand 0-gauge wire not being big enough for very sustained time of use12:51
juri_kanzure: I'm on month 2 of a rewrite of the linux kernel's built-in implementation of iscsi.12:51
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juri_other that that.. moving infrastructure to a series of pcduino3 boards, and building a pick-and-place-and-print-and-laser machine.12:52
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juri_nmz787: docs, please. ;)12:52
juri_that's something i'm discussing with a student, tonight.12:53
kanzurebad kernel scifi might be interesting, though12:57
juri_but where do the cats come in? people want the cats.12:57
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archels.g A shared neural ensemble links distinct contextual13:02
yoleauxarchels: Sorry, that command (.g) crashed.13:02
archelsfail²13:03
archels.title http://www.nature.com/nature/journal/v534/n7605/full/nature17955.html13:03
yoleauxA shared neural ensemble links distinct contextual memories encoded close in time : Nature : Nature Publishing Group13:03
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nmz787_iit would be interesting to try printing a semiconductor device using a finely focused laser and various starting powders (silicon, dopants) in a laser-induced melting process13:49
nmz787_itheorhetically it might then be possible to use solar irradiation coupled with a fresnel lens and some wavelenght filtering somehow (grating, prism or or metalens)13:49
nmz787_iand demo a solar-powered chip printer13:50
kanzurehttp://diyhpl.us/~bryan/papers2/bio/open-electroporator/homemade-electroporator-1991.pdf13:50
nmz787_iyeah, depends on that C1 capacitor13:51
nmz787_iso can't change the pulse shape13:51
chris_99i think i looked at a diy electroporator a while ago, am i right in thinking the BOM comes out >= £40013:58
nmz787_ithere are several DIY builds, with varying BOM costs13:59
nmz787_ithat one in particular looks closer to $20013:59
chris_99ah interesting13:59
nmz787_ithe one kanzure is (I think and hope) funding should be around $30 BOM13:59
chris_99oh wow, i thought the caps needed where expensive for some reason13:59
nmz787_ithis design eliminates the caps ;)14:00
nmz787_iusing induction14:00
chris_99oh interesting14:00
nmz787_iPWM some FETs, they pulse a low-side of a coil with low or medium voltage, coil produces HV... have parallel channels of this setup, and overlap pulses to elongate14:01
nmz787_iPWM duty cycle on FETs should allow variable voltage on the pulse as well14:01
nmz787_ifor varying the field strength14:01
chris_99what voltage/current do you need to produce for it?14:01
nmz787_ihe says it will drive a 30kOhm load, so you can do the math based on say 3 kV14:02
nmz787_ibut then there will be some wiggle room, since cuvettes vary (electrode spacing) and species and strains vary as far as needs14:03
chris_99is that 300W then14:03
nmz787_ichris_99: the terms are usually in volts/cm for field strength14:03
chris_99ahh14:04
nmz787_ierr MOhm maybe?14:04
nmz787_iI can't remember14:04
nmz787_ierr14:04
nmz787_ino it says kohms14:04
chris_99oh btw, it was an ADC i used, with a PGA, not sure if that's of any help14:04
nmz787_i"E.Coli 12-18kV/cm, test at 5msec pulse, adjust from that starting point for efficiency tuning                             S.cerevisieae ~7.5kV/cm, start at 5msec pulse"14:05
nmz787_iah, I was looking for MCU integrated14:05
chris_99ah gotcha14:05
nmz787_ihttp://imgur.com/TmwPOho14:05
nmz787_ihttp://imgur.com/a/swOXq14:05
nmz787_ichris_99: ^14:05
chris_99cool, will have a look, is there a simple experiment you can do with electroporation, without needing really expensive plasmids (if that's the right term)14:06
nmz787_iyep14:08
nmz787_iGFP or glowing e coli14:08
nmz787_ibasically it makes transforming organisms generally easier and less reagent intensive14:09
chris_99is there a kit for glowing yeast, i thought it was harder to get a plasmid for them?14:09
nmz787_iprobably is, not sure how easily obtainable14:09
nmz787_iI wish this existed for non-Apple:http://structure.io/14:12
nmz787_i.title14:12
yoleauxnmz787_i: Sorry, that command (.title) crashed.14:12
nmz787_i.title http://structure.io/14:12
yoleauxStructure Sensor - 3D scanning, augmented reality, and more for mobile devices14:12
chris_99did you see the google radar-y type thing14:12
nmz787_ihmm, no, project tango?14:12
chris_99https://atap.google.com/soli/14:13
kanzurenmz787_i: yep sent over the money last night14:13
nmz787_iis it ready to use?14:15
nmz787_iI think they sent me an invite a while ago14:15
nmz787_ibut I didn't have any steam to work on it14:15
nmz787_ioh, but they sent it to me for the whole project tango device14:15
nmz787_ithis seems different or new14:15
chris_99yeah i think this is new14:16
chris_99i think this is RF, isn't tango ToF14:16
chris_99with light14:16
nmz787_ii thought it was many sensors being used at once14:16
chris_99oh14:17
chris_99hmm14:17
nmz787_i(as in maybe this will be incorporated)14:17
nmz787_inot sure14:17
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kanzure"the task should be to build the analog circuit and connect it to any simple square wave generator  (which can be soldered together in 10 mins from an LM556 chip and needs no software).  Then see if the HV pulse has any real working characteristics using an HV probe to an oscilloscope.    what I see instead, is wizz-bang hitech sounding device ("wow! it has bluetooth!") with no prototype bench testing at all."14:37
kanzure"micropython is completely unsuitable for this task.  Look up the instruction cycle time and latency of micropython.  It is great but not good enough for a control system.  The timing and control loops need to be written in assembly for a stable product i.e. instruction cycles counted.  Lightening will create biology so sure, zapping something with any kind of shape might work sometimes, but obviously, repeatability and yield needs to be ...14:37
kanzure... maximum."14:37
kanzure"Basically he's saying:  let's take a microcontroller and some transistors with the transistors connected to a medium voltage rail (28VDC), and have the microcontrollers switch these, to make a square wave, which can then be assumed to become like a sine wave AC. (It won't)    Then let's take that supposed-to-be-AC signal and run it thru a transformer to boost the AC voltage x57.   So let's see.  28VDC minus let's say 3VDC for FET loss = ...14:38
kanzure... 0.5 to 25VDCmax at 1 mA  [No mention of how to remove DC from the output waveform; it needs filtering]  * 57 = 1425VAC peak-to-peak (theoretically but really less) at 0.015 mA, then suggested to double that with a capacitor diode bridge (which will add incredible amounts of EM noise)"14:38
kanzure"perhaps it could yield high voltage output at very low current like 1 uA.  The microcontroller will reset itself due to EM noise.   The diode doubler will arc on the output because there is no discharge path, so it will be more like a very unreliably shapen spark, rather than a HV square pulse.   I have doubts that a diode doubler is useful for reliable HV output.  Forget building the enclosure, forget the microcontroller, do some ...14:38
kanzure... measurements and prototyping with that analog circuit first.  A bunch of time will be saved, showing that the circuit doesn't transform anything with suitable yield"14:38
kanzure"A better design would not use FETs at all, it would use a sine wave generator directly (very simple circuit) with dual rail power supply (ie -9V and 9V is very common, or -12V and 12V) to drive a clean AC signal into the transformer.  Start with a dirty input like the FET idea and the output can never be clean."14:38
kanzure"14:39
kanzure"Also no mention of HV digital switch on the output, which is critical"14:39
nmz787_iwhere is this from, and why is he mentioning sine waves?14:39
nmz787_i(they)14:39
kanzurehttp://chimera.labs.oreilly.com/books/1234000002036/ch06.html14:39
kanzuresheeet i forgot about that article. damn.14:40
nmz787_ithat really isn't that related though14:40
nmz787_ias in, the HV supply can be had as an available part14:40
nmz787_ialso, his micropython blast seems muted by this: https://micropython.org/doc/tut-asm14:41
kanzuredon't worry about his micropython blast, replacing a single chip in a design is trivial14:42
nmz787_iI also really don't get this AC sine wave reference14:42
kanzureor, if the chip supports non-micropython stuff, then all the better... it doesn't matter.14:42
nmz787_iwhere is this stemming from, as in what tipped this line of thinking off?14:42
nmz787_ikanzure: exactly, that is firmware level and can be changed14:42
kanzurei could ask him a question about his sine wave obsession, what should be asked?14:42
nmz787_i"why are you talking about sine waves and AC?"14:43
kanzureis it possible that he thinks the output needs to be AC?14:43
nmz787_ipossible, but why, and if no reason, then seems unfamiliarity with the desired application14:44
nmz787_ior didn't read carefully14:44
kanzure"I quickly reskimmed and saw the voltage is generated directly from the battery which is what, 3.7VDC max. Yea, pretty much I don't think this prototype is going to work. No mention of precision voltage regulator either compared to the amount of details on the microcontroller (honestly who cares about the microcontroller they are all the same).   Imagine what happens when a digital IC with the common ground near an HV circuit gets noise ...14:45
kanzure... from a discharge arc of several hundred volts.  Very unstable."14:45
nmz787_ithis guy is seeming out of touch with reality... voltage regulators are not advertising points, they are common knowledge and easily sourced dime-a-dozen parts14:46
kanzuresent.14:47
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nmz787_iAlso where is this person seeing a diode voltage doubler? I can't find a block diagram myself now14:53
kanzurehttp://diyhpl.us/~bryan/papers2/bio/open-electroporator/pyzappa-open-electroporator-project-proposal.v0.3.pdf14:54
kanzurefirst paragraph14:54
kanzurenear the end14:54
nmz787_ihmm14:55
nmz787_inot sure why there wouldn't be a discharge path... that is the electrolyte solution14:55
kanzure"The suggested transformer & diode doubler requires AC input.  If input is a malformed wave then the output will also be malformed. There are many many articles on electroporation wave shape in EE journals, that are really good hard data articles.. (because, they're written by engineers)  IEEE journals or Electrophoresis journal."14:56
nmz787_ior a bleed-down/snubber resistor or capacitor maybe14:56
kanzure"Lightening is not a clean wave and it will transform "some" bacteria when it hits the ground.  But to maximize yield and reproducability in a lab, the output signal has to also be as clean and reproducible as possible, not just some long chain of dirty sparks.   The output does not have to be sine shaped AC HV but it does have to have a clean, reproducible shape.  Ideal would be an HV square wave pulse train.  But that will be ...14:56
kanzure... impossible to achieve in a circuit."14:56
nmz787_iwave shape really doesn't matter for this14:56
nmz787_ieven biorad says that14:57
nmz787_iwell maybe it was not biorad14:57
nmz787_imaybe it is the electroporation review manual/book I have14:57
nmz787_ialso not sure why he is referring to a geological/natural occurence of lightning14:58
nmz787_ithis is not randomly sourced high-voltage14:58
nmz787_iand there isn't AC needed when the pulser is paralleled, I believe14:58
nmz787_iagain, I think this person is low on details14:59
chris_99is there a schematic out of curiosity14:59
nmz787_iand I have a feeling I know who it is by their response and tone14:59
nmz787_i/me NLP14:59
kanzurei already leaked who it is14:59
nmz787_ioh14:59
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nmz787_iJon Cline?14:59
kanzureyea14:59
nmz787_iyeah14:59
kanzurehe's wonderful.15:00
kanzurechris_99: nope i don't think there's a schematic at the moment15:00
nmz787_ihe generally seems unconstructive/unhappy though, he could be more persuasive and helpful.15:00
nmz787_iI mean, his comments are well thought out, but they lack insight, and he is too quick/busy/high-and-mighty to ask, seeminly.15:01
kanzurethis is his way of being constructive.15:01
nmz787_isemingly&15:01
nmz787_i*15:01
kanzurei would bet that a lot of his magic would go away if you forced him to adopt another attitude; i'm fine with how he is.15:02
nmz787_iok so lots of iteration is needed for this feedback to become useful then15:02
nmz787_ibecause he is definitely not on the same page as I think John and I are15:02
kanzurehehe.15:08
kanzurei am going to chalk this up to mostly assuming AC output is a requriement15:12
nmz787_iwell his reply was regarding the input to the coil15:13
nmz787_ibut AC is just DC with a middle-ground15:13
nmz787_iso really I think he just doesn't understand that pulses are desired, single pulses, and potentially these single pulses will want to be overlapped using paraallel circuitry15:14
nmz787_imaybe we need to pay him for an hour of his time, sliced into a few 10 -20 minute blocks15:14
nmz787_i(long enough to read a message, google some stuff, and rant off a few lines/paragraphs)15:15
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kanzurenmz787_i: i'd be happy to do that, but you would have to organize that or whatever.15:31
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fennjuri_: http://fennetic.net/irc/keroserene_kernland_scaled.png16:42
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FourFireHi kanzure!17:02
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fennthe bit about noise crashing the microcontroller seems pretty relevant17:02
FourFireSo my a biohacking group is starting at my hackerspace17:02
fennmaybe optocouplers and a separated/heavily filtered power rail design could isolate it enough to not crash17:04
FourFireI'm in it, and although the threat of "bioethics comittee" already looms am excited about even the possibilities within the law in this, one of the most strictly regulating countries17:04
fennthere's a lot of stuff you can do, especially if you consider collaborating with people in other countries17:05
fennlike, you don't need to actually have the GMO to do science or whatever17:06
fennyou just design the plasmid and order things through the mail to a different address17:06
FourFireI was wondering about a thing  kanzure mentioned earlier, the symbiotic organisms which secrete nootropic in the brain17:06
fennlol17:06
FourFireof course, I was immediately thinking of you guys17:06
fennnon-human cells living in a brain is generally a bad idea17:06
FourFirethis starup/inestor/acceleator guy was there at the start with slides lol17:06
nmz787_i1fenn: its possible a piece of screen-door metal screen would be enough of a faraday cage to shield things17:07
fennnmz787_i1: not if the controller is connected to the HV circuit with a wire17:07
FourFire"we're restricting all these techs and our tax laws are quite stiffiling, and even though we're pouring 9 billion nok per year on biotech all the startps seem to sell out or move to other countries for some reason?"17:08
fenni havent really looked at the schematic in detail17:08
FourFirehe had a talk basically saying to everyone that if anything "interesting" resulted from the group, then it wold be funded17:09
fennif he's getting transformers custom made, why bother with the voltage doubler? just get a 100:1 turns ratio transformer instead17:09
fennbut why get custom transformers at all?17:09
fennFourFire: welp have fun with brain drain17:10
fennsee also BSD17:10
FourFirefenn yeah I eouldn't want to do a human mod for my first bio project ever, but i'm flining ideas at the wall, I want to do something "real" as in interesting, but with potential sale/open source value17:10
FourFirefebn hilarious because he brough up cambridge; "there's like 4000 biotech compaies in cambridge" but only 12 per year in Norway17:11
FourFireMy plan was generally to get a degree and the travel either to cambridge/oxford, germany,or some USAplace if I had no choice17:12
nmz787_i1fenn: you aren't using a ton of current, so you only have to worry about induction17:13
fennfourfire you know its cambridge massachusetts right?17:13
kanzureFourFire: there's a lot of potential projects listed here http://diyhpl.us/wiki/dna/projects/17:13
FourFirefenn I may be mixing up my important UK places es17:13
fennit's in USA17:13
fennMIT and harvard17:13
kanzure"Cambridge is a university city and the county town of Cambridgeshire, England"17:13
FourFirekanzure, what are the limitations of uhh what's it called when you force mutation rate really high and recursively kill off the population which doesn't exhibit the trait you want17:14
kanzuremutagenesis, selection, antibody selection, etc.17:14
fennUK has the typical EU anti-GMO insanity17:14
FourFirekanzure, can I get ecoli to excrete modafinil ?17:14
nmz787_i1FourFire: eventually17:15
FourFirenmz787_i1,  does that mean this decade?17:15
FourFireor would that require 1000 lines to select between or othewise ndoable things?17:15
FourFireheh immediately thought hasn't the plastic eating bactria been done?, *read the page title*17:17
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FourFireoh yeah the accelerator guy specifically mentioned iGEM and CuttingEdge (that conference where A Sandberg talked at my workplace last year) when he meant interesting projects17:18
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FourFirehah, I used "magnetic bacteria" as a bullshit example to explain mutagenesis selection, I didn't think it actually exsisted17:21
FourFireAlright, thanks for that I'll probably be popping in with more stupid questions.17:22
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kanzurehi.19:00
kanzureultrasound imaging proposal stuff: https://docs.google.com/document/d/1xvLWDbp0x6z0Ft3AsfxjIsLUNsg5smkTcYb1g4WVo5U/edit19:00
seanphhello19:02
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seanph@Ivan_ is working with me on hardware projects19:02
seanphwe are here to discuss the ultrasound proposal19:02
Ivan_Hi guys!19:03
kanzurefenn: are you around19:03
kanzurenmz787 is grocery shopping because he is mortal and requires food still19:03
kanzurenmz787 was talking about this one https://github.com/kelu124/murgen-dev-kit19:06
kanzurebeam power measurement is by hydrophone i think, right?19:08
seanph@kanzure are you talking about safety calibration?19:10
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fennhi19:11
kanzurehydrophones iirc are used for output measurement19:12
seanph@kanzure yeah, I can imagine doing that to characterize the system19:12
kanzurei'm making this up, you have done more work with these projects than i have at this point19:12
seanph@kanzure in normal operation, the piezo transducer both sends and receives19:12
kanzurefenn: nmz787 was pointing out that murgen-dev-ket.git has done a bunch of this work already, although not portable and it seems they use commercial probes (only?)19:13
kanzure12:43 < nmz787_i> kanzure: 'upgrade murgen's ADC/AFE (analog front end)' or 'enhance image decoding pipeline' or 'add doppleror 3D functionality' are interesting and immediate murgen possible-next-steps (or would make good proposals)19:13
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fennseanph: what do you mean "test on chicken legs" exactly? how do you know if it's safe based on chicken legs?19:15
seanph@fenn you don't, I hadn't thought that safety characterization would be a part of this initial prototyping project19:15
kanzureyeah i liked the beef/meat testing idea, not sure what to do with chicken bones though19:15
seanph@fenn thus the use of dead meat19:15
kanzurewith dead meet you can cut the meat and then see if there was any visually-detectable thermal damage19:16
kanzure*meat19:16
fennthat's not very comforting19:16
fennanyway my only major concern was the use of altium, since basically nobody but professional EEs have it due to the cost19:16
seanph@fenn we're not doing anything unusual, so I think basically there's a step of calibration later on to get the beam strength in safe limits19:17
seanph@fenn that's a valid concern, we are willing to use open source PCB CAD if desired19:17
kanzure19:49 < fenn> The first full-body human ultrasound -- conducted in the turret of a disused B-29 bomber  http://criticalmedia.uwaterloo.ca/courses/necromedia/19:17
seanph@fenn Ivan is familiar with EAGL, if that's cheap enough. He's also used DesignSpark19:18
fenneagle would be fine19:19
fennkicad is best of course, but it can be frustrating19:19
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Ivan_Sorry guys, my vpn went down19:20
seanphIvan_ is sitting next to me, saw the messages19:21
kanzureIvan_: http://gnusha.org/logs/2016-06-13.log19:21
kanzurealright19:21
Ivan_I have tried KiCad before, but it handles libraries components differently from eagleCAD, so I reverted back to that19:22
kanzurelooks like the only complaint on the google doc was something about motor sweep, but i think mechanical sweep is fine for this version19:23
kanzureall the signal processing will be fpga icestorm things, so that should work in real-time ish19:24
seanph@kanzure phased array is better for sure, but motor sweep is simpler19:24
seanph@kanzure we were actually thinking lately about just using an FTDI chip and an ADC and processing all on the PC, for simplicity's sake. also makes it more accessible to more people19:24
seanph@kanzure since few people are familiar with HDL19:24
seanph@kanzure but I do have an ICE devkit here we can fall back on if need be19:25
kanzurei have no idea what the processing requirements are19:25
seanph@kanzure I was thinking of a FT232H USB FTDI and LTC2315-12 ADC19:25
Ivan_@kanzure also if we use the PC for processing, the final BOM cost is cheaper19:25
seanph@kanzure PCB design is also easier without an FPGA to place19:26
seanph@kanzure phased array almost certainly needs fpga19:26
kanzurewhat actual components would be on the FPGA19:26
Ivan_@kanzure the processing requirements can be modest at first19:26
streetyIs the aim a 512x256 image refreshed 5 times per second? Seems somewhat ambitious for a mechanical movement, could be totally wrong though19:26
Ivan_hence no fpga19:26
kanzurein the motor sweep (for fpga)19:27
kanzurewell if we don't use an fpga then this adds a beaglebone or something to the project (or whatever small board linux is in style these days)19:28
fennwhy not an android phone?19:28
kanzurebecause android ndk makes people miserable? :)19:28
kanzurehm19:28
fennbeaglebone doesn't really add anything though, just realtime guarantees i guess19:28
seanph@streety 60 sweeps is only 30 rpm right? (5 * 60)/219:29
seanph@kanzure maybe we can even do it on a raspberry pi. but I had figured that most users would have a PC handy anyway19:29
kanzureoh i wouldn't assume a PC19:29
fennyou need a display of some kind19:29
seanph@streety, sorry, 5 sweeps per second19:29
kanzurephone probably makes the most sense....19:29
fennadding a display to a raspberry pi is just silly when phones are so plentiful19:30
seanph@kanzure we can target the phone. battery usage will probably be high, but I guess one would only use this for a short time19:30
kanzurewere you thinking power over usb?19:31
seanph@kanzure no19:31
fennwhat powers the ultrasound emitter?19:31
juri_fenn: nice. ;)19:31
seanph@kanzure power over USB was a major constraint of mobisante. I think it adds too much complexity to optimize for that in this first phase19:31
streetywould you need to pause the movement at each pixel or would it be a smooth movement?19:31
juri_nmz787: documentation! :P19:31
seanph@streety yes, it's a stepper motor19:31
nmz787sup19:32
kanzureseanph: btw this place is publicly logged so maybe mobisante/confidentiality stuff (i dunno what applies there)19:32
nmz787seanph: myHDL for Python ;)19:32
seanph@kanzure ah okay. I think what I said was public, but I will be careful :_19:32
seanph@kanzure thanks :)19:32
nmz787reading backlog for last hour or so19:32
kanzurehaha myhdl/python... nah, i think seanph could be convinced to write regular HDL things... but yeah, i guess it makes sense to reduce the amount of HDL written even if we do use an fpga....19:33
seanph@kanzure I figure that a super simple thing that uses C++ is accessible to a lot more people19:33
nmz787I like the condom with gel balls inside... seemed like a good non-rottable test subject19:34
seanph@kanzure then can get fancier in later phases19:34
seanph@nmz787 definitely the place to start19:34
fennso does the probe have its own battery or is it plugged into a wall wart?19:35
nmz787eagle should be avoided if you're avoiding Altium... otherwise just use altium (they're both closed)19:35
kanzurewhat19:35
fenneagle has a free version which is good enough for most people19:35
fenni'm more concerned about accessibility than open source purity19:36
kanzurealright that's verging on navelgazing19:36
kanzureyes19:36
seanph@fenn we can add a battery without much trouble if that's desired19:36
kanzurebut what was the plan w/o battery?19:36
kanzurewithout19:36
seanph@kanzure wall wart19:37
nmz787fenn: srsly?19:37
nmz787fenn: you disappoint my open-source computation engine19:37
Ivan_the free eagle version makes the board size limited and only lets you use two layers19:38
fennmaybe kicad has improved in the past five years, but i wouldn't force the version i used on anyone19:38
nmz787kicad is amazing19:38
nmz787it has improved dramatically over the past 2 years19:38
nmz787thanks to CERN money19:38
kanzurei predict much timewasting on this topic19:39
Ivan_I gave it a shot about four years ago19:39
Ivan_didn't work out, tried DesignSpark19:39
nmz787we can just move on and screw re-usability for poor kids in africa19:39
nmz787or pay someone $4 an hour somewhere to convert it later19:39
kanzurepoor kids... haha.19:40
kanzureyes to that plan19:40
nmz787send them GIFs of each section and layer of the final closed-board19:40
nmz787so is power really a concern?19:40
Ivan_@nmz787 that can be done19:40
nmz787seems like a plan for improvement19:40
seanph@nmz787 I think that the power can be optimized for, to run off of the phone, but this is just a prototype phase19:41
seanph@nmz787 MVP19:41
nmz787getting /something/ for a reasonable price, that is easy to produce and reproduce (by lesser skilled folks), and that has a hackable processing pipeline (that software neckbeards can jump into contributing DSP for) would be nice19:41
fennso.. stepper motors have 200 steps/rev which means only 33 full steps in a 60 degree scan window, how do you end up with 512x256 resolution?19:42
nmz787would an FTDI be high enough bandwidth for raw dumping to PC?19:42
seanph@fenn there would be gearing for sure19:42
fennhuh i hadn't considered gears19:43
fenndo you know about microstepping?19:43
nmz787seanph: Ivan_ have you heard of the Daisho project? It aimed to provide an HDL USB 3.0 superSpeed module19:43
nmz787gears will add more of a state-machine to your this-step-means-this-physical-position calculation19:44
fennyeah gears have backlash19:44
nmz787well not just that, but if youre rotating, 0-degrees tilt may not be the same tooth of the gear19:45
nmz787so mechanical fab will come into play with non-uniformity of the gear19:46
fennmeh even cheap gears are pretty precise19:46
seanph@fenn yeah, perhaps microstepping is a better idea. the motor driver DRV8833 that I am thinking of using can do 32 microsteps19:46
seanph@fenn so that solves that issue19:46
streetythe movement is going to be fast, there is not much time to play with. If you consider 256 positions visited 5 times a second and a max depth of 10cm just sending the sound wave and waiting for it to return will take 0.166 seconds19:47
streety* going to need to be fast19:47
streetythat's based on a speed of sound of 1540 m/s19:48
kanzurespeed of sound changes for different materials like human organs19:48
kanzureor rather, propagation of sound changes19:48
kanzureoops i mean "definitely non-human organs"19:48
fennstreety: .166 ms19:49
fennassuming a ~12 cm path19:50
Ivan_@nmz787  I looked at the Daisho project, but I couldnt find the exact price tag19:51
seanph@streety 1540 meters per second / 20 cm = 7.7khz no?19:51
streety0.1 * 2 (there and back) * 5 * 256 / 1540 = 0.166 s19:51
Ivan_@nmz787 also, like we previously mentioned it would be great to keep the first prototype, simple, no fpga and processing on the PC19:52
nmz787Ivan_: it is a block of code, free and open19:52
seanphas for the FTDI, the datarate we need at 8 bits per sample is 40Mbit, and the FT232H should support that. there may be an issue with the SPI interface being limited to 30MBit, now that I review the datasheet19:53
nmz787Ivan_: yeah I was just mentioning it because of USB 3, versus FTDI is limited to 2.019:53
Ivan_@nmz787 thought that you are refering to the USB 3.0 FPGA platform19:53
streetyI just got that speed from a number of sites as a ballpark figure19:53
seanphI'm not sure why we need USB 3 for 40MBit?19:54
nmz787Ivan_: yep, not saying to process on an FPGA, but if you're were comfortable with an FPGA and an FTDI wouldn't do the full bandwidth... maybe you were comfortable enough to just use the daisho for USB transfer19:55
nmz787if it is 40 Mbit then no, 2.0 should be fine19:55
fennam i the anonymous capybara?19:59
fennguess i'm just "anonymous"20:00
kanzureis that a philosophical question?20:00
fennno20:00
nmz787it is confusing as hell20:00
nmz787imagines a rampant varmint who can't be caught20:01
fennhttp://fennetic.net/irc/anonymous_capybara.png20:02
kanzureoh, well you're not logged in20:02
fennfor a moment i thought google might be cool again20:03
fennseanph: if you haven't used it, i highly recommend thermomorph/polycaprolactone/fantastic plastic for prototypes20:05
seanph@fenn we have some here I think :)20:05
seanph@fenn we work out of http://www.xinfab.com/ and http://xinchejian.com/20:06
nmz787sooo20:11
nmz7873D and doppler20:11
nmz787what are the requirements hardware wise?20:11
nmz787would they exist in the first plan? how many iterations to get to that?20:11
nmz787(non software)20:11
nmz787(also, software is important but decoupled... I cannot do such software)20:11
seanph@nmz787 we think we can do doppler with this hardware, just a software thing20:11
Ivan_@nmz787 for the 3d we will need a phased array most probably20:12
nmz787just thinking in terms of evolutionary design20:12
nmz787ok, how about the hardware then20:12
fennit would help to add an accelerometer and gyro for 3D20:12
nmz787are you taking an existing design, or just design pattern? are you taking i.e. murgen into account?20:12
kanzurenmz787: i don't think we're short on software people, and we can probably coerce seanph into doing software things if needed20:13
kanzureagreed re accelerometer and gyro20:13
seanph@fenn adding those shouldn't be a big deal. we were planning to have an Atmel micro to control and inject frame and line headers into the FTDI data stream, so we could have it talk to MEMS sensors and insert that metadata20:15
seanph@fenn and from there it's software20:15
fenna simple matter of programming :)20:16
seanph@fenn heh'. yeah not so simple of course. Ivan has experience working with radar signal processing tho, building up the algorithms in matlab first20:16
seanph@fenn it's certainly a stretch goal / out of scope here. but we can toss the MEMS sensors on the PCB so it's possible to do20:16
kanzurealso there's some open-source ultrasound signal processing stuff out there. i forget where. i think at least one of them was a "sample" api dev kit thingy from texas instruments.20:17
seanph@kanzure ah cool, definitely will search it20:17
kanzurehttp://www.ti.com/tool/s2meddus20:17
kanzure"The TI Embedded Processor Software Toolkit for Medical Imaging (STK-MED) is a collection of several standard ultrasound and optical coherence tomography (OCT) algorithms for TI’s C66x™ and C64x+™ architecture. The algorithms showcase how medical imaging functions can leverage the C66x and C64x+ architecture for efficient performance and low power consumption."20:17
fennyes TI has a bunch of stuff20:18
fenn.title http://www.ti.com/lit/wp/sprab12/sprab12.pdf20:18
yoleauxfenn: Sorry, that doesn't appear to be an HTML page.20:18
fenn"Signal Processing Overview of Ultrasound Systems for Medical Image Processing"20:18
fennImaging*20:19
fennhonestly i would be happy with just a volumetric render of raw data that's only been aligned by gyro and accelerometer20:23
fennisosurfaces are not all that useful really20:23
kanzurefenn: https://www.youtube.com/watch?v=hKH1e38B1is20:24
fennbonus points if the phone can be used to change angle of view by moving it around the patient, but that's getting into a different can of worms20:24
fennno that youtube video is wrong and dumb and you should be ashamed :P20:25
seanph@fenn would be great to be able to reproduce that. it makes the image a lot more understandable to the untrained eye20:26
fenneasy, just stick a QR code on the probe20:27
fenni'm talking about something different20:27
kanzureyou are talking about visualizing slices in 3 space?20:27
fennyes like the visible human project20:28
kanzurei don't remember that one20:28
fennit would probably look more like this http://vis.lbl.gov/Research/ChomboVis99/misc-art/vtk-volume.gif20:29
kanzurei was thinking http://staff.washington.edu/leotta/research/ortho_planes.gif20:29
kanzureor (if this wasn't PET) https://upload.wikimedia.org/wikipedia/commons/d/d7/CT_Scan_of_Dale_Mahalko's_brain-skull.jpg20:30
fennonce you get it into a volumetric representation you can slice it however you want20:30
fennthe second one is easy to fake with just opengl textures20:31
kanzuregosh if only we had some opengl folks in here20:31
fennyeah scan of dale mahalko's brain is a good inspirational image20:34
seanphhehe, yeah I have a lot of experience with graphics and OpenGL20:34
seanphwould be fun to do20:34
seanphespecially on the phone in realtime O.o20:34
kanzurei think that's called "webgl" these days :(20:34
nmz787so is the hardware pretty standard then?20:34
nmz787i.e. nothing to innovate on here?20:34
seanph'eh, I probably wouldn't use webgl for this. native C++20:35
nmz787just BOM cost reduction and opennes?20:35
seanph@nmz787 I think using the ftdi is innovative, in the sense that there are fast enough ones at a reasonable price these days20:35
nmz787well they20:35
seanph@nmz787 but yeah, it's basically commodification of an old school ultrasound design20:35
seanph@nmz787 taking advantage of modern components, computing power on the phone20:35
nmz787it is funny and interesting to hear that an FTDI chip is considered innovative, but I believe it :) (especially in this biomed imaging stuff, which is always sold as super expensive to 'us')20:37
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nmz787but then again, it was pretty innovative when I first learned they could be used as a logic analyzer too http://www.ebay.com/itm/24MHz-8CH-USB-Logic-Analyzer-8-Channel-Logic-Analyzer-Compatible-to-Saleae-/17120292718220:38
fennwhat's in the box?20:40
nmz787FTDI20:40
nmz787see this slide https://docs.google.com/presentation/d/1UGdLO5VJuHQRMvgvawBwe7E5R5H7_XczCERFo2DVMIk/edit#slide=id.g1084b242f_03620:40
nmz787err, maybe a cypress chip actually20:40
nmz787but it is essentially the same function20:41
nmz787its a USB to serial converter, where each bit of the byte is tied to a GPIO input20:41
fenni'm seeing numbers like 50kHz to 500kHz for the FT232, now 24MHz20:42
fennnot*20:42
nmz787so effectively you can just connect digital signals to the GPIO and parse the bit field on the PC side20:42
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nmz787isn't that just USB or USB 2 bandwidth?20:43
nmz787i mean transfer rate20:43
seanph_@nmz787 8 euro, nice20:43
nmz787or clock or something20:44
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nmz787fenn: https://sigrok.org/wiki/Fx2lafw20:44
nmz787fenn: the FT232H can do a bunch of modes though20:45
nmz787i think one is parallel in20:45
nmz787so effectively the same thing is possible20:45
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fennwell i never actually needed a logic analyzer so i guess i'll stick to poking at RTL-USB tv tuners20:47
seanphsorry for popping in and out, having vpn issues (China)20:47
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seanphso yeah, we will hang out in the channel at least while we're working on the project20:51
seanphwill be logging out now since we were up all night playing with superconductors, and badly need sleep20:51
fenng'night20:51
kanzureseeya. we can setup a vps for you to have stable irc.20:51
seanphthanks for your input everyone. the microstepping thing in particular seems like it will simplify things and make it better20:51
seanph@kanzure no worries, I'll sort that out. I actually have one that I'm not using20:52
kanzurenight21:00
* kanzure sleeps21:00
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fenn.title https://youtu.be/VIRCybGgHts23:22
yoleauxStanford Seminar - Geoffrey Hinton of Google & University of Toronto - YouTube23:22
fenn"Can the brain do back-propagation?"23:22
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--- Log closed Tue Jun 14 00:00:29 2016

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