2013-03-29.log

--- Log opened Fri Mar 29 00:00:41 2013
@kanzureoh look00:09
@kanzurethere's a prusa300:09
@kanzurehttps://github.com/josefprusa/Prusa300:09
@kanzureand it has thingdoc documentation00:09
@kanzurehttps://github.com/josefprusa/Prusa3/blob/master/box_frame/common.tdoc00:09
@kanzure/box_frame/inc looks like a primitive library system :\00:10
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BioGuyAnyone alive at this hour?01:40
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archelsonly the Euros and kanzure03:13
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diginetI'm not interested in it for biological applications, but what is there in the way of DIY microfluidics07:31
superkuhpaperbot: http://www.nature.com/nature/journal/v495/n7442/full/nature11990.html08:02
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/X-ray%20analysis%20on%20the%20nanogram%20to%20microgram%20scale%20using%20porous%20complexes.pdf08:03
@ParahSailindiginet: not much08:03
diginetParahSailin: couldn't you just use standard lithography techniques but on glass? (I guess HF as the etchant)08:04
diginetnot that litho is "easy," but it's not impossible, and we're not talking nanoscale here08:04
@ParahSailinfor glass you wouldnt even have to go to hf unless you were really in a hurry08:08
diginetwhat else could you use?08:09
diginet(for wet etching anyhow, not really interested in plasma etching)08:09
@ParahSailintmah could probably do it in a reasonable time, regular ammonia would do it a bit slower08:10
diginetinteresting08:10
@ParahSailinstrong acids will etch glass too08:10
@ParahSailinjust look up the etch rate you want to see which is most acceptable08:11
diginetlike which ones? I thought HF was the only common acid that etched glass08:11
diginetalthough I know hot phosphoric acid will08:11
diginetwhat about for the resist? PMMA has the advantage of being cheap, but IIRC it needs deep UV to be developed (or e-beam but that's obviously out of the picture)08:11
@ParahSailinits a question of rate, a lot of stuff will etch glass, but HF is the fastest08:14
diginetI see08:14
@ParahSailinHF is probably the most practical08:16
diginetwell HF does have the advantage of not attacking plastics (in general), I've heard of people making DIY photopolymer plates08:19
diginetmaybe I could use those as a resist08:20
@ParahSailinphotoresist works08:21
diginetlike SU-8? isn't that really pricey though?08:22
@ParahSailinthe regular novolac kind08:24
diginetwhere do you find that?08:24
diginetI've been looking for novolac for ages (for other stuff)08:25
diginetnovolac, like bakelite right?08:28
@ParahSailinwhat, no, like AZ[0-9]*08:29
diginetbakelite was a phenolic resin, as I understand it so is novolac, right?08:30
@ParahSailinyes08:47
@kanzurehttps://github.com/SpiderLabs/BurpNotesExtension08:55
@kanzurehttps://github.com/aglane for a UPnP browser soonish08:55
@kanzureopencascade 6.5.5 has been released08:58
@ParahSailinpaperbot: http://pubs.acs.org/doi/abs/10.1021/bi980942509:14
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Thermodynamic%20Parameters%20for%20an%20Expanded%20Nearest-Neighbor%20Model%20for%20Formation%20of%20RNA%20Duplexes%20with%20WatsonCrick%20Base%20Pairs.pdf09:14
@ParahSailini wonder if idt has done secret experiments more recently to make their oligoanalyzer more accurate09:15
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@kanzuremaradydd would be the person to talk with about that (since she worked at idt for a while and then repented to diybio)09:16
@kanzurepaperbot: http://www.nature.com/news/taking-the-crystals-out-of-x-ray-crystallography-1.1269909:18
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/788fffaa32f2b8b8118aa1d28c521831.txt09:18
@kanzurewait.. /news :(09:18
@kanzurepaperbot: http://www.nature.com/nature/journal/v495/n7442/full/nature11990.html09:18
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/X-ray%20analysis%20on%20the%20nanogram%20to%20microgram%20scale%20using%20porous%20complexes.pdf09:18
@kanzure"We demonstrate that as little as 80 nanograms of a sample is enough for X-ray single-crystal diffraction analysis."09:20
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@ParahSailinwow thats pretty big09:36
@ParahSailinoh, they only did small molecules09:38
superkuhThere is talk about proteins too.09:39
superkuhhttp://www.sciencemag.org/content/336/6084/1018.full09:39
superkuhpaperbot: http://www.sciencemag.org/content/336/6084/1018.full09:39
paperboterror: HTTP 300 http://diyhpl.us/~bryan/papers2/paperbot/Large-Pore%20Apertures%20in%20a%20Series%20of%20Metal-Organic%20Frameworks.pdf09:39
@ParahSailinwell there is no mention of peptide or protein in that nature one09:40
* superkuh nods.09:41
@ParahSailinpaperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1277807/09:45
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/b5f68ff1cd1f5306a7f3a0aab50f9fa3.txt09:45
@ParahSailinpaperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1277807/pdf/gki918.pdf09:45
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/7bcc57d4c29ce24a4b3d856414ae0089.pdf09:45
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@ParahSailinpaperbot: http://pubs.acs.org/doi/abs/10.1021/bi034621r11:03
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Effects%20of%20Sodium%20Ions%20on%20DNA%20Duplex%20Oligomers%3A%20Improved%20Predictions%20of%20Melting%20Temperatures.pdf11:03
@kanzurewasn't there also a thing about hairpins increasing the melting temperature11:04
@ParahSailinim not sure how that would affect it if you have the exact complement to duplex with11:13
@ParahSailinshould have some sort of effect11:14
@ParahSailinthis stuff is actually me using paperbot for work related stuff11:15
@kanzurework is too cheap to buy subscriptions?11:17
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@ParahSailinpaperbot: http://pubs.acs.org/doi/abs/10.1021/bi962590c11:56
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Thermodynamics%20and%20NMR%20of%20Internal%20GT%20Mismatches%20in%20DNA.pdf11:56
@ParahSailini couldnt condone paying these crooks on principle11:59
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@ParahSailinpaperbot: http://pubs.acs.org/doi/abs/10.1021/bi702363u13:31
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Predicting%20Stability%20of%20DNA%20Duplexes%20in%20Solutions%20Containing%20Magnesium%20and%20Monovalent%20Cations.pdf13:31
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@kanzurebah ipython has closed my pull request14:01
@kanzurehttps://github.com/ipython/ipython/issues/128614:01
@kanzurehttps://github.com/ipython/ipython/issues/289514:01
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@kanzure"East Bay DIYbio meeting 6pm at Sudoroom"14:53
@kanzurewin 514:53
@kanzurefidjklada14:53
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@kanzurehttp://news.yahoo.com/blogs/this-could-be-big-abc-news/teen-scientist-amazing-breakthrough-her-home-lab-165831291.html15:38
@kanzure"In her research she developed a process of artificial selection where she killed off algae with low levels of acetyl-CoA carboxylase (ACCase), an enzyme crucial to lipid synthesis. Left behind in the beakers under her bed were an efficient bunch of high yield algae, which she discovered produced a significant increase in lipid production."15:38
@kanzurei wonder what selection procedure this was15:38
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@kanzure"Dear Colleagues, An assertion such as below is ridiculous. Pharmaceutical companies would not spend the $1,000,000,000 for research it takes to bring each product to market if it were not for the brief period of market exclusivity that the patent system provides. Signed, Research Professor of Chemistry."16:00
@kanzureblah i can't remember the right links that debunk this16:00
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jonathancbuy more guns16:07
chris_99?16:09
@fennour sponsor, the NRA16:15
@kanzurejonathanc: hello16:17
@kanzurejonathanc: welcome back16:17
@kanzurealso i think your yaml>xml stance is respectable16:17
jonathancgcode vs. ?16:22
@kanzurecontext?16:29
jonathanc""Cool presentation and I want one of those things to make an incubator16:36
jonathancfor the repstrap I am building with Tecan/Biomek like attributes, I16:36
jonathancgot a  ... blah blah .. Anyway the repstrap firmware, I am planning on using Marlin which16:36
jonathancprocesses Gcode. I guess at first I will have the gcode thing going on16:36
jonathancfor position control of steppers and some way to send commands  ....""16:36
@kanzureah, well at least he's not writing his own gcode firmware16:36
@kanzurei think you can wire up linuxcnc directly to your actuators without a gcode intermediate16:38
jonathanci could just implement multiple command sets on my device.  auto-detect g-code and then switch to that, easy.16:39
@kanzurei don't think re-implementing gcode every time one of us makes anything that moves is a good use of our time16:39
jonathancmeh, that only takes a day16:40
@kanzurebut then you end up with lots of implementations that have poor edge case handling16:41
@kanzurewhat's wrong with repstrap? i haven't actually used it. the last i checked the main problem was that it was a java monstrosity? that might have been another reprap firmware though..16:41
jonathancSeems to me that gcode is pretty simple as an API16:45
@kanzurefenn: ping?16:45
jonathancsimple/dumb16:46
@kanzureoh wow linuxcnc is unable to find a grammar for gcode16:47
@kanzurehttp://www.mailinglistarchive.com/html/emc-users@lists.sourceforge.net/2012-02/msg00984.html16:47
@kanzurethere are "extensions" that must be allowed in real-time? what is this.16:47
@kanzurefenn is our resident linuxcnc developer and gcode user so i imagine he might know more specifics than i do16:48
jonathancis this what happens when meche's attempt to program?16:48
@kanzurewell afaik gcode was never really standardized with a grammar and it just "sort of happened"16:49
jonathanchence my curiousity regarding alternatives to gcode16:51
jonathancalthough any complexity pales in comparison to hacking proprietary workarounds into any networking protocol so...  it really is not that complex of a problem at all, it is no big deal16:52
@fennjonathanc: have you considered stealing large chunks from grbl?16:53
@fennof code*16:53
@kanzurealso if you really do have that file it would be nice to put it somewhere on the internets16:54
@fennkanzure: the reason for lack of standardization is vendor lock-in16:54
@fennthere's a perfectly good standard published by nist (RS274-NGC) but nobody implements it16:54
jonathancwell i'd never re-use code written by someone for arduino but might use it as documentation so that's a good pointer to have, will look at grbl16:55
jonathancI assume devices do not have to implement all g-code commands if they do not support them anyway16:56
@fennhere's the closest you'll get to a grammar for g-code: http://fennetic.net/irc/rs274ngc.ast.g although it's not particularly enlightening (g-code doesn't have much grammar to begin with)16:57
jonathancsimply, gimme a break, these commands are just turning on a motor or turning it off...  if the complex coordinate stuff is ignored16:57
@fennoh. in context http://fennetic.net/irc/emc3/src/emc/interpreter/rs274ngc/rs274ngc.ast.g16:58
jonathancexcellent16:59
@fenni'm not sure if that's actually correct; it was in the early stages of development16:59
jonathancok, i'll use it as a cross reference16:59
@fenni'm sort of confused what the goal is here. are you going to be running an embedded g-code interpreter on the robot? if so why not just use grbl running on an arduino?17:01
@kanzurethis doesn't seem to explain all the "gcode extensions" stuff. it seems to also support functions and it has to have a vm?17:01
jonathancbecause arduino is a toy?17:02
@fennwell, any avr17:02
@fennif it's against your religion, i guess that's an answer17:02
jonathancwell from superficial reading of gcode on wikipedia, gcode does allow registers (variables) to be set, so if you want to call that a vm, so be it17:02
@kanzure"remap gcodes half way through a swarf-making job"17:03
@kanzure"the language we have *is already runtime extensible* at the word level"17:03
jonathancg-code is just an api17:03
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@kanzurehttp://www.linuxcnc.org/docs/devel/html/remap/structure.html#_introduction_extending_the_rs274ngc_interpreter_by_remapping_codes17:04
@kanzureuhh "Embedded Python functions in the Interpreter started out as glue code, but turned out very useful well beyond that."17:04
@fennkanzure: various people in the emc project have tried to put lipstick on the pig, but custom functions and subroutines isn't generally considered part of the language17:04
@kanzureis python the lipstick or the pig?17:04
@fenng-code is the pig, fancy programming tricks is the lipstick17:04
@kanzurealso, it would be nice to have something that is not subject to vendor-lockin-guided-evolution17:05
@kanzureso even if you want to use gcode, why not just publish a grammar, then a specific standard, and just say let's use that subset17:05
@kanzurefenn: is the "3.3.4. Advanced example: Remapped codes in pure Python" section sane? it seems to have some python that accesses the gcode's interpreter's state.17:06
@fenni dont know, i've never used any of the embedded python stuff17:07
@fennalso you keep asking for a standard, but there is a standard, published by a standards organization, with a grammar, and a reference implementation of that17:08
@fennso i dont know what more you want17:08
@fenngoogle "nist rs274 production rules", the PDF has basically the same as what was in that antlr file i linked to earlier17:09
@kanzurewell, there's a pile of complaints about gcode that i keep hearing and it was always about incompatibility or something. and how could that happen if there's an actual standard?17:09
@fennbecause nobody follows the standard17:10
@kanzurebecause there's no reference implementation?17:10
@fennno, because the reference implementation wasn't good enough, so people extended it, and now nobody uses the original version17:10
@fennthat's what linuxcnc is17:10
@fennthen you have all the other vendors, whose names i forget now17:11
@fennanyway the core stuff like G0 G1 G2 is almost always the same17:12
@fennsome machines require fixed decimal point input, or no spaces, or must have spaces, or capital letters, or only parameters on their own line, and various stupid rules like that17:12
@kanzurebecause people chose not to use a parser parser?17:13
@fennso there's a thing called a post-processor, which takes a config file for your specific target machine and makes it work17:13
@fennit capitalizes the letters or adds zeroes to the end of numbers or whatever17:14
@kanzurehaha grand, i wasn't aware that there are gcode postprocessors17:14
@fennit's usually part of the CAM program17:14
@fennthere are people who make a living installing these config files :\17:15
@kanzurei suppose there might be some embedded environments where embedding an entire parser that can work on standard input might be impractical, maybe, but parsing decimals vs integers or capitals.. that's some pretty extreme optimization?17:15
@fennit's not optimization, it's for compatibility with crap written 50 years ago17:15
@fennpunch cards man17:16
@fennNC came first, then CNC. originally there was no computer in the loop17:16
@kanzurei'm aware.17:16
@fenna "toy" arduino is a supercomputer in comparison17:17
jonathancwell like I said, still simple compared to mucking with proprietary/standard internet protocol differences, so it is no big deal17:18
jonathancdoesnt need lex yacc for that17:18
jonathancthe trick would be to detect which dialect is required and then change on the fly17:19
jonathancby querying things on the device for example17:19
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@fennhow do you query a brain-dead serial protocol?17:20
jonathancwell from my superficial reading, gcode has registers that you can read, right.  so that's one way.17:21
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jonathancalternatively, send it a command, if it responds with errors, then go down the list until a dialect variant succeeds17:22
jonathancif it's transmit only with no detected errors, then there's still tricks that can be done17:22
jonathancpower cycle and read registers not yet initialized, see if there are characteristic values17:23
jonathancworst case, require the end user to select their device from a large list, which then selects the dialect17:23
jonathancit's no worse than any typical device driver on linux or something17:23
jonathanchowever.. if it's implemented on arduino I can see where there would be problems17:26
@kanzurei still want a package manager for pulling in maintained libraries for microcontrollers (including arduinos)17:27
@kanzure"oh just paste in the binary/source code once, you'll be fine"17:27
jonathancwell you'll have to design a package manager for installing the cross compilers first17:28
jonathancsome of which only run on windows17:28
@fenndpkg etc already does that17:28
jonathancused to be that 80% of all 8051 microcontroller code was written on keil compiler/toolchain17:29
* fenn puts his open-source zealot blinders on17:29
jonathancplus those libraries wont run on arbitrary hardware17:29
jonathancthere's 15 firmware engineers taking directions from me and guess how much reusable code they write and how many libraries are created even for in-house use?17:30
jonathancbasically I am saying there is no such thing as a library for microcontrollers unless you want to say a math library is all you want17:31
jonathancthere is no "application library"17:31
jonathancthe firmware is monolithic17:31
DonnchaCpaperbot: https://www.thieme-connect.com/ejournals/abstract/10.1055/s-2004-81597717:31
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/96286a67a3ade429ef9d1804eadab404.txt17:31
@fennhow is a FAT filesystem not reusable?17:31
jonathancwhy is there a FAT filesystem on a microcontroller project?17:32
jonathancthat's pretty dumb imho17:32
@fennso you can read and write to an SD card?17:32
jonathancwhat are you gonna do, stick a floppy disc in your avr?17:32
@kanzurejonathanc: opencv is very much reused everywhere in microcontrollers17:32
@kanzurejonathanc: maybe your firmware engineers suck, by the way.. reusable code is important.17:33
@fennum, opencv? you must be thinking of something else17:33
@kanzureopencv? no i'm thinking of opencv.17:33
jonathancin microcontrollers?  no you are thinking of something else17:33
@kanzurethen what are all these embedded projects doing with opencv17:34
jonathancshow me a FAT filesystem on an 8051 and I will show you a product that didn't sell17:34
@fennkanzure are you thinking of this? http://www.jrobot.net/Projects/AVRcam.html17:34
jonathancmaybe you are thinking of firmware which isn't really firmware.17:35
@fennalso today "embedded" could mean using a cellphone, i guess17:35
jonathancno, a smart phone is not really embedded17:35
@fennwell i dont know what to call it17:35
@kanzuretake qualcomm for example, their firmware surely has at least a few internal libraries.. it seems crazy that libraries are valid everywhere except one area of computing because...? because it's annoying to debug ?17:36
@fennjonathanc: say you have a spectrometer in your lab, how do you get data off it?17:36
jonathanctheir libraries are machine specific17:37
@fennso you have a custom windows driver that plugs into the machine with a serial port? and that's the best we can ever hope for?17:37
@kanzurecross compiling is fake, don't listen to the non-believers!17:37
@kanzurei think i messed that up17:38
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@fenni'm pretty sure there are lab instruments that write to a usb key when you plug it in17:38
jonathancnot sure where you are going with this convo17:38
@kanzureopenpcr :(17:38
@kanzureoh wait openpcr was by sdcard17:38
jonathancembedded has many meanings.  microcontroller is typically something very small memory, lets say 32K17:39
@fennwell anyway, my point was there are reusable chunks of code that have nothing to do with microcontroller-specific hardware, but still need to be implemented on a microcontroller17:39
jonathancsure, lets say usb stack17:39
jonathancor bluetooth stack17:40
jonathancor can bus protocol for ford autos17:40
jonathancor i2c protocol for lm temperature chip17:40
jonathancor even more common17:40
jonathanclets say math library17:40
@fennsure but all of that is implemented in hardware these days17:40
jonathancha wrong17:40
yashgarothok I'm assuming jonathanc is jcline17:41
@kanzurehe is a very good approximation of jonathan cline17:41
jonathancdo you work for a law enforcement agency?17:41
@fennyou'd think he would just /nick jcline17:41
yashgarothI imagine there's very few jonathan C's that know of this channel and electronics17:41
yashgarothme, law enforcement? heh17:42
jonathancsure libraries exist17:42
jonathancbut they are often machine specific, that means optimized, otherwise why "pay" for a library if it is not optimized?17:42
@kanzurehe was using FAT as a common software-implemented thing to argue for libraries i think17:42
@kanzurewell usually a compiler will help you optimize for instruction set quirks17:43
jonathancnot compiler optimization.  more like architecture-driver optimization17:43
@fenni think we're optimizing for coder time17:43
jonathancfor example FAT on a microcontroller is dumb becuase why are directories needed? they are not17:43
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jonathanchence they are not implemented17:43
@fennbut someone already wrote the code so why not17:44
jonathancyea tell me how many you sell by "optimizing for coder time"17:44
jonathancthat's not how you sell product17:44
@fennwho's selling anything17:44
@fenni thought we were making custom lab equipment17:44
jonathancengineering time is cheap if you're producing a million units17:44
jonathancnre cost vs manufacturing cost17:45
jonathanci thought we were making LOW COST equipment for the masses17:45
@kanzurenah.. mostly just for me. others are welcome to do it if they like too.17:45
@kanzure*if they would like to too17:45
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jonathanctell me why you want to optimize for coder time if your goal is to make widely-used equipment?17:45
@fennso, if the difference is using a $0.50 microcontroller instead of a $3 microcontroller, i'm not sure it's worth optimizing17:46
@kanzurebecause i can't be bothered to write custom libraries for the 100s of machines i work with17:46
yashgarothjonathanc: well, assuming it is you, this is max from the carlsbad lab17:46
jonathancIf your device must sell for $3 then it sure the hell is worth optimizing17:46
jonathanchow are you going to sell it for $3 if it costs you $317:46
jonathanchey max17:47
@kanzure$0.50 vs. $3 is nothing compared to the actual lab equipment costs17:47
@kanzures/costs/prices/17:47
jonathanceverything adds into FOB cost17:47
jonathancgo ahead and choose your $3 microcontroller17:47
jonathancthen add in the pcb area to add it in17:47
jonathancthat's where feature creep starts17:48
@kanzureso you believe there are *no* contexts in which libraries make sense for my microcontroller software adventures?17:48
jonathanchow much do you want to pay for openpcr, $599 ?17:48
@fennwhat you call feature creep, i call progress17:48
jonathancwhat you call progress, I call socialism17:48
@kanzurejonathanc: we both know that openpcr was terribly overpriced for what it was anyway17:50
jonathancmax what are you up to?17:50
@kanzurefor its marketing, it was probably priced okay17:50
jonathancopenpcr profit margin was what, 30%?  Work backwards from there to see how it's costs added up. every piece.17:50
@kanzurebut it's no where near an example of lowest cost, compared to the other thermocyclers we've seen out of the community17:50
@kanzurelike wiremound-pcr17:50
yashgarothright now? not much, just got home17:50
@kanzurejonathanc: for one, the chasis made no sense. why was it laser cut? who cares?17:50
@fenni liked the lightbulb in a pvc pipe thingy17:51
@fennhow much did that cost, $10?17:51
jonathancwiremound-pcr, are you kidding.  $85????17:51
jonathancwhy so high???17:51
@kanzurejonathanc: are you trolling?17:51
jonathancno seriously17:51
@kanzurejonathanc: is it so hard to believe that someone can manage 15 engineers inefficiently?17:52
@kanzurewell, the other indicator was the socialism jibe17:52
@fennwiremound is a heatsink with two holes drilled in it and power resistors attached?17:53
jonathancarduino mini17:53
@kanzureyeah, stacey made some suspicious choices on that one17:54
@fennffs is there any official documentation on this17:54
@fenni was confused, the heatsink is openpcr17:54
@kanzurewell, no, there was an instructables thing and then i put some of the copy-pasted source code somewhere https://github.com/kanzure/wiremound-pcr17:54
@kanzure(i was no-ing the documentation question)17:55
@fennokay, the box with the gigantic dna helix picture laser cut on the side, what is that called17:55
jonathanc$85, so arduino mini costs $15 of that17:55
jonathancI dunno should be able to do it in a PIC12F508 which costs $1.00 or so17:59
jonathancoptimize that down and there is no library17:59
jonathancthere are no functions, there is only main()17:59
@fenn2 resistors ($10), arctic silver epoxy ($14), solid state relay ($8.50), MAX31885 breakout board ($17.50), thermocouple wire ($10) and various hardware17:59
jonathancthere is no stack17:59
@kanzureno stack?17:59
@kanzurehm18:00
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jonathanc2 stack levels, in hardware not software18:00
jonathanccall depth more than 2 causes exception reset to save the processor18:00
jonathancthat's optimization18:00
@fennjonathanc: people use the arduino because it's pre-built and has a usb bootloader18:00
@fennthe idea is to make it something people can build without a full electronics lab with board production capability18:01
@fennyou start optimizing from the beginning and there's no room for improvement18:02
jonathancwell an 8 pin processor which only requires 1 resistor and 1 capacitor to complete does not really need board production...18:02
@fennyeah well how do you program it18:02
jonathancwith a programmer of course, common equip18:02
@fennso, call me spoiled but i'd like at least some kind of status indicator showing how much time is left in the PCR cycle18:04
jonathancsave resources by saving $$18:04
@kanzurealso why would it be taking 15 engineers to make a thermocycler?18:04
@kanzurei'm probably grumpy. i've been writing a caching server all day.18:05
jonathancthe socialism comment relates to "the public paying" rather than allowing price (capitalism) to dictate success18:06
jonathanc"well let's just be lazy and optimize for my time, and let the end user pay for my lack of optimization skills"18:06
jonathancto paraphrase18:06
@fennprice isn't the only variable; if price were the only thing that mattered, people would still be doing PCR by hand with water baths18:06
@kanzureno, in that scenario i am my own user18:06
@fennanyway i stick to my position of optimizing for coder/hacker time18:07
@kanzurein a stackless architecture i think you could still possibly use libraries if your compiler is good18:08
jonathancwhat is the library going to do? there's only 1024 bytes of memory.18:08
jonathancthere is only 1 .c file18:08
jonathancthere is no linker18:08
jonathancthere is no .ld file18:08
@fennwhat kind of broken system are you using18:08
jonathanchaha18:08
@fennffs man join this millennium18:08
@fennwhy even bother with C if there's no linker and you can't port your code18:09
jonathancthe code is portable to a chip with similar architecture18:09
@fennjust do it in raw bytecode, it's the most optimal18:09
@kanzureyeah we should hire 100 engineers to stare at hex editors all day18:10
@kanzureanyone who can't write in raw hex is fired18:10
jonathancit depends on how much % you save18:10
jonathancassembly vs C only saves 1-3% in most cases with this stuff18:10
jonathancthat's why risc is so good18:10
@fennso i think we've firmly established that optimizing the controller will at best save 20% of the project cost for our example project (wiremound-pcr)18:12
jonathancthere's more that could be saved I think18:13
jonathancthermocoupler dealio could be cut as well18:13
@fennbut there's still all sorts of costs unaccounted for: mechanical fabrication assembly and testing18:14
@fennparts procurement, "marketing"18:14
jonathancmax31885 why?18:14
jonathancmechanical, you guys would have to comment on18:15
@fennsomething about bandgaps changing with ambient temperature.. i didnt design it18:15
jonathanclemme guess you want to use the pid c++ library next18:16
@kanzurewhich library?18:16
jonathanccheese ball library previously discussed on the group18:17
jonathancused by openpcr I think18:17
@kanzurehow much of openpcr was adobe air?18:17
jonathancagain with same rationalization "trying to save developer time"18:17
@fennprobably this http://playground.arduino.cc/Code/PIDLibrary18:17
@kanzureadobe air was not rationalized by "saving developer time".. it was "saving time so i don't have to become a developer".18:17
@kanzureactually wait that doesn't make sense, josh can write code18:18
@kanzurewtf18:18
@kanzurewhy did josh let openpcr use adobe air?18:18
@fennwhy would anyone use adobe air18:18
@fennyou still have to write code, right?18:19
@fennThe Adobe AIR runtime enables developers to deploy standalone applications built with HTML, JavaScript, ActionScript, Flex, Adobe Flash Professional, yadda yadda yadda18:19
@kanzureand then you add this proprietary pile of crap in between you and your code too18:19
@kanzureand then your users have to use it too because you're sadistic or something18:19
@kanzure"To bring the age of the biological computer to a much speedier reality, Endy and his team have contributed all of BIL gates to the public domain so that others can immediately harness and improve upon the tools."18:20
@fennwhy not just implement a web server on the device and have it serve up all that fancy html18:20
@kanzurepaperbot: http://www.sciencemag.org/content/early/2013/03/27/science.123275818:21
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/9eeb0dfaf790e08cc2bcd8433b656816.txt18:21
@kanzureoh ffff18:21
@kanzurefuck aaas18:21
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@kanzureeast bay diybio meeting notes http://ec2-107-21-158-78.compute-1.amazonaws.com/wiki/index.php/General_Meeting_3/29/1319:18
@kanzurehttp://docs.google.com/document/d/1lDLnSkcqjfKTrSMu1SE2RdejCbxehzo786py3WbDo8c/edit19:18
@kanzurestalk: Patrik D'haeseleer, Shanee Stopnitzky, Ryan Bethencourt, Matt Harbowy, Jason Euren, Javier, Romy Ilano, Ron Shigeta, Marc Juul19:18
jonathancthe thing about an $85 fan-based thermocycler is this:   at any hardware store for $25 there's a space heater with 1500 BTU and heating element and fan in a great case with great user controls.  only $25.19:22
jonathancbio kids have $25 not $85.19:23
jonathanc$25 including manufacturing and even UL approval.19:23
jonathancand marketing and box and retail stickers.19:23
jonathancIf the overhead is removed let's say the product retail price drops $5-7 or so19:24
jonathancdo direct sale and drop another $4-519:24
jonathanchere's a much better one. Heater Project by Mike Pearce19:27
jonathancFrom readme.txt: The Heater 3 project is used to control waterbath heaters and other specialist temperature controlled equipment within the Chemistry Department.19:27
jonathancThis project combines the use of the 1-wire routines, serial routines, a P.I.D (Proportional, Integral, Derivative) calculation, ADC, and a interrupt driven burst mode heater control.19:27
jonathancEntire archive. Download (158KB).19:27
jonathanchttp://www.microchipc.com/sourcecode/PIC_Hi-Tech_C_Mike_Pearces_heater_project.zip19:28
jonathancthe "libraries" are .c files19:28
@kanzureyes, what else would they be? magic?19:29
jonathanc.a19:29
jonathancwith linker file19:29
@kanzureok good point19:30
jonathanchere, it is monolithic19:30
@kanzurethere are many other environments where libraries are pulled in with source19:30
jonathancyou can see from the source that it is not appropriate to make these into libraries19:30
* kanzure looks19:30
jonathancfor optimization, the code uses registers etc, and the delay loop for example, requires specific architecture for clock cycles19:31
@kanzurechecksum.c seems fairly standard, but i haven't finished reading its preamble19:31
jonathancthe 1-wire protocol for example is relatively portable except maybe 20 lines would need modification, for example you do not abstract the i/o pins in real embedded code, you reference them directly19:31
jonathanci.e. linux would create some structure blah blah to set an io pin shadow register which later the lower layer driver then pushes to the hardware blah blah overhead19:32
jonathancin fact during a code review this week we will restructure code to remove abstraction purposely because the flash is 92% full19:33
@kanzureoh look someone is bothering to do code reviews. great.19:33
jonathancto switch to another micro with bigger memory is the next step up in chip cost which ultimately impacts end user cost19:33
jonathancin a comp sci project these abstraction layers would be added not subtracted19:34
jonathancbecause resources are infinite.19:34
@kanzurenobody said it's a comp sci project19:34
@kanzureyou don't need comp sci to see that checksum.c is pretty standard19:34
jonathancdate time19:35
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@kanzuredid i fail his test?19:35
@kanzureoh he means it's time for a date, not... okay.19:36
@kanzurethe clock/timing issue is legitimate, because you need to be careful about which functions you either call/include that might block for too long, but that's always been the case.19:37
@kanzureand perhaps you could say that such a library manager shouldn't be used for stackless architectures.. but there's still lots of microcontroller environments that have more resources available.19:39
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@kanzurehttp://sudoroom.org/wiki/Biohacking19:49
@kanzurehttp://sudoroom.org/wiki/Projects#Biology_Projects19:49
@kanzurehttp://ec2-107-21-158-78.compute-1.amazonaws.com/wiki/index.php/Main_Page19:49
@kanzurehah there's a bit of an obsessive list of hackerspaces that tried crowdfunding here http://ec2-107-21-158-78.compute-1.amazonaws.com/wiki/index.php/Fundraising_Ideas19:50
@kanzure"unallocated space".. heh.19:51
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@kanzureJuul: meeting update?19:57
Juulkanzure, right now talking about what kind of space we want and whether we _need_ bsl219:58
@kanzurei think you can't get to bsl2 without bsl1, not sure19:58
Juulyeah19:58
Juuli mean, it depends on the county/city implementation20:01
Juulbut BSL1 requirements as I've seen them are a subset of BSL2 requirements20:02
@kanzurejust gotta map out the zoning laws20:04
Juulhmm20:04
Juulwe have a couple of people working on that20:04
Juuli think the result will be that we should go for oakland20:09
Juulit seems like they may have little/no regulation20:09
browniesoakland eh?20:10
Juulyep20:12
@kanzureit's weird that this was from 2004 http://www.futureofwipo.org/futureofwipodeclaration.html and it mentions wikipedia. wikipedia wasn't that big in 2004. it wasn't exactly a stellar example.20:37
@kanzureit would be a more relevant example since maybe 2007.20:37
browniesi was using wikipedia in '0420:43
brownies...before it went mainstream...20:43
@kanzurewe all were.. but it wasn't exactly something worth mentioning to the World Intellectual Property Organization if you wanted them to understand wtf you're talking about?20:44
@kanzurein 2004.20:44
ParahSail1npaperbot: http://www.sciencedirect.com/science/article/pii/S001910351300079120:47
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/The%20Wow%21%20signal%20of%20the%20terrestrial%20genetic%20code.pdf20:47
ParahSail1naliens in ur dnas20:47
ParahSail1ni think the ! in the file name broke the python20:48
ParahSail1nah, nevermind, it just took a while to get pdfparanoia'd20:48
@kanzurewow i just realized your github username20:57
@kanzurei don't know why that wasn't more obvious20:57
@kanzureit would be more useful if i could make these realizations while i am reading your bug reports20:59
@kanzureyou even used your name.. how did i miss that?21:00
ParahSail1nyeah, that's more of a "professional" username21:07
@kanzureheh21:09
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@kanzurepaperbot: http://users.ece.cmu.edu/~aavgerin/papers/mayhem-oakland-12.pdf22:05
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/e35c98abc8251f971cb1952d115c656b.txt22:05
@kanzurepaperbot: http://users.ece.cmu.edu/~ejschwar/papers/usenix11.pdf22:05
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/d1033e87cf00119c59ec698d23a2eac3.txt22:05
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jonathancmicrocontroller libraries http://mbed.org/explore/22:09
@kanzurehttp://moflow.org/#%5B%5BReference%20Library%5D%5D22:09
@kanzure.title22:09
yoleaux.: moflow :. - software security workflow22:09
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diginetdid anyone mirror the NTRS before it got taken down?22:10
@kanzurelink?22:10
diginetthe NASA technical report service22:10
@kanzurethe whole thing was taken down? those guys have balls. they are really trying to make a statement huh.22:10
diginetthey got paranoid because they realized people were actually reading things they put on the internet22:11
diginetI'm still trying to figure out a way that makes any sense22:11
@kanzureno it's because of sequestration. nasa has been canceling all sorts of public programs to make people angry.22:11
diginetare you sure? I read several news reports that it got shut down as a response to the fact that some Chinese national had been mass downloading docs from the server22:12
@kanzurethat's... interesting.22:12
@kanzureoh no somebody might be actually using our site, pull the plug22:12
diginetyeah, it's mind-numbingly stupid22:12
@kanzurejonathanc: is this a commercial product? what's going on here?22:12
@kanzurehmm http://mbed.org/handbook/Homepage22:13
@kanzurewhat are the target architectures?22:13
@kanzure"Prototype to hardware - How to move from your mbed prototype to your custom PCB."22:13
diginet"we fear people might be reading stuff we put on the internet for people to read"22:14
@kanzureare they selling only their own chips here?22:14
diginetmbed is ARM22:14
jonathanctarget soc is arm-based22:14
@kanzurei see. well that's nice.22:14
jonathancarm cortex is popular22:14
jonathanc32-bit22:14
@kanzureif they are a business, what is their model? selling devkits? support?22:14
jonathanclow power, reduced instruction set22:14
diginetreduced instruction set?22:14
jonathancsoc vendors fund sw dev22:14
diginetin name only22:14
jonathanci have a freescale board in front of me22:14
diginetthe RISC/CISC distinction is all but meaningless these days22:15
jonathancno, the cortex really is reduced instruction set22:15
@kanzuresoc vendors fund sw development because "maybe the developers will use our socs" ?22:15
jonathancyes22:15
@kanzureneat22:15
@kanzureassuming this works. i should play with this.22:15
@kanzurethis looks better than that bugslabs bullshit.22:15
jonathancdude soc vendors funded major eclipse dev effort22:15
@kanzureeclipse is like pure evil22:15
jonathancit is what it is, at least it works22:16
@kanzureheh22:16
digineteclipse is like "let's see just how shitty we can make our dev environment, you know, for fun"22:16
jonathancit is a common rallying point22:16
diginetRISC has not been a relevant argument in at least 15 years22:16
@kanzuretrue, eclipse is very good at getting attention22:16
jonathancits goal was to run on linux eh22:16
diginetRISC predates Linux22:17
jonathancarduino killer http://www.freescale.com/webapp/sps/site/prod_summary.jsp?code=FRDM-KL25Z&tid=vanFRDM-KL25Z22:17
diginetit was designed with the fact that developers were abandoning directly coding in asm for "high-level" (for the time) languages like C22:17
jonathanc$13 for the board, includes onboard jtag debugger22:18
diginetor you could, you know, just use the chip22:18
jonathancfreescale also supplies rtos22:18
diginetplenty of open source ones22:18
jonathancimportant feature is usb otg22:19
jonathancwith enough flash to actually embed a usb stack22:19
diginetugh, I'm so sick of the arduino bullshit22:19
jonathancalthough i'd have to see proof of that22:19
diginetjust use an AVR22:19
diginetit's simple22:20
diginetand much cheaper22:20
jonathancor dump avr and get a real chip you mean22:20
diginetI don't care for AVR, but pick your poison22:20
diginetI'm just sick of overpriced, glorifed dev boards22:20
jonathancwhatever.  you wont be able to make it for under $1022:21
diginetAVRs cost like $122:21
jonathanci'm talking about kinetis board, not an avr breakout board22:22
diginetoh22:22
jonathancadafruit obviously has a huge profit margin22:23
jonathanclike lego22:23
jonathancinfineon has a similar setup now too, also reduced footprint arm22:29
jonathancthey have these funky boards which are hexagonal and plug in together, rather than stackable22:31
jonathancthis is it http://www.freertos.org/FreeRTOS-for-Infineon-XMC4000-Cortex-M4.html22:32
jonathancinfineon's mini stick shaped boards and their hex boards http://www.infineon.com/cms/en/product/microcontrollers/32-bit-xmc4000-industrial-microcontrollers-arm®-cortex™-m4/xmc4000-development-tools,-software-and-kits/channel.html?channel=db3a30433580b3710135a0790288387222:36
@kanzureif anyone cares i've dumped some more security things into here http://diyhpl.us/~bryan/papers2/security/22:36
jonathancdude what a crazy url, it has the copyright symbol and tm mark in the url. that's whack22:36
@kanzurethey just want to make sure your browser is utf8 compliant, haha22:37
jonathancgoogle XMC Development Tools, Software & Kits22:37
@kanzureyou knew about mbed earlier tonight?22:37
jonathanci've had this board for a while22:37
jonathancdid an rtos evaluation a couple months back22:38
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@kanzureany complaints?22:38
jonathancproblem with mbed is it is online development22:38
@kanzurewhat why22:38
jonathancwell i told you about the toolchain problem22:39
jonathanchow are you going to compile a library if you can't get the toolchain without a $3000-per-seat license?22:39
jonathancthe "free" toolchain is online, i.e. virtual license supported by the vendors22:40
jonathancwho knows how long it will last22:40
jonathancintel had a similar system when the 80960 came out22:40
jonathanclog in, compile embedded code for 80960j I think it was, get the static binary, then burn to local board22:40
jonathancthey don't want to kill the 3rd party dev companies which make the toolchains, then they will be s.o.l.22:41
jonathancanother limitation with mbed is it is nxp which I'll never use again22:41
jonathancalso, while freescale does give away the rtos, and it is a really good rtos, it is only to be used on their own soc, not on others22:43
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jonathanccheck this one http://www.kickstarter.com/projects/paulstoffregen/teensy-30-32-bit-arm-cortex-m4-usable-in-arduino-a22:44
jonathancsame freescale chip.  freescale is solid but tries to lock in via offering software for their chip only, same story as always22:45
jonathancfunny quote  "...the Galago might just be the perfect ARM board for tinkerers weaning themselves off the Arduino."    "...the Galago might just be the perfect ARM board for tinkerers weaning themselves off the Arduino."22:47
jonathancgalago uses the same nxp chip as the mbed platform  http://www.kickstarter.com/projects/kuy/galago-make-things-better22:47
@kanzurethe arm toolchains are $3k/seat?22:48
jonathancdepends on the jtag22:48
@kanzuredoesn't llvm target arm just fine?22:49
jonathanci don't know if it does cortex instruction set or not22:53
jonathancthis is a different isa22:53
jonathancisa=instruction set architectur22:54
jonathancisa=instruction set architecture22:54
@kanzurearm cortex is not normal arm isa?22:54
@kanzurei should probably look into this huh22:54
jonathanccortex is reduced set like I said22:55
jonathanceither way it basically kills avr so why bother with that I dunno22:56
jonathancmore libraries for you http://www.pjrc.com/teensy/td_libs.html23:02
jonathanc"Linaro is a not-for-profit engineering organization consolidating and optimizing open source Linux software and tools for the ARM architecture."   http://www.linaro.org/23:04
@kanzurethat's quite a string of words23:05
@kanzureoh i see i can read it now23:05
@kanzureseems to be an industry consortium thing23:06
jonathancthis is the toolchain for the arm cortex apparently23:06
jonathanchttps://launchpadlibrarian.net/126639247/readme.txt23:06
jonathanc-mthumb -mcpu=cortex-m323:06
jonathanc-mthumb -mcpu=cortex-m423:06
jonathanclink https://launchpad.net/gcc-arm-embedded/4.7/4.7-2012-q4-major23:07
jonathancI am spoiled because I haven't used gcc in years now, thank darwin23:07
jonathancthere's something to be said for buying a commercial toolchain and just building, vs all kinds of bootstrap junk with gnu23:08
jonathancthis is a pretty sweet cortex board too, teensy 3.0 https://www.sparkfun.com/products/1178023:09
jonathancI played with teensy 2.0 when it came out (avr) but a little too slow and limited chip.  a great starter for beginners though, drag-and-drop firmware download interface is neat23:10
jonathanctoolchain install is a gnu p.o.s. though23:10
jonathancmbed nxp soc board  from sparkfun  https://www.sparkfun.com/products/956423:12
jonathanc$60, that aint cheap23:13
jonathancin that case, UBW32 is a better option23:14
@kanzuremaybe the open source options wouldn't suck so much if companies were actually trying to make something usable that doesn't cost $50k/seat23:16
jonathancwhat do you mean23:17
jonathancdudes get a lot done with the iar toolchain here23:21
jonathanctons done23:21
jonathancactually work on the project instead of working on makefile hell23:22
jonathancchange linker params in a couple minutes compared to .ld nonsense23:22
jonathancfor the cost of 2 weeks employment, gain more than that back in productivity23:23
jonathancplus a much better optimizer for sure23:24
@kanzure:fear: http://www.libcrack.so/2012/10/13/hacking-the-ar-drone-parrot/23:24
@kanzuresomeone is offering a rom dump sometime tomorrow. can't wait to start picking at it.23:26
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jonathancI found out from the director of sweng at the office that another hw/sw development office of ours was using  UBW boards like crazy for development, same as our office23:35
@kanzurei am being distracted by security things at the moment. this stuff is like candy to me. :(23:35
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--- Log closed Sat Mar 30 00:00:42 2013

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