--- Log opened Fri Mar 29 00:00:41 2013
00:09 <@kanzure> oh look
00:09 <@kanzure> there's a prusa3
00:09 <@kanzure> https://github.com/josefprusa/Prusa3
00:09 <@kanzure> and it has thingdoc documentation
00:09 <@kanzure> https://github.com/josefprusa/Prusa3/blob/master/box_frame/common.tdoc
00:10 <@kanzure> /box_frame/inc looks like a primitive library system :\
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01:40 < BioGuy> Anyone alive at this hour?
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03:13 < archels> only the Euros and kanzure
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07:31 < diginet> I'm not interested in it for biological applications, but what is there in the way of DIY microfluidics
08:02 < superkuh> paperbot: http://www.nature.com/nature/journal/v495/n7442/full/nature11990.html
08:03 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/X-ray%20analysis%20on%20the%20nanogram%20to%20microgram%20scale%20using%20porous%20complexes.pdf
08:03 <@ParahSailin> diginet: not much
08:04 < diginet> ParahSailin: couldn't you just use standard lithography techniques but on glass? (I guess HF as the etchant)
08:04 < diginet> not that litho is "easy," but it's not impossible, and we're not talking nanoscale here
08:08 <@ParahSailin> for glass you wouldnt even have to go to hf unless you were really in a hurry
08:09 < diginet> what else could you use?
08:09 < diginet> (for wet etching anyhow, not really interested in plasma etching)
08:10 <@ParahSailin> tmah could probably do it in a reasonable time, regular ammonia would do it a bit slower
08:10 < diginet> interesting
08:10 <@ParahSailin> strong acids will etch glass too
08:11 <@ParahSailin> just look up the etch rate you want to see which is most acceptable
08:11 < diginet> like which ones? I thought HF was the only common acid that etched glass
08:11 < diginet> although I know hot phosphoric acid will
08:11 < diginet> what 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)
08:14 <@ParahSailin> its a question of rate, a lot of stuff will etch glass, but HF is the fastest
08:14 < diginet> I see
08:16 <@ParahSailin> HF is probably the most practical
08:19 < diginet> well HF does have the advantage of not attacking plastics (in general), I've heard of people making DIY photopolymer plates
08:20 < diginet> maybe I could use those as a resist
08:21 <@ParahSailin> photoresist works
08:22 < diginet> like SU-8? isn't that really pricey though?
08:24 <@ParahSailin> the regular novolac kind
08:24 < diginet> where do you find that?
08:25 < diginet> I've been looking for novolac for ages (for other stuff)
08:28 < diginet> novolac, like bakelite right?
08:29 <@ParahSailin> what, no, like AZ[0-9]*
08:30 < diginet> bakelite was a phenolic resin, as I understand it so is novolac, right?
08:47 <@ParahSailin> yes
08:55 <@kanzure> https://github.com/SpiderLabs/BurpNotesExtension
08:55 <@kanzure> https://github.com/aglane for a UPnP browser soonish
08:58 <@kanzure> opencascade 6.5.5 has been released
09:14 <@ParahSailin> paperbot: http://pubs.acs.org/doi/abs/10.1021/bi9809425
09:14 < paperbot> error: 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.pdf
09:15 <@ParahSailin> i wonder if idt has done secret experiments more recently to make their oligoanalyzer more accurate
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09:16 <@kanzure> maradydd would be the person to talk with about that (since she worked at idt for a while and then repented to diybio)
09:18 <@kanzure> paperbot: http://www.nature.com/news/taking-the-crystals-out-of-x-ray-crystallography-1.12699
09:18 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/788fffaa32f2b8b8118aa1d28c521831.txt
09:18 <@kanzure> wait.. /news :(
09:18 <@kanzure> paperbot: http://www.nature.com/nature/journal/v495/n7442/full/nature11990.html
09:18 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/X-ray%20analysis%20on%20the%20nanogram%20to%20microgram%20scale%20using%20porous%20complexes.pdf
09:20 <@kanzure> "We demonstrate that as little as 80 nanograms of a sample is enough for X-ray single-crystal diffraction analysis."
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09:36 <@ParahSailin> wow thats pretty big
09:38 <@ParahSailin> oh, they only did small molecules
09:39 < superkuh> There is talk about proteins too.
09:39 < superkuh> http://www.sciencemag.org/content/336/6084/1018.full
09:39 < superkuh> paperbot: http://www.sciencemag.org/content/336/6084/1018.full
09:39 < paperbot> error: HTTP 300 http://diyhpl.us/~bryan/papers2/paperbot/Large-Pore%20Apertures%20in%20a%20Series%20of%20Metal-Organic%20Frameworks.pdf
09:40 <@ParahSailin> well there is no mention of peptide or protein in that nature one
09:41  * superkuh nods.
09:45 <@ParahSailin> paperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1277807/
09:45 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/b5f68ff1cd1f5306a7f3a0aab50f9fa3.txt
09:45 <@ParahSailin> paperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1277807/pdf/gki918.pdf
09:45 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/7bcc57d4c29ce24a4b3d856414ae0089.pdf
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11:03 <@ParahSailin> paperbot: http://pubs.acs.org/doi/abs/10.1021/bi034621r
11:03 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Effects%20of%20Sodium%20Ions%20on%20DNA%20Duplex%20Oligomers%3A%20Improved%20Predictions%20of%20Melting%20Temperatures.pdf
11:04 <@kanzure> wasn't there also a thing about hairpins increasing the melting temperature
11:13 <@ParahSailin> im not sure how that would affect it if you have the exact complement to duplex with
11:14 <@ParahSailin> should have some sort of effect
11:15 <@ParahSailin> this stuff is actually me using paperbot for work related stuff
11:17 <@kanzure> work is too cheap to buy subscriptions?
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11:56 <@ParahSailin> paperbot: http://pubs.acs.org/doi/abs/10.1021/bi962590c
11:56 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Thermodynamics%20and%20NMR%20of%20Internal%20GT%20Mismatches%20in%20DNA.pdf
11:59 <@ParahSailin> i couldnt condone paying these crooks on principle
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13:31 <@ParahSailin> paperbot: http://pubs.acs.org/doi/abs/10.1021/bi702363u
13:31 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Predicting%20Stability%20of%20DNA%20Duplexes%20in%20Solutions%20Containing%20Magnesium%20and%20Monovalent%20Cations.pdf
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14:01 <@kanzure> bah ipython has closed my pull request
14:01 <@kanzure> https://github.com/ipython/ipython/issues/1286
14:01 <@kanzure> https://github.com/ipython/ipython/issues/2895
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14:53 <@kanzure> "East Bay DIYbio meeting 6pm at Sudoroom"
14:53 <@kanzure> win 5
14:53 <@kanzure> fidjklada
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15:38 <@kanzure> http://news.yahoo.com/blogs/this-could-be-big-abc-news/teen-scientist-amazing-breakthrough-her-home-lab-165831291.html
15:38 <@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 <@kanzure> i wonder what selection procedure this was
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16:00 <@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 <@kanzure> blah i can't remember the right links that debunk this
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16:07 < jonathanc> buy more guns
16:09 < chris_99> ?
16:15 <@fenn> our sponsor, the NRA
16:17 <@kanzure> jonathanc: hello
16:17 <@kanzure> jonathanc: welcome back
16:17 <@kanzure> also i think your yaml>xml stance is respectable
16:22 < jonathanc> gcode vs. ?
16:29 <@kanzure> context?
16:36 < jonathanc> ""Cool presentation and I want one of those things to make an incubator
16:36 < jonathanc> for the repstrap I am building with Tecan/Biomek like attributes, I
16:36 < jonathanc> got a  ... blah blah .. Anyway the repstrap firmware, I am planning on using Marlin which
16:36 < jonathanc> processes Gcode. I guess at first I will have the gcode thing going on
16:36 < jonathanc> for position control of steppers and some way to send commands  ....""
16:36 <@kanzure> ah, well at least he's not writing his own gcode firmware
16:38 <@kanzure> i think you can wire up linuxcnc directly to your actuators without a gcode intermediate
16:39 < jonathanc> i could just implement multiple command sets on my device.  auto-detect g-code and then switch to that, easy.
16:39 <@kanzure> i don't think re-implementing gcode every time one of us makes anything that moves is a good use of our time
16:40 < jonathanc> meh, that only takes a day
16:41 <@kanzure> but then you end up with lots of implementations that have poor edge case handling
16:41 <@kanzure> what'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..
16:45 < jonathanc> Seems to me that gcode is pretty simple as an API
16:45 <@kanzure> fenn: ping?
16:46 < jonathanc> simple/dumb
16:47 <@kanzure> oh wow linuxcnc is unable to find a grammar for gcode
16:47 <@kanzure> http://www.mailinglistarchive.com/html/emc-users@lists.sourceforge.net/2012-02/msg00984.html
16:47 <@kanzure> there are "extensions" that must be allowed in real-time? what is this.
16:48 <@kanzure> fenn is our resident linuxcnc developer and gcode user so i imagine he might know more specifics than i do
16:48 < jonathanc> is this what happens when meche's attempt to program?
16:49 <@kanzure> well afaik gcode was never really standardized with a grammar and it just "sort of happened"
16:51 < jonathanc> hence my curiousity regarding alternatives to gcode
16:52 < jonathanc> although 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 deal
16:53 <@fenn> jonathanc: have you considered stealing large chunks from grbl?
16:53 <@fenn> of code*
16:54 <@kanzure> also if you really do have that file it would be nice to put it somewhere on the internets
16:54 <@fenn> kanzure: the reason for lack of standardization is vendor lock-in
16:54 <@fenn> there's a perfectly good standard published by nist (RS274-NGC) but nobody implements it
16:55 < jonathanc> well 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 grbl
16:56 < jonathanc> I assume devices do not have to implement all g-code commands if they do not support them anyway
16:57 <@fenn> here'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 < jonathanc> simply, gimme a break, these commands are just turning on a motor or turning it off...  if the complex coordinate stuff is ignored
16:58 <@fenn> oh. in context http://fennetic.net/irc/emc3/src/emc/interpreter/rs274ngc/rs274ngc.ast.g
16:59 < jonathanc> excellent
16:59 <@fenn> i'm not sure if that's actually correct; it was in the early stages of development
16:59 < jonathanc> ok, i'll use it as a cross reference
17:01 <@fenn> i'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 <@kanzure> this doesn't seem to explain all the "gcode extensions" stuff. it seems to also support functions and it has to have a vm?
17:02 < jonathanc> because arduino is a toy?
17:02 <@fenn> well, any avr
17:02 <@fenn> if it's against your religion, i guess that's an answer
17:02 < jonathanc> well 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 it
17:03 <@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 < jonathanc> g-code is just an api
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17:04 <@kanzure> http://www.linuxcnc.org/docs/devel/html/remap/structure.html#_introduction_extending_the_rs274ngc_interpreter_by_remapping_codes
17:04 <@kanzure> uhh "Embedded Python functions in the Interpreter started out as glue code, but turned out very useful well beyond that."
17:04 <@fenn> kanzure: 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 language
17:04 <@kanzure> is python the lipstick or the pig?
17:04 <@fenn> g-code is the pig, fancy programming tricks is the lipstick
17:05 <@kanzure> also, it would be nice to have something that is not subject to vendor-lockin-guided-evolution
17:05 <@kanzure> so even if you want to use gcode, why not just publish a grammar, then a specific standard, and just say let's use that subset
17:06 <@kanzure> fenn: 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.
17:07 <@fenn> i dont know, i've never used any of the embedded python stuff
17:08 <@fenn> also you keep asking for a standard, but there is a standard, published by a standards organization, with a grammar, and a reference implementation of that
17:08 <@fenn> so i dont know what more you want
17:09 <@fenn> google "nist rs274 production rules", the PDF has basically the same as what was in that antlr file i linked to earlier
17:09 <@kanzure> well, 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?
17:10 <@fenn> because nobody follows the standard
17:10 <@kanzure> because there's no reference implementation?
17:10 <@fenn> no, because the reference implementation wasn't good enough, so people extended it, and now nobody uses the original version
17:10 <@fenn> that's what linuxcnc is
17:11 <@fenn> then you have all the other vendors, whose names i forget now
17:12 <@fenn> anyway the core stuff like G0 G1 G2 is almost always the same
17:12 <@fenn> some 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 that
17:13 <@kanzure> because people chose not to use a parser parser?
17:13 <@fenn> so there's a thing called a post-processor, which takes a config file for your specific target machine and makes it work
17:14 <@fenn> it capitalizes the letters or adds zeroes to the end of numbers or whatever
17:14 <@kanzure> haha grand, i wasn't aware that there are gcode postprocessors
17:14 <@fenn> it's usually part of the CAM program
17:15 <@fenn> there are people who make a living installing these config files :\
17:15 <@kanzure> i 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 <@fenn> it's not optimization, it's for compatibility with crap written 50 years ago
17:16 <@fenn> punch cards man
17:16 <@fenn> NC came first, then CNC. originally there was no computer in the loop
17:16 <@kanzure> i'm aware.
17:17 <@fenn> a "toy" arduino is a supercomputer in comparison
17:18 < jonathanc> well like I said, still simple compared to mucking with proprietary/standard internet protocol differences, so it is no big deal
17:18 < jonathanc> doesnt need lex yacc for that
17:19 < jonathanc> the trick would be to detect which dialect is required and then change on the fly
17:19 < jonathanc> by querying things on the device for example
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17:20 <@fenn> how do you query a brain-dead serial protocol?
17:21 < jonathanc> well from my superficial reading, gcode has registers that you can read, right.  so that's one way.
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17:22 < jonathanc> alternatively, send it a command, if it responds with errors, then go down the list until a dialect variant succeeds
17:22 < jonathanc> if it's transmit only with no detected errors, then there's still tricks that can be done
17:23 < jonathanc> power cycle and read registers not yet initialized, see if there are characteristic values
17:23 < jonathanc> worst case, require the end user to select their device from a large list, which then selects the dialect
17:23 < jonathanc> it's no worse than any typical device driver on linux or something
17:26 < jonathanc> however.. if it's implemented on arduino I can see where there would be problems
17:27 <@kanzure> i 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"
17:28 < jonathanc> well you'll have to design a package manager for installing the cross compilers first
17:28 < jonathanc> some of which only run on windows
17:28 <@fenn> dpkg etc already does that
17:29 < jonathanc> used to be that 80% of all 8051 microcontroller code was written on keil compiler/toolchain
17:29  * fenn puts his open-source zealot blinders on
17:29 < jonathanc> plus those libraries wont run on arbitrary hardware
17:30 < jonathanc> there'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?
17:31 < jonathanc> basically I am saying there is no such thing as a library for microcontrollers unless you want to say a math library is all you want
17:31 < jonathanc> there is no "application library"
17:31 < jonathanc> the firmware is monolithic
17:31 < DonnchaC> paperbot: https://www.thieme-connect.com/ejournals/abstract/10.1055/s-2004-815977
17:31 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/96286a67a3ade429ef9d1804eadab404.txt
17:31 <@fenn> how is a FAT filesystem not reusable?
17:32 < jonathanc> why is there a FAT filesystem on a microcontroller project?
17:32 < jonathanc> that's pretty dumb imho
17:32 <@fenn> so you can read and write to an SD card?
17:32 < jonathanc> what are you gonna do, stick a floppy disc in your avr?
17:32 <@kanzure> jonathanc: opencv is very much reused everywhere in microcontrollers
17:33 <@kanzure> jonathanc: maybe your firmware engineers suck, by the way.. reusable code is important.
17:33 <@fenn> um, opencv? you must be thinking of something else
17:33 <@kanzure> opencv? no i'm thinking of opencv.
17:33 < jonathanc> in microcontrollers?  no you are thinking of something else
17:34 <@kanzure> then what are all these embedded projects doing with opencv
17:34 < jonathanc> show me a FAT filesystem on an 8051 and I will show you a product that didn't sell
17:34 <@fenn> kanzure are you thinking of this? http://www.jrobot.net/Projects/AVRcam.html
17:35 < jonathanc> maybe you are thinking of firmware which isn't really firmware.
17:35 <@fenn> also today "embedded" could mean using a cellphone, i guess
17:35 < jonathanc> no, a smart phone is not really embedded
17:35 <@fenn> well i dont know what to call it
17:36 <@kanzure> take 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 <@fenn> jonathanc: say you have a spectrometer in your lab, how do you get data off it?
17:37 < jonathanc> their libraries are machine specific
17:37 <@fenn> so 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 <@kanzure> cross compiling is fake, don't listen to the non-believers!
17:38 <@kanzure> i think i messed that up
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17:38 <@fenn> i'm pretty sure there are lab instruments that write to a usb key when you plug it in
17:38 < jonathanc> not sure where you are going with this convo
17:38 <@kanzure> openpcr :(
17:38 <@kanzure> oh wait openpcr was by sdcard
17:39 < jonathanc> embedded has many meanings.  microcontroller is typically something very small memory, lets say 32K
17:39 <@fenn> well 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 microcontroller
17:39 < jonathanc> sure, lets say usb stack
17:40 < jonathanc> or bluetooth stack
17:40 < jonathanc> or can bus protocol for ford autos
17:40 < jonathanc> or i2c protocol for lm temperature chip
17:40 < jonathanc> or even more common
17:40 < jonathanc> lets say math library
17:40 <@fenn> sure but all of that is implemented in hardware these days
17:40 < jonathanc> ha wrong
17:41 < yashgaroth> ok I'm assuming jonathanc is jcline
17:41 <@kanzure> he is a very good approximation of jonathan cline
17:41 < jonathanc> do you work for a law enforcement agency?
17:41 <@fenn> you'd think he would just /nick jcline
17:41 < yashgaroth> I imagine there's very few jonathan C's that know of this channel and electronics
17:42 < yashgaroth> me, law enforcement? heh
17:42 < jonathanc> sure libraries exist
17:42 < jonathanc> but they are often machine specific, that means optimized, otherwise why "pay" for a library if it is not optimized?
17:42 <@kanzure> he was using FAT as a common software-implemented thing to argue for libraries i think
17:43 <@kanzure> well usually a compiler will help you optimize for instruction set quirks
17:43 < jonathanc> not compiler optimization.  more like architecture-driver optimization
17:43 <@fenn> i think we're optimizing for coder time
17:43 < jonathanc> for example FAT on a microcontroller is dumb becuase why are directories needed? they are not
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17:43 < jonathanc> hence they are not implemented
17:44 <@fenn> but someone already wrote the code so why not
17:44 < jonathanc> yea tell me how many you sell by "optimizing for coder time"
17:44 < jonathanc> that's not how you sell product
17:44 <@fenn> who's selling anything
17:44 <@fenn> i thought we were making custom lab equipment
17:44 < jonathanc> engineering time is cheap if you're producing a million units
17:45 < jonathanc> nre cost vs manufacturing cost
17:45 < jonathanc> i thought we were making LOW COST equipment for the masses
17:45 <@kanzure> nah.. mostly just for me. others are welcome to do it if they like too.
17:45 <@kanzure> *if they would like to too
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17:45 < jonathanc> tell me why you want to optimize for coder time if your goal is to make widely-used equipment?
17:46 <@fenn> so, if the difference is using a $0.50 microcontroller instead of a $3 microcontroller, i'm not sure it's worth optimizing
17:46 <@kanzure> because i can't be bothered to write custom libraries for the 100s of machines i work with
17:46 < yashgaroth> jonathanc: well, assuming it is you, this is max from the carlsbad lab
17:46 < jonathanc> If your device must sell for $3 then it sure the hell is worth optimizing
17:46 < jonathanc> how are you going to sell it for $3 if it costs you $3
17:47 < jonathanc> hey max
17:47 <@kanzure> $0.50 vs. $3 is nothing compared to the actual lab equipment costs
17:47 <@kanzure> s/costs/prices/
17:47 < jonathanc> everything adds into FOB cost
17:47 < jonathanc> go ahead and choose your $3 microcontroller
17:47 < jonathanc> then add in the pcb area to add it in
17:48 < jonathanc> that's where feature creep starts
17:48 <@kanzure> so you believe there are *no* contexts in which libraries make sense for my microcontroller software adventures?
17:48 < jonathanc> how much do you want to pay for openpcr, $599 ?
17:48 <@fenn> what you call feature creep, i call progress
17:48 < jonathanc> what you call progress, I call socialism
17:50 <@kanzure> jonathanc: we both know that openpcr was terribly overpriced for what it was anyway
17:50 < jonathanc> max what are you up to?
17:50 <@kanzure> for its marketing, it was probably priced okay
17:50 < jonathanc> openpcr profit margin was what, 30%?  Work backwards from there to see how it's costs added up. every piece.
17:50 <@kanzure> but it's no where near an example of lowest cost, compared to the other thermocyclers we've seen out of the community
17:50 <@kanzure> like wiremound-pcr
17:50 < yashgaroth> right now? not much, just got home
17:50 <@kanzure> jonathanc: for one, the chasis made no sense. why was it laser cut? who cares?
17:51 <@fenn> i liked the lightbulb in a pvc pipe thingy
17:51 <@fenn> how much did that cost, $10?
17:51 < jonathanc> wiremound-pcr, are you kidding.  $85????
17:51 < jonathanc> why so high???
17:51 <@kanzure> jonathanc: are you trolling?
17:51 < jonathanc> no seriously
17:52 <@kanzure> jonathanc: is it so hard to believe that someone can manage 15 engineers inefficiently?
17:52 <@kanzure> well, the other indicator was the socialism jibe
17:53 <@fenn> wiremound is a heatsink with two holes drilled in it and power resistors attached?
17:53 < jonathanc> arduino mini
17:54 <@kanzure> yeah, stacey made some suspicious choices on that one
17:54 <@fenn> ffs is there any official documentation on this
17:54 <@fenn> i was confused, the heatsink is openpcr
17:54 <@kanzure> well, no, there was an instructables thing and then i put some of the copy-pasted source code somewhere https://github.com/kanzure/wiremound-pcr
17:55 <@kanzure> (i was no-ing the documentation question)
17:55 <@fenn> okay, the box with the gigantic dna helix picture laser cut on the side, what is that called
17:55 < jonathanc> $85, so arduino mini costs $15 of that
17:59 < jonathanc> I dunno should be able to do it in a PIC12F508 which costs $1.00 or so
17:59 < jonathanc> optimize that down and there is no library
17:59 < jonathanc> there are no functions, there is only main()
17:59 <@fenn> 2 resistors ($10), arctic silver epoxy ($14), solid state relay ($8.50), MAX31885 breakout board ($17.50), thermocouple wire ($10) and various hardware
17:59 < jonathanc> there is no stack
17:59 <@kanzure> no stack?
18:00 <@kanzure> hm
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18:00 < jonathanc> 2 stack levels, in hardware not software
18:00 < jonathanc> call depth more than 2 causes exception reset to save the processor
18:00 < jonathanc> that's optimization
18:00 <@fenn> jonathanc: people use the arduino because it's pre-built and has a usb bootloader
18:01 <@fenn> the idea is to make it something people can build without a full electronics lab with board production capability
18:02 <@fenn> you start optimizing from the beginning and there's no room for improvement
18:02 < jonathanc> well an 8 pin processor which only requires 1 resistor and 1 capacitor to complete does not really need board production...
18:02 <@fenn> yeah well how do you program it
18:02 < jonathanc> with a programmer of course, common equip
18:04 <@fenn> so, call me spoiled but i'd like at least some kind of status indicator showing how much time is left in the PCR cycle
18:04 < jonathanc> save resources by saving $$
18:04 <@kanzure> also why would it be taking 15 engineers to make a thermocycler?
18:05 <@kanzure> i'm probably grumpy. i've been writing a caching server all day.
18:06 < jonathanc> the socialism comment relates to "the public paying" rather than allowing price (capitalism) to dictate success
18:06 < 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 < jonathanc> to paraphrase
18:06 <@fenn> price isn't the only variable; if price were the only thing that mattered, people would still be doing PCR by hand with water baths
18:06 <@kanzure> no, in that scenario i am my own user
18:07 <@fenn> anyway i stick to my position of optimizing for coder/hacker time
18:08 <@kanzure> in a stackless architecture i think you could still possibly use libraries if your compiler is good
18:08 < jonathanc> what is the library going to do? there's only 1024 bytes of memory.
18:08 < jonathanc> there is only 1 .c file
18:08 < jonathanc> there is no linker
18:08 < jonathanc> there is no .ld file
18:08 <@fenn> what kind of broken system are you using
18:08 < jonathanc> haha
18:08 <@fenn> ffs man join this millennium
18:09 <@fenn> why even bother with C if there's no linker and you can't port your code
18:09 < jonathanc> the code is portable to a chip with similar architecture
18:09 <@fenn> just do it in raw bytecode, it's the most optimal
18:10 <@kanzure> yeah we should hire 100 engineers to stare at hex editors all day
18:10 <@kanzure> anyone who can't write in raw hex is fired
18:10 < jonathanc> it depends on how much % you save
18:10 < jonathanc> assembly vs C only saves 1-3% in most cases with this stuff
18:10 < jonathanc> that's why risc is so good
18:12 <@fenn> so 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)
18:13 < jonathanc> there's more that could be saved I think
18:13 < jonathanc> thermocoupler dealio could be cut as well
18:14 <@fenn> but there's still all sorts of costs unaccounted for: mechanical fabrication assembly and testing
18:14 <@fenn> parts procurement, "marketing"
18:14 < jonathanc> max31885 why?
18:15 < jonathanc> mechanical, you guys would have to comment on
18:15 <@fenn> something about bandgaps changing with ambient temperature.. i didnt design it
18:16 < jonathanc> lemme guess you want to use the pid c++ library next
18:16 <@kanzure> which library?
18:17 < jonathanc> cheese ball library previously discussed on the group
18:17 < jonathanc> used by openpcr I think
18:17 <@kanzure> how much of openpcr was adobe air?
18:17 < jonathanc> again with same rationalization "trying to save developer time"
18:17 <@fenn> probably this http://playground.arduino.cc/Code/PIDLibrary
18:17 <@kanzure> adobe air was not rationalized by "saving developer time".. it was "saving time so i don't have to become a developer".
18:18 <@kanzure> actually wait that doesn't make sense, josh can write code
18:18 <@kanzure> wtf
18:18 <@kanzure> why did josh let openpcr use adobe air?
18:18 <@fenn> why would anyone use adobe air
18:19 <@fenn> you still have to write code, right?
18:19 <@fenn> The Adobe AIR runtime enables developers to deploy standalone applications built with HTML, JavaScript, ActionScript, Flex, Adobe Flash Professional, yadda yadda yadda
18:19 <@kanzure> and then you add this proprietary pile of crap in between you and your code too
18:19 <@kanzure> and then your users have to use it too because you're sadistic or something
18:20 <@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 <@fenn> why not just implement a web server on the device and have it serve up all that fancy html
18:21 <@kanzure> paperbot: http://www.sciencemag.org/content/early/2013/03/27/science.1232758
18:21 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/9eeb0dfaf790e08cc2bcd8433b656816.txt
18:21 <@kanzure> oh ffff
18:21 <@kanzure> fuck aaas
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19:18 <@kanzure> east bay diybio meeting notes http://ec2-107-21-158-78.compute-1.amazonaws.com/wiki/index.php/General_Meeting_3/29/13
19:18 <@kanzure> http://docs.google.com/document/d/1lDLnSkcqjfKTrSMu1SE2RdejCbxehzo786py3WbDo8c/edit
19:18 <@kanzure> stalk: Patrik D'haeseleer, Shanee Stopnitzky, Ryan Bethencourt, Matt Harbowy, Jason Euren, Javier, Romy Ilano, Ron Shigeta, Marc Juul
19:22 < jonathanc> the 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.
19:23 < jonathanc> bio kids have $25 not $85.
19:23 < jonathanc> $25 including manufacturing and even UL approval.
19:23 < jonathanc> and marketing and box and retail stickers.
19:24 < jonathanc> If the overhead is removed let's say the product retail price drops $5-7 or so
19:24 < jonathanc> do direct sale and drop another $4-5
19:27 < jonathanc> here's a much better one. Heater Project by Mike Pearce
19:27 < jonathanc> From readme.txt: The Heater 3 project is used to control waterbath heaters and other specialist temperature controlled equipment within the Chemistry Department.
19:27 < jonathanc> This 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 < jonathanc> Entire archive. Download (158KB).
19:28 < jonathanc> http://www.microchipc.com/sourcecode/PIC_Hi-Tech_C_Mike_Pearces_heater_project.zip
19:28 < jonathanc> the "libraries" are .c files
19:29 <@kanzure> yes, what else would they be? magic?
19:29 < jonathanc> .a
19:29 < jonathanc> with linker file
19:30 <@kanzure> ok good point
19:30 < jonathanc> here, it is monolithic
19:30 <@kanzure> there are many other environments where libraries are pulled in with source
19:30 < jonathanc> you can see from the source that it is not appropriate to make these into libraries
19:30  * kanzure looks
19:31 < jonathanc> for optimization, the code uses registers etc, and the delay loop for example, requires specific architecture for clock cycles
19:31 <@kanzure> checksum.c seems fairly standard, but i haven't finished reading its preamble
19:31 < jonathanc> the 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 directly
19:32 < jonathanc> i.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 overhead
19:33 < jonathanc> in fact during a code review this week we will restructure code to remove abstraction purposely because the flash is 92% full
19:33 <@kanzure> oh look someone is bothering to do code reviews. great.
19:33 < jonathanc> to switch to another micro with bigger memory is the next step up in chip cost which ultimately impacts end user cost
19:34 < jonathanc> in a comp sci project these abstraction layers would be added not subtracted
19:34 < jonathanc> because resources are infinite.
19:34 <@kanzure> nobody said it's a comp sci project
19:34 <@kanzure> you don't need comp sci to see that checksum.c is pretty standard
19:35 < jonathanc> date time
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19:35 <@kanzure> did i fail his test?
19:36 <@kanzure> oh he means it's time for a date, not... okay.
19:37 <@kanzure> the 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.
19:39 <@kanzure> and 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.
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19:49 <@kanzure> http://sudoroom.org/wiki/Biohacking
19:49 <@kanzure> http://sudoroom.org/wiki/Projects#Biology_Projects
19:49 <@kanzure> http://ec2-107-21-158-78.compute-1.amazonaws.com/wiki/index.php/Main_Page
19:50 <@kanzure> hah 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_Ideas
19:51 <@kanzure> "unallocated space".. heh.
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19:57 <@kanzure> Juul: meeting update?
19:58 < Juul> kanzure, right now talking about what kind of space we want and whether we _need_ bsl2
19:58 <@kanzure> i think you can't get to bsl2 without bsl1, not sure
19:58 < Juul> yeah
20:01 < Juul> i mean, it depends on the county/city implementation
20:02 < Juul> but BSL1 requirements as I've seen them are a subset of BSL2 requirements
20:04 <@kanzure> just gotta map out the zoning laws
20:04 < Juul> hmm
20:04 < Juul> we have a couple of people working on that
20:09 < Juul> i think the result will be that we should go for oakland
20:09 < Juul> it seems like they may have little/no regulation
20:10 < brownies> oakland eh?
20:12 < Juul> yep
20:37 <@kanzure> it'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 <@kanzure> it would be a more relevant example since maybe 2007.
20:43 < brownies> i was using wikipedia in '04
20:43 < brownies> ...before it went mainstream...
20:44 <@kanzure> we 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 <@kanzure> in 2004.
20:47 < ParahSail1n> paperbot: http://www.sciencedirect.com/science/article/pii/S0019103513000791
20:47 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/The%20Wow%21%20signal%20of%20the%20terrestrial%20genetic%20code.pdf
20:47 < ParahSail1n> aliens in ur dnas
20:48 < ParahSail1n> i think the ! in the file name broke the python
20:48 < ParahSail1n> ah, nevermind, it just took a while to get pdfparanoia'd
20:57 <@kanzure> wow i just realized your github username
20:57 <@kanzure> i don't know why that wasn't more obvious
20:59 <@kanzure> it would be more useful if i could make these realizations while i am reading your bug reports
21:00 <@kanzure> you even used your name.. how did i miss that?
21:07 < ParahSail1n> yeah, that's more of a "professional" username
21:09 <@kanzure> heh
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22:05 <@kanzure> paperbot: http://users.ece.cmu.edu/~aavgerin/papers/mayhem-oakland-12.pdf
22:05 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/e35c98abc8251f971cb1952d115c656b.txt
22:05 <@kanzure> paperbot: http://users.ece.cmu.edu/~ejschwar/papers/usenix11.pdf
22:05 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/d1033e87cf00119c59ec698d23a2eac3.txt
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22:09 < jonathanc> microcontroller libraries http://mbed.org/explore/
22:09 <@kanzure> http://moflow.org/#%5B%5BReference%20Library%5D%5D
22:09 <@kanzure> .title
22:09 < yoleaux> .: moflow :. - software security workflow
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22:10 < diginet> did anyone mirror the NTRS before it got taken down?
22:10 <@kanzure> link?
22:10 < diginet> the NASA technical report service
22:10 <@kanzure> the whole thing was taken down? those guys have balls. they are really trying to make a statement huh.
22:11 < diginet> they got paranoid because they realized people were actually reading things they put on the internet
22:11 < diginet> I'm still trying to figure out a way that makes any sense
22:11 <@kanzure> no it's because of sequestration. nasa has been canceling all sorts of public programs to make people angry.
22:12 < diginet> are 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 server
22:12 <@kanzure> that's... interesting.
22:12 <@kanzure> oh no somebody might be actually using our site, pull the plug
22:12 < diginet> yeah, it's mind-numbingly stupid
22:12 <@kanzure> jonathanc: is this a commercial product? what's going on here?
22:13 <@kanzure> hmm http://mbed.org/handbook/Homepage
22:13 <@kanzure> what are the target architectures?
22:13 <@kanzure> "Prototype to hardware - How to move from your mbed prototype to your custom PCB."
22:14 < diginet> "we fear people might be reading stuff we put on the internet for people to read"
22:14 <@kanzure> are they selling only their own chips here?
22:14 < diginet> mbed is ARM
22:14 < jonathanc> target soc is arm-based
22:14 <@kanzure> i see. well that's nice.
22:14 < jonathanc> arm cortex is popular
22:14 < jonathanc> 32-bit
22:14 <@kanzure> if they are a business, what is their model? selling devkits? support?
22:14 < jonathanc> low power, reduced instruction set
22:14 < diginet> reduced instruction set?
22:14 < jonathanc> soc vendors fund sw dev
22:14 < diginet> in name only
22:14 < jonathanc> i have a freescale board in front of me
22:15 < diginet> the RISC/CISC distinction is all but meaningless these days
22:15 < jonathanc> no, the cortex really is reduced instruction set
22:15 <@kanzure> soc vendors fund sw development because "maybe the developers will use our socs" ?
22:15 < jonathanc> yes
22:15 <@kanzure> neat
22:15 <@kanzure> assuming this works. i should play with this.
22:15 <@kanzure> this looks better than that bugslabs bullshit.
22:15 < jonathanc> dude soc vendors funded major eclipse dev effort
22:15 <@kanzure> eclipse is like pure evil
22:16 < jonathanc> it is what it is, at least it works
22:16 <@kanzure> heh
22:16 < diginet> eclipse is like "let's see just how shitty we can make our dev environment, you know, for fun"
22:16 < jonathanc> it is a common rallying point
22:16 < diginet> RISC has not been a relevant argument in at least 15 years
22:16 <@kanzure> true, eclipse is very good at getting attention
22:16 < jonathanc> its goal was to run on linux eh
22:17 < diginet> RISC predates Linux
22:17 < jonathanc> arduino killer http://www.freescale.com/webapp/sps/site/prod_summary.jsp?code=FRDM-KL25Z&tid=vanFRDM-KL25Z
22:17 < diginet> it was designed with the fact that developers were abandoning directly coding in asm for "high-level" (for the time) languages like C
22:18 < jonathanc> $13 for the board, includes onboard jtag debugger
22:18 < diginet> or you could, you know, just use the chip
22:18 < jonathanc> freescale also supplies rtos
22:18 < diginet> plenty of open source ones
22:19 < jonathanc> important feature is usb otg
22:19 < jonathanc> with enough flash to actually embed a usb stack
22:19 < diginet> ugh, I'm so sick of the arduino bullshit
22:19 < jonathanc> although i'd have to see proof of that
22:19 < diginet> just use an AVR
22:20 < diginet> it's simple
22:20 < diginet> and much cheaper
22:20 < jonathanc> or dump avr and get a real chip you mean
22:20 < diginet> I don't care for AVR, but pick your poison
22:20 < diginet> I'm just sick of overpriced, glorifed dev boards
22:21 < jonathanc> whatever.  you wont be able to make it for under $10
22:21 < diginet> AVRs cost like $1
22:22 < jonathanc> i'm talking about kinetis board, not an avr breakout board
22:22 < diginet> oh
22:23 < jonathanc> adafruit obviously has a huge profit margin
22:23 < jonathanc> like lego
22:29 < jonathanc> infineon has a similar setup now too, also reduced footprint arm
22:31 < jonathanc> they have these funky boards which are hexagonal and plug in together, rather than stackable
22:32 < jonathanc> this is it http://www.freertos.org/FreeRTOS-for-Infineon-XMC4000-Cortex-M4.html
22:36 < jonathanc> infineon'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=db3a30433580b3710135a07902883872
22:36 <@kanzure> if anyone cares i've dumped some more security things into here http://diyhpl.us/~bryan/papers2/security/
22:36 < jonathanc> dude what a crazy url, it has the copyright symbol and tm mark in the url. that's whack
22:37 <@kanzure> they just want to make sure your browser is utf8 compliant, haha
22:37 < jonathanc> google XMC Development Tools, Software & Kits
22:37 <@kanzure> you knew about mbed earlier tonight?
22:37 < jonathanc> i've had this board for a while
22:38 < jonathanc> did an rtos evaluation a couple months back
22:38 -!- diginet [~kevin@107-213-84-107.lightspeed.hstntx.sbcglobal.net] has left ##hplusroadmap ["Leaving"]
22:38 <@kanzure> any complaints?
22:38 < jonathanc> problem with mbed is it is online development
22:38 <@kanzure> what why
22:39 < jonathanc> well i told you about the toolchain problem
22:39 < jonathanc> how are you going to compile a library if you can't get the toolchain without a $3000-per-seat license?
22:40 < jonathanc> the "free" toolchain is online, i.e. virtual license supported by the vendors
22:40 < jonathanc> who knows how long it will last
22:40 < jonathanc> intel had a similar system when the 80960 came out
22:40 < jonathanc> log in, compile embedded code for 80960j I think it was, get the static binary, then burn to local board
22:41 < jonathanc> they don't want to kill the 3rd party dev companies which make the toolchains, then they will be s.o.l.
22:41 < jonathanc> another limitation with mbed is it is nxp which I'll never use again
22:43 < jonathanc> also, 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 others
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22:44 < jonathanc> check this one http://www.kickstarter.com/projects/paulstoffregen/teensy-30-32-bit-arm-cortex-m4-usable-in-arduino-a
22:45 < jonathanc> same freescale chip.  freescale is solid but tries to lock in via offering software for their chip only, same story as always
22:47 < jonathanc> funny 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 < jonathanc> galago uses the same nxp chip as the mbed platform  http://www.kickstarter.com/projects/kuy/galago-make-things-better
22:48 <@kanzure> the arm toolchains are $3k/seat?
22:48 < jonathanc> depends on the jtag
22:49 <@kanzure> doesn't llvm target arm just fine?
22:53 < jonathanc> i don't know if it does cortex instruction set or not
22:53 < jonathanc> this is a different isa
22:54 < jonathanc> isa=instruction set architectur
22:54 < jonathanc> isa=instruction set architecture
22:54 <@kanzure> arm cortex is not normal arm isa?
22:54 <@kanzure> i should probably look into this huh
22:55 < jonathanc> cortex is reduced set like I said
22:56 < jonathanc> either way it basically kills avr so why bother with that I dunno
23:02 < jonathanc> more libraries for you http://www.pjrc.com/teensy/td_libs.html
23:04 < 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/
23:05 <@kanzure> that's quite a string of words
23:05 <@kanzure> oh i see i can read it now
23:06 <@kanzure> seems to be an industry consortium thing
23:06 < jonathanc> this is the toolchain for the arm cortex apparently
23:06 < jonathanc> https://launchpadlibrarian.net/126639247/readme.txt
23:06 < jonathanc> -mthumb -mcpu=cortex-m3
23:06 < jonathanc> -mthumb -mcpu=cortex-m4
23:07 < jonathanc> link https://launchpad.net/gcc-arm-embedded/4.7/4.7-2012-q4-major
23:07 < jonathanc> I am spoiled because I haven't used gcc in years now, thank darwin
23:08 < jonathanc> there's something to be said for buying a commercial toolchain and just building, vs all kinds of bootstrap junk with gnu
23:09 < jonathanc> this is a pretty sweet cortex board too, teensy 3.0 https://www.sparkfun.com/products/11780
23:10 < jonathanc> I 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 neat
23:10 < jonathanc> toolchain install is a gnu p.o.s. though
23:12 < jonathanc> mbed nxp soc board  from sparkfun  https://www.sparkfun.com/products/9564
23:13 < jonathanc> $60, that aint cheap
23:14 < jonathanc> in that case, UBW32 is a better option
23:16 <@kanzure> maybe the open source options wouldn't suck so much if companies were actually trying to make something usable that doesn't cost $50k/seat
23:17 < jonathanc> what do you mean
23:21 < jonathanc> dudes get a lot done with the iar toolchain here
23:21 < jonathanc> tons done
23:22 < jonathanc> actually work on the project instead of working on makefile hell
23:22 < jonathanc> change linker params in a couple minutes compared to .ld nonsense
23:23 < jonathanc> for the cost of 2 weeks employment, gain more than that back in productivity
23:24 < jonathanc> plus a much better optimizer for sure
23:24 <@kanzure> :fear: http://www.libcrack.so/2012/10/13/hacking-the-ar-drone-parrot/
23:26 <@kanzure> someone is offering a rom dump sometime tomorrow. can't wait to start picking at it.
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23:35 < jonathanc> I 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 office
23:35 <@kanzure> i am being distracted by security things at the moment. this stuff is like candy to me. :(
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--- Log closed Sat Mar 30 00:00:42 2013