| --- Log opened Mon May 21 00:00:16 2012 | ||
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| kanzure | ok maybe not.. one last one: | 00:02 |
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| kanzure | http://www.violentacres.com/archives/193/what-would-happen-if-you-bought-25-bottles-of-nyquil/ | 00:02 |
| yashgaroth | hell yeah dxm | 00:05 |
| Mokbortolan_ | yeah, I guess it just shows a group of people's response to what they perceive as a threat to their community | 00:07 |
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| joshcryer | Blender + BMesh + Precision Modelling Tools = Usable CAD Solution, imo: http://wiki.blender.org/index.php/User:Kellpossible | 02:26 |
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| kanzure | beebooop | 06:20 |
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| kanzure | nmz787: sorry for cutting out last night | 08:15 |
| kanzure | "makerbot robot petting zoo".. man, why can't i have a robot petting zoo? | 08:23 |
| chris_99 | lol | 08:23 |
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| strages_work | kanzure: you can http://en.wikipedia.org/wiki/BEAM_robotics | 08:33 |
| kanzure | strages_work: paperclip robots were some of my first :) | 08:34 |
| strages_work | you can get surprisingly complex when combining simple sensors | 08:36 |
| strages_work | no one's in charge, it's all just feedback loops | 08:36 |
| audy | http://xkcd.com/1058/ you've all ready it | 08:40 |
| audy | already* read it | 08:40 |
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| nmz787 | its cool | 08:57 |
| nmz787 | if i can't convince you to write a toolpath generator with me, i'm not sure what needs to be done CAD wise other than some simple metadata bookkeeping | 08:58 |
| kanzure | huh? all i said was that svg/xml-based inputs to a toolpath generator didn't make sense | 08:59 |
| nmz787 | if there is open cad software, i.e. it draws vectors and curves... other than toolpath generation, i think keeping track of metadata is all that would be needed to add-on | 09:02 |
| nmz787 | where metadata would be z direction to defocus the laser to make a wider channel | 09:02 |
| nmz787 | which would correllate to the line thickness you drew | 09:03 |
| kanzure | well, most laser cutters are accessed with a silly print driver, and then postscript is sent directly to the laser cutter | 09:04 |
| kanzure | i don't really feel like writing a postscript parser or porting one to atmega or whatever parallax is | 09:04 |
| nmz787 | thats not how it would work though, right? | 09:08 |
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| ThomasEgi | how about converting postscript to hpgl? | 09:10 |
| nmz787 | isn't the path generated by dijkstras method on the largest closed/cyclic paths, then on the noncyclic remaining lines | 09:10 |
| kanzure | ThomasEgi: i don't really want to write a hpgl driver for parallax either. why is everyone so against linux all the sudden? | 09:11 |
| ThomasEgi | not quite sure what parallax is in this context. but hpgl is pretty easy to interpret on an atmega. | 09:12 |
| nmz787 | so you have your binary image after your cad is all done, curves rendered, all at laser cutter resolution... then dijkstras etc... pre-build the paths... save to SD card, microcontroller merely reads pixels and moves to them | 09:12 |
| nmz787 | space intensive, but nothing a 32gb sd card couldn't handle | 09:12 |
| nmz787 | parallax propeller is an 8 core microcontroller at up to 80MHz | 09:12 |
| nmz787 | as easy to get into as arduino | 09:12 |
| ThomasEgi | should be no problem to get a gcode or hpgl interpreter running on one. | 09:13 |
| nmz787 | it doesnt have hardware multiply/divide though | 09:13 |
| nmz787 | but they are builtin with the interpreter | 09:13 |
| ThomasEgi | doesnt reprap feature some arduino based gcode interpreter? | 09:14 |
| nmz787 | and optimized assembly routines exist online... as the assembly language for the propeller is actually pretty easy and useful | 09:14 |
| ThomasEgi | with reduced instruction set? | 09:14 |
| nmz787 | i don't see why you wouldn't just waste space on storing a precomputed pixel-based path on the PC, at the cost of SD card space | 09:15 |
| kanzure | i don't think it should be a binary image.. it's just vector data | 09:15 |
| nmz787 | curves arent vectors | 09:16 |
| nmz787 | well, they could be, but the grain is still pixels | 09:16 |
| kanzure | not in the cad software | 09:16 |
| nmz787 | no | 09:16 |
| nmz787 | but for driving a stepper | 09:17 |
| ThomasEgi | wouldnt call it pixels. but steps instead. | 09:18 |
| ThomasEgi | one easy way would be to aproximate all curves by straigth line segments. those can be dealt with easily on a microcontroller. | 09:19 |
| kanzure | i don't think it should be on a microcontroller. it should be on a normal computer. | 09:19 |
| kanzure | no reason to constrain yourself so much. | 09:19 |
| ThomasEgi | normal computers have terrible timing | 09:20 |
| kanzure | you can offload the timing operations to a microcontroller, but that's about all i'd do | 09:20 |
| ThomasEgi | that's the idea of using straigth lines | 09:20 |
| ThomasEgi | you basically tell the microcontroller how many steps to take in which direction at what speed | 09:21 |
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| kanzure | yes i know how steppers work (to the extent that electromagnetism doesn't make me scratch my head) | 09:21 |
| ThomasEgi | so.. taking an arduino as "instruction buffer" and stepper controller. which receives the new commands over rs232 seems most reasonable to me | 09:23 |
| kanzure | ok. so why would an sd card be used there? | 09:24 |
| nmz787 | high speed | 09:27 |
| nmz787 | no interruptions in data stream | 09:27 |
| nmz787 | no dependence on computer | 09:27 |
| nmz787 | 20 MIPs on 8 cores with perfect timing | 09:28 |
| kanzure | i want a computer :( | 09:28 |
| kanzure | we'll stick in a whole box there if we have to | 09:28 |
| ThomasEgi | a computer is definetly easier. | 09:28 |
| nmz787 | reading and writing to an SD card is very easy | 09:28 |
| nmz787 | computer can have a joystick mode | 09:28 |
| ThomasEgi | nmz787, if you have premade libraries for it. | 09:28 |
| nmz787 | but i still think the shortest vector is literally going to be 1 movement unit up, and 1 movement unit right | 09:29 |
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| nmz787 | yeah SD is all done | 09:29 |
| nmz787 | download a library from parallax object repo | 09:29 |
| nmz787 | uses 1 of 8 cores | 09:30 |
| ThomasEgi | guess the computer version allows ways more flexibility and interaction | 09:30 |
| nmz787 | the problem i've heard in the past is the data rate from the computer and the microcontroller's buffer | 09:31 |
| nmz787 | which is why precomputed paths seem best to me | 09:31 |
| ThomasEgi | an atmega can have kilobytes of ram. | 09:31 |
| ThomasEgi | given each vector only takes a couple of bytes, buffering should not be a problem | 09:32 |
| nmz787 | but we have 10s of meters for total path length, cutting as fast as we can at micron resolution | 09:32 |
| ThomasEgi | not an issue as long as you can supply the instructions faster than you execute them | 09:33 |
| kanzure | so, i talked with fenn for a bit | 09:34 |
| nmz787 | if the vectors are each 1 micron on a curve, the best resolution this thing can do, with the cutting rate we want it would be about 34716microns per second | 09:34 |
| ThomasEgi | oh. that's quite fast | 09:34 |
| kanzure | if we have a 16 micron step size, linuxcnc is fine | 09:35 |
| nmz787 | not for the speed we want though | 09:35 |
| kanzure | i agree that 1 micron step size would be great, but i'm not sure it's required | 09:35 |
| kanzure | no it should be okay at 16 microns? | 09:35 |
| kanzure | why do you say that? | 09:35 |
| nmz787 | i think it is | 09:35 |
| nmz787 | we need to microstep so its smooth | 09:35 |
| nmz787 | or we're not accomplishing much over the existing desktop lasers | 09:36 |
| kanzure | we should probably use the word tolerance and radians to describe curves | 09:36 |
| nmz787 | which give 25 micron steps now | 09:36 |
| kanzure | my laser cutter didn't give me 25 micron step sizes.. also it was on a giant belt, and i'm pretty sure it wasn't that precise | 09:36 |
| ThomasEgi | anyway. at that stepping speed i really would recommend to buffer the entire programm on a fast accessible medium | 09:37 |
| ThomasEgi | either sd card. or eeprom or so. | 09:37 |
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| nmz787 | kanzure: 1000dpi is 25micron | 09:46 |
| nmz787 | well as fenn said, as long as its repeatable | 09:47 |
| nmz787 | btw you said you talked to him | 09:48 |
| kanzure | caught him on the phone real quick | 09:48 |
| kanzure | apparently he's sleeping | 09:48 |
| nmz787 | gotta do what you gotta do | 09:49 |
| nmz787 | so i think there are really well made lasers that project a + sign that you can use for aligning thing perpendicular | 09:50 |
| kanzure | you mean a mask? | 09:50 |
| nmz787 | no for the gantry rails | 09:50 |
| kanzure | no i mean you can shine light through a mask to get a perpendicular jig | 09:51 |
| nmz787 | i had asked about how to get them perfectly perpendicular | 09:51 |
| nmz787 | right but then you need a good jig | 09:51 |
| nmz787 | but yeah | 09:51 |
| nmz787 | they sell them alltogether | 09:52 |
| nmz787 | audy: great comic! | 09:56 |
| kanzure | copenhagen suborbitals test fire 2012-05-20 http://www.youtube.com/watch?v=Sk5S5Q3M4Ek | 09:56 |
| nmz787 | boring video | 10:01 |
| nmz787 | where is the action? | 10:01 |
| kanzure | :/ | 10:01 |
| kanzure | win 6 | 10:01 |
| kanzure | dkjawdksjfkasdfa | 10:01 |
| kanzure | ignore that. | 10:01 |
| nmz787 | kanzure the spambot | 10:01 |
| kanzure | it's just an irssi problem | 10:02 |
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| mensch | k | 10:54 |
| mensch | eh, wrong window | 10:55 |
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| kanzure | http://www.kickstarter.com/projects/incident/gtar-the-first-guitar-that-anybody-can-play | 11:48 |
| kanzure | not sure why they are forcing it to play through the iphone? | 11:48 |
| nmz787 | prob made development easier with the dock | 12:08 |
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| nmz787 | http://www.youtube.com/watch?v=pOTWEPF925c&feature=g-all-u | 13:25 |
| kanzure | what is it? | 13:27 |
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| yashgaroth | well, it could be an improvement over less-specific molecules for blocking protein interactions | 13:53 |
| kanzure | the video is about ligand binding? i haven't clicked yet, just want a title or something | 13:54 |
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| yashgaroth | cup-shaped, negatively charged molecule that binds to parts of cytochrome c | 13:54 |
| yashgaroth | (and any other protein with a positively charged region) | 13:55 |
| yashgaroth | they seem to be stretching it a bit with the promises, but you never know | 13:55 |
| HEx1 | wrt parallax: I have to recommend against the propeller, there's nothing even approaching a free toolchain | 14:03 |
| HEx1 | sorry, Free toolchain. you can write in their proprietary interpreted Spin language, for which they don't even document the bytecodes, or you can write in assembler. anything else you're on your own. no gcc port, for example | 14:05 |
| nmz787 | HEx1: they offer their toolchain for free, and you can use gcc | 14:06 |
| nmz787 | and propeller assembly is easy and quite powerful | 14:06 |
| HEx1 | there's a gcc port? where? | 14:06 |
| nmz787 | http://code.google.com/p/propgcc/ | 14:06 |
| HEx1 | ooh,will check | 14:06 |
| nmz787 | but i don't see it as a big issue, they've been around for a long time and their software is pretty decent | 14:07 |
| nmz787 | there is other more IDE and debugger compilers from a 3rd party too, i think for a fee | 14:08 |
| nmz787 | the propeller definitely is as easy to start playing with as the arduino | 14:08 |
| HEx1 | (yes, propeller assembly is nice. but you very much have to design your project specifically for the propeller, as it's so unlike any other architecture) | 14:08 |
| nmz787 | why is that a problem? it has the right hardware for the job IMO | 14:08 |
| nmz787 | specifically the 8 cores with a sensible way to program parallelzation and synchronized independent control loops | 14:10 |
| nmz787 | and $8 | 14:10 |
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| HEx1 | it's not, necessarily. but it does mean that existing code, even existing microcontroller-targeted code, is unlikely to be of any use, and you'll have to start from scratch | 14:10 |
| nmz787 | what code though? no one has built a micro CNC for microfluidics | 14:12 |
| nmz787 | SD card code is out there and modular and ready for use | 14:12 |
| HEx1 | maybe I'm just coming at this from too much of a free software bent | 14:12 |
| kanzure | linuxcnc already exists, and doesn't have a parallax port | 14:13 |
| nmz787 | http://sourceforge.net/projects/fsrw/?source=directory | 14:13 |
| nmz787 | FSRW is a FAT16/FAT32 filesystem for the Parallax Propeller. This sourceforge project supports further concurrent development of the popular existing fsrw project. | 14:13 |
| nmz787 | linuxcnc is booty slow | 14:13 |
| kanzure | i don't think fat16/fat32 is a good idea for a laser cutter | 14:13 |
| nmz787 | i dont see your logic | 14:14 |
| kanzure | that's a file system format | 14:14 |
| nmz787 | not format | 14:14 |
| nmz787 | the filesystem | 14:14 |
| nmz787 | it takes 1 of the 8 cores | 14:14 |
| HEx1 | I just know that, for all that's it's easy to get started if you're on windows, when I got my dev board (~Aug 2010) I spent several days trolling the wiki, IRC etc. for free linux dev tools, preferably with source and under an open license. with arduino it's apt-get, done | 14:14 |
| nmz787 | and gets you 2 wire access to SD cards | 14:14 |
| nmz787 | that looks like a file stream in code | 14:14 |
| kanzure | i still don't understand why an SD card is necessary | 14:14 |
| kanzure | just have a computer.. done. | 14:14 |
| nmz787 | your computer has memory, done | 14:15 |
| kanzure | if you think linuxcnc is too slow, we could do a small atmel chip to offload crap to | 14:15 |
| nmz787 | but we should just use a propeller | 14:15 |
| kanzure | well, no, usually a computer means something general purpose, so with ethernet, wifi, a keyboard, other things | 14:15 |
| nmz787 | its better than atmel for this purpose | 14:15 |
| nmz787 | just because its multicore | 14:15 |
| nmz787 | it might be possible with USB 2.0 high-speed to accomplish pure computer contorl | 14:16 |
| nmz787 | control | 14:16 |
| nmz787 | but in reality computers can hang | 14:16 |
| nmz787 | its not real-time | 14:16 |
| nmz787 | if the buffer dies, the job is interrupted | 14:16 |
| nmz787 | linuxcnc uses a parallel port for control I/O, it has a bandwidth limit, its limited by the length of the wires looking like transmission lines | 14:17 |
| nmz787 | its limited to using linux | 14:17 |
| nmz787 | with a $10 SD card and a $9 propeller it just seems worth it to get rid of buffer issues and timing concerns | 14:18 |
| kanzure | it is real-time. that's what a kernel does. | 14:19 |
| kanzure | or, that's what the rt-kernel does. | 14:19 |
| nmz787 | thats way too complex for this | 14:19 |
| nmz787 | and the code will be way uglier | 14:20 |
| kanzure | all of that code is already written and is open source. | 14:20 |
| nmz787 | the beauty of 8 cores that program like a microcontroller is breaking out of that paradigm | 14:20 |
| HEx1 | finding out that there was no open source spin compiler for any platform, that the only open source (well, available source, no license) assembler was written as part of a demo (and in Prolog to boot) that the internals of Spin were undocumented to the extent that they'd encrypted their ROM that interprets it (they claim, for example, that it's not possible to call spin code from assembly, which is blatantly false but admitting otherwise would require rev | 14:20 |
| nmz787 | i still dont see how you get around the transmission line and buffer issue | 14:20 |
| HEx1 | </rant> | 14:20 |
| kanzure | 'spin' compiler? | 14:21 |
| nmz787 | we're not proposing to build a chip foundry just to say its open and free | 14:21 |
| nmz787 | spin is their interpreted language name | 14:21 |
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| kanzure | the buffer issue- if it becomes one- can be solved with a downstream extra chip. | 14:22 |
| nmz787 | whats your proposed use of said chip? | 14:23 |
| kanzure | well it sounds like you're concerned about timing on the steps, so if you need the extra precision we can offload that later, but that's /only/ a very tiny scheduler.. probably 10 lines of code | 14:24 |
| nmz787 | whatever the case, i don't think we can rely on linuxcnc purely based on the number of steps per second we want to take... the computer needs to tell the motors to turn on, quite fast... if the lines are too long from a GP computer, then they need to be shortened or boosted with some sort of 'buffer' | 14:29 |
| nmz787 | if the computer is sending direct pixel by pixel step movements out, it just seems like throwing those steps pre-computed onto and SD card ENSURES we have no timing errors creep in... that if something crashes, it doesn't waste PDMS or some other thing thats under the laser... if the GP computer freezes in place with the laser running, it could start a fire, etc | 14:30 |
| * HEx1 only now backlogs for the context in which his mental keyword matching triggered | 14:31 | |
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| kanzure | http://peerj.com/ seems to be $100/mo for unlimited papers? | 17:15 |
| kanzure | oh, no | 17:15 |
| kanzure | that's just for publishing paper. how awful. | 17:15 |
| kanzure | man, i already hate peerj | 17:20 |
| joshcryer | I hate $$$ for papers. | 17:21 |
| docl | icky | 17:23 |
| docl | pretty website tho | 17:24 |
| docl | which to be blunt is much more than I can say for the SKDB project page | 17:24 |
| kanzure | haha | 17:25 |
| kanzure | it's just twitter bootstrap | 17:25 |
| kanzure | don't be too impressed | 17:25 |
| jrayhawk | kanzure: how can the skdb project page be made uglier? | 17:25 |
| kanzure | unrendered svg markup | 17:25 |
| docl | hmm. it suddenly occurs to me that I should make a pretty website with twitter bootstrap to panhandle with. | 17:26 |
| jrayhawk | a monospace fixed-size font would help, i suppose | 17:26 |
| docl | comic sans maybe? | 17:27 |
| jrayhawk | good lord, man, even i have my limits | 17:27 |
| kanzure | so the fbi just called me | 17:27 |
| kanzure | due to budget issues, they are moving the workshop | 17:27 |
| kanzure | in addition, they want to know if i will do the brochure graphics design for them since they ran out of money | 17:28 |
| jrayhawk | moving the workshop temporally, or proximally | 17:28 |
| kanzure | am i the only one wondering why the weapons of mass destruction division is underfunded? | 17:28 |
| kanzure | geographically | 17:28 |
| kanzure | if i do their brochure, it's totally going to be some biohacking manifesto | 17:29 |
| jrayhawk | well, i guess that's getting into the diy spirit of things | 17:30 |
| jrayhawk | try to trick people with an abundance of time and motivation into scratching itches for you | 17:30 |
| kanzure | it occurs to me that this might not be the fbi | 17:30 |
| kanzure | i have never asked to review their badges/identification | 17:31 |
| kanzure | although the agents' names appear in the news often | 17:31 |
| yashgaroth | moving...where? | 17:41 |
| yashgaroth | don't say DC | 17:41 |
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| kanzure | yashgaroth: just across the bay. past oakland. | 17:44 |
| kanzure | so they are picking another hotel or something | 17:44 |
| yashgaroth | if it's nearer berkeley I can stay with relatives, so hey | 17:44 |
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| n_bentha | hi | 20:39 |
| kanzure | howdie | 20:39 |
| n_bentha | still no new news :( | 20:39 |
| nmz787 | news about? | 20:40 |
| n_bentha | diybionews2 | 20:41 |
| kanzure | oh. i haven't updated it because i'm lame. | 20:42 |
| kanzure | you should give me things to add to it | 20:42 |
| n_bentha | not in my job description | 20:43 |
| nmz787 | are you expecting something there? | 20:43 |
| n_bentha | not really | 20:44 |
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| nmz787 | Rewritable digital data storage in live cells via | 21:32 |
| nmz787 | engineered control of recombination directionality | 21:32 |
| nmz787 | http://www.pnas.org/content/early/2012/05/14/1202344109.full.pdf | 21:32 |
| nmz787 | still pretty far away from something useful | 21:32 |
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| LionClan | hello | 23:35 |
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| LionClan | how much would it cost, you think, to set up a sequencer to make the skip over 51-55 happen for duchenne muscular dystrophy patients with the 51-55 deletion | 23:42 |
| LionClan | the cure of a sort is in the form of a truncated dystrophin, that begins and ends like normal dystrophin, but is missing the middle parts of the molecule | 23:43 |
| LionClan | treated muscle cells of patient with the 51-55 deletion showed dystrophin in the correct place on the cell walls the functional place, this is indication of normal cell integrity | 23:43 |
| LionClan | the effect was still there at the end of the trial | 23:44 |
| LionClan | there is no way of knowing it would ever stop working, that has not been observed | 23:44 |
| LionClan | for this exact deletion the skip lands in a readable frame; one of the few successes, this is a fortunate situation for these patients, while diappointing for the many more it does not cure | 23:45 |
| yashgaroth | please define "set up a sequencer to make the skip" | 23:46 |
| LionClan | the exact sequence required is known | 23:47 |
| yashgaroth | yes it is | 23:48 |
| yashgaroth | so what is this 51-55 variant, the sequence is missing those 5 codons? | 23:48 |
| LionClan | yes | 23:49 |
| yashgaroth | and you want to deliver the gene for a version that I assume is truncated by more than those 5 codons? | 23:49 |
| yashgaroth | links to papers are not required, but very useful | 23:50 |
| yashgaroth | ...also, since kanzure doesn't seem to be around, welcome to the channel | 23:51 |
| LionClan | the relevant parts of the truncated dystrophin created by the skip are the beginning and end, so though missing part of the sequence, the truncated dystrophin expresses in the cell walls, indicating functionality | 23:51 |
| LionClan | thank you | 23:51 |
| LionClan | I'm searching my logs for the relevant links | 23:52 |
| LionClan | and explaining as I go | 23:52 |
| yashgaroth | ohhh so you don't mean adding a truncated form of the gene, just making the already-present copy skip over the middle exons | 23:52 |
| LionClan | yes | 23:52 |
| LionClan | this has been done, however it was not the intent of the experiment | 23:52 |
| LionClan | the patient with the 51-55 deletion was included as an expected negative, and was accidentally cured | 23:53 |
| yashgaroth | heh | 23:53 |
| LionClan | the target, was the much more common 51 deletion | 23:54 |
| LionClan | they failed, because the skip lands in an unreadable frame | 23:54 |
| yashgaroth | oligos are not difficult to manufacture, which are what I assume they're using, or possibly plasmids encoding the oligos | 23:55 |
| NonFish[ | I believe the idea is to make antisense oligonucleotides used for causing exon skipping yes | 23:55 |
| LionClan | for this exact deletion, the 51-55 deletion, the skip lands in a readable frame; an accidental success | 23:55 |
| NonFish[ | targeted exon skipping that results in production of a slightly shorter but functional dystrophin | 23:56 |
| LionClan | NonFish[ and I have been talking about this for some time | 23:56 |
| yashgaroth | the more difficult part is delivering enough of the drug to every muscle in a useful amount | 23:56 |
| LionClan | it'sx injected into each muscle | 23:56 |
| LionClan | and was still functioning at the end of the trial some six months later | 23:57 |
| yashgaroth | using what delivery method? DNA injected by itself won't even enter cells, much less the nucleus | 23:57 |
| yashgaroth | are we talking viruses or what | 23:57 |
| LionClan | the truncated dystrophin created expressed in the cell walls, it's functional | 23:58 |
| LionClan | MDA is continuing their pursuit of a 51 skip, with no success | 23:59 |
| yashgaroth | minor aside, animals cells don't have cell walls, but it would be on the cell membrane or wherever dystrophin normally goes | 23:59 |
| LionClan | there's a picture of the stain, let me find that | 23:59 |
| --- Log closed Tue May 22 00:00:17 2012 | ||
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