--- Log opened Mon May 21 00:00:16 2012
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00:02 < kanzure> ok maybe not.. one last one:
00:02 < kanzure> http://www.violentacres.com/archives/193/what-would-happen-if-you-bought-25-bottles-of-nyquil/
00:05 < yashgaroth> hell yeah dxm
00:07 < Mokbortolan_> yeah, I guess it just shows a group of people's response to what they perceive as a threat to their community
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02:26 < joshcryer> Blender + BMesh + Precision Modelling Tools = Usable CAD Solution, imo: http://wiki.blender.org/index.php/User:Kellpossible
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06:20 < kanzure> beebooop
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08:15 < kanzure> nmz787: sorry for cutting out last night
08:23 < kanzure> "makerbot robot petting zoo".. man, why can't i have a robot petting zoo?
08:23 < chris_99> lol
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08:33 < strages_work> kanzure: you can http://en.wikipedia.org/wiki/BEAM_robotics
08:34 < kanzure> strages_work: paperclip robots were some of my first :)
08:36 < 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
08:40 < audy> http://xkcd.com/1058/ you've all ready it
08:40 < audy> already* read it
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08:57 < nmz787> its cool
08:58 < 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
08:59 < kanzure> huh? all i said was that svg/xml-based inputs to a toolpath generator didn't make sense
09:02 < 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
09:03 < nmz787> which would correllate to the line thickness you drew
09:04 < 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
09:08 < nmz787> thats not how it would work though, right?
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09:10 < 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
09:11 < kanzure> ThomasEgi: i don't really want to write a hpgl driver for parallax either. why is everyone so against linux all the sudden?
09:12 < 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
09:13 < 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
09:14 < 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?
09:15 < 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
09:16 < 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
09:17 < nmz787> but for driving a stepper
09:18 < ThomasEgi> wouldnt call it pixels. but steps instead.
09:19 < 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.
09:20 < 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
09:21 < ThomasEgi> you basically tell the microcontroller how many steps to take in which direction at what speed
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09:21 < kanzure> yes i know how steppers work (to the extent that electromagnetism doesn't make me scratch my head)
09:23 < ThomasEgi> so.. taking an arduino as "instruction buffer" and stepper controller. which receives the new commands over rs232 seems most reasonable to me
09:24 < kanzure> ok. so why would an sd card be used there?
09:27 < nmz787> high speed
09:27 < nmz787> no interruptions in data stream
09:27 < nmz787> no dependence on computer
09:28 < 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.
09:29 < nmz787> but i still think the shortest vector is literally going to be 1 movement unit up, and 1 movement unit right
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09:29 < nmz787> yeah SD is all done
09:29 < nmz787> download a library from parallax object repo
09:30 < nmz787> uses 1 of 8 cores
09:30 < ThomasEgi> guess the computer version allows ways more flexibility and interaction
09:31 < 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.
09:32 < 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
09:33 < ThomasEgi> not an issue as long as you can supply the instructions faster than you execute them
09:34 < 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
09:35 < 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
09:36 < 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
09:37 < 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.
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09:46 < nmz787> kanzure: 1000dpi is 25micron
09:47 < nmz787> well as fenn said, as long as its repeatable
09:48 < 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
09:49 < nmz787> gotta do what you gotta do
09:50 < 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
09:51 < 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
09:52 < nmz787> they sell them alltogether
09:56 < nmz787> audy: great comic!
09:56 < kanzure> copenhagen suborbitals test fire 2012-05-20 http://www.youtube.com/watch?v=Sk5S5Q3M4Ek
10:01 < 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
10:02 < kanzure> it's just an irssi problem
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10:54 < mensch> k
10:55 < mensch> eh, wrong window
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11:48 < 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?
12:08 < nmz787> prob made development easier with the dock
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13:25 < nmz787> http://www.youtube.com/watch?v=pOTWEPF925c&feature=g-all-u
13:27 < kanzure> what is it?
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13:53 < yashgaroth> well, it could be an improvement over less-specific molecules for blocking protein interactions
13:54 < kanzure> the video is about ligand binding? i haven't clicked yet, just want a title or something
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13:54 < yashgaroth> cup-shaped, negatively charged molecule that binds to parts of cytochrome c
13:55 < 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
14:03 < HEx1> wrt parallax: I have to recommend against the propeller, there's nothing even approaching a free toolchain
14:05 < 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
14:06 < 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
14:07 < 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
14:08 < 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
14:10 < nmz787> specifically the 8 cores with a sensible way to program parallelzation and synchronized independent control loops
14:10 < nmz787> and $8
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14:10 < 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
14:12 < 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
14:13 < 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
14:14 < 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.
14:15 < 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
14:16 < 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
14:17 < 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
14:18 < nmz787> with a $10 SD card and a $9 propeller it just seems worth it to get rid of buffer issues and timing concerns
14:19 < 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
14:20 < 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>
14:21 < 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
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14:22 < kanzure> the buffer issue- if it becomes one- can be solved with a downstream extra chip.
14:23 < nmz787> whats your proposed use of said chip?
14:24 < 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
14:29 < 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'
14:30 < 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
14:31  * HEx1 only now backlogs for the context in which his mental keyword matching triggered
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17:15 < 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.
17:20 < kanzure> man, i already hate peerj
17:21 < joshcryer> I hate $$$ for papers.
17:23 < docl> icky
17:24 < docl> pretty website tho
17:24 < docl> which to be blunt is much more than I can say for the SKDB project page
17:25 < 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
17:26 < 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
17:27 < 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
17:28 < 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
17:29 < kanzure> if i do their brochure, it's totally going to be some biohacking manifesto
17:30 < 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
17:31 < kanzure> i have never asked to review their badges/identification
17:31 < kanzure> although the agents' names appear in the news often
17:41 < yashgaroth> moving...where?
17:41 < yashgaroth> don't say DC
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17:44 < 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
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20:39 < n_bentha> hi
20:39 < kanzure> howdie
20:39 < n_bentha> still no new news :(
20:40 < nmz787> news about?
20:41 < n_bentha> diybionews2
20:42 < kanzure> oh. i haven't updated it because i'm lame.
20:42 < kanzure> you should give me things to add to it
20:43 < n_bentha> not in my job description
20:43 < nmz787> are you expecting something there?
20:44 < n_bentha> not really
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21:32 < 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
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23:35 < LionClan> hello
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23:42 < 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
23:43 < 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
23:44 < 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
23:45 < 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
23:46 < yashgaroth> please define "set up a sequencer to make the skip"
23:47 < LionClan> the exact sequence required is known
23:48 < yashgaroth> yes it is
23:48 < yashgaroth> so what is this 51-55 variant, the sequence is missing those 5 codons?
23:49 < 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?
23:50 < yashgaroth> links to papers are not required, but very useful
23:51 < 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
23:52 < 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
23:53 < LionClan> the patient with the 51-55 deletion was included as an expected negative, and was accidentally cured
23:53 < yashgaroth> heh
23:54 < LionClan> the target, was the much more common 51 deletion
23:54 < LionClan> they failed, because the skip lands in an unreadable frame
23:55 < 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
23:56 < 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
23:57 < 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
23:58 < LionClan> the truncated dystrophin created expressed in the cell walls, it's functional
23:59 < 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
--- Log closed Tue May 22 00:00:17 2012