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| gmaxwell | So... self/less semi-scifi action movie; which is arguably kind of anti-transhumanism. Though I wonder if, to the extent it has any effect at all, if it would have a pro-transhumanism or anti-transhumanism effect. E.g. "bad rich people do mind-transfer immortality" vs "holy shit maybe mind-transfer immortality could be possible?" | 01:46 |
|---|---|---|
| * fenn blinks | 01:50 | |
| fenn | thought i had switched to the wrong channel for a sec | 01:50 |
| fenn | stargate had a whole thing about the ancients and mind uploading technology that went on forever (i didn't watch most of it) | 01:53 |
| fenn | are you proposing making a movie, or asking about existing movies? | 01:54 |
| gmaxwell | There is an existing move, just out in theaters; that I'm semi-whining about. | 01:56 |
| gmaxwell | I could (not too accurately) describe it as a remake of freejack. | 01:57 |
| gmaxwell | in any case, without giving too much away. Not super nice Billionare is dying of cancer. Mysterious scientists offer him a process to trasfer into a new body. Process works, but then a bunch of stuff happens mostly because a "sci fi" movie can't exist without lots of explosions. | 01:58 |
| gmaxwell | Misses a great oppturnity to paint an interesting morally grey story; instead opts for cartoon villany. But the on topic context is I wonder if (in the unlikely event the movie influences public opinion at all) if that influence might be anti-transhumanist (as the movie seems to be at face value) or pro- just by virtue of getting people thinking. | 02:00 |
| fenn | oh i had dismissed that offhand because it should have been based on "i will fear no evil" in the first place | 02:04 |
| fenn | https://en.wikipedia.org/wiki/I_Will_Fear_No_Evil | 02:04 |
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| fenn | it's not like any of this is new | 02:08 |
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| fenn | a movie like "limitless" seems more down to earth, while actually representing enhancements in a positive light | 02:12 |
| fenn | most pop culture portrays technology as ambivalent at best, as if it would have existed anyway and we're all just along for the ride | 02:16 |
| fenn | there's almost never a sense that hey, we have this problem, and it sucks, but then someone fixed the problem with technology | 02:17 |
| fenn | something about story archetypes | 02:17 |
| gmaxwell | yea, limitless was fun. Yea, well a fun thing to watch in movies: no one ever reads, researches, designs, thinks, invents.. I think because these processes are mostly inward and thus boring to show in a movie. | 02:18 |
| Adlai | Gattaca was about as good as it can get while maintaining homage to the indomitable human spirit | 02:18 |
| fenn | -_- | 02:18 |
| Adlai | no? | 02:19 |
| fenn | gattaca is a lame straw man | 02:19 |
| fenn | not a shining example | 02:19 |
| * Adlai isn't citing it as a strawman | 02:19 | |
| fenn | ok so you're saying gattaca is promoting technology as a positive force? please explain | 02:20 |
| Adlai | so terrible, that the kid's dream is to fly to mars | 02:20 |
| Adlai | this requires a bit of technology | 02:21 |
| Adlai | sure there's also "misuse" of technology in that movie, but there are plenty of cool aspects | 02:21 |
| fenn | it only requires him passing an onerous entrance exam based mostly on societal prejudices | 02:21 |
| Adlai | which stick with you is largely a matter of biases and maybe having the movie presented as a strawman too many times | 02:21 |
| gmaxwell | Gattaca appeared to have a considerable public policy impact in the US. (GINA) | 02:22 |
| gmaxwell | Fortunately not a greviously bad one (AFAIK) | 02:22 |
| * Adlai saw it many years after the fact, in an open minded context | 02:22 | |
| Adlai | gmaxwell: which movie did you semi-whine about? | 02:25 |
| gmaxwell | Adlai: "self/less" | 02:26 |
| * Adlai parsed that as adjectival | 02:26 | |
| Adlai | ... and there's another terminator movie!? maybe this one i'll skip. | 02:27 |
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| fenn | has anyone read "the terminal experiment"? | 02:29 |
| * Adlai has begun the long-overdue GEB | 02:31 | |
| JayDugger | Yes, fenn. | 02:31 |
| gmaxwell | Adlai: oh wow, you've not read GEB? | 02:32 |
| JayDugger | Never too late to read GEB. | 02:32 |
| Adlai | "metamagical themas" got me programming for fun, but that was years ago and it's time to fix the omission | 02:34 |
| fenn | http://fennetic.net/irc/the_terminal_experiment.pdf haven't read it but the plot summary on wikipedia sounded relevant | 02:35 |
| JayDugger | I read it when serialized, and well, I think you can do better with your reading time. | 02:37 |
| fenn | hum ok | 02:37 |
| JayDugger | I am not a fan of Robert Sawyer, to put it politely. | 02:37 |
| JayDugger | If you want to read philosophical SF, pick a random book by Lem or Egan. You'll do better. | 02:38 |
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| fenn | i like ted chiang's books; they're similar | 02:38 |
| JayDugger | If you want to read SF that explores religion, pick, in order of relevance, Blish's A Case of Conscience, Zebrowski's Cave of Stars, or anything by Stapledon. | 02:39 |
| JayDugger | Let me look at a list of Chiang's works. I might not have read anything by him. | 02:39 |
| fenn | oh i thought "the terminal experiment" was about mind uploads escaping into the internet, and the "soul wave" thing was just technobabble | 02:40 |
| gmaxwell | Adlai: GEB was essential to meeting my partner, in fact. | 02:40 |
| JayDugger | No, more like the other way around, IIRC. | 02:40 |
| JayDugger | Read Platt's The Silicon Man for a better uploading story. | 02:40 |
| gmaxwell | Re uploading stories. gwillen related to me a story he forgot the name of where someone was scanned and the data open sourced after the simulation failed to work... anyone know what story that was? | 02:42 |
| JayDugger | For the record, I've nothing against religion or OOBE or NDE or the like in SF. I think Sawyer's overrated, and that he won his various awards through lack of competition. | 02:42 |
| JayDugger | Do you remember what year, gmaxwell, and what length? Novel? Short story? | 02:43 |
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| fenn | http://fennetic.net/irc/Charles_Platt_-_The_Silicon_Man.pdf | 02:43 |
| gmaxwell | JayDugger: I believe a novel, impression I had was that it was relatively recent. (also because if it were fairly old the liklyhood that I would have read it would be much greater). | 02:44 |
| JayDugger | That's it, yes. | 02:44 |
| JayDugger | This decade? This century? | 02:44 |
| gmaxwell | This decade seems more likely. | 02:45 |
| gmaxwell | Are there many uploading stories outside of this century? Ah do I need to specify that I'm talking about a book that has already been written (date is not in the future). :) | 02:46 |
| JayDugger | Platt wrote in the 1990s. | 02:46 |
| JayDugger | If I did a little research, I could probably find older stories too, though I doubt many if any before 1970 or so. | 02:46 |
| JayDugger | Failed uploads show up in Alastair Reynolds Conjoiner setting, Revelation Space, etc. | 02:47 |
| JayDugger | Those are from the 2000s. | 02:47 |
| JayDugger | Egan wrote Permutation City in the 1990s, too. | 02:48 |
| JayDugger | fenn, I don't think I've read anything by Chiang. | 02:48 |
| gmaxwell | I've recommended permutation city in the past to lots of people; basically required reading before any of the more recent singularity fiction the asks you to accept an awful lot of stuff. | 02:49 |
| Adlai | what about zindell? | 02:50 |
| * Adlai hasn't read the lightbringer series, but neverness & its sequels were great | 02:50 | |
| fenn | JayDugger: mostly short stories.. i recommend "understand" and "story of your life" | 02:51 |
| Adlai | http://www.infinityplus.co.uk/stories/shanidar.htm | 02:51 |
| JayDugger | https://en.wikipedia.org/wiki/Mind_uploading_in_fiction | 02:52 |
| JayDugger | My guess of 1970 was too late. | 02:52 |
| JayDugger | What about Zindell? | 02:53 |
| Adlai | philosophical SF that explores religion | 02:54 |
| JayDugger | Good point, but you could say the same about Frank Herbert's major works. | 02:55 |
| Adlai | sure | 02:55 |
| Adlai | but herbert's name is thrown around a lot more often than zindell's | 02:55 |
| JayDugger | I stick with the examples I gave earlier, because they don't pussyfoot around with fictional religions. | 02:56 |
| JayDugger | Except for Stapledon, but he gets mentioned because of the early time when he wrote. | 02:56 |
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| JayDugger | Reading the Wikipedia article (above), I'd forgotten Benford's Eater. | 02:57 |
| JayDugger | That's not really about religion per se, but it does involve mind uploading, human sacrifice, and propitiating an angry god. | 02:58 |
| JayDugger | gmaxwell, I am sorry I couldn't help, but I have no idea what work you have in mind. | 03:01 |
| gmaxwell | JayDugger: thanks in any case; I only asked because the subject came up. | 03:02 |
| gmaxwell | :) | 03:02 |
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| kanzure | "And even they often do not succeed in correcting the problem. Cryonics cases involve hugely varying clinical presentations, disease histories, ischemic intervals, available technical, social and financial resources, and on and on. This kind of situation cannot currently be automated, and to truly automate it would require something approaching global, or mature AI. It would also (currently) be unbelievably expensive since in order not ... | 06:10 |
| kanzure | ... be overridden, it would require robotic control of the patient from pre-pronouncement through long term storage in LN2." | 06:10 |
| kanzure | "You should also look at what nature has done vis a vis the problem of freezing in living organisms. There is huge, indeed absolutely enormous evolutionary pressure to adapt complex living systems like big mammals to tolerate freezing. Energetically, it is by far the most economical approach. And yet, beyond very small scales nature does not do this. Antarctica is littered with the corpses of mammals and birds who froze death and full of ... | 06:13 |
| kanzure | ... mammals and birds who go to absurd and very energetically costly extremes to AVOID freezing at all costs. Penguins, the Weddel and Elephant seals all avoid freezing, even though it would be far more energetically and practically sensible to simple to just solidify and wait until till summer comes. Why? Why does nothing bigger than a tree frog freeze? Why are the few organisms that do tolerate "freezing" all very small and all ... | 06:13 |
| kanzure | ... carefully control where and how much ice forms?" | 06:13 |
| kanzure | "Let me put it to you another way. If you set out to create mammals that could tolerate being run over by a steam roller by progressively crushing them generation after generation what you end up with if you succeeded? And how applicable would it be the mammals you stated with? Maybe even more to the point, would it be physically possible and how long would it take and what would it cost? Remember also that not every thing we want living ... | 06:13 |
| kanzure | ... systems to do is doable." | 06:13 |
| kanzure | heh | 06:13 |
| kanzure | so for his comment about why don't penguins just wait it out, that's not really fair because perhaps they stumbled into the method of avoiding freezing first (local minima/maxima) | 06:17 |
| JayDugger | What source has that pasted quote? | 06:31 |
| kanzure | private correspondence with mike darwin, lord of the frozen realm | 06:33 |
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| JayDugger | Got it. Thanks. | 06:42 |
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| kanzure | .title http://spaceprob.es/ | 06:46 |
| yoleaux | spaceprob.es catalogs the active human-made machines that freckle our solar system | 06:46 |
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| heath | https://github.com/ruuvi | 09:00 |
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| heath | they are moving from the da14581 to a nrf52 in v2 of ruuvitag | 09:01 |
| heath | i'm so excited to see this | 09:01 |
| * heath hopefully doesn't have to depend upon estimote in the future | 09:02 | |
| heath | announcement: http://ruuvi.com/blog/ruuvi-goes-fully-open-source.html | 09:04 |
| heath | firmware will be released in about a week i'm told | 09:04 |
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| juri_ | yay, more Free Hardware. :) | 10:46 |
| juri_ | I need to get my Pick and Place system going. | 10:47 |
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| CaptHindsight | kanzure: updated specs sent | 10:53 |
| kanzure | coolio, lunch first then i will review | 10:53 |
| kanzure | CaptHindsight: reasons for vacuum chuck? just curious | 11:08 |
| kanzure | phosphoramidite images are hard to figure out | 11:09 |
| kanzure | (photos) | 11:10 |
| CaptHindsight | kanzure: that is how they held the sample slides in place | 11:15 |
| kanzure | hm well okay, makes sense- it's easier than the clip that microscopes use | 11:15 |
| CaptHindsight | it also would remove any excess wash fluid from the underside of the sample slides | 11:15 |
| CaptHindsight | yeah | 11:16 |
| kanzure | CaptHindsight: juri_ is willing to do some reverse engineering for the piezo control. should we just have her do the fpga + board? | 11:18 |
| CaptHindsight | I already have it | 11:19 |
| CaptHindsight | i just need to verify the new 1420 head | 11:20 |
| juri_ | you already have the head reverse engineered? | 11:20 |
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| CaptHindsight | kanzure: this image? http://imagebin.ca/v/28P4N0YwuKK6 this | 11:21 |
| CaptHindsight | juri_: yes, it's not just reversing | 11:21 |
| kanzure | yeah... i see something being held, i see some tubes. uh.. | 11:22 |
| kanzure | i see some stuff behind the tubes | 11:22 |
| juri_ | what's needed? | 11:22 |
| CaptHindsight | the original POSaM team did not understand the printhead operation | 11:22 |
| CaptHindsight | they just saw a firing pulse and tried to copy it | 11:22 |
| CaptHindsight | the firing pulse shape is the heart of piezo inkjet | 11:23 |
| CaptHindsight | juri_: I need to merge Mesa hm2 cnc control VHDL with printhead VHDL | 11:23 |
| CaptHindsight | and make it open | 11:23 |
| juri_ | since you're using different fluids that have a different surface tension.. | 11:24 |
| CaptHindsight | the Mesa stuff already is | 11:24 |
| juri_ | OK. i can do that. | 11:24 |
| juri_ | what's the timescale? | 11:24 |
| CaptHindsight | yes, waveforms are even patented to block competitors | 11:24 |
| CaptHindsight | I can have the printer up in August | 11:25 |
| juri_ | damn. then i need to start now-now. | 11:25 |
| CaptHindsight | I'm also going to out whatever doesn't fit into the Mesa IO board onto the printhead controller | 11:26 |
| CaptHindsight | out/put | 11:27 |
| CaptHindsight | juri_: you have a drop watcher? | 11:27 |
| juri_ | Nope. | 11:27 |
| juri_ | SEM, and CNC'd microscopes (with lasers!)... | 11:27 |
| CaptHindsight | nice but not how it works | 11:28 |
| CaptHindsight | I have to build the analog board for the printhead as well | 11:29 |
| juri_ | yea, i'm behind the curve on this. been busy 3d printing metals... | 11:29 |
| CaptHindsight | we can stuff the cnc control and printhead control into the Mesa FPGA | 11:29 |
| CaptHindsight | then use the provided IO on the Mesa board to get the digital signals off to the DAC/analog board | 11:30 |
| CaptHindsight | Mesa also has some new control blocks for the FPGA in the works that might be used for the printhead | 11:31 |
| juri_ | you got links to what you're currently running on the mesa? | 11:31 |
| CaptHindsight | talking to them right now | 11:31 |
| juri_ | It's been a few years since i've touched VHDL. | 11:31 |
| CaptHindsight | it's all on the Mesa site | 11:31 |
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| CaptHindsight | kanzure: the images from the POSaM doc aren't too clear | 11:33 |
| kanzure | agreed | 11:33 |
| CaptHindsight | they just run line from the vials to the printhead | 11:34 |
| CaptHindsight | needle through septum, line , line over fluid inlets to printhead | 11:34 |
| kanzure | i think the abi machines had two lines into each vial, one for gas and another for material to be pushed up (or down?) | 11:34 |
| CaptHindsight | another thing that the POSaM team did not understand | 11:35 |
| kanzure | perhaps they just didn't specify it | 11:35 |
| CaptHindsight | printheads require the right amount of negative pressure behind the jet, you also want positive pressure to flush if clogged or purge the chamber | 11:36 |
| juri_ | POSaM doc? link? | 11:37 |
| kanzure | http://bioinformatics.org/pogo/ | 11:38 |
| kanzure | http://bioinformatics.org/pogo/POSAM_Man_Ch1_Assembly_v1-2_040601.pdf | 11:38 |
| kanzure | http://bioinformatics.org/pogo/POSAM_Man_Ch2_User_v1-0_040414.pdf | 11:38 |
| CaptHindsight | http://imagebin.ca/v/28PAVbNVLF7x the other pic with the vials and drying nozzles | 11:40 |
| CaptHindsight | http://www.mesanet.com/software/parallel/5i24.zip Mesa hm2 files | 11:41 |
| CaptHindsight | I listed the Epson 1420 as the printhead earlier, it is actually the 1430 | 11:44 |
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| juri_ | ok, i'm going to need a few hours to digest all of this. | 11:46 |
| CaptHindsight | it has 90 nozzles per channel for a total of 540 nozzles vs the POSaM's Epson 700 printhead that had only 192 nozzles | 11:47 |
| CaptHindsight | the Epson spec in the POSaM doc does not apply | 11:48 |
| CaptHindsight | the analog (DAC) board is for the Epson 700 | 11:48 |
| CaptHindsight | the new analog board will mop up anything that doesn't fit into the off the off the shelf Mesa cards | 11:49 |
| CaptHindsight | I'm going to take my VHDL for the printhead control and build a block that will work with Mesa's hm2 blocks in the FPGA | 11:52 |
| CaptHindsight | kanzure: gets the fun of writing a g-code generator that starts with DNA sequences | 11:53 |
| CaptHindsight | and cuts them up into smaller pieces that will be printed onto the slides | 11:54 |
| CaptHindsight | he gets to also generate the bitmaps for each print layer | 11:54 |
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| juri_ | sounds like fun. ;) | 12:44 |
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| kanzure | is the fpga going to have a gcode parser/interpreter? | 12:54 |
| CaptHindsight | Linuxcnc does | 12:59 |
| CaptHindsight | Linuxcnc does it all! well almost | 12:59 |
| CaptHindsight | http://www.linuxcnc.org/binary.hybrid.iso | 13:00 |
| CaptHindsight | kanzure: http://wiki.linuxcnc.org/cgi-bin/wiki.pl?EMC_Components for a quick overview of how Linuxcnc is put together and features | 13:03 |
| CaptHindsight | is has a simulators so you can preflight the printing | 13:04 |
| CaptHindsight | you also get a choice of several GUI's | 13:05 |
| CaptHindsight | you gave to decide if you want something all together new or just modify something that's been done for machine control | 13:06 |
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| CaptHindsight | there is also a HAL to make it easy to configure and tie components or signals together | 13:22 |
| CaptHindsight | http://linuxcnc.org/docs/html/hal/intro.html | 13:22 |
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| CaptHindsight | http://linuxcnc.org/docs/html/hal/basic_hal.html | 13:22 |
| CaptHindsight | http://linuxcnc.org/docs/html/hal/tutorial.html | 13:23 |
| CaptHindsight | the DNA printer is pretty simple so the HAL config take only a few minutes | 13:23 |
| kanzure | looking at hal things | 13:36 |
| kanzure | "The command loadusr loads a user space HAL component. User space programs are their own separate processes, which optionally talk to other HAL components via pins and parameters. You cannot load real time components into user space." | 13:37 |
| kanzure | ah i see, | 13:38 |
| kanzure | "The command loadrt loads a real time HAL component. Real time component functions need to be added to a thread to be updated at the rate of the thread. You cannot load a user space component into the real time space." | 13:38 |
| kanzure | okay then | 13:38 |
| kanzure | aha, http://linuxcnc.org/docs/html/hal/halmodule.html | 13:39 |
| kanzure | while 1: time.sleep(1); h['out'] = h['in'] | 13:40 |
| kanzure | simple enough, fire up the patent machine..... | 13:44 |
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| kanzure | "Wood frog adaptations to overwintering in Alaska: new limits to freezing tolerance" http://jeb.biologists.org/content/217/12/2193.full | 14:07 |
| kanzure | "Lower lethal temperatures in wood frogs have been reported as near −7°C (Layne et al., 1998), with a recent account, however, of survival of frogs from Alaska cooled to −16°C in the laboratory (Costanzo et al., 2013). In subarctic Interior Alaska, wood frogs overwinter in the subnivean space covered by duff and leaf litter (Kirton, 1974), where temperatures can remain below freezing for over 6 months with minima near −20°C ... | 14:11 |
| kanzure | ... (Barnes et al., 1996; Sformo et al., 2010). These extreme temperatures combined with previously reported limits to freeze tolerance would suggest that high mortality of wood frogs occurs in Interior Alaska." | 14:12 |
| kanzure | "We considered that wood frogs began to freeze when soil temperatures were below −1.6°C (lowest observed exotherm in 2011 and 2012) and thawed when temperatures were above −0.16°C, based on the melting point of wood frogs determined previously (Sinclair et al., 2013)." | 14:12 |
| kanzure | melting point of wood frogs... well, okay. | 14:12 |
| drethelin | heh | 14:15 |
| kanzure | .wik https://en.wikipedia.org/wiki/Mark_Roth_(scientist) | 14:21 |
| yoleaux | kanzure: Sorry, that command (.wik) crashed. | 14:21 |
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| kanzure | dpk: isbugmuch | 14:22 |
| dpk | god fucksake dammit | 14:22 |
| dpk | why the fuck is that fucking broken | 14:22 |
| kanzure | .wik http://en.wikipedia.org/wiki/Mark_Roth_(scientist) | 14:24 |
| yoleaux | kanzure: Sorry, that command (.wik) crashed. | 14:24 |
| kanzure | .wik mark roth (scientist) | 14:24 |
| yoleaux | "Mark Roth (born 1957) is an American biochemist, and director of the Roth Lab at the Fred Hutchinson Cancer Research Center. He is a professor at the University of Washington." — https://en.wikipedia.org/wiki/Mark_Roth_(scientist) | 14:24 |
| dpk | ah | 14:25 |
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| juri_ | is there a page where we have documented which print head comes from which epson printer, or gotten that from the vendor? | 14:37 |
| CaptHindsight | Epson 1430 and I can get them from the factory in bulk | 14:38 |
| CaptHindsight | Epson only releases specs under multiple NDA's | 14:38 |
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| CaptHindsight | the inkjet industry makes Intel and BIOS docs look like open source :) | 14:39 |
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| juri_ | figgures. i had arleady standardized on the 440/600/640 for my PCB printing. | 14:39 |
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| CaptHindsight | we can print pcb's including the substrates and the conductors all from fluids | 14:43 |
| CaptHindsight | it's more like multiwire than a pcb with layers since you're not plating and bonding multiple 2 layer boards together | 14:44 |
| CaptHindsight | SLA + Injket | 14:45 |
| CaptHindsight | it should cost less and be faster than traditional multilayer fabrication | 14:45 |
| juri_ | sounds like a winner to me. i was just laying down resist. | 14:46 |
| CaptHindsight | it's another patent minefield | 14:47 |
| juri_ | I'm not interested in patents. in fact, i develop 3d printing technologies in the open explicitly to prevent others from patenting the good stuff. | 14:47 |
| juri_ | you watch my video yet? | 14:48 |
| CaptHindsight | the aluminum? yes | 14:48 |
| CaptHindsight | the problem is that others patent the obvious | 14:49 |
| juri_ | yes, the system is broken. | 14:50 |
| CaptHindsight | even after watching your videos | 14:50 |
| CaptHindsight | "hey I have a video on youtube for that process" | 14:50 |
| juri_ | it's good prior art.. :) | 14:51 |
| CaptHindsight | too bad you did file since megacorp X did, now they have the patent, we invalidated your video | 14:51 |
| CaptHindsight | did not file | 14:51 |
| juri_ | I've got a good lawyer for this... ;) | 14:51 |
| CaptHindsight | the problem is that they don't look for prior art | 14:52 |
| juri_ | while it's not a situation i want to be in... | 14:52 |
| CaptHindsight | or ignore it | 14:52 |
| CaptHindsight | once they get the patent it's difficult to remove it | 14:52 |
| CaptHindsight | yeah, it's very broken | 14:53 |
| juri_ | well then, let's invent this stuff, thes argue about what to do about it. ;) | 14:53 |
| CaptHindsight | the inkjet is pretty simple | 15:00 |
| CaptHindsight | V2 DNA synthesizer will be a bit more elaborate | 15:01 |
| CaptHindsight | there are lots of tools to make for sub-micron manufacturing | 15:01 |
| CaptHindsight | tools used to make much more complex machines | 15:02 |
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| juri_ | we've been building a giant cnc setup here. we're going to mount lasers on it, but if you want me to help, i'll just add one of these inkjet heads. | 15:03 |
| CaptHindsight | low cost Focused Ion Beam, SEM, lithography equipment, etc | 15:03 |
| juri_ | exxactly. hense, our SEM. | 15:04 |
| juri_ | do you happen to be in the DC area? | 15:04 |
| CaptHindsight | I'm near Chicago and I'm often in China/Taiwan | 15:05 |
| juri_ | ah. no dice. :) | 15:05 |
| juri_ | tell, i'm a director of http://hacdc.org/ . our equipment is listed on the wiki, and as expected, our designs are all online. | 15:07 |
| CaptHindsight | I usually work with industrial printheads | 15:07 |
| CaptHindsight | so if the Epsons are a problem in the long run we can change to something else | 15:07 |
| CaptHindsight | Fuji, Xaar, RPSA, Seiko, ITW etc | 15:09 |
| juri_ | so, are we thinking the mesa 5i24? | 15:12 |
| CaptHindsight | 6i24 PCIe version | 15:13 |
| CaptHindsight | same files as the 5i24 | 15:13 |
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| CaptHindsight | I already talked to Mesa about using their new blocks for raster applications | 15:14 |
| CaptHindsight | I didn't know they were working on something similar | 15:16 |
| juri_ | Interesting. | 15:17 |
| juri_ | do we have prices yet? i need to know how much i'm about to sink... | 15:17 |
| juri_ | my current FPGA is only half of one of those. | 15:17 |
| CaptHindsight | I already have them | 15:17 |
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| juri_ | neat. | 15:18 |
| CaptHindsight | we build machines all the time | 15:20 |
| kanzure | :-) | 15:21 |
| CaptHindsight | mesa 6i24 is $140 | 15:22 |
| streety | I would love to see mass spec added to the list of low cost equipment to work on | 15:22 |
| CaptHindsight | streety: yes another good one that is not too complicated | 15:22 |
| streety | indeed | 15:24 |
| kanzure | CaptHindsight: thanks for the links, makes 100% sense now | 15:25 |
| kanzure | (HAL stuff) | 15:26 |
| CaptHindsight | kanzure: no problem | 15:26 |
| CaptHindsight | we won't even have to touch it except for the config file | 15:26 |
| CaptHindsight | HAL can also run stand alone | 15:26 |
| kanzure | HAL is how i'll do the integration with a custom application | 15:26 |
| kanzure | to read/write on pins | 15:27 |
| CaptHindsight | yeah, thats how it's done | 15:27 |
| kanzure | i wonder if i can run linuxcnc in a virtual machine, without the realtime stuff | 15:28 |
| CaptHindsight | if you don't need real time | 15:28 |
| kanzure | ah good. i suspect not (for development). | 15:28 |
| CaptHindsight | otherwise nope | 15:29 |
| juri_ | I'm way too used to just procgramming a microcontroller to do this stuff. | 15:29 |
| juri_ | you played with the propeller chips? | 15:30 |
| kanzure | technically no | 15:30 |
| kanzure | but don't tell nobody | 15:30 |
| juri_ | the VHDL is available, so we can always just upload one into the FPGA... | 15:30 |
| CaptHindsight | kanzure: the SIM's will run on the VM | 15:32 |
| CaptHindsight | so you can make your mods to HAL and test, just not in real time | 15:33 |
| kanzure | excellent | 15:34 |
| kanzure | we're going to have to name this thing | 15:34 |
| kanzure | let's throw a few webcams into the system too | 15:36 |
| kanzure | "oligoweaver" (yuck) | 15:39 |
| CaptHindsight | olig-o-matic | 15:40 |
| kanzure | i think that one might be taken already | 15:40 |
| CaptHindsight | Ernie? | 15:40 |
| kanzure | oh weird maybe not... dr. oligo is taken. | 15:40 |
| kanzure | "deep space probe 3" (perhaps a little too absurd....) | 15:47 |
| juri_ | v'ger 12. | 15:56 |
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| CaptHindsight | My First Little Oligo Printer | 16:00 |
| CaptHindsight | Mr Mutate | 16:01 |
| juri_ | easy bake monster creation kit. | 16:01 |
| kanzure | heh | 16:02 |
| CaptHindsight | Hybrids-r-us | 16:02 |
| CaptHindsight | the fun is yours | 16:03 |
| kanzure | genesis 2 | 16:03 |
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| juri_ | welp, i'm going to read all of this. the FPGA boards look like the right call. | 17:30 |
| kanzure | peacemaker / piecemaker | 18:36 |
| kanzure | "necessary evil" (just kidding... that name was used by uh, something else) | 18:39 |
| kanzure | maybe it should be called "mutually assured peace" | 18:42 |
| kanzure | "nucleic peacemaker" has a nice ring to it, i dunno | 18:42 |
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| juri_ | We've got a drop detection system here for medical purposes that we've designed, based on an LED and photodiode. this system is using red lasers. hmmm... | 18:47 |
| juri_ | i guess the big question is just what parts of this you want help with, and what sort of time scale you're looking at. | 18:49 |
| juri_ | I'd like a microfluidic distribution system on my big printer, but not for the purposes of biology. I'm still building things. | 18:50 |
| kanzure | turns out that he has all of the parts ready to go, just needs me to write a bitmap to HAL program | 18:50 |
| kanzure | and some other gcode things that i'm not entirely clear about (perhaps my program is supposed to generate gcode?) | 18:50 |
| CaptHindsight | either g-code or we use the same g-code | 18:51 |
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| juri_ | i noticed how primitive the waveform documentation is in this. | 18:51 |
| CaptHindsight | with the same preplanned scans for the head | 18:51 |
| CaptHindsight | and just the bipmap changes for each layer | 18:52 |
| juri_ | i mean, functionality first, but not enough math. | 18:52 |
| CaptHindsight | juri_: they were working without specs for the printhead | 18:53 |
| CaptHindsight | plus they were using a printhead from 3-4 generations ago | 18:54 |
| juri_ | do you want a better spec for the printhead you're dealing with? | 18:54 |
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| kanzure | CaptHindsight: so is my program responsible for generating gcode and sending it down the pins? | 18:54 |
| CaptHindsight | no, I'm all set | 18:54 |
| CaptHindsight | kanzure: linuxcnc takes the gcode for motion control | 18:55 |
| juri_ | wow. ok, so you don't need my help afterall. ;) | 18:55 |
| kanzure | but then how does the gcode keep in sync with the other commands? | 18:55 |
| CaptHindsight | we can use custom M codes to tell the printhead controller when a scan has started | 18:55 |
| CaptHindsight | what the printhead controller needs is the strip of bitmap for each scan pass in the direction it is traveling | 18:56 |
| CaptHindsight | the strip that matches the print swath of the printhead | 18:56 |
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| CaptHindsight | the g-code interpreter in Linuxcnc will handle all the motion commands, and it can toggle a pin in HAL when it gets M code to tell the printhead controller when it is going to start a scan | 18:59 |
| CaptHindsight | then the printhead controller will need the bitmap for that scan | 19:00 |
| CaptHindsight | the printhead controller will be synched to the encoder output that can be gated by HAL | 19:00 |
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| CaptHindsight | but to directly answer you question, the gcode gets run by Linuxcnc line by line | 19:02 |
| CaptHindsight | Linuxcnc is keeping track of the machine position by counting pulses from the encoders | 19:03 |
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| CaptHindsight | when Linuxcnc reaches the end of the last command it runs the next command | 19:04 |
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| CaptHindsight | be back in a bit | 19:07 |
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| kanzure | oh, linuxcnc generates gcode in real-time as well? hm. got any links? | 19:32 |
| wrldpc1 | Richard Stallman has the strangest list of demands for giving a speech I have ever read. | 19:34 |
| wrldpc1 | .title https://groups.google.com/a/mysociety.org/forum/#!msg/mysociety-community/zkyZpOXjgoQ/_8xyXSxv9zYJ | 19:34 |
| yoleaux | Google Groups | 19:34 |
| wrldpc1 | ^ heh | 19:34 |
| kanzure | lots of people have various demands like that | 19:34 |
| kanzure | my demand list is "just let me speak" at the moment | 19:34 |
| kanzure | oh and pay me | 19:35 |
| kanzure | and wine and dine me i think | 19:35 |
| kanzure | .. hm maybe i should write these down. | 19:35 |
| wrldpc1 | :) | 19:35 |
| wrldpc1 | “If you can find a host for me that has a friendly parrot, I will be | 19:35 |
| wrldpc1 | very very glad. If you can find someone who has a friendly parrot I | 19:35 |
| wrldpc1 | can visit with, that will be nice too.” | 19:35 |
| drethelin | heh | 19:36 |
| wrldpc1 | I need to learn how to irc. | 19:36 |
| drethelin | that kind of thing might be just a check | 19:37 |
| drethelin | to see if they read all his demands | 19:37 |
| wrldpc1 | haha yeah | 19:37 |
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| wrldpc1 | What is the coolest or most notable research currently being conducted at SRI? | 19:59 |
| wrldpc1 | Also .. | 19:59 |
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| wrldpc1 | My San Fran trip next month is still on. I know I asked this before (and I got a lot of good feedback) but if anyone has any access to any strange/interesting science/technology-related places please holler at me. Does anyone know anyone at Cambrian Genomics who could arrange a visit? On my list so far .. Tech Museum of Innovation, Noisebridge, Google (S.F. offices), The Computer Museum, Moffett Field (Ames Research tour) | 20:01 |
| wrldpc1 | I’d like to get more substantive access to Google .. particularly Moffett Google but know no one. PARC, Tesla, Apple, Pixar .. all on my list as well. | 20:02 |
| wrldpc1 | SRI as well but I feel like I need some reason beyond “I’m interested in science.” | 20:02 |
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| CaptHindsight | kanzure: Linuxcnc does not generate G-code | 20:09 |
| CaptHindsight | G-code is input to Linuxcnc and the interpreter turns that into motion | 20:10 |
| CaptHindsight | I think I'll have to write up a spec on our options for the G-code | 20:11 |
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| CaptHindsight | kanzure: what you or someone will have to write is a G-code generator that start with oligo sequences | 20:14 |
| CaptHindsight | then take those sequences and break them up into target locations on the tray | 20:15 |
| CaptHindsight | each base layer looks like it has a pretty similar preset routine | 20:16 |
| CaptHindsight | if the drop size and nozzle pitch match what the sample patterns are then you can fire up to 90 of the same base channel nozzles at the same time | 20:19 |
| CaptHindsight | if the nozzel pitch for the other channels also lines up to the sample patterns then you can fire 4 base channels at the same time (90 nozzles to each channel) | 20:20 |
| CaptHindsight | G-codes for the positions of the samples, M-codes to fire drops | 20:23 |
| CaptHindsight | M-codes to turn the drying nozzles on and off | 20:24 |
| CaptHindsight | M-codes to turn wash solenoids on/off | 20:25 |
| super` | Hi, I've assembled an OpenPCR.. and I'm wondering what would be the best approach to get a readout on my saliva as a test.. is the gel electrophoresis with agarose gel still the best approach? (FYI: The DNA Computing course I took was ~15yrs ago and didn't have any lab time, so I know the theory but lack in practical) Are there better ways to get a readout now? | 20:25 |
| super` | ..and I'm more interested in working with oligo on combinatorial problems than I am Bioinformatics (once I'm sure my setup works, if that [D[Dmakes a difference) | 20:27 |
| kanzure | CaptHindsight: okay understood. so once i generate the gcode, the fpga will interpret the gcode? or should i interpret the gcode and convert to pin firing patterns. | 20:29 |
| kanzure | oh wait, nevermind. you already answered this. | 20:30 |
| CaptHindsight | kanzure: linuxcnc will interpret the motion G-code and be able to toggle pins for M-codes | 20:30 |
| CaptHindsight | but we still have to sync bit maps in a frame buffer to the positions of the printhead or drying nozzles | 20:31 |
| CaptHindsight | the printer will need 2 files | 20:31 |
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| CaptHindsight | one being G-code, and the other being bit maps for all the layers of printing | 20:32 |
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| kanzure | i'll have to figure out how to dump gcode in real-time into linuxcnc. looking... | 20:33 |
| CaptHindsight | along with that there are all subroutines for operations like PURGE, WASH, DRY etc | 20:33 |
| CaptHindsight | all the G-code gets put in up front, or can be | 20:34 |
| CaptHindsight | and all the bitmaps can be in memory | 20:34 |
| CaptHindsight | I guess you can send G-code line by line into linuxcnc but then you lose the trajectory planner stuff beyond one line | 20:35 |
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| kanzure | looks like linuxcnc expects to consume gcode by stdout (line by line) | 20:35 |
| CaptHindsight | not to big a deal since we aren't planning on printing arcs | 20:36 |
| CaptHindsight | i was thinking that you would slave the printing to the G-code and position info | 20:37 |
| kanzure | there's no need to include valve toggles in gcode output if the program is just toggling valves using HAL anyway | 20:37 |
| kanzure | or, the other way around, which is: there's no need to use HAL if the gcode output includes the valve toggles | 20:37 |
| kanzure | perhaps that's not true | 20:37 |
| kanzure | hm | 20:37 |
| CaptHindsight | yeah toggling an IO is just part of G-code | 20:38 |
| kanzure | ok | 20:38 |
| abetusk | is there any reason you're using linuxcnc vs. something else, like arduino + grbl, marlin or smotthieboard? | 20:38 |
| CaptHindsight | or can be done by HAL | 20:39 |
| kanzure | "HAL pin I/O (M62-M68)." | 20:39 |
| CaptHindsight | yes, Linuxcnc does it all, if someone wants to go nuts with a duino they can follow a working example | 20:39 |
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| CaptHindsight | I look at it this way. Linuxcnc is your 5000 pc tool set, if you want to only focus on the 100 pcs that you only think you need now then use a micro | 20:41 |
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| kanzure | hm looks like it might have a concept of streaming gcode maybe | 20:42 |
| CaptHindsight | it's an open design so you're free to use drawer slides, hot melt for framing, wooden parts etc if you wish | 20:43 |
| CaptHindsight | kanzure: some people do over ethernet | 20:43 |
| kanzure | http://linuxcnc.org/docs/html/common/python-interface.html | 20:44 |
| kanzure | "gcodes: (returns tuple of 16 integers) - currently active G-codes." | 20:44 |
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| CaptHindsight | abetusk: how is the support on duino or smoothie for closed loop/servos? | 20:57 |
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| abetusk | afaik in terms of grbl and smoothie it assumes stepper. I don't know about marlin and such but I assume they assume the same. Don't take my word for it but that's what I've seen. | 20:59 |
| abetusk | They all assume low end steppers and such. The smoothie has a4982 chips on board | 21:00 |
| CaptHindsight | we are going to be done with this whole printer in weeks, maybe someone will spend months reinventing the wheel for a micro | 21:00 |
| abetusk | It depends on what you mean by reinventing the wheel. You're using linuxcnc to control closed loop servos? | 21:01 |
| CaptHindsight | there could be enough problems with chemistry and yield, we don't need any with machine control on top of it | 21:01 |
| super` | is this conversation about the project i saw on kickstarter for automating lab work? | 21:02 |
| super` | OpenTrons | 21:03 |
| CaptHindsight | super`: no, but is the one you saw made of t-slot and yeah..... | 21:03 |
| super` | i don't know.. | 21:03 |
| CaptHindsight | I hope they are working an easy for lab worker to use front end | 21:04 |
| CaptHindsight | everything else is done | 21:04 |
| CaptHindsight | we use G-code and Linuxcnc to make custom lab robots all the time | 21:04 |
| CaptHindsight | their project made it sound like they have some sort of breakthrough | 21:05 |
| CaptHindsight | like makerbot | 21:05 |
| abetusk | people had reprap before makerbot | 21:05 |
| CaptHindsight | linuxcnc or ladder logic + PLC is common | 21:06 |
| super` | yah.. that site was sort of deceptive.. they tried to make it seem like they created self-replicating automata or something | 21:06 |
| super` | but it just prints the parts from what i could see | 21:07 |
| CaptHindsight | https://www.kickstarter.com/projects/932664050/opentrons-open-source-rapid-prototyping-for-biolog | 21:07 |
| CaptHindsight | just a Cartesian 3 axis stage with a t-slot frame | 21:07 |
| CaptHindsight | a couple of syringe pumps are mounted on it | 21:08 |
| CaptHindsight | you can get all that off the shelf for years | 21:08 |
| abetusk | Why the hate? They're trying to make an appliance for people who don't want to | 21:09 |
| CaptHindsight | looks like belt drive with steppers | 21:09 |
| CaptHindsight | no hate | 21:09 |
| CaptHindsight | it's just nothing new unless they are making some easier to use software | 21:09 |
| CaptHindsight | most t-slot distributors will design that same system for you in a few days | 21:10 |
| CaptHindsight | hopefully they will have some software | 21:12 |
| CaptHindsight | " Mix.Bio, Download and share biology protocols to run on the OT.One. coming soon!" | 21:17 |
| CaptHindsight | maybe an easy to use set of G-codes for lab operations | 21:18 |
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| drethelin | lab techs getting obselete | 21:21 |
| CaptHindsight | are they using monkeys instead just like PC manufacturers? :) | 21:22 |
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| CaptHindsight | drethelin: are machines replacing them? | 21:22 |
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| CaptHindsight | juri_: I'm working on an lathe type inkjet printer to make parts larger than this https://www.youtube.com/watch?v=o4Ok0LQx0Uc | 22:00 |
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| kanzure | cool | 22:01 |
| CaptHindsight | 8m long, 2m dia and ~10 ton parts | 22:01 |
| kanzure | CaptHindsight: unnamed oligomakerthing user interface will be web-based. probably i'll use websockets for streaming data reasons. | 22:02 |
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| kanzure | CaptHindsight: i think either we should talk about or the document should talk about who's going to be ordering the phosphoramidites, argon, acetonitrile, etc., and also about testing procedures- for example, there's probably going to be a few iterations of "mail dna into some other company" for testing | 22:05 |
| kanzure | this isn't a big deal; it's just unspecified and something we haven't hashed out | 22:06 |
| CaptHindsight | kanzure: are you able to order the chems? | 22:06 |
| kanzure | unknown- but if i am, i'm probably going to be shipping them to you :-) | 22:06 |
| kanzure | also; it's not clear to me whether you want to keep the machine? | 22:06 |
| CaptHindsight | it's yours | 22:06 |
| kanzure | right but keep as in host | 22:07 |
| CaptHindsight | I thought you had a space for it | 22:07 |
| CaptHindsight | lets see | 22:07 |
| kanzure | put another way; say it works and prints dna, aren't you going to want to use it? | 22:08 |
| CaptHindsight | it'll work | 22:08 |
| CaptHindsight | lets talk | 22:09 |
| CaptHindsight | about where will this end up | 22:09 |
| kanzure | heh | 22:09 |
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| kanzure | btw drying nozzles are going to blow away the chemicals unless they are tied to the surface | 22:09 |
| CaptHindsight | if there is enough pressure | 22:10 |
| kanzure | i'd also like to figure out tighter target specs for number of spots per run | 22:11 |
| kanzure | repeatability of 10 microns means 10 micron spacing between center of each spot? | 22:11 |
| CaptHindsight | some of this is TBD like spaces and size of each well | 22:12 |
| kanzure | ok | 22:12 |
| CaptHindsight | repeatability of dropping on drop on top of another | 22:12 |
| CaptHindsight | drop size at 1.5pL will be ~75um, well depending on the surface tension | 22:13 |
| kanzure | you haven't estimated cost of argon, reagents, etc., right? | 22:13 |
| CaptHindsight | not included | 22:13 |
| kanzure | ok | 22:13 |
| CaptHindsight | no chems or gas | 22:13 |
| CaptHindsight | just the guts | 22:13 |
| kanzure | worked with gas before? | 22:13 |
| CaptHindsight | plenty | 22:14 |
| kanzure | win 5 | 22:14 |
| kanzure | whoops | 22:15 |
| kanzure | irc fail | 22:15 |
| CaptHindsight | we have lost of mixes here for welding, reactors etc | 22:15 |
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| CaptHindsight | I think it needs a home where it will have a frequent user like yourself | 22:16 |
| kanzure | understood. i'll have to think about optimal place to put it- nmz787, juri_, juul, etc. | 22:18 |
| CaptHindsight | I'll probably build a V2 down the line | 22:20 |
| CaptHindsight | version 2, not the WWII rocket | 22:20 |
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| kanzure | hmm i guess i should organize my list of "dna things i want to print" projects | 22:26 |
| kanzure | all i gots are http://diyhpl.us/wiki/genetic-modifications/ | 22:26 |
| kanzure | and http://diyhpl.us/wiki/dna/projects | 22:26 |
| kanzure | although i sort of need to know how much i can print, to pick good projects | 22:27 |
| kanzure | hm. vicious cycle. | 22:27 |
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| kanzure | we really need to aim for some target number of spots, or else it's always going to be cheaper to just order 100 bp from a current vendor | 22:30 |
| CaptHindsight | is anyone making GMO yeasts for brewing? | 22:30 |
| kanzure | yes.... someone made a non-alcoholic brew? i don't remember the details. i wonder who did that... | 22:31 |
| kanzure | was that yashgaroth? or maybe anselm... | 22:31 |
| CaptHindsight | nozzle spacing is 282um (1/90") | 22:35 |
| kanzure | well if we can fire at 50 kHz then really it's a matter of step size or something... hmm. | 22:37 |
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| CaptHindsight | so ~1m is possible on the 12" x 12" tray | 22:37 |
| CaptHindsight | epson aren't that fast | 22:37 |
| CaptHindsight | IIRC ~14Khz is max | 22:39 |
| kanzure | oops | 22:40 |
| CaptHindsight | the $3K-10K printheads fire to 50khz and more | 22:40 |
| CaptHindsight | now thats 14khz per channel so 14khz x 90 = 1.2m drops per second | 22:41 |
| CaptHindsight | thats with ideal fluids | 22:42 |
| CaptHindsight | we have to jet what we get and it's shear luck that they jet ok | 22:42 |
| kanzure | gotta sleep, brb | 22:47 |
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| --- Log closed Mon Jul 13 00:00:09 2015 | ||
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