| --- Day changed Wed Sep 02 2009 | ||
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| genehacker | kanzure | 01:11 |
|---|---|---|
| genehacker | are you up? | 01:11 |
| genehacker | ever hear of a part classification table? | 01:12 |
| genehacker | or shape classification | 01:13 |
| genehacker | or group technology | 01:13 |
| genehacker | http://en.wikipedia.org/wiki/Group_technology | 01:14 |
| genehacker | cause that sounds an awful lot like skdb | 01:14 |
| genehacker | mind telling me what skdb really is? | 01:15 |
| genehacker | or what the purpose of it is? | 01:17 |
| Utopiah | genehacker: reading up that page and http://en.wikipedia.org/wiki/Cellular_manufacturing , there is no mention of those in http://books.google.fr/books?id=oaBOuo4mId8C but leading principles seem similar . I guess the main purpose of SKDB related to this is to make it fully automated (or at least "automatable" by providing proper formats and related tools) rather than "just a philosophy principle" | 01:37 |
| Utopiah | (but that's just my view) | 01:37 |
| Utopiah | skimming through http://www.ohiolink.edu/etd/view.cgi?acc_num=ucin990649367 too | 01:39 |
| Utopiah | (very interesting, especially since I don't know most of those refs :-# ) | 01:48 |
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| kanzure | genehacker, the point of skdb is to be able to say "apt-get install me a robot army" | 06:48 |
| kanzure | "“Self-Assembled Single-Crystal Silicon Circuits on Plastic,” by Sean A. | 06:55 |
| kanzure | Stauth and Babak A. Parviz, in Proceedings of the National Academy of | 06:55 |
| kanzure | Sciences, 19 September 2006." | 06:55 |
| kanzure | oh, it's parviz | 06:58 |
| kanzure | other parviz papers: http://heybryan.org/books/papers/parviz/ | 06:59 |
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| kanzure | http://xkcd.com/612/ <-- he must have authored scp too | 07:53 |
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| CIA-32 | skdb: fenn * r df4c2dd /packages/lego/data.yaml: add ldraw id | 11:37 |
| CIA-32 | skdb: fenn * r 1846d85 /core/ (package.py skdb.py yamlcrap.py): split package into a new file, move load() into yamlcrap | 11:37 |
| kanzure | how did you figure out the ldraw IDs? | 11:53 |
| kanzure | was it from the book? | 11:53 |
| kanzure | yet another wonderful day of chemistry: http://heybryan.org/school/ch301/2009-09-02.html | 12:03 |
| fenn | i looked them up on peeron | 12:18 |
| fenn | http://adl.serveftp.org/lab/fenn/pngs/lego_cgraph.png | 12:18 |
| fenn | not quite as good as lego assembly instructions :P | 12:19 |
| kanzure | is that generated? | 12:23 |
| fenn | ya | 12:23 |
| kanzure | hehe | 12:23 |
| fenn | sort of hard to believe i'm the first person to ever do this | 12:23 |
| kanzure | kind of lame isn't it | 12:23 |
| kanzure | typical lego gallery-style instructions could be done if my screenshot mechanism worked | 12:24 |
| kanzure | because you already add the legos sequentially | 12:24 |
| kanzure | so you just show the images in a gallery in the order in which they were added | 12:24 |
| fenn | right | 12:24 |
| kanzure | (although that's not necessarily the most optimal sequence) | 12:24 |
| fenn | "most optimal" for generating instructions, or for some other metric | 12:25 |
| kanzure | well the goal is assembly | 12:25 |
| kanzure | it's easy to generate a sequence of steps that are not conducive to physical assembly | 12:25 |
| kanzure | er | 12:25 |
| kanzure | this requires some testing | 12:25 |
| fenn | yeah, i don't take that into account | 12:26 |
| kanzure | too bad we can't color-highlight the lego studs or something | 12:26 |
| kanzure | is there a way to color surfaces in opencascade? | 12:26 |
| fenn | yes | 12:26 |
| kanzure | because if we can detect the most near surface to an interface, | 12:26 |
| kanzure | we can change its color | 12:26 |
| kanzure | and then take an image of that and use it as the icon in the graph | 12:26 |
| fenn | well, i'll let you do that | 12:26 |
| kanzure | does it matter? | 12:26 |
| fenn | it wouldn't be too hard to project the 3d interface coords to 2d coords on the icon | 12:27 |
| fenn | but then you're sort of leaving graph lala-land | 12:27 |
| fenn | bah. ok i'm not the first http://journals.cambridge.org/download.php?file=/AIE/AIE17_02/S0890060403172046a.pdf&code=23e3638afdb973f190aecae20ceafeb1 | 12:28 |
| fenn | wtf.. if there are all these papers on assembly graphs you'd at least expect ONE relevant google image result | 12:29 |
| kanzure | if you want some papers, | 12:30 |
| kanzure | http://adl.serveftp.org/papers/review/ | 12:30 |
| fenn | NO | 12:30 |
| fenn | bad packer! | 12:30 |
| kanzure | IIRC, you were the one who selected these | 12:31 |
| kanzure | also your link is "file not available" | 12:31 |
| kanzure | (not even a proper 404) | 12:31 |
| fenn | http://www.google.com/url?q=http://journals.cambridge.org/production/action/cjoGetFulltext?fulltextid=183050&sa=U&start=2&ei=l6qeSq_4EJngsAPKr_jZBg&usg=AFQjCNFjozOZi3Di6t-rP_hvYH6KxZVrHQ | 12:31 |
| fenn | blah | 12:31 |
| fenn | 'using assembly representations to enable evolutionary design of lego structures' by regli and peysakhov | 12:32 |
| kanzure | that's just regli | 12:32 |
| kanzure | yeah we already say that in their repo | 12:32 |
| kanzure | remember? legoGA java bullshit? | 12:32 |
| fenn | yeah | 12:33 |
| kanzure | it's on /mnt/maxtor/software/legoGA/ on leibniz if you want to take a look | 12:33 |
| fenn | actually i really doubt regli wrote any of the code | 12:33 |
| kanzure | yeah it was just peysakhov | 12:33 |
| xp_prg | It is confirmed, the father of synthetic biology is presenting tomorrow | 12:47 |
| kanzure | he's not the father of synthetic biology | 12:53 |
| kanzure | fenn: where is igraph in debian? | 12:55 |
| xp_prg | yes he is | 12:56 |
| xp_prg | how dare you | 12:56 |
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| kanzure | xp_prg: ask him | 12:59 |
| xp_prg | He is, you seriously, seriously, seriously don't know what your talking about right now | 12:59 |
| xp_prg | very surprising to me actually | 12:59 |
| xp_prg | how could you get that wrong? | 13:00 |
| genehacker | ??? | 13:00 |
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| fenn | python-igraph | 13:12 |
| kanzure | couldn't find package python-igraph | 13:27 |
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| fenn | wtf it's not in debian? | 13:39 |
| fenn | now i'm really confused | 13:39 |
| kanzure | thought you said it was? | 13:39 |
| fenn | i thought it was.. it's in ubuntu :( | 13:40 |
| kanzure | ha ha | 13:43 |
| fenn | so anyway, why is clear() not resetting all_bricks (or cgraph) | 13:43 |
| kanzure | do I have to answer | 13:45 |
| fenn | looks like it never did | 13:46 |
| kanzure | all_bricks=[] | 13:47 |
| kanzure | what's wrong with that? | 13:47 |
| fenn | i dunno | 13:47 |
| fenn | i also tried global all_bricks on its own line | 13:47 |
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| kanzure | fenn: your bug will be fixed if you do "import paths" and access it as paths.all_paths | 14:27 |
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| kanzure | what? http://erights.org/ | 14:29 |
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| kanzure | fenn: | 14:58 |
| kanzure | in add_key, what you want to use functools.partial(clear, my_argument=blah) | 14:59 |
| CIA-32 | skdb: kanzure * r a4c0919 / (gui/gui.py paths.py): partially fix global with functools.partial | 15:04 |
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| CIA-32 | skdb: fenn * r ee8fd0a /core/interface.py: pretty lego graphs | 15:11 |
| CIA-32 | skdb: fenn * r b167b67 / (gui/gui.py paths.py): Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb | 15:11 |
| CIA-32 | skdb: fenn * r 571a690 /gui/gui.py: grunt. | 15:11 |
| CIA-32 | skdb: fenn * r 9e70a4c /packages/lego/grammar.yaml: claw->clip to match ldraw terminology | 15:14 |
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| fenn | "the Technical Ref Manual for the OMAP3530 is 3517 pages long" | 15:57 |
| genehacker | what are you doing with processors? | 15:59 |
| fenn | nothing | 16:00 |
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| genehacker | nothing? | 16:06 |
| genehacker | whoa | 16:06 |
| genehacker | linkage based linear motion guides might be able to make themselves | 16:07 |
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| kanzure | hey ve :p | 17:05 |
| ve | hey :p | 17:07 |
| kanzure | how goes it? | 17:07 |
| ve | ok apparently | 17:08 |
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| wonklab | yo | 17:27 |
| xp_prg | hi wonkylab person :> | 17:34 |
| * bkero omnoms | 17:35 | |
| kanzure | hey wonklab | 17:38 |
| kanzure | wonklab: check the link in the /topic :) | 17:38 |
| kanzure | wrldpc2: why not talk in here | 17:38 |
| -!- Irssi: #hplusroadmap: Total of 33 nicks [0 ops, 0 halfops, 0 voices, 33 normal] | 17:39 | |
| wrldpc2 | cool | 17:40 |
| wonklab | kanzure: What is all that? | 17:40 |
| wonklab | python stuff | 17:40 |
| wonklab | What's hplus? | 17:41 |
| kanzure | wonklab: it's like apt-get but for real stuff | 17:41 |
| wrldpc2 | I wonder how to write this email. | 17:41 |
| kanzure | hplus stands for "transhuman". it's like transsexualism except for being human. | 17:41 |
| kanzure | wrldpc2: in english? | 17:41 |
| wrldpc2 | LOL | 17:41 |
| wrldpc2 | clever | 17:41 |
| wrldpc2 | "Dear Uncle Steve, I'm currently seeking to assist an elite group of transhuman geniuses ..." | 17:42 |
| wrldpc2 | "They are not bound to this earth ..." | 17:42 |
| kanzure | are you sure about that | 17:42 |
| wrldpc2 | lol | 17:42 |
| wrldpc2 | yea .. | 17:42 |
| wonklab | I saw an article about novel genes in the human genome today. | 17:43 |
| kanzure | was it the mutation article? | 17:43 |
| wrldpc2 | link? | 17:43 |
| wonklab | http://www.physorg.com/news171051139.html | 17:43 |
| kanzure | http://news.bbc.co.uk/2/hi/science/nature/8227442.stm | 17:43 |
| wonklab | nope | 17:44 |
| kanzure | yay it gives a DOI | 17:44 |
| kanzure | ah but the DOI is not found | 17:44 |
| wonklab | It's about totally new genes that humans have and chimps/gorillas/macaques don't. | 17:44 |
| wonklab | yeah | 17:44 |
| kanzure | Recent de novo origin of human protein-coding genes. | 17:44 |
| wonklab | I tried to citeulike it, but it didn't work. | 17:44 |
| wonklab | I got the paper, though. | 17:45 |
| kanzure | try this: http://genome.cshlp.org/content/early/2009/08/31/gr.095026.109.full.pdf | 17:45 |
| kanzure | and for future reference: http://adl.serveftp.org/papers/Recent%20de%20novo%20origin%20of%20human%20protein-coding%20genes.pdf | 17:47 |
| kanzure | wonklab: so, the idea of skdb is to be able to download hardware over the internet | 17:47 |
| kanzure | plus the ability to generate instructions for making various parts | 17:48 |
| kanzure | for instance, here is an assembly diagram that was made today (beta) http://adl.serveftp.org/lab/fenn/pngs/lego_cgraph.png | 17:48 |
| kanzure | pre-beta | 17:48 |
| kanzure | pre-alpha I should say | 17:48 |
| wonklab | What's that supposed to make? | 17:51 |
| kanzure | well when you run paths.py, the demo presently randomly adds legos together | 17:51 |
| kanzure | so that diagram makes whatever random creation was on fenn's screen | 17:51 |
| kanzure | there are some screenshots in this presentation: | 17:52 |
| kanzure | http://adl.serveftp.org/lab/presentations/updates-from-austin.pdf | 17:52 |
| wonklab | You want to make a standard way of describing diybio experiments? | 17:57 |
| kanzure | that's one part of this project | 17:58 |
| kanzure | one of the "packages" in skdb is going to be a simple thermocycler, for instance | 17:58 |
| kanzure | there are some CAD models for an AFM floating around .. those are definitely going to be added. maybe a parametric atomic force microscope package? :) | 17:58 |
| kanzure | there's already some descriptions of common materials and tools in biology labs, let me dig up the links | 17:59 |
| kanzure | http://adl.serveftp.org/skdb/doc/BOMs/analytical-instrumentation (this isn't complete) | 17:59 |
| kanzure | it's just a list .. doesn't currently contain CAD information or instructions on how to build those devicesz | 17:59 |
| kanzure | same with this PCR document: http://adl.serveftp.org/skdb/doc/BOMs/pcr | 17:59 |
| wonklab | I'd like to try out the diy pcr one of these days. | 18:04 |
| kanzure | :) | 18:04 |
| wonklab | I read that cheapo thermocycler paper. | 18:04 |
| kanzure | ah, good | 18:05 |
| kanzure | there's a few other on the server if you stare long enough | 18:05 |
| wonklab | But I've got no lab skillz as of yet. | 18:05 |
| kanzure | wait, I thought you were a wet lab guy? | 18:05 |
| kanzure | bbiab | 18:05 |
| wonklab | And no real plans to learn any on the job. | 18:05 |
| wonklab | Nope, I'm computational. | 18:05 |
| wonklab | About to move one of my simulations over to the TeraGrid. | 18:06 |
| xp_prg | wow what is TeraGrid? | 18:07 |
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| wonklab | http://www.teragrid.org/ | 18:17 |
| wonklab | The US, mostly-academic grid of supercomputers. | 18:17 |
| wonklab | It includes NCSA, SDSC, PSC, and TACC. | 18:18 |
| wonklab | http://www.top500.org/list/2009/06/100 | 18:19 |
| wonklab | kraken and ranger are on the teragrid. | 18:19 |
| kanzure | ranger is local to me | 18:25 |
| * kanzure has ssh access to horseshoe (I think) | 18:25 | |
| wonklab | I can use ranger and lonestar. | 18:30 |
| wonklab | There's some other one. | 18:30 |
| wonklab | abe and lonestar are on the top 100, too. | 18:31 |
| wonklab | ranger's crazy. | 18:31 |
| wonklab | 63,000 cores. | 18:32 |
| wonklab | The TACC is great. | 18:32 |
| wonklab | It makes me want to do a postdoc at UT. | 18:33 |
| kanzure | they have a visualization center at UT | 18:33 |
| kanzure | have you seen it? | 18:33 |
| kanzure | it's wall to wall monitors and projectors | 18:33 |
| wonklab | I have time on it, but it's no good to me. | 18:33 |
| wonklab | spur | 18:33 |
| wonklab | We've got a GPU cluster up at NCSA called lincoln. | 18:33 |
| wonklab | They're building some petascale machine. | 18:34 |
| wonklab | It's going to have its own building. | 18:34 |
| wonklab | Near the power plant. | 18:34 |
| xp_prg | wonklab how do you get time on it? | 18:36 |
| wonklab | You apply for a computer time grant. | 18:37 |
| wonklab | If you're accepted, you get a certain CPU-hour allotment for a year. | 18:37 |
| wonklab | It's funny working that out into CPU-years. | 18:38 |
| wonklab | Last year I used something like 60 CPU-years. | 18:38 |
| wonklab | There's other machines, though. | 18:39 |
| wonklab | Lots of universities and computational groups have their own clusters. | 18:39 |
| wonklab | The big national labs have clusters, too. | 18:39 |
| wonklab | roadrunner is at Los Alamos. | 18:39 |
| wonklab | It's funny using these machines when there's so much hype about the "cloud". | 18:41 |
| kanzure | the cloud is bullshit | 18:41 |
| wonklab | But the cloud is only really good for embarrassingly parallel stuff. | 18:41 |
| wonklab | Lots of problems aren't embarrassingly parallel. | 18:42 |
| wonklab | Basically, the hard ones. | 18:42 |
| xp_prg | wonklab tell me about your program and what it does | 18:46 |
| wonklab | It's not really my program. | 18:47 |
| wonklab | I'm most just a user. | 18:47 |
| wonklab | I've added some small things to it, though. | 18:47 |
| wonklab | It's NAMD, an atomic molecular dynamics simulator. | 18:48 |
| kanzure | anything like CHARMM? | 18:48 |
| wonklab | You basically put in a bunch of molecules. | 18:48 |
| wonklab | yeah | 18:48 |
| wonklab | Then calculate the forces per atom and move everything one timestep. | 18:48 |
| kanzure | so you configure a program and pop you get a phd? is that how it works? | 18:48 |
| wonklab | I use NAMD to study certain proteins and RNAs. | 18:49 |
| wonklab | Most MD people don't do much programming on MD code. | 18:49 |
| wonklab | My systems are in the 100,000-200,000 range. | 18:50 |
| wonklab | But some people have pushed NAMD up into multiple millions of atoms. | 18:50 |
| wonklab | They've done whole ribosome simulations. | 18:50 |
| kanzure | do you have the config files? | 18:51 |
| wonklab | And small viruses. | 18:51 |
| wonklab | yep | 18:51 |
| kanzure | can you upload them or send them to me? | 18:51 |
| wonklab | Everyone makes their own config files. | 18:51 |
| kanzure | no, for the viruses | 18:51 |
| kanzure | or ribosomes | 18:51 |
| wonklab | oh, no | 18:51 |
| wonklab | Those large systems are a pain to deal with. | 18:51 |
| wonklab | Once you actually manage to simulate something, the data analysis is difficult. | 18:52 |
| wonklab | Actually, just doing stuff like preparing the water box and putting in ions gets difficult. | 18:52 |
| wonklab | And assigning histidine protonation states. | 18:53 |
| drazak | how does that work? | 19:02 |
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| kanzure | genehacker: did you see the skdb presentation yet? | 19:21 |
| genehacker | what skdb presentation | 19:22 |
| genehacker | where? | 19:22 |
| kanzure | http://adl.serveftp.org/lab/presentations/updates-from-austin.pdf | 19:23 |
| genehacker | so can we compete with thingiverse? | 19:26 |
| kanzure | hell yes | 19:26 |
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| genehacker | I have some ideas on how we could make a profit on something like this | 19:26 |
| kanzure | the first step is getting somebody to fund us | 19:27 |
| genehacker | so how do you want to make a profit with this? | 19:28 |
| kanzure | selling kits | 19:28 |
| kanzure | for people who are too lazy to do it themselves | 19:28 |
| genehacker | ok | 19:28 |
| kanzure | didn't I tell you this before? | 19:28 |
| genehacker | yeah | 19:30 |
| genehacker | just making sure | 19:32 |
| kanzure | what were you thinking? | 19:32 |
| genehacker | so what would we sell as a kit at this point? | 19:32 |
| kanzure | thermocycler kit might be a good start | 19:32 |
| kanzure | but I'm open to suggestions | 19:33 |
| kanzure | maybe an AFM | 19:33 |
| genehacker | good idea | 19:33 |
| genehacker | perhaps a CNC mill? | 19:33 |
| genehacker | or is there already too much competition in that field | 19:33 |
| kanzure | no there's only one open source cnc mill (mechmate) | 19:34 |
| kanzure | and it's really just a giant router | 19:34 |
| kanzure | and it kind of sucks a lot | 19:34 |
| genehacker | so why not redesign it? | 19:34 |
| kanzure | right | 19:34 |
| kanzure | yeah I think that's reasonable | 19:34 |
| genehacker | ADL research gave part mating a probability curve? | 19:35 |
| genehacker | that's amazing | 19:35 |
| kanzure | it sucked immensely | 19:35 |
| kanzure | it was six if statements | 19:35 |
| kanzure | this is the part where you go "LOL" | 19:35 |
| genehacker | LOL | 19:36 |
| genehacker | LOL indeed | 19:36 |
| genehacker | did it work though? | 19:36 |
| kanzure | er.. sort of. let me dig out the code for you. give me a few seconds. | 19:36 |
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| genehacker | hey if you can compute part interfacing tolerances that would be awesome | 19:37 |
| genehacker | because that's determines some of what puts the parts together | 19:37 |
| kanzure | yes we're working on that in skdb | 19:37 |
| genehacker | that matt moses paper called that part entropy or something | 19:37 |
| kanzure | maybe you should come in to the lab to see a live demo some time | 19:38 |
| kanzure | fenn is there all day tomorrow | 19:38 |
| kanzure | so just stop by some time | 19:38 |
| * kanzure is uploading the probability code | 19:38 | |
| kanzure | our current method is somewhat better though | 19:38 |
| genehacker | cool | 19:38 |
| kanzure | what we're doing is checking whether or not two interfaces or two parts are compatible | 19:39 |
| genehacker | anyway on the processes | 19:39 |
| kanzure | yeah? | 19:39 |
| genehacker | would it help if I input data into the system on them | 19:39 |
| genehacker | I'm taking materials processing | 19:39 |
| kanzure | probably | 19:39 |
| kanzure | this is taking forever to upload | 19:40 |
| genehacker | what do you mean by general geometry constraint language? | 19:40 |
| kanzure | oh it was already on there | 19:41 |
| kanzure | oh it was already on therehttp://adl.serveftp.org/lab/2007-05-04_manasi_tamhankar.zip | 19:41 |
| kanzure | er | 19:41 |
| kanzure | http://adl.serveftp.org/lab/2007-05-04_manasi_tamhankar.zip | 19:41 |
| kanzure | so anyway | 19:41 |
| kanzure | well a geometry constraint language would be useful to say that a band saw can only go in certain directions | 19:41 |
| kanzure | and no 90 degree turns, for instance | 19:41 |
| genehacker | so my materials processing book talks about using geometry classification tables to figure out how makeable something is by various processes | 19:43 |
| genehacker | do you mean something like that | 19:43 |
| kanzure | nope, this was fenn's idea | 19:43 |
| kanzure | his plan was to take a process and then make it randomly generate shapes | 19:43 |
| kanzure | shapes that it can most definitely manufacture | 19:43 |
| kanzure | then by doing that a lot, you can make shapes that match the thing that you want to make | 19:43 |
| kanzure | this way, you can only make stuff that is actually possible | 19:43 |
| kanzure | and you'll never end up with something fucking crazy | 19:43 |
| genehacker | at the left end of the table you start out with primitive shapes | 19:43 |
| kanzure | maybe you could scan in the page? | 19:44 |
| genehacker | like uniform cross sections | 19:44 |
| genehacker | yeah | 19:44 |
| genehacker | but there's no standard method of doing this | 19:44 |
| genehacker | everyone has there own method | 19:45 |
| kanzure | can you give me a link? | 19:47 |
| genehacker | WTF | 19:50 |
| genehacker | scan was not successful | 19:50 |
| genehacker | shoot it's now in a document | 19:51 |
| genehacker | rescan | 19:51 |
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| genehacker | uploading | 20:06 |
| genehacker | http://imgur.com/HRM1w&1jPYH&8h7BZ | 20:09 |
| genehacker | enjoy | 20:10 |
| kanzure | thanks | 20:11 |
| genehacker | welcome | 20:12 |
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| genehacker | did you present that kanzure? | 20:22 |
| genehacker | did you present that kanzure? | 20:24 |
| kanzure | ytes | 20:24 |
| genehacker | to who? | 20:24 |
| kanzure | campbell, rob stone and matt bohm. rob and bohm are up at oregon state uni. | 20:24 |
| genehacker | oh at adl conference | 20:25 |
| kanzure | no it was just a telephone call a few weeks ago | 20:26 |
| genehacker | ok | 20:26 |
| genehacker | What do FS, CFG, and DAM stand for | 20:28 |
| kanzure | bullshit | 20:28 |
| kanzure | ignore it for now | 20:28 |
| kanzure | fs is "function structure" | 20:28 |
| kanzure | CFG is "configuration flow graph" | 20:28 |
| kanzure | DAM is "design assembly matrix" | 20:28 |
| kanzure | you'll get it when you go into your machine elements class probably | 20:28 |
| kanzure | or whichever one campbell does | 20:29 |
| kanzure | it's basically just this way of using arrows to point from one thing to the other | 20:29 |
| ybit | 01:14 < genehacker> mind telling me what skdb really is? | 20:29 |
| ybit | 01:16 < genehacker> or what the purpose of it is? | 20:29 |
| genehacker | that's sort of why I quit machine elements | 20:29 |
| genehacker | because I didn't have a very good professor | 20:29 |
| kanzure | well if you have any questions I guess I can answer them | 20:29 |
| kanzure | since I've worked in the lab for about a year now | 20:29 |
| genehacker | mind explaining each | 20:29 |
| kanzure | well I can tell you what they are, but not what they are good for, because they are bullshit | 20:30 |
| kanzure | so, a function structure is this graph with nodes and edges | 20:30 |
| kanzure | the nodes are tagged with a "function name" like "translates mechanical energy into electrical energy" | 20:30 |
| kanzure | the edges in the graph are "flows" | 20:30 |
| kanzure | graphsynth (and maybe soon skdb?) translates these function structures into CFGs, which are more like .. | 20:30 |
| genehacker | the lines connecting nodes? | 20:30 |
| kanzure | "use a gear to change mechanical rotational motion" | 20:30 |
| kanzure | the lines connecting nodes are called "edges" | 20:30 |
| genehacker | ok | 20:31 |
| kanzure | unidirectional edges go from node A to node B | 20:31 |
| kanzure | bidirectional edges go from node A to node B and node B to node A | 20:31 |
| kanzure | there's also hyperedges but they are hyperbullshit | 20:31 |
| kanzure | anyway, a CFG is kind of like an assembly graph | 20:31 |
| kanzure | except not as advanced | 20:31 |
| kanzure | a DAM is even more weird and I doubt you'll ever encounter it | 20:31 |
| kanzure | basically it's a way of saying "this component is adjacent to this component and secures it" | 20:32 |
| kanzure | it's an adjacency matrix or incidence matrix usually | 20:32 |
| genehacker | where can I learn about that? | 20:32 |
| kanzure | DAMs? probably by emailing campbell, to be honest | 20:32 |
| genehacker | well all of this | 20:32 |
| kanzure | there's a paper actually | 20:33 |
| kanzure | let me find it | 20:33 |
| kanzure | http://heybryan.org/~bbishop/docs/repo/presentations/Wed3-KurtogluCampbell-From%20Black-Box%20To%20Component%20Selection.ppt | 20:33 |
| kanzure | http://heybryan.org/~bbishop/docs/repo/presentations/2008-12/Exploring%20The%20Worth%20Of%20Automatically%20Generated%20Design%20Alternatives.ppt | 20:33 |
| kanzure | paper: http://heybryan.org/books/Manufacturing/campbell/Exploring%20the%20worth%20of%20automatically%20generated%20design%20alternatives%20based%20on%20designer%20preferences.pdf | 20:34 |
| kanzure | anyway I hope that helps | 20:34 |
| kanzure | campbell wrote a paper this year that goes over the basics, but I don't seem to have a digital copy | 20:35 |
| kanzure | if you want, I can bring it tomorrow for you | 20:35 |
| kanzure | it goes over the basics pretty well | 20:35 |
| genehacker | ok cool | 20:35 |
| kanzure | ok let me throw it in the pack | 20:35 |
| ybit | 18:01 < kanzure> there are some CAD models for an AFM floating around .. those are definitely going to be added. maybe a parametric atomic force microscope package? :) | 20:35 |
| * ybit wants the cad files | 20:36 | |
| kanzure | they are in the papers-dir | 20:36 |
| kanzure | also I sent an email to diybio about it | 20:36 |
| kanzure | http://heybryan.org/books/papers/AFM.zip | 20:36 |
| genehacker | how do you make the probes? | 20:36 |
| kanzure | contents of the zip file: http://heybryan.org/books/papers/AFM/ | 20:36 |
| kanzure | you can make a probe via a few different methods | 20:37 |
| kanzure | one method is the flame method | 20:37 |
| kanzure | where you put the tip in a flame | 20:37 |
| kanzure | another method is this acidic drip method | 20:37 |
| kanzure | where you dunk your tip into some acid | 20:37 |
| kanzure | and as you slowly pull it vertically, | 20:37 |
| kanzure | the acid has to drip in a way that constraints the tip into becoming a sharp tip | 20:37 |
| kanzure | also there's a way to do it like sharpening a knife IIRC... :) | 20:37 |
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| genehacker | flame method? | 20:38 |
| kanzure | I may have been mistaking that for the acid method | 20:38 |
| genehacker | dang | 20:38 |
| genehacker | that's surprising | 20:38 |
| genehacker | I though it involved some weird 3d photolithography | 20:39 |
| kanzure | no | 20:39 |
| kanzure | it could, but no | 20:39 |
| genehacker | anyway what would you use an AFM for at this point? | 20:39 |
| kanzure | DNA sequencing? | 20:39 |
| genehacker | nice | 20:40 |
| kanzure | oh shit :) | 20:40 |
| kanzure | sympy solves my calculus homework just fine | 20:40 |
| genehacker | so what makes skdb better than thingiverse? | 20:40 |
| genehacker | heh | 20:40 |
| kanzure | with skdb you can say "I want a milling machine, what do I need to make one?" | 20:40 |
| genehacker | I wonder if it's ok to show the work by posting the code | 20:41 |
| kanzure | and it will automatically download everything you need | 20:41 |
| kanzure | there are a lot of reasons I guess | 20:41 |
| kanzure | thingiverse is just this website where you upload some CAD files | 20:41 |
| genehacker | so we don't have files for a milling machine | 20:41 |
| kanzure | so what? we can make them | 20:41 |
| kanzure | and once we do, | 20:41 |
| kanzure | we say that the milling machine works in such-and-such-way | 20:41 |
| genehacker | we need to develop the machine | 20:41 |
| kanzure | for instance right now we have some legos in skdb | 20:41 |
| kanzure | and the legos have these holes, studs, and anti studs, etc. | 20:41 |
| kanzure | these are labeled as "interfaces" | 20:42 |
| kanzure | so that they can be automatically mated with other parts | 20:42 |
| kanzure | this way you can say "find me a bearing that is compatible with this flywheel" | 20:42 |
| kanzure | or something | 20:42 |
| kanzure | but yeah, someone needs to make a milling machine | 20:42 |
| genehacker | the point is how could we make this into something that somebody will fund? | 20:42 |
| genehacker | heh I've got some ideas for that... | 20:43 |
| kanzure | dunno. I have a hard time explaining it to people. | 20:43 |
| kanzure | these days I'm just telling them "it's a way to download hardware over the internet, and no I'm not talking about drivers" | 20:43 |
| ybit | genehacker: what book is that scanned page from? | 20:43 |
| genehacker | I want to make turn those ideas in that moses paper into something real | 20:43 |
| genehacker | THE MECHANOMICON | 20:44 |
| kanzure | you should install skdb | 20:44 |
| kanzure | or at least come by the lab to see it in action | 20:45 |
| genehacker | how do I install skdb? | 20:45 |
| kanzure | well right now you have to install opencascade and pythonOCC first, | 20:45 |
| kanzure | fenn wrote some instructions for this | 20:45 |
| kanzure | http://adl.serveftp.org/dokuwiki/pythonocc | 20:45 |
| kanzure | once you do that, skdb is ready to work | 20:46 |
| genehacker | I'll have to go to my linux partition to do that | 20:47 |
| kanzure | yes | 20:48 |
| genehacker | btw why does linux make my laptop's battery last shorter then when it's running winblows? | 20:48 |
| kanzure | how much shorter? | 20:48 |
| ybit | could be that you have wifi turned on unknowingly | 20:49 |
| genehacker | 4-5 hours shorter | 20:49 |
| kanzure | wtf? | 20:49 |
| genehacker | nope | 20:49 |
| kanzure | have you ran it down to 0? | 20:49 |
| ybit | 19:27 < genehacker> so how do you want to make a profit with this? | 20:49 |
| ybit | 19:28 < kanzure> selling kits | 20:49 |
| genehacker | 6 hours with winblows 2 hours with linux | 20:49 |
| genehacker | yup | 20:49 |
| genehacker | down to zero | 20:49 |
| kanzure | hmm | 20:49 |
| ybit | i am trying to convince my boss to take a different direction with the company eventually to see skdb kits | 20:50 |
| genehacker | I think it has something to do with the drivers | 20:50 |
| ybit | s/see/sell | 20:50 |
| kanzure | genehacker: yes it probably does | 20:50 |
| kanzure | genehacker: ubuntu has to pack in so many different drivers | 20:50 |
| genehacker | anyway if we want to make skdb kits how shall we make them? | 20:50 |
| kanzure | it might be using something that is not optimal for your hardware | 20:50 |
| kanzure | probably manually at first | 20:50 |
| kanzure | see, skdb solves that problem | 20:50 |
| kanzure | by telling us how to make the kits | 20:50 |
| genehacker | then contract out to china? | 20:51 |
| genehacker | it may tell how to make the kits | 20:51 |
| genehacker | but it may not tell us how to make them economically | 20:51 |
| kanzure | economically like what? | 20:51 |
| genehacker | as cheap as possible | 20:51 |
| kanzure | oh that's easy we can just include price information | 20:51 |
| genehacker | there are many ways to produce essentially the same part | 20:51 |
| kanzure | and make it minimize for price | 20:51 |
| kanzure | yeah | 20:51 |
| kanzure | that's kinda the point though | 20:51 |
| genehacker | price changes over time | 20:52 |
| kanzure | so we'll see | 20:52 |
| kanzure | yes | 20:52 |
| ybit | genehacker: what was the name of the book? | 20:52 |
| genehacker | THE MECHANOMICON | 20:52 |
| ybit | it wasn't THE MECHANOMICON from what i gather | 20:52 |
| genehacker | no | 20:52 |
| genehacker | why? | 20:52 |
| ybit | it seemed interesting | 20:52 |
| kanzure | the title seems interesitng | 20:52 |
| kanzure | *interesting | 20:52 |
| ybit | i don't know if that's the title or just the title chapter | 20:53 |
| ybit | because a search for it shows nothing but papers | 20:53 |
| genehacker | intro to manuf processes schey | 20:53 |
| ybit | title of the chapter* | 20:53 |
| kanzure | well I just totally lost motivation to do my homework | 20:53 |
| * kanzure writes a program | 20:53 | |
| genehacker | what sort of problem? | 20:53 |
| * ybit wants to see how sympy solved your cal homework, kanzure :) | 20:54 | |
| ybit | and schey's books isn't in ebook format on the interwebs from what i gather | 20:54 |
| genehacker | I dare you to turn in a copy of the code show as work | 20:54 |
| ybit | s/books/book | 20:54 |
| genehacker | that sucks | 20:54 |
| kanzure | blah = exp(1)**(3*x) | 20:55 |
| genehacker | try your local library | 20:55 |
| kanzure | blah2 = Derivative(blah) | 20:55 |
| kanzure | blah2._eval_derivative(x) | 20:55 |
| kanzure | result: 3*e^(3*x) | 20:55 |
| genehacker | you don't need a sympy to do that | 20:55 |
| kanzure | yeah I know | 20:55 |
| genehacker | that's easy | 20:55 |
| kanzure | it was just a simple test | 20:55 |
| kanzure | you don't want to test it on the complicated stuff first :) | 20:55 |
| genehacker | derivers don't really work for complex stuff | 20:55 |
| kanzure | give me something commplex | 20:56 |
| kanzure | *complex | 20:56 |
| genehacker | on those problems you have to show work | 20:56 |
| genehacker | and the teacher will probably count off points if you use an autoderiver | 20:57 |
| genehacker | does sympy have a solve function? | 20:57 |
| kanzure | don't worry, I'm not an idiot | 20:57 |
| kanzure | yes | 20:57 |
| genehacker | that can find zeros? | 20:57 |
| kanzure | and series | 20:57 |
| ybit | first project for skdb: a book scanner | 20:57 |
| ybit | based on legos | 20:57 |
| genehacker | well then once I get my fluids homework back I'll give it something that gave my calculator trouble | 20:58 |
| ybit | screw afm and others :) | 20:58 |
| genehacker | ybit a lego universal constructor would be far more useful | 20:58 |
| * ybit wants to know what military grade soldering circuit board work is | 20:58 | |
| ybit | maybe i should have asked the boss man, supposedly that's what i'll be doing tomorrow | 20:59 |
| ybit | maybe he just means strictness in how much solder is applied to the components.. | 20:59 |
| genehacker | when it needs to work after being shot at or shot out of a gun | 20:59 |
| ybit | genehacker, you work on that. i'm going to scan a few books with this lego scanner | 20:59 |
| ybit | quite a few of those type projects here, but i don't think that's what he was referencing | 21:00 |
| genehacker | what lego scanner? | 21:00 |
| ybit | http://www.geocities.jp/takascience/lego/fabs_en.html | 21:03 |
| ybit | www.youtube.com/watch?v=KkwERsAyDzU | 21:03 |
| ybit | Grouping parts based on geometrical shapes and manufacturing attributes using a neural network | 21:05 |
| ybit | think that was on adl | 21:05 |
| ybit | it's what google found when searching for genehacker's book | 21:06 |
| ybit | is a neural network necessary, what's the advantage... | 21:06 |
| ybit | Retrieving of parts with geometric similarity | 21:06 |
| ybit | that's a chapter from the book Foundations of Data Organization and Algorithms | 21:08 |
| wrldpc2 | has anyone seen the television show "the colony" ? | 21:11 |
| ybit | kanzure: oh.. the plastic afm | 21:11 |
| ybit | right.. i don't think it was an entire afm | 21:12 |
| ybit | wrldpc2: no | 21:12 |
| ybit | why do you ask? | 21:12 |
| wrldpc2 | http://dsc.discovery.com/videos/the-colony-safety-and-security-full-episode.html | 21:12 |
| wrldpc2 | lots of neat diy shit, they assembled this team of various specialists from different disciplines ... marine biologist, electronics specialist, martial artist, doctor, mechanical engineer, etc. | 21:13 |
| wrldpc2 | it's a post-apoc Fallout type of situation. They cordoned off a sector of LA and shot the entire series there. | 21:13 |
| kanzure | wrldpc2: yes I've seen "the colony" | 21:13 |
| genehacker | I don't have a TV | 21:14 |
| kanzure | I watched one episode | 21:14 |
| wrldpc2 | you have a comp you don't need a tv | 21:14 |
| kanzure | not sure how likely it is that they just so happen to have an 80-bajillion-year-old mechanical and electrical engineer laying around | 21:14 |
| wrldpc2 | haha | 21:14 |
| kanzure | "oh we simply make a particle accelerator" | 21:14 |
| kanzure | fuck that | 21:14 |
| wrldpc2 | the electrical engineer is awesome | 21:14 |
| kanzure | he was probably planted | 21:15 |
| wrldpc2 | he looks like Dr. Wiley ... only anefarious | 21:15 |
| wrldpc2 | totally | 21:15 |
| genehacker | TV what is this obscure techonoly | 21:15 |
| genehacker | so what did they have and and what did they make? | 21:18 |
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| genehacker | I wonder if they could've grown chorella... | 21:20 |
| genehacker | oh wait no water | 21:20 |
| genehacker | a solenoid valve | 21:25 |
| genehacker | lucky | 21:25 |
| genehacker | what'd they do for growing food? | 21:57 |
| genehacker | where'd they get the oranges | 21:58 |
| ybit | there was a post-apacolyptic orange tree planting festival | 22:01 |
| genehacker | oh | 22:01 |
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| wrldpc2 | wtf | 23:43 |
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