--- Day changed Wed Sep 02 2009
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01:11 < genehacker> kanzure
01:11 < genehacker> are you up?
01:12 < genehacker> ever hear of a part classification table?
01:13 < genehacker> or shape classification
01:13 < genehacker> or group technology
01:14 < genehacker> http://en.wikipedia.org/wiki/Group_technology
01:14 < genehacker> cause that sounds an awful lot like skdb
01:15 < genehacker> mind telling me what skdb really is?
01:17 < genehacker> or what the purpose of it is?
01:37 < 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)
01:39 < Utopiah> skimming through http://www.ohiolink.edu/etd/view.cgi?acc_num=ucin990649367 too
01:48 < Utopiah> (very interesting, especially since I don't know most of those refs :-# )
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06:48 < kanzure> genehacker, the point of skdb is to be able to say "apt-get install me a robot army"
06:55 < 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."
06:58 < kanzure> oh, it's parviz
06:59 < kanzure> other parviz papers: http://heybryan.org/books/papers/parviz/
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07:53 < kanzure> http://xkcd.com/612/ <-- he must have authored scp too
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11:37 < 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
11:53 < kanzure> how did you figure out the ldraw IDs?
11:53 < kanzure> was it from the book?
12:03 < kanzure> yet another wonderful day of chemistry: http://heybryan.org/school/ch301/2009-09-02.html
12:18 < fenn> i looked them up on peeron
12:18 < fenn> http://adl.serveftp.org/lab/fenn/pngs/lego_cgraph.png
12:19 < fenn> not quite as good as lego assembly instructions :P
12:23 < 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
12:24 < 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)
12:25 < 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
12:26 < 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?
12:27 < 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
12:28 < fenn> bah. ok i'm not the first http://journals.cambridge.org/download.php?file=/AIE/AIE17_02/S0890060403172046a.pdf&code=23e3638afdb973f190aecae20ceafeb1
12:29 < fenn> wtf.. if there are all these papers on assembly graphs you'd at least expect ONE relevant google image result
12:30 < kanzure> if you want some papers,
12:30 < kanzure> http://adl.serveftp.org/papers/review/
12:30 < fenn> NO
12:30 < fenn> bad packer!
12:31 < 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
12:32 < 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?
12:33 < 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
12:47 < xp_prg> It is confirmed, the father of synthetic biology is presenting tomorrow
12:53 < kanzure> he's not the father of synthetic biology
12:55 < kanzure> fenn: where is igraph in debian?
12:56 < xp_prg> yes he is
12:56 < xp_prg> how dare you
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12:59 < 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
13:00 < xp_prg> how could you get that wrong?
13:00 < genehacker> ???
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13:12 < fenn> python-igraph
13:27 < kanzure> couldn't find package python-igraph
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13:39 < fenn> wtf it's not in debian?
13:39 < fenn> now i'm really confused
13:39 < kanzure> thought you said it was?
13:40 < fenn> i thought it was.. it's in ubuntu :(
13:43 < kanzure> ha ha
13:43 < fenn> so anyway, why is clear() not resetting all_bricks (or cgraph)
13:45 < kanzure> do I have to answer
13:46 < fenn> looks like it never did
13:47 < 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
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14:27 < kanzure> fenn: your bug will be fixed if you do "import paths" and access it as paths.all_paths
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14:29 < kanzure> what? http://erights.org/
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14:58 < kanzure> fenn: 
14:59 < kanzure> in add_key, what you want to use functools.partial(clear, my_argument=blah)
15:04 < CIA-32> skdb: kanzure * r a4c0919 / (gui/gui.py paths.py): partially fix global with functools.partial
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15:11 < 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.
15:14 < CIA-32> skdb: fenn * r 9e70a4c /packages/lego/grammar.yaml: claw->clip to match ldraw terminology
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15:57 < fenn> "the Technical Ref Manual for the OMAP3530 is 3517 pages long"
15:59 < genehacker> what are you doing with processors?
16:00 < fenn> nothing
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16:06 < genehacker> nothing?
16:06 < genehacker> whoa
16:07 < genehacker> linkage based linear motion guides might be able to make themselves
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17:05 < kanzure> hey ve :p
17:07 < ve> hey :p
17:07 < kanzure> how goes it?
17:08 < ve> ok apparently
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17:27 < wonklab> yo
17:34 < xp_prg> hi wonkylab person :>
17:35  * bkero omnoms
17:38 < kanzure> hey wonklab
17:38 < kanzure> wonklab: check the link in the /topic :)
17:38 < kanzure> wrldpc2: why not talk in here
17:39 -!- Irssi: #hplusroadmap: Total of 33 nicks [0 ops, 0 halfops, 0 voices, 33 normal]
17:40 < wrldpc2> cool
17:40 < wonklab> kanzure: What is all that?
17:40 < wonklab> python stuff
17:41 < 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
17:42 < 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 ..
17:43 < 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
17:44 < 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.
17:45 < 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
17:47 < 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
17:48 < 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
17:51 < 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
17:52 < kanzure> there are some screenshots in this presentation:
17:52 < kanzure> http://adl.serveftp.org/lab/presentations/updates-from-austin.pdf
17:57 < wonklab> You want to make a standard way of describing diybio experiments?
17:58 < 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? :)
17:59 < 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
18:04 < 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.
18:05 < 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.
18:06 < wonklab> About to move one of my simulations over to the TeraGrid.
18:07 < xp_prg> wow what is TeraGrid?
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18:17 < wonklab> http://www.teragrid.org/
18:17 < wonklab> The US, mostly-academic grid of supercomputers.
18:18 < wonklab> It includes NCSA, SDSC, PSC, and TACC.
18:19 < wonklab> http://www.top500.org/list/2009/06/100
18:19 < wonklab> kraken and ranger are on the teragrid.
18:25 < kanzure> ranger is local to me
18:25  * kanzure has ssh access to horseshoe (I think)
18:30 < wonklab> I can use ranger and lonestar.
18:30 < wonklab> There's some other one.
18:31 < wonklab> abe and lonestar are on the top 100, too.
18:31 < wonklab> ranger's crazy.
18:32 < wonklab> 63,000 cores.
18:32 < wonklab> The TACC is great.
18:33 < 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.
18:34 < 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.
18:36 < xp_prg> wonklab how do you get time on it?
18:37 < 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.
18:38 < wonklab> It's funny working that out into CPU-years.
18:38 < wonklab> Last year I used something like 60 CPU-years.
18:39 < 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.
18:41 < 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.
18:42 < wonklab> Lots of problems aren't embarrassingly parallel.
18:42 < wonklab> Basically, the hard ones.
18:46 < xp_prg> wonklab tell me about your program and what it does
18:47 < 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.
18:48 < 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?
18:49 < wonklab> I use NAMD to study certain proteins and RNAs.
18:49 < wonklab> Most MD people don't do much programming on MD code.
18:50 < 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.
18:51 < 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.
18:52 < 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.
18:53 < wonklab> And assigning histidine protonation states.
19:02 < drazak> how does that work?
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19:21 < kanzure> genehacker: did you see the skdb presentation yet?
19:22 < genehacker> what skdb presentation
19:22 < genehacker> where?
19:23 < kanzure> http://adl.serveftp.org/lab/presentations/updates-from-austin.pdf
19:26 < genehacker> so can we compete with thingiverse?
19:26 < kanzure> hell yes
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19:26 < genehacker> I have some ideas on how we could make a profit on something like this
19:27 < kanzure> the first step is getting somebody to fund us
19:28 < 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?
19:30 < genehacker> yeah
19:32 < 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
19:33 < 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
19:34 < 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
19:35 < 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"
19:36 < 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.
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19:37 < 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
19:38 < 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
19:39 < 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
19:40 < kanzure> this is taking forever to upload
19:40 < genehacker> what do you mean by general geometry constraint language?
19:41 < 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
19:43 < 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
19:44 < 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
19:45 < genehacker> everyone has there own method
19:47 < kanzure> can you give me a link?
19:50 < genehacker> WTF
19:50 < genehacker> scan was not successful
19:51 < genehacker> shoot it's now in a document
19:51 < genehacker> rescan
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20:06 < genehacker> uploading
20:09 < genehacker> http://imgur.com/HRM1w&1jPYH&8h7BZ
20:10 < genehacker> enjoy
20:11 < kanzure> thanks
20:12 < genehacker> welcome
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20:22 < genehacker> did you present that kanzure?
20:24 < 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.
20:25 < genehacker> oh at adl conference
20:26 < kanzure> no it was just a telephone call a few weeks ago
20:26 < genehacker> ok
20:28 < 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
20:29 < 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
20:30 < 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"
20:31 < 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
20:32 < 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
20:33 < 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
20:34 < 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
20:35 < 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? :)
20:36  * 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/
20:37 < 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... :)
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20:38 < 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
20:39 < 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?
20:40 < 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?"
20:41 < 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.
20:42 < 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?
20:43 < 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
20:44 < genehacker> THE MECHANOMICON
20:44 < kanzure> you should install skdb
20:45 < 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
20:46 < kanzure> once you do that, skdb is ready to work
20:47 < genehacker> I'll have to go to my linux partition to do that
20:48 < 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?
20:49 < 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
20:50 < 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
20:51 < 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
20:52 < 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
20:53 < 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?
20:54  * 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
20:55 < 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
20:56 < kanzure> give me something commplex
20:56 < kanzure> *complex
20:56 < genehacker> on those problems you have to show work
20:57 < 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
20:58 < 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
20:59 < 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 
21:00 < 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?
21:03 < ybit> http://www.geocities.jp/takascience/lego/fabs_en.html
21:03 < ybit> www.youtube.com/watch?v=KkwERsAyDzU
21:05 < ybit> Grouping parts based on geometrical shapes and manufacturing attributes using a neural network 
21:05 < ybit> think that was on adl
21:06 < 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
21:08 < ybit> that's a chapter from the book Foundations of Data Organization and Algorithms
21:11 < wrldpc2> has anyone seen the television show "the colony" ?
21:11 < ybit> kanzure: oh.. the plastic afm
21:12 < 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
21:13 < 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"
21:14 < 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
21:15 < 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
21:18 < genehacker> so what did they have and and what did they make?
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21:20 < genehacker> I wonder if they could've grown chorella...
21:20 < genehacker> oh wait no water
21:25 < genehacker> a solenoid valve
21:25 < genehacker> lucky
21:57 < genehacker> what'd they do for growing food?
21:58 < genehacker> where'd they get the oranges
22:01 < ybit> there was a post-apacolyptic orange tree planting festival
22:01 < genehacker> oh
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23:43 < wrldpc2> wtf
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