--- Day changed Tue Nov 04 2008
00:07 < willPow3r> it didn't work for me, no
00:08 < willPow3r> i think the graph displays in that window, but i can't make it larger
00:13 < kanzure_> Making it larger? Bah.
00:13 < kanzure_> Just switch to ASCII instead of HTML.
00:19 < willPow3r> i can't figure it out. where's the f'ing manual?
00:19 < kanzure_> There is none yet. What is there to figure out?
00:19 < kanzure_> Btw, in the end I'll probably do a webcast/video.
00:19 < kanzure_> screencast/video.
00:20 < willPow3r> the MAKE function. for building CFGs. it doesn't do anything, just prints out "Match in 12681.dot with transfer"  but that number changes
00:20 < willPow3r> unless that *is* the function
00:21 < kanzure_> Notice the sorry not implemented message.
00:21 < willPow3r> oh right
00:21 < kanzure_> So, what this is going to do is convert the given graph that you have drawn, into possible designs.
00:21 < kanzure_> So, a component that "converts" might be a particular engine.
00:21 < willPow3r> thats a great fucking idea!
00:22 < willPow3r> and it uses a database of parts/processes?
00:22 < kanzure_> SKDB? yes, it is.
00:22 < kanzure_> Yes.
00:22 < willPow3r> you're an industrial engineer right?
00:22 < willPow3r> makes perfect sense.
00:22 < kanzure_> So this is also what I'm doing for synbioss/biobricks
00:23 < kanzure_> if xp_prg ever finishes the work I gave him over a month ago.
00:23 < willPow3r> but you could feasibly datamine the entinre intarweb for useable parts/processes
00:23 < kanzure_> no shit ;-)
00:23 < kanzure_> Also the patent database.
00:23 < kanzure_> "Reverse engineering of the entire patent database"
00:23 < willPow3r> so skdb != serial killer database
00:24 < kanzure_> plus seekda.com (maybe) to search for ..
00:24 < kanzure_> uh
00:24 < kanzure_> right.
00:24 < willPow3r> ;)
00:24 < kanzure_> http://heybryan.org/shots/2008-11_02_supermetal_2.png <- What I made yesterday.
00:25 < kanzure_> Today the doc for ADL was going over some Hod Lipson videos. 
00:25 < kanzure_> He showed the evolved robotics stuff.
00:25 < willPow3r> The requested URL /shots/2008-11_02_supermetal_2.png was not found on this server.
00:25 < kanzure_> Hod apparently had a simulator for showing different designs of bots, that moved around on the screen
00:25 < kanzure_> http://heybryan.org/shots/ <- look for 'supermetal' on this page. Choose the second one.
00:26 < kanzure_> Anyway, the doc commented that "this was the work of like three or four grad students over their time at his lab - many years"
00:26 < kanzure_> and he pointed to the typical checkerboard OpenGL terrain
00:26 < kanzure_> plus a cube on it and kinda twitching
00:26 < kanzure_> Now, I don't mean to brag, or be an ass or anything,
00:26 < kanzure_> but that's like tutorial 2 of NeHe
00:27 < kanzure_> So, given that 'supermetal 2008' work that I did yesterday,
00:27 < kanzure_> plus some twitching, I could probably mimic the same work in a relatively short amount of time
00:27 < willPow3r> it doesn't seem that complicated really
00:27 < kanzure_> Hod's group was then printing out the parts to the automatically generated bots via a 3D printer
00:28 < kanzure_> plus some provided motors or something (which is where I personally get stuck)
00:28  * kanzure_ fetches the video
00:28 < kanzure_> oh, it's his ted talk
00:28 < willPow3r> link
00:28 < kanzure_> Anyway, it's not a servo, but rather some sort of pneumatic system in the formfactor of a servo
00:28  * kanzure_ gets up to move to the other machine
00:29 < kanzure-> http://www.ted.com/talks/view/id/165
00:29 < kanzure-> http://ccsl.mae.cornell.edu/research/golem/golem480x240.wmv
00:29 < kanzure_> Anyway, I'm _pretty sure_ it's simple. Maybe I'm not seeing something here.
00:30 < kanzure_> I don't understand the actuator for the tubular form factor or whatever. It somehow "crawls" but it's made out of a triangle. Not a wheel or anything. How is this possible?
00:31 < willPow3r> looks like how an inchworm moves
00:31 < kanzure_> An inchworm has muscles that 'stretch' via a molecular mechanism. Doesn't count.
00:34 < kanzure_> I guess it's like rotating a screw. Rotate to the right to go away, to the left to go inward. 
00:36 < willPow3r> this is in the cornell vid?
00:37 < kanzure_> It's in both I think.
00:37 < kanzure_> One shows more of the simulations, the ted talk shows the physical implementations.
00:37 < willPow3r> for all of 5 seconds
00:37 < kanzure_> heh'
00:37 < xp_prg> kanzure_ it is coming along nicely as you have already seen :>
00:37 < kanzure_> Where's the rest of it?
00:37 < xp_prg> still working on it, been quite busy
00:42 < willPow3r> they should have ran more evolutionary simulations than just "which ever bots move fastest get to move on"
00:43 < kanzure_> I think they did.
00:43 < kanzure_> Not sure. I would have hoped so.
00:44 < willPow3r> "the only rule was that the machines that move faster will replace the ones that move slower"
00:44 < kanzure_> That's the selection portion of the GA.
00:45 < willPow3r> its hard for me to believe that this is state of the art robotics research.
00:45 < kanzure_> Go to Japan for that. ;-)
00:45 < willPow3r> its far too pragmatic.
00:45 < kanzure_> But that's more "trying to make up AI".
00:45 < kanzure_> Hm?
00:46 < kanzure_> What do you mean?
00:46 < willPow3r> these robots could be designed with legos.
00:46 < kanzure_> This is more about evolutionary algorithms than it is about robotics AFAIK.
00:46 < kanzure_> But yeah, it's not "new materials" or new shapes and designs, that's for sure.
00:46 < kanzure_> that's something fixable methinks
00:47 < willPow3r> nanotech should be able to bridge the gap
00:47 < kanzure_> The problem with letting it randomly generate shapes and new parts and so on, like in Supermetal, is that the possibility space explodes
00:47 < kanzure_> Uh?
00:47 < kanzure_> What gap?
00:48 < willPow3r> the servo/actuator model is far to coarse to be used seriously. we need to use something that has many, many more degrees of freedom
00:48 < willPow3r> but this is definitely a good starting place i suppose
00:49 < willPow3r> they're using an evolutionary process to weed out bad designs
00:50 < willPow3r> but the designs aren't elaborate enough to seriously be subjected to those kind of selective forces
00:50 < kanzure_> On the contrary.
00:50 < kanzure_> http://heybryan.org/~bbishop/docs/repo/ Check out this and the subdirectories. Anything in PNG too.
00:50 < kanzure_> http://heybryan.org/~bbishop/docs/repo/CDD/
00:50 < kanzure_> http://heybryan.org/~bbishop/docs/repo/CDDs/
00:50 < kanzure_> one of those ..
00:51 < willPow3r> 45 KBps?
00:52 < kanzure_> Hrm?
00:52 < kanzure_> Anyway, there's giant graphs, lots of parts and so on.
00:52 < willPow3r> your upload speed.
00:52 < kanzure_> hm.
00:53 < willPow3r> what opens .cdd files?
00:53 < kanzure_> Something commercial. conceptdraw or something. Avoid it.
00:53 < kanzure_> Try the PNG. I took a few screenshots/exports when I was running conceptdraw.
00:54 < willPow3r> all the files in CDD are .cdd...
00:54 < willPow3r> i'll check png then
00:54 < kanzure_> Sorry. Try CDDs. I don't know where I put it.
00:54 < kanzure_> yeah.
00:55 < willPow3r> time for bfast. bbl
01:29 < willPow3r> it would be funny if somebody pulled a bel-air during a ted talk
01:29 < kanzure_> A what?
01:29 < willPow3r> a bel-air.
01:30 < willPow3r> http://encyclopediadramatica.com/Bel-Air
01:31 < willPow3r> except remove all references to 4chan and /b/
02:01 < kanzure_> So yeah, this isn't really working out for me.
02:02 < kanzure_> There are about 46 different types of nodes, so at least *46 more graphs per depth into the trees that you go for possible graphs, so at 3 nodes it's already 46^3. 
02:03 < kanzure_> I generated a million rules that could be used to transform the function structure (what the user provides) to possible configurations of parts and items, but.
02:03 < kanzure_> But if the idea is to apply a million rules to each applied million rules, and go on for a few depths, that's many, many trillions of results..
02:03 < kanzure_> I need a simple way of extracting interesting specimens for now.
02:04 < kanzure_> The problem is that if the user chooses something ridiculously exotic, as if the rules are not evenly distributed for all 46 options, then it's all shot to hell, if you're doing a small 150-rulecount system.
02:05 < willPow3r> use a weighted rule system perhaps?
02:05 < kanzure_> *if the case is that the rules are not evenly distributed for all 46 options (i.e., if the generated ruleset just so happens to be centering around one section)
02:05 < kanzure_> Hrm?
02:06 < kanzure_> I need a balance between the number of possible options in the ontology versus expected interesting stuff turning up, for now.
02:07 < kanzure_> So maybe only 10 types of nodes, which would allow depth, but there's very little breadth here. You wouldn't get a weird "gasoline line connected to a parachute". :-/
02:09 < kanzure_> Meh. Maybe it's better that there's too many rules to explore. 
02:16 < kanzure_> Aha.
02:16 < kanzure_> The idea was always that the users would build up a library of interesting rules for their own personal use. 
02:16 < kanzure_> But since the newbie will not have a set of rules, just let it be random. 
02:16 < kanzure_> If there turns out to be a rule of thumb for figuring out interesting rules, then I'm sure they'll start putting those into the db and having their fun
02:17 < kanzure_> Ok. Food, star wars, then some programming.
05:06 < wrldpc> http://d.scribd.com/docs/11eq9u1ilefgk830irm6.pdf
05:06 < wrldpc> ^TSIN, Kurzweil
05:07 < wrldpc> Didn't know if you guys had this in PDF yet.
05:07 < wrldpc> If anyone has Ending Aging in PDF holler or scribd it.
05:14 < drazak> I wonder how much it costs to double barrel sequence a whole human genome
05:43 < willPow3r> i accidentally a whole human genome
06:00 < willPow3r> the *whole* thing
06:12 < splicer_> you ate a whole human genome?
06:13 < willPow3r> no, i accidentally it
06:14 < willPow3r> i dont know if i should be worried or what
06:16 < splicer_> just on purpose it next time, you should be fine
06:17 < willPow3r> not sure, because if you it, then you're supposed to or else the consequences 
06:18 < splicer_> there is always the risk of that of course. and we don't want that.
06:20 < willPow3r> thats what it says in the. and you're not supposed to everything you, as they say.
06:22 < splicer_> ah.. they, the ones doing both it and that.
06:24 < ybit> http://www.youtube.com/watch?v=Li5nMsXg1Lk "pinky and the brain on parts of the brain"
07:06 < wrldpc> lol
13:31 < kanzure_> wtf?
13:31 < kanzure_> "Out of socket memory"
14:12 < fenn> another buzzword to add to your list: http://en.wikipedia.org/wiki/Knowledge-based_engineering
14:12 < UtopiahGHML> as opposed to emotion based engineering
14:15 < fenn> RTFA
14:46 < fenn> this makes me sad: http://commons.wikimedia.org/wiki/Commons:Screenshots
14:47 < UtopiahGHML> try http://www.fractaluniverse.org/ instead
14:48 < fenn> emotion-based physics :(
14:52 < fenn> everyone knows the universe is patterned after the flying spaghetti monster
14:59 < fenn> heh first time i've come across a wingnut championing a "flat sun" theory
15:09 < faceface> kanzure_, have you seen this wrt. your journal dump? http://www.myjournals.org
15:42 < faceface> "Wiki for *executable* English" over databases?
15:44 < UtopiahGHML> ?
15:44 < UtopiahGHML> another rewrite of SQL?
15:50 < fenn> gellish?
15:56 < faceface> aparently information is 'in google', but I didn't query yet
15:56 < faceface> http://www.nature.com/news/2008/080903/full/455022a.html
15:56 < faceface> can you see that link?
15:57 < faceface> there reference is in the comments part
15:57 < faceface> Big data: Wikiomics - http://www.nature.com/news/2008/080903/full/455022a.html
16:15 < nsh> Low input, high throughput, no output
17:22 < faceface> have you guys seen this?
17:22 < faceface> In Google we trust
17:22 < faceface> This paper considers information safety and accuracy in the digital age using Google as an entry point.
17:23 < faceface> http://www.firstmonday.org/issues/issue11_4/shaker/
17:23 < faceface> its a really interesting paper.
17:25 < UtopiahGHML> firstmonday usually have interesting questions
17:26 < UtopiahGHML> without reading it Im pretty sure the conclusion will be to, as always, cross check information and have multiple sources of information and the danger of having some information blackhole like Google.
17:29 < UtopiahGHML> (but they don't provide DOI :(
17:38 < faceface> UtopiahGHML, don't know where its published
17:38 < faceface> UtopiahGHML, the results are a bit more nuanced
17:38 < faceface> but its interesting to read what they write about trust.
17:39 < faceface> what is that registry that SMW can be 'published' to?
17:44 < kanzure__> Screenshots are subject to the copyright of the displayed program? waaaht??
17:45 < kanzure__> faceface: Are those for open access journals only or what?
17:45 < faceface> what?
17:45 < kanzure__> myjournals.org
17:45 < faceface> oh... don't know the deets
17:45 < faceface> I think its for any journal... like a login aggrigator...
17:45 < faceface> perhaps
17:46 < kanzure__> They are asking users for usernames and passwords?
17:46 < faceface> anyone know how to use Chanserv
17:46 < kanzure__> Good god, people fall for this shit?
17:46  * kanzure__ makes a clone ASAP
17:46 < faceface> hehehe... did you get that email from me asking you to join some company?
17:46 < kanzure__> Maybe. Let me check.
17:46 < faceface> I gave them my gmail addressbook and they went to town
17:46 < faceface> nevermind if you did!
17:46 < kanzure__> Recent email?
17:46 < faceface> some time earlier this year
17:47 < kanzure__> ThirdGen?
17:48 < kanzure__> Anyway.
18:11 < faceface> yo dudes... http://www.google.com/base/a/dan.bolser/1084695/D12391011315988090326
18:11 < faceface> feedback ... good bad or otherwise...
18:12 < faceface> its a 'journal club' of this... http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060175&ct=1
18:12 < faceface> l8r
18:13 < bkero> Isn't biobricks a wiki?
18:13 < bkero> Sorry, not biobricks, http://partsregistry.org/Main_Page
18:13 < faceface> crap... can you even see that
18:14 < bkero> Yes, I have the PDF loaded
18:14 < kanzure__> Biobricks is a wiki, but there's a database behind it that they like to hide.
18:14 < kanzure__> I mean, not just the mediawiki db.
18:18 < bkero> Have you seen the parts registry?
18:18 < kanzure__> Me?
18:18 < kanzure__> Are you kidding?
18:18 < bkero> Heh
18:18 < kanzure__> http://heybryan.org/books/biobricks/
18:18 < kanzure__> http://heybryan.org/graph/
18:18 < bkero> Moreover talking to faceface
18:18 < kanzure__> http://heybryan.org/graph/synbioss/
18:18 < kanzure__> Are you kidding?
18:18 < kanzure__> Dan works in bioinformatics
18:19 < bkero> Ok
18:19 < kanzure__> :)
18:24 < kanzure__> xp_prg: Do you have it done yet?
18:51 < xp_prg> kanzure still working on it, want me send you what I have so far?
18:51 < xp_prg> to send you
18:53 < kanzure__> yes?
18:53 < xp_prg> ok
19:09 < xp_prg> sent it
20:24 < UtopiahGHML> anybody used DBpedia? Id like to have a list of the US stats with name, area and coordinates
20:27 < UtopiahGHML> actually maybe there is a mashup to directly query DBpedia, process it with R and display a nice graph all online, no?
20:58 < xp_prg> kanzure__ did you see it?
21:08 < kanzure_> xp_prg: Does this fully (re)generate the SBML?
21:08 < kanzure_> ScienceDirect just called me.
21:08  * kanzure_ grins
21:11 < xp_prg> yes it does
21:11 < willPow3r> kanzure_, prank call
21:11 < xp_prg> but it is not complete
21:11 < xp_prg> its about 70% there
21:20 < UtopiahGHML> (failure, Freebase doesn't have the area, I have the list of states and other useful info but not that one :\
21:27 < kanzure_> if it's not complete then how would you say it fully regenerates it?
21:31 < kanzure-> https://www323.livemeeting.com/rm/elsevier/webJoin?id=UsabilityTest&pw=presenter&role=present
21:32 < kanzure-> http://concepts.elsevier.com/sciencedirect/2009-1/UsabilityTest_2009_1.html
21:33 < kanzure-> http://concepts.elsevier.com/sdrevamp
21:40 < kanzure_> These people are not secure.
21:40 < kanzure_> user: demo / pass: feed8ack
21:40 < kanzure_> gasp! googleable usernames and passwords!
21:40 < willPow3r> it certainly isn't palin's yahoo email
21:41 < kanzure-> http://concepts.elsevier.com/sciencedirect/2009-1/ <-- teh hell?
21:42 < kanzure-> What are they doing here?
21:42 < kanzure-> Hrm.
21:43 < willPow3r> looks like getting ready for next year
21:44 < kanzure-> hm.
21:44 < kanzure-> must corrupt their md5 scheming system
21:44 < kanzure-> muuust
21:48 < kanzure_> http://oxzaps6.elsevier.co.uk maps to http://concepts.elsevier.com/
21:50 < kanzure-> xpharm-oxzweb5.elsevier.co.uk/
21:53 < kanzure-> https://secure.elsevier.co.uk/ane-server/login
21:54 < kanzure-> shratz and skiddaw..
21:56 < kanzure-> http://www2.elsevier.co.uk/~tony/rss_demo/ sample.rdf
21:59 < kanzure-> rse13.ritense.com
22:00 < kanzure-> http://rse12.rittense.com/
22:30 < xp_prg4> kanzure?
22:34 < kanzure_> Yes?
22:34 < xp_prg4> so did the email help you?
22:35 < kanzure_> Did you send another one?
22:35 < xp_prg4> no
22:35 < xp_prg4> did the one I sent you help you?
22:36 < kanzure_> No. I asked you what's remaining.
22:36 < kanzure_> You said 30% and didn't tell me.
22:36 < xp_prg4> what's remaining is to add math rate functions and prompting the user for input etc...
22:39 < kanzure_> Which math rate functions?
22:41 < xp_prg4> you specify rates for a reaction etc...
22:41 < xp_prg4> just compare the testmodel.xml and the one I gave you that tells what is missing
22:42 < kanzure_> User input supplies the rates?
22:43 < xp_prg4> yup
23:01 < xp_prg4> so does that help you kanzure_ or not?
23:24 < kanzure_> xp_prg4: I don't see "complex specifics" support.
23:24 < kanzure_> I also don't see "binding specifics".
23:24 < kanzure_> Nor anything about protein inducers
23:25 < kanzure_> or "bound complexes" for each of the inducers
23:35 < kanzure-> http://voiced.device.mst.edu/groups/voiced/
23:44 < kanzure_>  /whois kanzure__
23:51 < kanzure_> I wonder how drug commercials are made these days. Does the advertizing firm go to the scientists that published the papers and ask, "Okay, great, now what's the best way to fuck this up in the ad?"
23:51 < kanzure_> "Using a powerful ingredient, this product strengthens bone marrows by __magic elves__."
23:52 < procto> I made contact today with a guy who runs a clinic in ethiopea
23:52 < procto> we discussed orgs like diybio producing blueprints of medecines and medical equipment
23:52 < kanzure_> The clinics don't do the ads.
23:52 < procto> to be produced on-site in africa
23:53 < kanzure_> procto: You should talk to Guido about that. He's been popping up on the diybio mailing list recently, but he's more from Joseph Jackson's side of things on the internet.
23:53 < willPow3r> yeah, why bring the slave labor here?
23:53 < kanzure_> I met him with Joseph u pin CA.
23:55 < kanzure_> procto: If I gave him schematics, would he put them to use?
23:56 < procto> not yet
23:56 < procto> I just introduced him to the idea of fablabs, etc.
23:57 < kanzure_> Also, if you talk with Andrew Hessell and convince him to show us something working from his automated diy biotech toolchain *cough*, then that's good too.
23:57 < kanzure_> Ah.
23:57 < kanzure_> *Hessel
23:57 < procto> thing is, he's a fellow student here
23:57 < procto> so I have close contact
23:57 < procto> anyways, off to my math midterm review session