--- Day changed Tue Sep 02 2008
00:00 < fenn> i think people like tabs because windows doesn't give much in the way of window management
00:01 < kanzure> even my vertical scrollbar hack isn't all that helpful
00:01 < kanzure> still have to scroll
00:02 < kanzure> how do you keep a bajillion things going at once
00:02 < newgenome> WOAH
00:02 < kanzure> and still keep it easily addressable
00:02 < newgenome> just looked up the figures for graphene paper
00:02 < kanzure> yeah?
00:02 < newgenome> it has a tensile strength of 35000 gigapascals
00:02 < fenn> that doesnt sound right
00:03 < newgenome> carbon nanotubes have a tensile strength of 62000 gpa
00:03 < newgenome> spider silk is 1200 gpa
00:03 < kanzure> link
00:04 < newgenome> no wait it's all in megapascals
00:04 < newgenome> sorry got it wrong there
00:04 < fenn> *bonk*
00:04 < newgenome> facepalm
00:04 < newgenome> all measurements above are in Mpa
00:05 < newgenome> so this graphene paper stuff is half the strength of single molecule carbon nanotubes
00:05 < fenn> that figures
00:05 < fenn> it's basically the same stuff, but with rough edges
00:06 < newgenome> yep
00:06 < newgenome> and it is easy to make
00:06 < kanzure> http://heybryan.org/graphene.html
00:06 < kanzure> oh
00:06 < kanzure> let me export this to a wiki for you
00:07 < newgenome> but it gets messed up with water
00:07 < newgenome> tensile modulus
00:08 < newgenome> that is what I put
00:08 < newgenome> http://ttp.northwestern.edu/abstracts/viewabs.php?id=316
00:08 < newgenome> I don't know if that is any different
00:08 < kanzure> http://heybryan.org/mediawiki/index.php/Graphene
00:08 < kanzure> have fun
00:08 < kanzure> oh
00:08 < kanzure> I already had stuff on it
00:08 < kanzure> huh
00:09 < fenn> tensile modulus is stiffness
00:09 < kanzure> Feel free to edit and dump notes.
00:09 < newgenome> so it isn't strong enough for building incredible strong things
00:11 < fenn> graphene paper is not the same thing, it's like the difference between wood and paper
00:11 < newgenome> yeah I figured that out
00:12 < newgenome> there really needs to be a way to synthesize huge sheets of single molecule graphene
00:12 < kanzure> melt graphene down
00:12 < kanzure> let it cool on a surface
00:12 < newgenome> I don't think you can melt graphite
00:13 < newgenome> most single molecule graphene is made by CVD
00:14 < newgenome> I believe
00:14 < fenn> why do you want huge sheets of it?
00:15 < fenn> hmm interesting, monocrystaline silicon has a tensile strength of 7GPa vs 5.5GPa for carbon fiber (62GPa for carbon nanotube)
00:16 < kanzure> fenn: I think the biobricks registry might be useless
00:16 < kanzure> when it comes to using the xml data
00:16 < newgenome> so you can somehow weld the sheets together to make a container that holds metallic hydrogen
00:16 < kanzure> so far I haven't "cracked" it
00:16 < fenn> what do you mean "cracked" it? its all right there
00:16 < newgenome> or make a graphene balloon and pump it up to 6000 psi
00:17 < kanzure> 1008 1062 0.0 - BBa_R0062
00:17 < kanzure> that tells me nothing
00:17 < kanzure> that's the same data they use for all of the parts
00:17 < kanzure> the same variables I mean
00:17 < kanzure> so what's distinguishing these parts in the XML data ?
00:17 < kanzure> not much ..
00:17 < kanzure> it's all the semantic descriptions of the parts more than anything else
00:17 < fenn> the XML data is just annotations
00:17 < kanzure> annotations re: the sequences, right?
00:18 < fenn> showing where the promoters, gene products, etc are
00:18 < fenn> it doesnt say what the part is supposed to do, that's on the wiki page
00:18 < fenn> there's no formal way of describing how to use the part
00:19 < kanzure> kinda like skdb in general
00:19 < kanzure> how do you describe turtles ?
00:19 < kanzure> turtle societies especially
00:20 < fenn> skdb is supposed to have a formal description of how the parts fit together
00:20 < fenn> that's why we have all these classes and units and stuff
00:20 < kanzure> right
00:20 < fenn> otherwise its just a bunch of text like appropedia
00:21 < kanzure> so then what would it take to work for partsregistry.org ?
00:21 < fenn> you'd have to read each of the descriptions and stuff them into a formal category with parameters and hyperlinks etc
00:21 < fenn> and also write some code describing how the different categories interact
00:21 < fenn> same thing as skdb really
00:22 < fenn> turtle = class = category
00:22 < kanzure> right
00:24 < kanzure> they already have them in categories sorta
00:24 < kanzure> http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Signalling
00:24 < kanzure> Cell-Cell signalling section
00:24 < kanzure> http://partsregistry.org/Part_Types
00:24 < kanzure> does that count ?
00:24 < kanzure> it's kind of hard to make something reasonable with that methinks
00:24 < kanzure> it really requires external knowledge being hammered into the system I think
00:24 < kanzure> going through the bio literature and finding a new gene to play with using the same parts
00:25 < fenn> those categories (part_types) are useful but there's just not enough information on how they interact
00:26 < kanzure> there are some comments / descriptions that mention a relationship with another part
00:26 < kanzure> but it's not formalized
00:26 < fenn> right
00:26 < fenn> "produces fluorescence in either the absence of TetR or in the presence of the inducer aTC." could be easily formalized
00:27 < kanzure> okay, so let's fork it
00:27 < kanzure> what mechanisms will we add in to let those formalizations to occur
00:27 < kanzure> in the git-orized version of the db.
00:27 < kanzure> maybe each new type of relationship between two bricks
00:27 < kanzure> will be a separate set of files
00:28 < fenn> those are like the skdb classes
00:28 < kanzure> kind of like when you're doing mysql db tables you add in a new table to relate the unique id of some other table (the key) with some new property that you want to sort by
00:28 < fenn> whereas each part is an skdb project
00:28 < kanzure> the classes are the relationships?
00:28 < fenn> no, the classes have methods which define the relationships
00:28 < kanzure> and where in the proc do you run/call the methods?
00:28 < kanzure> just checking.
00:29 < fenn> when testing if the parts will work together the way you want?
00:29 < kanzure> I'm very confused
00:29 < kanzure> I agree that each part is an skdb project
00:29 < fenn> say signaller A makes ampicillin, and signaller B makes tetracycline, then measurement unit C that responds to tet will "work" with B but not with A
00:30 < kanzure> okay
00:30 < kanzure> A, B, C = 3 skdb projects
00:30 < fenn> so when you're looking around for stuff that works with C, you get a list of things that make tetracycline
00:30 < fenn> right
00:30 < kanzure> that kind of makes sese
00:30 < kanzure> sense
00:30 < kanzure> would it run through the list of all objects and run the make() method and if it produces 'tet' then it keeps it on the list ?
00:31 < kanzure> or is there something else you're thinking of
00:31 < kanzure> like would that be in the metadata spec of the part ?
00:31 < fenn> 'makes tet' would be in the metadata
00:31 < fenn> uh, that's turtle layer number 1
00:31 < fenn> what its supposed to do
00:32 < kanzure> this sounds like a good story
00:32 < kanzure> "Turtles and Python"
00:32 < kanzure> second ed. is "Turtles in Python"
00:32 < fenn> turtle was slow and stupid, but python knew how to tie himself in knots
00:33 < fenn> one day python ate turtle and became so bloated he couldn't tie himself in knots anymore
00:33 < fenn> the end
00:33 < kanzure> then a gnu appeared and set everything right
00:33 < kanzure> hrm
00:33 < kanzure> maybe also a camel
00:33 < kanzure> anyway
00:33 < fenn> nooo
00:33 < kanzure> pythons eat camels?
00:34 < fenn> pythons just ignore camels and hope they go away and die already, or maybe spit and hiss at them
00:34 < kanzure> so in the metadata turtle representation layers thingies
00:35 < kanzure> what's layer 2 specified at ? is it just another set of metadata that you could download, or would it be just extra stuff hidden in the package
00:35 < kanzure> hm, I like hidden extra stuff
00:35 < fenn> layer 2 is like, more introspection
00:36 < fenn> looking at inherited traits and building new models of what is going to happen
00:36 < fenn> i guess
00:36 < fenn> forget i said anything about layer 1 2 3
00:36 < kanzure> k, that helps
00:36 < fenn> nominal output products: tet, GFP
00:37 < kanzure> okay, so we can have a simple output specification for these biobricks
00:37 < fenn> actual output products: tet, GFP, NADP+, ADP, amino soup, tRNA
00:37 < kanzure> and input spec
00:37 < newgenome> hmmm
00:38 < newgenome> this gives me an idea
00:38 < kanzure> I'd be worried if it didn't
00:38 < newgenome> how fast can gfp be produced
00:38 < fenn> megatons per millisecond
00:38 < newgenome> and can it be turned off
00:38 < fenn> nevar!
00:38 < kanzure> polymerase per second will tell you sort of
00:38 < kanzure> PoPs
00:38 < fenn> newgenome: are you thinking about some kind of optical signalling mechanism?
00:39 < newgenome> as in could I make a cellular automata
00:39 < fenn> like a blinking led
00:39 < kanzure> kind of like Andy's lab's bacterial photography?
00:39 < kanzure> yeah
00:39 < newgenome> yeah
00:39 < kanzure> they're working on cellular automata
00:39 < kanzure> that's what we were doing in the lab
00:39 < kanzure> sort of
00:39 < kanzure> turing patterns aren't quite cellular automata but it's kinda close enough
00:39 < newgenome> except blinking all over
00:39 < newgenome> cool
00:39 < newgenome> wait turing patterns?
00:39 < kanzure> yes, but there's a discrete basis to it
00:39 < newgenome> how the heck are you getting turing patterns
00:40 < kanzure> I was going to try to implement "LiquidWars"
00:40 < kanzure> go play LiquidWars for about 2 seconds and you'll get it
00:40 < kanzure> 2D surface with patterns
00:40 < kanzure> it's not cellular automata rules, I know
00:40 < newgenome> http://www.bitstorm.org/gameoflife/
00:40 < newgenome> i want to implement this sort of
00:40 < kanzure> I know what CA is. ;-)
00:41 < newgenome> good
00:41 < newgenome> someone is working on literally cellular automata?
00:41 < newgenome> are they using luciferin?
00:42 < newgenome> does it have a faster response?
00:42 < kanzure> Not in Andy's lab .. all in vitro
00:42 < kanzure> anyway
00:42 < kanzure> nonprotein
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00:42 < fenn> you have sequence binding fluorophores right?
00:42 < kanzure> riight
00:43 < kanzure> right
00:43 < fenn> well something like that
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00:43 < kanzure> fenn: okay, so I'll rip the data set shortly and just automatically generate relationships based off of which category it's in, kinda randomly assume all of the data, and then the parts within each category will have some sort of relationship generated for starters (we don't need to be precise at this point)
00:43 < kanzure> and then we can just use that to try to build graphs, no ?
00:43 < kanzure> I don't know what the selection function will be though
00:43 < kanzure> once all of that data is filled out (even if half-assed / autogenerated)
00:44 < fenn> sounds good enough
00:44 < kanzure> no, I mean, let's say you're at your graph app thingy
00:44 < kanzure> http://bloodgate.com/graph-easy/
00:44 < kanzure> let's say you're here again
00:44 < kanzure> actually I might like http://bloodgate.com/graph-demo/more
00:44 < kanzure> http://bloodgate.com/graph-demo/ more
00:44 < fenn> ok, what about something like stupidfunclub.com?
00:45 < kanzure> is it flash?
00:45 < fenn> where instead of trying to see the whole graph at once, you tell a 'story' about what you want to do, one step at a time
00:45 < fenn> yes it's flash
00:45 < kanzure> ok, now I see it
00:45 < fenn> doesnt have to be flash though
00:45 < kanzure> had to switch browsers
00:45 < kanzure> hm
00:45 < kanzure> okay, I like that
00:45 < fenn> otherwise you just get a big hairball
00:45 < kanzure> entirely doable
00:46 < kanzure> right
00:46 < kanzure> but then what about parallel processes that you want to represent or something
00:46 < kanzure> don't know how to say that
00:46 < fenn> multiple branches in the story
00:46 < kanzure> you don't branch on a conditional?
00:46 < kanzure> that's important.
00:46 < fenn> huh?
00:46 < kanzure> imagine an rpg with a tree for the storyline
00:47 < kanzure> those are conditional branches
00:47 < kanzure> not "always running concurrently"
00:47 < kanzure> just an important difference to consider.
00:47 < fenn> sure
00:47 < fenn> i dont think of this story as being a chronological sequence
00:47 < fenn> more like a circuit diagram
00:47 < kanzure> signaler -> teh signal -> receptor
00:47 < fenn> but the point is, each step along the circuit you have a set of options for what to add next
00:47 < kanzure> odd, that's not how I design my electrical schematics
00:48 < kanzure> sometimes it is I guess
00:48 < kanzure> usually it's just me hearing somebody yelling at me "you forgot some damn resistors, that thing will fry like an egg"
00:48 < fenn> you could even work backwards from the end point, or work both directions if it's a loop
00:49 < fenn> fwiw graph-easy doesn't show up in konqueror
00:49 < kanzure> blah
00:49 < kanzure> graph-demo?
00:50 < kanzure> wahoo
00:50 < fenn> oh, wait, its just words with > between them
00:50 < fenn> nevermind
00:50 < kanzure> hm?
00:50 * kanzure checks.
00:51 < kanzure> yeah, that's an odd character blitting error
00:51 * kanzure wonders if this could be combined with collabedit.com just be to ridiculous .. ok, maybe not.
00:51 < kanzure> s/could/should/
00:52 < fenn> ew
00:52 < kanzure> collaborative mind maps
00:54 < newgenome> http://www.physorg.com/news139500643.html
00:54 < newgenome> check this out
00:54 < newgenome> meat anyone?
00:55 < kanzure> Depends, how complex is the synthesis of this polymer?
00:56 < kanzure> fenn: ok, so the storymaker interface here .. how should this be implemented?
00:56 < kanzure> I know how to make a storymaker in general,
00:56 < kanzure> but in the context of graph-demo I'm not so sure
00:56 < kanzure> maybe a couple of pages of a 'wizard' ?
00:56 < kanzure> a wizard to guide the pythons and turtles, you see
00:59 < fenn> the idea is to end up with a circuit diagram, right? so you draw it out as you go
00:59 < kanzure> where do you see your options for the next unit thingy
00:59 < fenn> at each vertex in the graph, you have all the edges from that vertex available to choose from
00:59 < kanzure> or your options for the relationship thingy
00:59 < fenn> like some kind of context menu or something
00:59 < kanzure> oh
00:59 < kanzure> ew
00:59 < fenn> ok, another frame
00:59 < kanzure> ew ew
00:59 < fenn> what?
00:59 < kanzure> you mean a listbox maybe?
00:59 < fenn> little icons with words on them doesn't help make good decisions
01:00 < kanzure> this is true
01:00 < fenn> you want to see what your options are and how they work
01:00 < fenn> um, bad phrasing
01:00 < fenn> you want to see probably some pictures, explanation of how it works, testing readiness level, cost, etc
01:01 < kanzure> all in one little window? yikes
01:01 < kanzure> interface nightmare
01:01 < kanzure> that should be stuff the user types into a cli and stuff pops up
01:01 < fenn> not really, basically it would just show you the wiki page for that skdb project
01:01 < kanzure> sorry ?
01:01 < kanzure> so at the bottom of the screen, have it dynamically load the project you're about to make an edge to?
01:01 < fenn> right
01:01 < kanzure> the wiki page of the project
01:02 < kanzure> ok, sounds good, but I still don't see how they're going to see their options of possible new vertices to choose from
01:02 < kanzure> listbox at the side of the widget/panel in which they are 'drawing' ?
01:02 < newgenome> man this is way over my head
01:02 < fenn> so on the left side you have little icons with names stuck to them, and on the right you have the detailed view of whatever you just selected or focused on
01:02 < kanzure> fenn: so you don't have an overall view of what you've written in the story so far?
01:02 < fenn> no, of course not
01:02 < kanzure> so you just go linearly ?
01:03 < fenn> if you knew what you were doing you wouldnt need this program
01:03 < kanzure> ah
01:03 < fenn> uh, you have a diagram of what you've picked so far, yes
01:03 < kanzure> okay
01:03 < kanzure> oh
01:03 < kanzure> left side -> little icons with names stuck to them, check
01:03 < kanzure> right side you have a detailed view of what you've just selected
01:03 < kanzure> but then where is your diagram of what you've picked so far?
01:04 < kanzure> maybe just a small little horizontal diagram at the top ?
01:04 < kanzure> hrm
01:04 < fenn> it's being built up in the window with little icons
01:04 < kanzure> oh
01:04 < fenn> on the left, same window
01:04 < kanzure> then where do they see their list of options for the new vertices to pick from ?
01:04 < fenn> each icon has edges going out of it
01:04 < kanzure> bah
01:04 < kanzure> time for you to do a mockup
01:04 < fenn> when you're at the bleeding edge, there's multiple edges to pick from
01:05 < fenn> they lead to 'ghost' icons that are the options available to you
01:05 < kanzure> uhm, so let's say that there's 10k options for the next part
01:05 < kanzure> 10k ghost icons, really ?
01:05 < fenn> well, maybe not
01:05 < fenn> the other option was a list
01:06 < fenn> you could click on an edge and get a list of things that fit that edge in the usual description window
01:07 < fenn> ok mockup time
01:07 < kanzure> heh
01:07 < fenn> kolourpaint wheee
01:07 < kanzure> yep, same here
01:07 < fenn> it always looks so much better in your head
01:07 < kanzure> btw, if there's such a "click an edge" feature, it's easy to implement in code at least for something like
01:07 < kanzure> examine_edge.py file.diagram edge-id-here
01:07 < kanzure> and then it could spit out the information or whatever
01:07 < kanzure> that's simple enough.
01:07 < kanzure> (of course, we're talking about a browser thingy)
01:07 < kanzure> ((but we both know it's not restricted to a browser thingy))
01:08 < kanzure> I'm almost tempted to go cold turkey and not use a graphical interface at all ;-)
01:09 < kanzure> maybe that's the way to go anyway
01:09 < kanzure> hack out the list of commands for the shell
01:09 < kanzure> then wrap those up into the web app
01:11 < bkero> do it
01:11 < bkero> Get the output to be through an irc bot.
01:11 < kanzure> aren't irc bots typically terrible?
01:11 < bkero> Yes, but they're an effective output mechanism.
01:12 < kanzure> You want to do engineering in a chat room with an irc bot ?
01:12 < kanzure> heh
01:12 < bkero> yes
01:12 < newgenome> hey
01:12 < kanzure> you're crazy :-)
01:12 < bkero> !run command3.pl
01:12 * kanzure adds it to his todo list
01:12 < newgenome> just found a cool biobrick
01:12 < bkero> < Bot> Hits: 0, Misses: 4, Anomolies: 8192, Entropy: 93%
01:12 < kanzure> bkero: no, I'm thinking of trying combinations/permutations in a chat room with collective community experience or something
01:13 < newgenome> http://partsregistry.org/wiki/index.php?title=Part:BBa_I742111
01:13 < newgenome> limonene synthase
01:13 < newgenome> limonene is a chemical that can dissolve polystyrene
01:13 < newgenome> it's also flammable
01:14 < bkero> Can't gasoline also?
01:14 < newgenome> and smell's like lemons
01:14 < newgenome> good point
01:14 < newgenome> you could make napalm with it
01:14 < bkero> I've done that
01:14 < bkero> Styrofoam + gasoline = gooey
01:14 < bkero> It absorbs about 1000:1
01:15 < kanzure> bkero: entropy? :)
01:15 < bkero> Yes
01:15 < bkero> Lots of entropy in your theoretical data. :P
01:16 < newgenome> bactonapalm
01:16 < kanzure> Doesn't make sense ..
01:16 < bkero> It was just sample output :P
01:16 < kanzure> okay
01:16 < kanzure> just had to know if there was something behind it
01:16 < kanzure> you know, just in case
01:16 < bkero> Nope
01:16 < bkero> You could have calculated entropy as an output
01:17 < fenn> blah.. god this is ugly
01:17 < fenn> http://fennetic.net/pub/irc/skdb-mockup/select-icon.png
01:17 < kanzure> hehe
01:17 < fenn> http://fennetic.net/pub/irc/skdb-mockup/select-edge.png
01:17 < kanzure> okay
01:18 < kanzure> instead of clicking, let's just do shift + left/right arrow
01:18 < kanzure> and then no-shift means switching the nodes
01:18 < kanzure> when you right-arrow over to something that doesn't exist, you're auto-transported to the list of options
01:18 < kanzure> to the right
01:18 < kanzure> where right arrow goes down, placing the blocks on the page
01:18 < kanzure> simple enough of course
01:18 < fenn> can do both
01:19 < kanzure> clicking lines in js just sounds hard
01:19 < fenn> keyboard and mouse interface is common in gui widgets
01:19 < kanzure> I don't think I know of a way to click on lines in javascript like that
01:19 < kanzure> unless you're pixel perfect
01:19 < fenn> i dont know any javascript so i probably wont be learning it just for this
01:19 < kanzure> or "snap on" action
01:19 < kanzure> don't bother
01:19 < kanzure> I feel impure even mentioning it
01:20 < kanzure> but I might do this mockup.
01:20 < fenn> you dont have to be pixel perfect, the line can light up based on which element the cursor is nearest
01:20 * kanzure wonders if the bloodgate script has something for that
01:20 < fenn> like in electrical cad
01:21 < fenn> i need to do something like this already for emc
01:21 < kanzure> gui/js thingy?
01:21 < fenn> no, a graph/list thingy
01:21 < kanzure> huh?
01:21 < kanzure> not your mockup?
01:21 < fenn> connecting boxes that can only be connected in certain ways
01:22 < fenn> its basically the same idea
01:22 < fenn> but totally different context
01:22 < kanzure> that's what the "validator" that we mentioned a long time ago should be doing
01:22 < kanzure> well, not just "validator"
01:22 < fenn> the validator is what gives you the list of options
01:22 < kanzure> but also the "find a compatable next part" idea
01:22 < kanzure> *compatible
01:23 -!- newgenome [n=chatzill@resnet-47-165.dorm.utexas.edu] has quit ["ChatZilla 0.9.83 [Firefox 3.0.1/2008070208]"]
01:23 < kanzure> the trick is that we have a data set with the biobricks stuff, sort of
01:23 < kanzure> or at least we can auto generate the data set
01:23 < kanzure> since they are already somewhat staggard
01:23 < kanzure> we could do the random rule stuff and have it be bad meta data
01:23 < kanzure> until they yell at us and are friendly enough to fork it for a while and then merge it when it's acceptable :)
01:24 < fenn> until they laboriously type all their sloppy plain english metadata into our system, you mean
01:24 < kanzure> they are welcome to come up with their own metadata system, I think
01:24 < kanzure> aren't they?
01:24 < fenn> indeed, but they havent
01:24 < kanzure> slackers
01:24 < fenn> sometimes its easier to let someone else tell you what to think (set up the metadata scheme)
01:25 < fenn> then filling out all the details is just grunt work
01:25 < kanzure> some poor undergrad
01:25 < fenn> or even just kids on the diybio list
01:25 < fenn> shrug
01:25 < kanzure> where do they have access to that info?
01:25 < kanzure> I don't think it's all in the descriptions all the time
01:25 < fenn> hmm
01:25 < kanzure> it's usually in the literature, which kids typically don't have access to
01:26 < kanzure> but
01:26 < kanzure> finding those papers and giving them out isn't hard either
01:26 < kanzure> okay, 8 am classes
01:26 < kanzure> I should sleep
01:26 < fenn> gn8
01:27 < bkero> ick 8am classes
01:28 < kanzure> ick 8 am calculus class
01:28 < kanzure> ick 8 am calculus class oh shit don't have the book homework due thursday
01:28 < kanzure> that sort of thing
01:28 < bkero> g2library
01:28 < kanzure> like everyone else?
01:29 < bkero> Mebbe
01:29 < bkero> Get there early in the morning, copy the pages, return the books, and figure out how to do the problems by wikipedia
01:29 < kanzure> oh, the content isn't the problem
01:29 < kanzure> it's the questions
01:29 < kanzure> so yes
01:29 < bkero> or find a torrent on textbooktorrents.com?
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01:32 < kanzure> 'You are not currently enrolled in any courses.'
01:32 < kanzure> hahah
01:32 < kanzure> beautiful ..
01:33 < kanzure> fairly popular book, it has been torrented
01:36 < kanzure> aha
01:36 < kanzure> demonoid hurrah
01:41 < bkero> Demonoid :P
01:41 < bkero> There you go
01:41 < bkero> Now you can be even lazier. Thank you internet.
01:41 < kanzure> the torrent isn't starting though
01:41 < kanzure> hm
01:42 < bkero> Tried textbook torrents?
01:43 < kanzure> registration is currently disabled
01:43 < kanzure> has been for a while IIRC
01:43 < bkero> I have an account
01:43 < bkero> Whats the book called?
01:46 < kanzure> http://www.demonoid.com/files/details/1552394/15625924/
01:46 < Depucelato1> There's a private tracker for textbook torrents?
01:47 < bkero> Didn't used to be private.
01:47 < Depucelato1> you're talking about Demonoid or one specifically for textbooks?
01:47 < Depucelato1> Because I'm in partickler sick of paying for latest edition textbooks
01:47 < kanzure> Depucelato1: textbooktorrents
01:48 < Depucelato1> I've taken to melting the binding off of my textbooks and putting them on the scanner/copier at work to scan and OCR
01:49 < Depucelato1> which is great for timed open-book texts where I supposedly wouldn't be fast enough to browse through the book for answers
01:55 < kanzure> damnit, wrong book
01:58 < bkero> http://labs.mozilla.com/2008/08/introducing-ubiquity/
02:04 < kanzure> "doing something" requires an art to construct the task
02:04 < kanzure> it doesn't just magically exist
02:04 < kanzure> so once one person puts in the effort, it should be much less effort to just copy/paste the file
02:04 < kanzure> just like my idea of having Austin2008.zip for all of the events around town
02:15 < kanzure> argh
02:15 < kanzure> how could this be ?
02:15 < kanzure> there's no question #85 in this section
02:15 < kanzure> so I'm pretty sure it's the wrong book
02:15 < kanzure> but amazon does not know of the right book's existence
02:24 < fenn> wow ubiquity is like surfraw v2.0
02:25 < kanzure> you have it running?
02:25 < fenn> no i'm watching the demo
02:25 < fenn> it runs in the browser though.. not sure how hard it would be to fix that
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04:22 < fenn> ubiquity is really quite fun to play with
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05:22 < bkero> Yes it is :)
05:22 < bkero> for i in *; do mencoder $i -ovc copy -oac copy -forceidx -of avi -o $i.new && mkvmerge -o `echo $i|sed -e '{ s/\.avi/\.mkv/ }'` $i.new && rm $i.new && rm $i; done
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06:24 < nsh> EGREEK
06:44 -!- faceface [n=dbolser@bioinformatics.org] has quit [Remote closed the connection]
06:59 < nsh> "In the past two years, a laboratory in France and another in the United States independently reconstructed a functioning HERV-K retrovirus from pieces found in the human genome. This summer, both showed that the gene sequences of some of those viruses bear the characteristic fingerprints of APOBEC3, a human enzyme that mutated them into submission."
06:59 < nsh> colour me dubious...
07:02 < nsh> --http://www.washingtonpost.com/wp-dyn/content/article/2008/08/31/AR2008083101759_pf.html
07:45 < kanzure> huh
07:49 < willPow3r> ...
07:49 * kanzure just woke up and isn't processing effectively
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08:49 < willPow3r> i hate when that happens
08:50 < kanzure> waking up?
08:51 < willPow3r> waking up is nice, but the need for sleep isn't
08:52 * kanzure vanishes
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12:59 < kanzure> somebody tempt me to use ubiquity
13:00 < bkero> kanzure: It's got context-sensitive verbs.
13:01 < bkero> You can use it to embed google maps into anything :P
13:01 < kanzure> also, the skdb app grapher thingy, is that just for structure? or is it for process? if I wanted to mesh a 3d object and call it a part, is the viewer thingy showing that I have an object "touching" other things? or what?
13:03 < kanzure> bkero: so, it's just greasemonkey userscripts all over again?
13:03 < bkero> kanzure: Sort of. It's more like quicksilver for firefox.
13:03 < bkero> Have you ever used quicksilver?
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13:33 < kanzure> I don't remember.
13:33 < kanzure> quickfox
13:33 < kanzure> not quicksilver
13:33 < kanzure> oh crap, 1 pm appointment with an automated professor
13:33 < kanzure> profbot or something
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14:10 < pk> hi
14:12 < willPow3r> pk
14:16 < pk> i want google chrome
14:19 < willPow3r> chrome is going to compete with firefox, not IE
14:20 < willPow3r> so keep that in mind when you decide to switch
14:25 < pk> I have great add-ons in firefox
14:26 < pk> chrome would have to blow firefox away for me to switch
15:06 < pk> it's released now
15:06 < pk> the beta is out
15:06 < pk> i can't get it from google though, must be getting hammered badly
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15:29 < kanzure> hahah
15:29 < kanzure> firefox has lots of problems
15:29 < kanzure> anyway
15:29 < kanzure> hahah
15:29 < kanzure> I met with the doc behind the automated design lab today
15:31 < kanzure> so here's what he's doing
15:31 < kanzure> given a bag of parts, make a graph to represent the design and their interconnections and so on
15:32 < kanzure> then, he wants to simulate the functionality of these designs
15:32 < kanzure> for example -- I didn't tell him this -- but a good example would be biobrick kinetics
15:32 < kanzure> *cough*
15:32 < kanzure> and then he wants to see what manipulations of the parameters when generating those designs (from 'seeds') produce good stuff, or whatever
15:33 < kanzure> you could manually optimize all of the parameters of a spaceship if you had to, for example
15:33 < kanzure> anyway,
15:33 < kanzure> for figuring out which parameters are interesting and the values that are interesting, he wants to use not genetic algorithms but simple neural networks with their own graph representation
15:33 < kanzure> then use graph rewriting 'grammar rules' to find a suitable amount of complexity in the 'neural net' (or hidden markov model, more appropriately?)
15:34 < kanzure> that can deal with the problem space that you are designing within
15:34 < kanzure> 'grammar rules' are the things that can be applied to a 'neural network graph' and add a new edge into it as a permutation
15:34 < kanzure> or whatever
15:35 < kanzure> anyway, I piped up at that point and suggested that you should learn which of these 'grammar rules' start to make for interesting parameter-variable-values in the solver/evaluator of the designs that you tree-generate
15:35 < kanzure> turns out that that's the project that he was going to pitch me
15:35 < kanzure> be careful what you say, you might be assigned to actually doing it
15:36 * kanzure is wondering about computational complexity classes and whether or not graph rewriting grammar rules are more appropriate for certain classes than others, and whether or not manufacturing problems can be reduced to comp sci
15:36 < kanzure> surely 'traveling salesman and routing' is a good example, but that's not the same context.
15:36 < kanzure> anyway, he mentioned there might be money involved
15:38 < kanzure> now, which biobricks would be particularly good for using in such a system
15:38 < kanzure> since we have chemical kinetics of some of them, I'm sure we do
15:40 < kanzure> then we can just use the random connections between the parts of each 'category' on partsregistry.org
15:40 < kanzure> that we were talking about last night
15:41 < kanzure> plug in some kinetic simulation stuff, and then generate a full tree of all of the possible designs and whatever, then optimize that by coming up with either the 'neural network' or 'markov model thingy' so that the designs can be better selected "somehow" -- not quite sure what the framework is going to look like ...
15:41 < kanzure> the trick is finding the designs that work best, so I'm pretty sure kinetics is a good place
15:48 < kanzure> this guy apologized *to me* for using C#
15:52 < kanzure> http://clm.utexas.edu/MM-MM08talk-med/
15:54 * kanzure is not so sure how cross-lateral these 'graph grammar rules' are going to be across the computational complexity domain
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16:12 < pk> is this guy talking to UT austin donors or something?
16:18 < kanzure> not sure
16:18 < kanzure> might be students?
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19:24 < bkero> http://www.engadget.com/2008/09/02/mythbusters-rfid-hacking-episode-canned-by-credit-card-company-l/
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19:39 < ybit> http://www.ted.com/index.php/talks/paul_rothemund_details_dna_folding.html
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19:50 < pk> nice, looks like a good one
19:50 < pk> I'll watch after dinner
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19:53 < bkero> Yay ted
20:42 < Nade> i love ted
20:42 < Nade> i've watched like nearly every vid on that site
21:09 < pk> oh my
21:09 < pk> that video is awesome
21:09 < kanzure> aughghghghgh
21:09 < kanzure> Hulk crush!
21:09 < pk> watching all those smileys floating around is surreal
21:10 < pk> thanks for sharing
21:10 < kanzure> okay
21:10 < kanzure> so
21:10 < kanzure> dr. campbell has me paid for doing his research
21:10 < kanzure> dr. mauk has his cerebellum simulator in fucking visualbasic
21:10 < kanzure> wants that over to C/C++ via OpenMP
21:10 < kanzure> he's doing his own fortran version, wtf
21:10 < kanzure> thought that was dead
21:10 < kanzure> overall great people
21:11 < kanzure> also went to the ASME meeting, the Engineers for a Sustainable World meeting (building a biodiesel reactor over at the pickle research center off campus, also poop bacteria for Mexico), and the Robotics and Automation Society with free 24/7 lab access in a trailer right off of the engineering 'square' of buildings
21:11 < kanzure> who the fuck codes a cerebellum in visual basic
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21:20 * kanzure turns into hulk
21:23 < kanzure>
21:23 < kanzure> Previous Claims of siRNA Therapeutic Effects Called into
21:23 < kanzure> Question by Report in Human Gene Therapy
21:28 < pk> human gene therapy is some kind of publication?
21:29 < pk> yup.
21:30 < kanzure> crap
21:30 < kanzure> where'd I send something about that yellow drum bot
21:30 < kanzure> anybody know which mailing list?
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22:06 < kanzure> http://heybryan.org/~bbishop/docs/mauksimzip.zip <-- visual basic hurray?
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22:59 < procto> kanzure: dunno if that's something you're interested in, by my research project this semester will be on qualitative spatial reasoners
23:00 < kanzure> what does this mean
23:00 < kanzure> qualitative?
23:00 < kanzure> reasoners?
23:01 < procto> well, reasoners use logics and calculi to infer conclusions from premises
23:01 < kanzure> eww
23:01 < kanzure> :)
23:02 < procto> prolog is an example of a language and a particular logic
23:02 < kanzure> right
23:02 < procto> well, qualitative spatial reasoning has to do with spatial things
23:03 < procto> so, for example you say "there's a bum near the mcdonald's on main st"
23:03 < procto> what does "near" mean?
23:03 < procto> it's a qualitative spatial operator
23:03 < procto> there are ways to treat such statements in a formal mannel
23:03 < procto> I plan on using this to augment my gargoyle system
23:04 < procto> or imagine saying something like this to a system: "I'm on a building on the 3rd floor. out the windown I can see X, Y and Z. Where am I?"
23:05 < procto> things like that
23:05 < procto> the specific area I will be working on, I'm not sure yet
23:07 < kanzure> reverse reasoning to figure out where an agent is, would certainly be interesting
23:07 < kanzure> that's worthwhile methinks
23:08 < kanzure> to reconstruct overall location from clues
23:08 < procto> that's one application
23:08 < procto> in general, you don't always have perfect spatial information
23:08 < kanzure> right
23:08 < kanzure> rarely do I :-)
23:08 < procto> especially in unfamiliar locations
23:09 < kanzure> today I found myself staring at a 12 by 9 foot neural tissue slice on a wall
23:09 < kanzure> it was beautiful
23:09 < kanzure> but I had no clue where I was.
23:09 < kanzure> beautiful in the evil way
23:10 < procto> hehe
23:10 < procto> with my system implemented, you can show it a photo, and then ask for the nearest bathroom
23:10 < procto> :>
23:10 < kanzure> cell phone pics
23:11 < procto> fully implemented. which probably won't quite happen very soon
23:11 < procto> realistically
23:11 < procto> thing is, no one ever told it where the bathrooms in the building are explicitely
23:12 < procto> it probably scraped it from a site fro a small symposium, where one of pages said the bathroom was "Across the hall"
23:12 < procto> that's the kind of thing I want
23:13 < kanzure> "download the poopfactor, dial 222 now."
23:24 < kanzure> I thought of a silly wearable computer idea
23:25 < kanzure> if you cross your hands to your alternate shoulders, there's a good place to strap on one half a keyboard on each outer edge of the arm
23:28 < procto> too tiring
23:28 < kanzure> yeah :(
23:29 < kanzure> okay, how about the old card trick
23:29 < kanzure> but with giant keyboards
23:29 < kanzure> card under the sleeve