| --- Day changed Tue Sep 02 2008 | ||
| fenn | i think people like tabs because windows doesn't give much in the way of window management | 00:00 |
|---|---|---|
| kanzure | even my vertical scrollbar hack isn't all that helpful | 00:01 |
| kanzure | still have to scroll | 00:01 |
| 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 | 00:02 |
| newgenome | carbon nanotubes have a tensile strength of 62000 gpa | 00:03 |
| newgenome | spider silk is 1200 gpa | 00:03 |
| kanzure | link | 00:03 |
| 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 | 00:04 |
| 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 | 00:05 |
| 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 | 00:06 |
| newgenome | but it gets messed up with water | 00:07 |
| newgenome | tensile modulus | 00:07 |
| 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 | 00:08 |
| 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 | 00:09 |
| 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 | 00:11 |
| 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 | 00:12 |
| newgenome | most single molecule graphene is made by CVD | 00:13 |
| newgenome | I believe | 00:14 |
| fenn | why do you want huge sheets of it? | 00:14 |
| fenn | hmm interesting, monocrystaline silicon has a tensile strength of 7GPa vs 5.5GPa for carbon fiber (62GPa for carbon nanotube) | 00:15 |
| 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 | 00:16 |
| kanzure | <START>1008</START> <END>1062</END> <SCORE>0.0</SCORE> <ORIENTATION></ORIENTATION> <PHASE>-</PHASE> <NOTE>BBa_R0062</NOTE> | 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? | 00:17 |
| 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 | 00:18 |
| kanzure | kinda like skdb in general | 00:19 |
| kanzure | how do you describe turtles ? | 00:19 |
| kanzure | turtle societies especially | 00:19 |
| 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 | 00:20 |
| 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 | 00:21 |
| fenn | turtle = class = category | 00:22 |
| kanzure | right | 00:22 |
| 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 | 00:24 |
| fenn | those categories (part_types) are useful but there's just not enough information on how they interact | 00:25 |
| 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 | 00:26 |
| 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 | 00:27 |
| 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. | 00:28 |
| 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 | 00:29 |
| 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 ? | 00:30 |
| 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 | 00:31 |
| 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 | 00:32 |
| 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? | 00:33 |
| 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 | 00:34 |
| 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 | 00:35 |
| 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 | 00:36 |
| 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 | 00:37 |
| 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? | 00:38 |
| 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 | 00:39 |
| 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. ;-) | 00:40 |
| newgenome | good | 00:41 |
| newgenome | someone is working on literally cellular automata? | 00:41 |
| newgenome | are they using luciferin? | 00:41 |
| 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 | 00:42 |
| -!- ybit [n=h@unaffiliated/ybit] has quit [Read error: 104 (Connection reset by peer)] | 00:42 | |
| fenn | you have sequence binding fluorophores right? | 00:42 |
| kanzure | riight | 00:42 |
| kanzure | right | 00:43 |
| fenn | well something like that | 00:43 |
| -!- ybit [n=h@unaffiliated/ybit] has joined #hplusroadmap | 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) | 00:43 |
| 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? | 00:44 |
| 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 | 00:45 |
| 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 | 00:46 |
| 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 | 00:47 |
| 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 | 00:48 |
| fenn | fwiw graph-easy doesn't show up in konqueror | 00:49 |
| kanzure | blah | 00:49 |
| kanzure | graph-demo? | 00:49 |
| 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. | 00:50 | |
| 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/ | 00:51 |
| fenn | ew | 00:52 |
| kanzure | collaborative mind maps | 00:52 |
| newgenome | http://www.physorg.com/news139500643.html | 00:54 |
| newgenome | check this out | 00:54 |
| newgenome | meat anyone? | 00:54 |
| kanzure | Depends, how complex is the synthesis of this polymer? | 00:55 |
| 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 | 00:56 |
| 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 | 00:59 |
| 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 | 01:00 |
| 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 | 01:01 |
| 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 ? | 01:02 |
| 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? | 01:03 |
| 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 | 01:04 |
| 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 | 01:05 |
| fenn | you could click on an edge and get a list of things that fit that edge in the usual description window | 01:06 |
| 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)) | 01:07 |
| kanzure | I'm almost tempted to go cold turkey and not use a graphical interface at all ;-) | 01:08 |
| 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 | 01:09 |
| 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. | 01:11 |
| 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 | 01:12 |
| 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 | 01:13 |
| 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 | 01:14 |
| kanzure | bkero: entropy? :) | 01:15 |
| bkero | Yes | 01:15 |
| bkero | Lots of entropy in your theoretical data. :P | 01:15 |
| 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 | 01:16 |
| 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 | 01:17 |
| 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 | 01:18 |
| 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 | 01:19 |
| 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 | 01:20 |
| 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 | 01:21 |
| 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 | 01:22 |
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| 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 :) | 01:23 |
| 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) | 01:24 |
| 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 | 01:25 |
| 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 | 01:26 |
| bkero | ick 8am classes | 01:27 |
| 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? | 01:28 |
| 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? | 01:29 |
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| kanzure | 'You are not currently enrolled in any courses.' | 01:32 |
| kanzure | hahah | 01:32 |
| kanzure | beautiful .. | 01:32 |
| kanzure | fairly popular book, it has been torrented | 01:33 |
| kanzure | aha | 01:36 |
| kanzure | demonoid hurrah | 01:36 |
| 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 | 01:41 |
| bkero | Tried textbook torrents? | 01:42 |
| 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? | 01:43 |
| kanzure | http://www.demonoid.com/files/details/1552394/15625924/ | 01:46 |
| Depucelato1 | There's a private tracker for textbook torrents? | 01:46 |
| 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 | 01:47 |
| 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 | 01:48 |
| Depucelato1 | which is great for timed open-book texts where I supposedly wouldn't be fast enough to browse through the book for answers | 01:49 |
| kanzure | damnit, wrong book | 01:55 |
| bkero | http://labs.mozilla.com/2008/08/introducing-ubiquity/ | 01:58 |
| 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 | 02:04 |
| 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 | 02:15 |
| fenn | wow ubiquity is like surfraw v2.0 | 02:24 |
| 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 | 02:25 |
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| fenn | ubiquity is really quite fun to play with | 04:22 |
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| 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 | 05:22 |
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| nsh | EGREEK | 06:24 |
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| 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... | 06:59 |
| nsh | --http://www.washingtonpost.com/wp-dyn/content/article/2008/08/31/AR2008083101759_pf.html | 07:02 |
| kanzure | huh | 07:45 |
| willPow3r | ... | 07:49 |
| * kanzure just woke up and isn't processing effectively | 07:49 | |
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| willPow3r | i hate when that happens | 08:49 |
| kanzure | waking up? | 08:50 |
| willPow3r | waking up is nice, but the need for sleep isn't | 08:51 |
| * kanzure vanishes | 08:52 | |
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| kanzure | somebody tempt me to use ubiquity | 12:59 |
| bkero | kanzure: It's got context-sensitive verbs. | 13:00 |
| 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? | 13:01 |
| 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? | 13:03 |
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| 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 | 13:33 |
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| pk | hi | 14:10 |
| willPow3r | pk | 14:12 |
| pk | i want google chrome | 14:16 |
| willPow3r | chrome is going to compete with firefox, not IE | 14:19 |
| willPow3r | so keep that in mind when you decide to switch | 14:20 |
| pk | I have great add-ons in firefox | 14:25 |
| pk | chrome would have to blow firefox away for me to switch | 14:26 |
| 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 | 15:06 |
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| 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 | 15:29 |
| 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 | 15:31 |
| 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 | 15:32 |
| 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?) | 15:33 |
| 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 | 15:34 |
| 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 | 15:35 |
| * 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 | 15:36 |
| 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 | 15:38 |
| 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 | 15:40 |
| 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 | 15:41 |
| kanzure | this guy apologized *to me* for using C# | 15:48 |
| kanzure | http://clm.utexas.edu/MM-MM08talk-med/ | 15:52 |
| * kanzure is not so sure how cross-lateral these 'graph grammar rules' are going to be across the computational complexity domain | 15:54 | |
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| pk | is this guy talking to UT austin donors or something? | 16:12 |
| kanzure | not sure | 16:18 |
| kanzure | might be students? | 16:18 |
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| bkero | http://www.engadget.com/2008/09/02/mythbusters-rfid-hacking-episode-canned-by-credit-card-company-l/ | 19:24 |
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| ybit | http://www.ted.com/index.php/talks/paul_rothemund_details_dna_folding.html | 19:39 |
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| pk | nice, looks like a good one | 19:50 |
| pk | I'll watch after dinner | 19:50 |
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| bkero | Yay ted | 19:53 |
| Nade | i love ted | 20:42 |
| Nade | i've watched like nearly every vid on that site | 20:42 |
| 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 | 21:09 |
| 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 | 21:10 |
| 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 | 21:11 |
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| * kanzure turns into hulk | 21:20 | |
| kanzure | 21:23 | |
| kanzure | Previous Claims of siRNA Therapeutic Effects Called into | 21:23 |
| kanzure | Question by Report in Human Gene Therapy | 21:23 |
| pk | human gene therapy is some kind of publication? | 21:28 |
| pk | yup. | 21:29 |
| kanzure | crap | 21:30 |
| kanzure | where'd I send something about that yellow drum bot | 21:30 |
| kanzure | anybody know which mailing list? | 21:30 |
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| kanzure | http://heybryan.org/~bbishop/docs/mauksimzip.zip <-- visual basic hurray? | 22:06 |
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| procto | kanzure: dunno if that's something you're interested in, by my research project this semester will be on qualitative spatial reasoners | 22:59 |
| kanzure | what does this mean | 23:00 |
| kanzure | qualitative? | 23:00 |
| kanzure | reasoners? | 23:00 |
| procto | well, reasoners use logics and calculi to infer conclusions from premises | 23:01 |
| kanzure | eww | 23:01 |
| kanzure | :) | 23:01 |
| 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 | 23:02 |
| 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 | 23:03 |
| 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?" | 23:04 |
| procto | things like that | 23:05 |
| procto | the specific area I will be working on, I'm not sure yet | 23:05 |
| kanzure | reverse reasoning to figure out where an agent is, would certainly be interesting | 23:07 |
| kanzure | that's worthwhile methinks | 23:07 |
| 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 | 23:08 |
| 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 | 23:09 |
| 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 | 23:10 |
| 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 | 23:11 |
| 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 | 23:12 |
| kanzure | "download the poopfactor, dial 222 now." | 23:13 |
| kanzure | I thought of a silly wearable computer idea | 23:24 |
| 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 | 23:25 |
| procto | too tiring | 23:28 |
| kanzure | yeah :( | 23:28 |
| kanzure | okay, how about the old card trick | 23:29 |
| kanzure | but with giant keyboards | 23:29 |
| kanzure | card under the sleeve | 23:29 |
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