| --- Day changed Sun Sep 07 2008 | ||
| kanzure | http://heybryan.org/~bbishop/docs/biobricks/ <-- Stuff. | 00:06 |
|---|---|---|
| kanzure | oops, fixed http://heybryan.org/~bbishop/docs/biobricks/types/ | 00:07 |
| * kanzure was using > instead of >> in his writes. hehe | 00:07 | |
| kanzure | In the types/ dir you will find a listing of each category to which each biobrick belongs (see also the data/ dir with the biobricks themselves). Now, I'm wondering how to apply http://bionetgen.org/index.php/Tutorial_Example -- the reaction rules should be on a per-brick level, right? | 00:23 |
| kanzure | I could just correlate the DNA files in the data/ dir back over to some database that uses BNG2 format (which has the 'reaction rules') | 00:23 |
| kanzure | but the question is whether the 'reaction rules' apply on a per-biobrick level, or is it per "class/types of biobricks" level ? | 00:23 |
| kanzure | (Either way, there's going to have to be some fancy variable find-and-replace in the 'rule set' in the BNG2 file format) | 00:24 |
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| kanzure | Hey Overand. | 00:31 |
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| kanzure | Hey. | 10:32 |
| kanzure | Hm. Server IP has changed again. | 10:32 |
| kanzure | http://grey.colorado.edu/emergent/index.php/Server_Protocol | 10:50 |
| kanzure | Hm. | 10:50 |
| kanzure | http://heybryan.org/free_will.html just because I don't want to keep writing it over and over again | 11:38 |
| * kanzure is willing to update that definition / approach, of course, since little of his ideas rely on it, but it's not a big deal either | 11:39 | |
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| kanzure | Hi Phreedom. | 12:27 |
| Phreedom | hi | 12:27 |
| kanzure | How goes the hackathon? | 12:27 |
| Phreedom | kanzure_: which one? | 12:31 |
| Phreedom | kanzure_: which one? | 12:31 |
| Phreedom | grrr | 12:31 |
| Phreedom | kanzure: :) | 12:31 |
| kanzure | Hm. | 12:32 |
| kanzure | Odd, kanzure_ highlights on this end too. | 12:32 |
| kanzure | desktop hackathon | 12:32 |
| kanzure | The one where you ranted at the gnomefolk. | 12:32 |
| Phreedom | kanzure_: not yet started | 12:32 |
| kanzure | hrm -> "The astonishing computation hypothesis is that “You”, your joys, your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than different forms of computation implemented by a vast assembly of biology." | 12:32 |
| Phreedom | what's so astonishing in this? | 12:32 |
| Phreedom | kanzure: it was a preliminary meeting, so nobody knows what's going to happen... | 12:33 |
| Phreedom | but I wouldn't count on miracles happening | 12:33 |
| Phreedom | it's gnome after all | 12:33 |
| kanzure | http://heybryan.org/phenogeno.html <-- An email I just sent out to Mike Tinter on the AGI mailing list. Nothing particularly new, but still worth saving. | 12:44 |
| kanzure | Can anybody help me figure out what the link was to the SBML model db? I think it was off of sbml.org, but I had it in the logs here somewhere. I've lost it. | 12:57 |
| kanzure | http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=home | 13:02 |
| fenn | "astonishing hypothesis" is more generally known as the church-turing hypothesis, as much as i hate naming things after dead guys | 13:50 |
| fenn | ho hum | 13:52 |
| fenn | the way to get those types of evolutionary processes going is through the general architectures of selection and optimization | 13:52 |
| fenn | in addition you need some kind of randomness and preferably a way to shuffle genes around in a novel yet not totally obliterative way | 13:52 |
| fenn | such as exons and introns | 13:53 |
| fenn | but i'm not convinced evolution will come up with every possible design (given an infinite amount of time) | 13:54 |
| fenn | assumption being that there exist an infinite number of stupid designs and a smaller infinity of good designs | 13:55 |
| kanzure | "the general architectures of selection and optimization" - i.e., need to hook into the selection somewhere, the already instantiated procs | 13:55 |
| kanzure | evolution will indeed *not* come up with every possible design | 13:55 |
| kanzure | not even iterative design generators will come up with every possible design | 13:56 |
| * fenn is reading "new kind of science" | 13:59 | |
| kanzure | I realized the source of my confusion with the automated design lab project that I've been (not) working on, | 14:06 |
| kanzure | I was confusing the conversation I had the night before the lab meeting and the one after the lab meeting | 14:06 |
| kanzure | for the cad app we were going to have the bricks connect in various ways for the users of the 'story creator' to select the next piece of the story | 14:06 |
| kanzure | then, after the meeting, it was something about also checking 'kinetics' or something, and thus conflating the issues of the stoichiometry or simulation of the designs with the circuit structure and how the bricks/legos connect | 14:07 |
| fenn | what does 'kinetics' and 'stoichiometry' refer to? chemistry or ecology? | 14:08 |
| kanzure | chemistry | 14:08 |
| kanzure | there's some "reaction rate rules" in the 'SBML model database' | 14:08 |
| kanzure | which looked like stoichiometry to me | 14:08 |
| kanzure | 3 parts this, get out 4 parts that, etc. | 14:08 |
| kanzure | each individual brick having its own set of "reaction rate rules" | 14:08 |
| fenn | oh but since you're doing molecular engineering it's the same thing.. n/m | 14:09 |
| kanzure | not sure if each brick should have their own rules - how would you evaluate the overall circuit? | 14:09 |
| fenn | i'm fairly certain the stoichiometry is intimately tied to the 'story' or sequence of reactions | 14:10 |
| kanzure | would you do it piece by piece, at each brick, and then sum it all up with a final evaluator to see that A+B+C, each with their solved differential equations (in an algebraic form), add up to something that has a certain energy rating? (efficiency would be where you don't lose products through the design , for instance) | 14:10 |
| kanzure | yes | 14:10 |
| kanzure | this is true | 14:10 |
| kanzure | I think each brick has ordinary differential equations, like http://bionetgen.org/index.php/Tutorial_Example has | 14:11 |
| kanzure | and then if you solve each ODE at each brick, then you sum up each solution-to-the-ODE-at-each-brick and can do an overall evaluation of the circuit | 14:11 |
| kanzure | circuit/design | 14:11 |
| fenn | sounds like a bad idea | 14:12 |
| kanzure | yeah? | 14:12 |
| fenn | its like doing your bank account once a month, but you might go below 0 at some time during the month and not know it | 14:12 |
| kanzure | wasted processing, you mean? | 14:13 |
| fenn | no, inaccurate results i mean | 14:13 |
| kanzure | why bother going down the story if the characters are already dead | 14:13 |
| kanzure | oh | 14:13 |
| fenn | the summary says it should work, but if you do it step by step it doesn't work | 14:13 |
| fenn | i'm not really sure what you're talking about though, so dont pay too much attention | 14:14 |
| kanzure | let's make it a bit more practical .. hold on | 14:14 |
| kanzure | you have your bricks: http://heybryan.org/~bbishop/docs/biobricks/data/ | 14:15 |
| kanzure | each brick has a type: http://heybryan.org/~bbishop/docs/biobricks/types/ | 14:15 |
| fenn | dns bugaboo | 14:15 |
| kanzure | hm? | 14:15 |
| kanzure | oh crap, again? | 14:15 |
| fenn | Could not connect to host heybryan.org | 14:15 |
| kanzure | ping, is it 66.112.232.129 ? | 14:15 |
| fenn | sorry it was on my end, n/m | 14:16 |
| kanzure | anyway, /data/ has dot BBF files taken from partsregistry.org | 14:16 |
| kanzure | and /types/ has text files with lists of BBF parts in each, representing the members of the class or type (given by the name of the txt file) | 14:17 |
| kanzure | a circuit could be represnted by a list of bricks/parts, so: BBa_01, BBa_02, BBa_03, <-- primitive sequential biobrick circuit format. | 14:17 |
| fenn | a specific instance would be a sequence of parts, but a general class would be a sequene of types | 14:18 |
| * fenn hates words | 14:19 | |
| kanzure | rawr | 14:19 |
| fenn | going back to my pretty 1200 page picture book | 14:19 |
| kanzure | two ideas: (1) each 'general class' (/types/) would interconnect with the other /types/ in a circuit way, all BBF files would be assigned a 'reaction rate constant' that would make that particular brick a unique play on the 'type'; | 14:22 |
| kanzure | or | 14:22 |
| kanzure | (2) all BBF files are given their own unique equation, to which any other biobrick must plug in to somehow with input/output variables on their metadata (i.e., produces 3 molecules of blah; well, that blah must be the input to the next item in the 'specific instance') | 14:22 |
| kanzure | Abstraction to another domain, back to SKDB-manufacturing: metadata of each part has to fit together (inputs/outputs); validator to make sure of this in a given design/circuit/system (collection of parts). | 14:31 |
| kanzure | This doesn't do the simulation / optimization stuff .. but it's my guess that there are some ODE solvers out there that can take an 'equation' from each part and then slap them all together into a giant differential equation mess, solve it, and then check to see if it fares better than another design (or whatever your rating func is). Surely this is possible .. | 14:32 |
| kanzure | What do they call these in calculus classes? | 14:32 |
| kanzure | "related rates" ? | 14:32 |
| kanzure | http://heybryan.org/mediawiki/index.php/Cal2#Related_rates | 14:33 |
| fenn | partial differential equations? | 14:33 |
| kanzure | 'Identify the known rates of change and the rate of change that is to be found. | 14:33 |
| kanzure | Construct an equation relating the quantities whose rates of change are known to the quantity whose rate of change is to be found. | 14:33 |
| kanzure | Differentiate both sides of the equation with respect to time (or other rate of change). | 14:33 |
| kanzure | Substitute the known rates of change and the known quantities into the equation. | 14:33 |
| kanzure | Solve for the wanted rate of change.' | 14:33 |
| kanzure | oh, PDEs too I guess | 14:33 |
| kanzure | uhm | 14:34 |
| kanzure | crap. | 14:34 |
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| kanzure | big crash | 14:39 |
| * kanzure asked #not-math | 14:39 | |
| kanzure | 'I'm wondering if I have a PDE on my hands: I have a number of "blocks" that each have an ODE within it; then, I want to string these blogs together so that the variables in the input and output of the blocks are in terms of their neighboring blocks, followed by a solving of all of the ODEs strung together simultaneously. Is this a PDE?' | 14:39 |
| kanzure | I'm pretty sure it is | 14:39 |
| kanzure | but they might be, you know, more knowledgeable | 14:40 |
| kanzure | 'In mathematics, partial differential equations (PDE) are a type of differential equation, i.e., a relation involving an unknown function (or functions) of several independent variables and its (resp. their) partial derivatives with respect to those variables.' | 14:40 |
| kanzure | then what are "related rate" problems? :-/ | 14:40 |
| kanzure | 'In differential calculus, related rates problems involve finding a rate that a quantity changes by relating that quantity to other quantities whose rates of change are known. The rate of change is usually with respect to time.' | 14:41 |
| kanzure | 'Suppose that there is a 10-meter ladder leaning against the wall of a building, and the base of the ladder is sliding away from the building at a rate of 3 meters per second. How fast is the top of the ladder sliding down the wall when the base of the ladder is 6 meters from the wall?' | 14:41 |
| kanzure | hm, so if there's a known rate of change function then it's a related rate | 14:41 |
| kanzure | if they are all unknown, then it's a PDE | 14:42 |
| kanzure | but didn't I assign the functions to each block in the first place ? | 14:42 |
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| kanzure | http://www.naken.cc/vb2c/ <-- wtf :-) | 15:01 |
| kanzure | http://web.archive.org/web/20040513050833/http://bcx.basicguru.com/ basic to c translator. | 15:10 |
| kanzure | http://bcx-basic.so | 15:11 |
| kanzure | who distributes their open source app as an exe anyway? | 15:14 |
| kanzure | http://www.bcxgurus.com/ | 15:14 |
| kanzure | http://support.microsoft.com/default.aspx?kbid=216388 | 15:20 |
| kanzure | 'Visual Basic Automation code' what? | 15:20 |
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| Phreedom | visual basic? open source? hmm | 15:26 |
| kanzure | http://heybryan.org/shots/2008-09-07_vb2c_bce.png <-- wtf | 15:28 |
| kanzure | note the nondistracting American flags | 15:29 |
| kanzure | what a nice touch ... | 15:29 |
| kanzure | That was absolutely no help whatsoever. | 15:31 |
| willPow3r_ | kanzure is unpatriotic. | 15:58 |
| willPow3r_ | freaking terrorist. | 15:58 |
| kanzure | bah | 16:02 |
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| * kanzure is converting the visual basic nonsense into perl just for the sake of rapidity | 17:48 | |
| kanzure | Has this ridiculously large list of global variables :-/ | 17:48 |
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| kanzure | Public Sub BS_TDV() | 18:33 |
| kanzure | GDecayGrBK = Exp(-Time_step_size / GTauGrBK) | 18:33 |
| kanzure | What could Exp possibly be? it's not an exponential function since there's no second parameter | 18:33 |
| kanzure | and it's not "evaluate this expression" since there's the line "GLeakBK = 0.2 / (6 - Time_step_size)" just after it without Exp() .. | 18:33 |
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| kanzure | inE = MF(Gr(x).MF(1)) + MF(Gr(x).MF(2)) + MF(Gr(x).MF(3)) + MF(Gr(x).MF(4)) | 19:27 |
| kanzure | what an annoying line | 19:27 |
| kanzure | Apparently MF is an array | 19:27 |
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| kanzure | argh | 19:30 |
| kanzure | even in my damn music | 19:30 |
| kanzure | http://rockautism.vh1classic.com/ | 19:30 |
| * kanzure doesn't need to hear KISS telling me to "Cure Autism Now" | 19:31 | |
| * kanzure just wants his rock | 19:31 | |
| kanzure | http://chromium.org/ | 19:53 |
| kanzure | http://dev.chromium.org/developers/how-tos/build-instructions-linux | 19:54 |
| kanzure | wait, they say that the browser ui layer is the only thing not compiling on linux | 19:59 |
| kanzure | so does that mean it has the HTML layout engine working? :) | 20:00 |
| kanzure | 'What currently builds? base, net, WebKit - WebCore, Javascript bindings, most of glue targets build, various other sub-projects, such as skia, libxml, etc' | 20:00 |
| kanzure | hurray | 20:00 |
| kanzure | http://ubuntuforums.org/showpost.php?p=5719331&postcount=45 wine instructions maybe | 20:34 |
| kanzure | reportedly ridiculously slow | 20:34 |
| kanzure | oh well | 20:48 |
| kanzure | http://pr.willowgarage.com/ ' The Personal Robotics program is a collaboration between Willow Garage, Stanford University, and other academics institutions to create an open-source codebase and freely available hardware platform for mobile manipulation.' | 20:51 |
| kanzure | 'Anybots [anybots.com] is probably further along. Take a look at their pictures. I've seen that machine in operation. Balance is automatic, but manipulation and movement are teleoperated.' | 20:52 |
| kanzure | hah, the "Indians behind the bot" gig | 20:52 |
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| pk | hi | 21:51 |
| pk | what's going on? | 21:51 |
| kanzure | The fan is making noises. | 22:03 |
| kanzure | Is this bad? | 22:03 |
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| kanzure | http://www.engr.utexas.edu/expo/students/hints.cfm 'Demonstrate knowledge the company' | 23:21 |
| kanzure | indeed, I shall "demonstrate knowledge the company" | 23:21 |
| kanzure | hm, need a "business" card | 23:39 |
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