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| * nsh reads buffer | 02:36 | |
| kanzure | :) | 02:41 |
|---|---|---|
| * nsh is rather dubious of measures like PoPS and RiPS | 02:41 | |
| kanzure | read on | 02:41 |
| kanzure | I solve it | 02:41 |
| kanzure | or at least that part | 02:41 |
| * nsh reads on | 02:42 | |
| nsh | so | 02:45 |
| kanzure | there's also stuff in #bioinformatics where faceface got whiff of what I'm doing | 02:45 |
| kanzure | *caught scent | 02:46 |
| nsh | you want to systematically optimise a simulated gene regulatory network by training a stochastic model, such as HMM or ANN against a simulation of the GRN itself, such that the model becomes successful at predicting whether a certain change in the configuration of the GRN variables will lead to greater or lower efficiency, according to some metric? | 02:47 |
| kanzure | correct | 02:47 |
| nsh | but rather than replicate the computational complexity redundantly in two models, you feel it would be possible to feed the stochastic efficiency predicter only the uniqueness-factor of the GRN model and have its implicit modeling recreate it somehow? | 02:48 |
| kanzure | but, not only is it (1) either a HMM or ANN or something -- this is variablized, and not only is (2) the GRN design circuit variablized, and not only is (3) the simulation results (obviously) variablized, but I'd also like to (4) variablize the fact that it's a GRN ... | 02:48 |
| kanzure | uhm | 02:48 |
| kanzure | hm | 02:48 |
| kanzure | No, what I'm interested in seeing is if the stochastic model predictor thingy applies across different problems | 02:49 |
| nsh | oh | 02:49 |
| kanzure | and the ranking of these 'stochastic models' | 02:49 |
| kanzure | particularly rules ("graph grammars") used to do some internal fixups on the 'stochastic models' | 02:49 |
| kanzure | which makes it even weirder | 02:49 |
| nsh | that sounds dangerously like an attempt to produce a general purpose solver | 02:49 |
| nsh | which is almost certain to not work well | 02:49 |
| kanzure | because then you have to ask, how many iterations of rule applications are you willing to go through as well? or will you just "lock it in" at some point | 02:49 |
| kanzure | right | 02:50 |
| kanzure | but it's not intended to do general purpose solving really | 02:50 |
| kanzure | I think i'd be good if it works for just a given problem | 02:50 |
| * nsh nods | 02:50 | |
| kanzure | problem space, something with context. i.e., a particular GRN that you're making | 02:50 |
| nsh | right | 02:50 |
| kanzure | faceface was happy that it sounded like it could possibly automatically generate all possible GRNs / biochem pathways from some unmodeled organism, and then the stochastic models could help fish out which one of those has the correct 'gaps' filled in that nobody knows about yet from the bioinformatics | 02:51 |
| kanzure | :-) which is one possibility :-) | 02:51 |
| nsh | mmm | 02:51 |
| kanzure | there's probably a simpler way to do it than a bruteforce tree search + dynamic programming / backpropagation | 02:52 |
| kanzure | but anyway. | 02:52 |
| nsh | bear in mind combinatorial explosion | 02:52 |
| kanzure | right right | 02:52 |
| nsh | complex networks scale terribly | 02:52 |
| kanzure | bear in mind we have supercomputer access | 02:52 |
| nsh | oh, we do? :-) | 02:52 |
| * nsh notes this | 02:52 | |
| * kanzure grins | 02:52 | |
| kanzure | so, | 02:53 |
| kanzure | you understand what it is that I'm doing, but | 02:53 |
| kanzure | what the hell do I feed into the ANN/HMM/stochastic-model-thingy ? | 02:53 |
| kanzure | something that is a function of a given generated/possible model, I know this much. | 02:53 |
| kanzure | that's not much of a start :) | 02:53 |
| nsh | aye | 02:53 |
| * nsh was thinking the same | 02:54 | |
| kanzure | so I was going to use biobricks as some seed content | 02:54 |
| nsh | you can convolute a set of data in many different ways and still retain its uniqueness. some forms will be more facile to predict from than others; the question is, why? | 02:55 |
| kanzure | and there's some ways I can get kinetic reaction or gene expression models for the biobrick parts, so that's a start | 02:55 |
| kanzure | right, you could conceivably take the ID number of the generated design | 02:55 |
| kanzure | or the md5 | 02:55 |
| nsh | well | 02:55 |
| kanzure | but that's not necessarily going to produce something interesting with a limited ANN | 02:55 |
| nsh | md5 is lossy | 02:55 |
| * nsh nods | 02:55 | |
| nsh | and the id number would only contain the data of the final model when coupled with the complexity of the GRN generating algorithm | 02:56 |
| kanzure | the idea is to somehow model the simulator in less steps, right? | 02:56 |
| * nsh nods | 02:56 | |
| kanzure | i.e., hidden variables that aren't really variables in the simulation, but rather represent some 'computational complexity wetdream of a mix of variables' | 02:56 |
| kanzure | computational complexity in the sense of complexity science, not the real deal | 02:57 |
| * nsh smiles | 02:57 | |
| nsh | but there's no free lunch, of course | 02:57 |
| nsh | you can't arbitrarily reduce the complexity of the model | 02:57 |
| nsh | only whatever is redundant in it | 02:57 |
| nsh | and if you can't tell for certain whether you're optimising or approximating | 02:57 |
| nsh | you run the risk of inaccuracy for certain marginal cases | 02:58 |
| kanzure | right. | 02:58 |
| nsh | so, maybe you can think of it like image compression, or mp3 | 02:59 |
| kanzure | it = ? | 02:59 |
| nsh | it, the optimisation of the GRN simulation | 02:59 |
| nsh | what features are extraneous to the final output variable | 03:00 |
| nsh | which is, for example, some measure of optimality | 03:00 |
| nsh | so, in testing efficiency, you're taking a large data set and reducing it finally to a very small one | 03:00 |
| kanzure | not optimizing the simulator, btw | 03:00 |
| nsh | mmm | 03:01 |
| kanzure | okay, so that's possible, | 03:01 |
| kanzure | maybe the stochastic models can figure out the 'interesting stuff' on the fringes | 03:01 |
| * nsh bbl | 03:01 | |
| kanzure | that don't "compress well" in the typical patterns of other generated designs (GRNs, or stoichiometrical chem, ..) | 03:01 |
| kanzure | hrm | 03:01 |
| kanzure | http://www.me.utexas.edu/~adl/graphsynth/images/flowchart.png <-- harder than this claims it to be | 03:04 |
| kanzure | wait | 03:05 |
| kanzure | isn't that the semantic search facilitator? | 03:05 |
| * kanzure scratches his head | 03:05 | |
| kanzure | Oh, maybe this is better described as a runtime/online interpreter to 'dynamic programming' | 03:09 |
| kanzure | do I need the stochastic model? if I can autogenerate all possible designs using a set of 'rules' for the manipulation of the circuits/designs, then surely some rules are going to be more useful in a certian problem domain than in others. These rules, that when applied, if they consistently make 'better stuff' then that's what should be used more often, no? | 03:35 |
| kanzure | hypothesis: there are hidden variables between genotype and phenotype | 03:37 |
| bkero | Perhaps you could adapt acovea for what you're doing? :) | 03:40 |
| kanzure | http://www.coyotegulch.com/products/acovea/ | 03:40 |
| kanzure | 'ACOVEA (Analysis of Compiler Options via Evolutionary Algorithm)' | 03:40 |
| kanzure | oh god | 03:40 |
| kanzure | just what I need :) | 03:40 |
| bkero | Bwahaha | 03:40 |
| bkero | btw the guy who runs it is insane | 03:41 |
| bkero | clinically | 03:41 |
| kanzure | How serious are you? | 03:41 |
| kanzure | insane as in insane in the sense that you'd have to be to do that code, | 03:42 |
| bkero | Heh | 03:42 |
| bkero | He does some weird shit | 03:42 |
| kanzure | or in an institution for the insane? | 03:42 |
| bkero | former | 03:42 |
| kanzure | neat | 03:42 |
| kanzure | wait, this is just for compiler flags? | 03:42 |
| bkero | Exactly | 03:42 |
| kanzure | Nothing more? | 03:42 |
| bkero | Hm? | 03:42 |
| kanzure | Compiler optimization usually looks at code and then tries to find a better way and fixes your mistakes | 03:43 |
| kanzure | evolutionary algorithms and backpropagation and such are what I've been thinking of | 03:43 |
| kanzure | and really this /is/ a compiler/optimization problem | 03:43 |
| bkero | This basically takes algorithms, and figures out what combinations of compiler options yield the fastest runtimes. | 03:43 |
| kanzure | if it's just "flags" in general, and not analyzing algorithms (loops?) in the code, then blah | 03:43 |
| kanzure | why not just implement the code from within the compiler in the first place ? | 03:44 |
| bkero | But it's built in such a modular way you could adapt it to running any dataset through a filter to see which performs better(less entropy, faster runtime, faster compile time, etc) | 03:44 |
| bkero | It's testing combinations of flags | 03:44 |
| bkero | based on evolution | 03:45 |
| kanzure | yes, I know | 03:45 |
| kanzure | it says that. | 03:45 |
| bkero | There might be a plugin for gcc that does this, but I've never heard of it. | 03:45 |
| fenn | "AMD’s products are not designed, intended, authorized or warranted for use as components in systems intended for surgical implant into the body" well shucks, so much for that idea | 03:47 |
| bkero | Fuck AMD | 03:48 |
| bkero | go arm | 03:48 |
| kanzure | from their legal mumbo jumbo? | 03:48 |
| kanzure | bkero: Atmel meeting later today :) | 03:48 |
| bkero | lol | 03:48 |
| kanzure | they're showing up for the local IEEE chapter | 03:48 |
| bkero | Gotta love those 8-bit microcontrollers | 03:48 |
| kanzure | methinks they've quadrupled that by now | 03:48 |
| bkero | Seriously though, ARM chips are where it's at if you need any serious cruning done in an embedded environment. | 03:49 |
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| fenn | there are 32 bit AVR's but most people use the 8 bit chips because they dont come in ridiculous BGA packages | 03:49 |
| fenn | and the free compiler yadda yadda | 03:49 |
| kanzure | I'm nearly convinced that the Semantic Search Facilitator project is equivalent to the Automated Design Lab project. | 03:49 |
| fenn | you've rediscovered the do what i mean interface | 03:50 |
| bkero | Heh | 03:50 |
| kanzure | does this mean I have to become Larry Wall ? | 03:50 |
| fenn | there can only be one | 03:50 |
| bkero | You're doomed to a terrible fate. | 03:50 |
| bkero | Dude, have you SEEN larry wall? | 03:50 |
| kanzure | No? | 03:50 |
| kanzure | Have YOU? | 03:50 |
| kanzure | srsly | 03:51 |
| bkero | yup | 03:51 |
| bkero | He was at oscon this year | 03:51 |
| kanzure | Oh. | 03:51 |
| kanzure | me was going to use GAs to mutate the search strings | 03:52 |
| kanzure | and then find those GA / rulesets that prove most lucrative in certain search domains | 03:53 |
| kanzure | that's basically the same thing here | 03:53 |
| kanzure | except not natural language | 03:53 |
| kanzure | and not the web | 03:53 |
| bkero | lol | 03:54 |
| bkero | Sounds like some bioperl | 03:56 |
| kanzure | Yes, I've toyed with bioperl.org before. | 03:56 |
| kanzure | the wikipedia article on ANNs vaguely references them as "systems that learn in an /optimal/ sense" | 03:57 |
| kanzure | all these darned things are really just ways of otherwise saying 'optimization' | 03:58 |
| bkero | lol | 03:58 |
| kanzure | life is a compiler, I am the optimizer and you sir are a very, very Big O notational headache | 03:58 |
| kanzure | hrm | 03:58 |
| kanzure | I'm sure that line could be improved | 03:58 |
| bkero | I'm actually bytecode. | 03:59 |
| bkero | Already interpreted and ready to be run | 03:59 |
| kanzure | Where's your virtual machine? | 03:59 |
| bkero | bvm | 03:59 |
| bkero | It has yet to be written. | 03:59 |
| bkero | So I'm actually useless bytecode, and very hard to reverse back into higher-level. | 03:59 |
| kanzure | http://heybryan.org/~bbishop/docs/2008-07-31/ | 04:04 |
| kanzure | http://www.cs.jyu.fi/ai/OntoGroup/InBCT_May_2004.html <-- Semantic Search Facilitator | 04:06 |
| kanzure | "Semantic Search Assistant hides from users the complexity of query language of concrete search engine and performs routine actions that most of users do in order to achieve better performance and get more relevant results." | 04:06 |
| faceface | kanzure, I was working with a guy who worked on that field | 04:19 |
| kanzure | 'that' ? | 04:20 |
| kanzure | bkero: I've found myself wanting a compiler optimization database of tricks and such. gcc is more of a hack IIRC. llvm looks more structured, maybe. | 04:20 |
| faceface | oh, semantic search facilitator type stuff | 04:20 |
| kanzure | Neat. | 04:21 |
| kanzure | What'd you come up with? | 04:21 |
| faceface | cant find his website | 04:21 |
| kanzure | btw, don't care about the semantic aspect .. just the facilitator part ;-) | 04:21 |
| faceface | actually we were working on protein-protein interactions | 04:22 |
| kanzure | excellent | 04:22 |
| kanzure | so, how did that work? | 04:22 |
| kanzure | helping researchers to find the right proteins to fit into the puzzle? | 04:22 |
| faceface | i.e. nothing to do with semantics | 04:22 |
| faceface | his idea was that ontologies should help you lean a new field | 04:22 |
| kanzure | damn right | 04:23 |
| bkero | science 8) | 04:23 |
| faceface | found it at last... http://www.vincent-wolowski.net/ | 04:25 |
| faceface | yup, science it is :-) | 04:25 |
| kanzure | polish | 04:25 |
| faceface | its just most tools don't let you use an ontology in that kind of didactic / explorative way | 04:25 |
| kanzure | right | 04:26 |
| kanzure | explorative = realtime/online debuggng, profiling or compiler optimization | 04:26 |
| kanzure | meaning some really funky code | 04:26 |
| faceface | http://www.vincent-wolowski.net/informatics.html | 04:26 |
| kanzure | or a giant virtual machine | 04:26 |
| faceface | well.. time to work | 04:26 |
| kanzure | what's your latest? | 04:27 |
| faceface | boring | 04:28 |
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| faceface | people hear are boring | 04:28 |
| kanzure | where? | 04:28 |
| willPow3r | hear | 04:28 |
| * kanzure gets ready to mark a place off his map | 04:28 | |
| kanzure | hehe | 04:28 |
| faceface | guess what... disks are getting larger... data is getting more... lets spend the morning talking about how much dna exists... | 04:28 |
| faceface | dundee, scotland | 04:29 |
| kanzure | eh? | 04:29 |
| kanzure | they want to calculate the amount of existing dna? | 04:29 |
| faceface | oh well... (I'm only jelous because they are having this conversation without me) | 04:29 |
| faceface | no that would be interesting | 04:29 |
| kanzure | oh | 04:29 |
| kanzure | :) | 04:29 |
| kanzure | then what are they talking about? | 04:29 |
| faceface | they can only see what people who do sequencing present to them | 04:29 |
| kanzure | they have no sequencer? | 04:30 |
| kanzure | wtf | 04:30 |
| faceface | sequening = faster, data = more | 04:30 |
| faceface | not here | 04:30 |
| faceface | oh if data = more then ... OMFG! | 04:30 |
| * kanzure wonders about an 'ecological search facilitator' to find unknown niches/links | 04:30 | |
| kanzure | in thermodynamic systems in general. hrm. | 04:30 |
| faceface | well.. have fun | 04:30 |
| kanzure | heh | 04:30 |
| kanzure | okay | 04:30 |
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| kanzure | oh | 04:40 |
| kanzure | it occurs to me that in the semantic search facilitator, or my 'autogoogler', if I had the 20 different queries up, I would only obviously select a few (or maybe all (eventually)), | 04:40 |
| marainein | kanzure: what thing are you talking about? | 04:41 |
| kanzure | from that selection information, the 'GA, rules, HMM, or ANN aspect'' that were used to generate those queries would be reinforced | 04:41 |
| kanzure | marainein: hold on | 04:41 |
| kanzure | as nsh said it: | 04:41 |
| kanzure | "you want to systematically optimise a simulated gene regulatory network by training a stochastic model, such as HMM or ANN against a simulation of the GRN itself, such that the model becomes successful at predicting whether a certain change in the configuration of the GRN variables will lead to greater or lower efficiency, according to some metric?" | 04:41 |
| kanzure | "but rather than replicate the computational complexity redundantly in two models, you feel it would be possible to feed the stochastic efficiency predicter only the uniqueness-factor of the GRN model and have its implicit modeling recreate it somehow?" | 04:42 |
| kanzure | applications include automatically generating genetic regulatory networks, factories, search queries, and filling in the gaps in our knowledge of genotype/phenotype relations. | 04:46 |
| kanzure | you know what I like, the simulator allows numeric output | 04:49 |
| kanzure | instead of flipping through google search results | 04:49 |
| kanzure | although google search results give semantic feedback | 04:50 |
| kanzure | hm, tradeoffs :) | 04:50 |
| * marainein nods | 04:50 | |
| kanzure | Suppose you took the opposite approach of limiting the search results and instead expanded it; perhaps you applied the probabilistic web crawling papers to the issue of design. Then, you have weird, strange variables that relate various models (out of the 10,000 generated models) together. | 04:57 |
| kanzure | By laws of connectivity, clicking from one to the next should only take a certain amount of time to find The Good One -- some upper-bound on the number of clicks/hops that it would take. But it has to be more links than the number of nodes overall, obviously. | 04:57 |
| kanzure | So, I'm interested in taking the 'Autogoogler' idea in terms of design. There's no "web" that is pre-generated. There's "not much" to search. The user input is, what? The results are ranked by simulator results, obviously -- whatever parameters the user is ultimately optimizing for. | 05:02 |
| kanzure | What's the user input? It has to be constrained - it's not going to be 'words' since there's no 'words' attached to the generated designs. I suppose the user input is the selection of different 'rules' to apply to rewrite the design-graphs (possible manipulations between, i.e., biobricks), by clicking on the equivalent of the 'list of 20 search queries'. | 05:02 |
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| kanzure | http://www.sustainabledave.org/ | 05:59 |
| kanzure | http://www.youtube.com/watch?v=fdJjyoHdnIA | 06:00 |
| kanzure | http://www.youtube.com/watch?v=opaTDxWUyZc | 06:00 |
| kanzure | the npr link might be beter | 06:00 |
| kanzure | *better | 06:00 |
| * nsh wonders how kanzure has time to find all the links he spouts, when he doesn't even have time to read them all | 06:26 | |
| nsh | he->I | 06:26 |
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| kanzure | nsh: the confused mumblings of /me, ah yes :-) | 06:27 |
| kanzure | silly mortal, there is no /me | 06:27 |
| kanzure | Anyway, the trick is to be not human. | 06:27 |
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| * nsh guesses as much | 06:49 | |
| kanzure | http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=measurement&show=1 | 06:56 |
| kanzure | grumble grumble, why does this have html output | 06:56 |
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| kanzure | http://www.biodas.org/wiki/Main_Page | 07:00 |
| kanzure | spec: http://www.biodas.org/documents/spec.html | 07:01 |
| * nsh reads http://www.nature.com/nrg/journal/v9/n9/full/nrg2414.html | 07:13 | |
| nsh | , cringes at capitalised wiki | 07:13 |
| kanzure | hrm | 07:15 |
| nsh | heh, type "nucleur" | 07:17 |
| nsh | Nature should hire a proofreader | 07:17 |
| * nsh will do it for 5 figures | 07:17 | |
| nsh | two typos "compute" | 07:18 |
| nsh | this is pretty kintergarten stuff :-/ | 07:20 |
| nsh | good that they have a concrete example problem though | 07:20 |
| kanzure | I got stupid and turned the televisional news on | 07:25 |
| nsh | :-/ | 07:26 |
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| nsh | usually it happens the other way around | 07:26 |
| nsh | hey dan | 07:26 |
| nsh | (people watch the television news and then become stupid) | 07:26 |
| kanzure | and there's this silly stuff saying "mmr vaccine doesn't cause autism - it's the nail in the coffin to the debate .. so stop talking about it." but they'll just say it's a conspiracy | 07:26 |
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| * nsh tries to ignore the crazies | 07:28 | |
| kanzure | yay, let's treat these there darned children with these thingies called brainers or somethin' | 07:30 |
| kanzure | that'll learn 'em | 07:30 |
| * kanzure fetches a pitchfork | 07:30 | |
| * nsh smiles | 07:31 | |
| kanzure | http://www.usautism.org/ | 07:31 |
| nsh | [[[ | 07:31 |
| nsh | A mature biology cyberinfrastructure should make this type of analysis much more straightforward (Fig. 2b). Ideally, the researcher would be able to design the experiment at a high level by describing the data sets he wishes to work with and the relationships he wishes to traverse (protein to gene to exon to conservation score) by using a graphical tool or a high-level description language. | 07:31 |
| nsh | The infrastructure would then do the hard work of finding databases, analysis services and compute resources that can satisfy the request, thereby transforming and integrating the data and returning the results. If the researcher desired, he could then easily share the method and results with the research community by pushing a 'publish' button; this information would then become a discoverable service that could be re-used by others. | 07:31 |
| nsh | Over time, other members of the research community could add value to this work by commenting on it, linking it to related work, contributing modifications to the method, and submitting new raw and analysed data sets that enrich it. | 07:31 |
| kanzure | I'm going to go yell at them | 07:31 |
| nsh | ]]] --http://www.nature.com/nrg/journal/v9/n9/full/nrg2414.html#B4 | 07:32 |
| kanzure | I think they're down the street | 07:32 |
| kanzure | screw them | 07:32 |
| kanzure | look at their wiki | 07:32 |
| nsh | (above is essentially saying: wouldn't it be cool if there was MAGIC!?!?!?!?!) | 07:32 |
| kanzure | they cite SKDB for a reason | 07:32 |
| kanzure | that's not quite magic | 07:32 |
| kanzure | just throw it into git repositories | 07:32 |
| kanzure | we'll do the rest, m'am | 07:32 |
| * nsh smiles | 07:33 | |
| * nsh actually believes all the above is quite possible | 07:34 | |
| kanzure | http://www.youtube.com/user/USAutismAndAsperger | 07:34 |
| kanzure | "how do we fix these kids" | 07:34 |
| nsh | do i really want to watch that? | 07:34 |
| kanzure | no | 07:34 |
| nsh | IGNORE THE CRAZIES | 07:34 |
| kanzure | but it's next door :-( | 07:34 |
| nsh | then leave your rubbish bags outside their porch | 07:35 |
| nsh | but don't give them brainspace | 07:35 |
| nsh | that's valuable finding-cool-links-for-nsh time | 07:35 |
| nsh | and coming-up-with-interesting-ideas time | 07:35 |
| kanzure | now wonder these kids "withdraw" (whatever that means) | 07:43 |
| kanzure | *no | 07:44 |
| nsh | mm | 07:46 |
| kanzure | find me my variables for my GRN optimizer | 07:52 |
| kanzure | heh | 07:52 |
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| kanzure | Hey kikl | 08:09 |
| kanzure | oh, probably ybit | 08:09 |
| kanzure | no fun. | 08:09 |
| kanzure | What's with the random nickjoins, anyway? | 08:09 |
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| faceface | ignore me | 08:36 |
| jimjim | I thought xchat had crashed | 08:37 |
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| faceface | nsh, thanks for the link - we were just talking about that at lunch | 08:40 |
| faceface | I saw it on nature networks forum | 08:40 |
| faceface | nsh, kanzure, are you on nature networks? | 08:41 |
| faceface | not that its good for anything really... | 08:41 |
| kanzure | No, is it a social community thingy? | 08:42 |
| * kanzure stole nature.com | 08:42 | |
| kanzure | All of it ... | 08:42 |
| faceface | sure | 08:42 |
| faceface | kanzure, you did that with a log in somewhere? | 08:42 |
| faceface | cus a guy over on #bioinformatics would be interested in dumping those PDF's into a P2p | 08:43 |
| kanzure | faceface: I need somebody god damned serious about it. | 08:43 |
| faceface | kanzure, yeah... | 08:44 |
| kanzure | I'm willing to invest some money into it for a machine to put behind a coffee shop. | 08:44 |
| kanzure | 40 GB is a *huge* torrent. | 08:44 |
| faceface | coffee shop? | 08:44 |
| faceface | kanzure, dont torrent the whole thing man! | 08:44 |
| kanzure | Right, just leave it on a hdd uploading or torrenting. | 08:44 |
| kanzure | Hm? | 08:44 |
| kanzure | Why not ? | 08:44 |
| faceface | cus its not what ppl want to download... a few yes | 08:44 |
| kanzure | you and me both | 08:44 |
| kanzure | that's about it :-) | 08:44 |
| kanzure | No, I'm sure some foreign universities would love to meet me | 08:44 |
| faceface | ppl want papers | 08:45 |
| faceface | oh yeah... them too | 08:45 |
| faceface | forgot about the poor folk | 08:45 |
| kanzure | cd3wd comes to mind | 08:46 |
| kanzure | Although CD3WD is only 700 MB. | 08:46 |
| kanzure | This would substantially increase their collection. Oops. | 08:46 |
| kanzure | von Neumann probe project here we come? | 08:46 |
| kanzure | (not with natural language) | 08:47 |
| kikl | kanzure, good guess | 08:50 |
| fenn | CD3WD is many GB | 08:50 |
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| fenn | about 14GB i think | 08:51 |
| ybit | do you guys ever sleep o.O | 08:51 |
| fenn | it's getting close to my bedtime | 08:51 |
| faceface | this week | 08:52 |
| kanzure | sleep? | 08:56 |
| kanzure | Sleep is for the weak! Food is for the weak! err .. | 08:57 |
| kanzure | (2008-08-26 11:21:12) kanzure: nsh: Food is for the weak. Sleep is for the weak. Fight entropy: start doing nothing today! | 08:57 |
| ybit | :) | 09:02 |
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| faceface | bot? | 10:04 |
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| nsh | []_+````{ pk: STATE PURPOSE. }''''+_[] | 10:21 |
| pk | lawl what? | 10:22 |
| * nsh smiles | 10:23 | |
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| kanzure | And now I know the Great Evils of CAD. | 13:45 |
| kanzure | while the interface isn't as bad as blender, it doesn't promote the cleanest thinking | 13:46 |
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| kanzure | specifically solidworks | 13:46 |
| bkero | How about CAM? | 13:47 |
| kanzure | Haven't tried yet. | 13:50 |
| kanzure | 'There is a plate of dark chocolate cookies with tiny chocolate chips in the middle office. It has been brought to our attention that, if these cookies are not consumed by the end of the business day, certain peril might doom every PCR ever carried out in this building henceforth. | 13:50 |
| kanzure | It is our suspicion that super intelligent bears have laid plans to dope DNAses into every tiny 200 uL eppendorf in every lab, and they are using the chocolate chips within the cookies as a homing signal to know where their target lies. In order to safeguard the success of the work carried out within the MBB, we highly encourage you, the brave citizens of Ellingtonia, to consume these cookies with all due haste. ' | 13:50 |
| kanzure | Ah yes, interlab politics | 13:50 |
| kanzure | I'll (never?) miss it | 13:50 |
| bkero | Mmm cookies. | 13:51 |
| bkero | kanzure: fscking awesome | 13:52 |
| kanzure | :) | 13:52 |
| kanzure | oh the terror http://heybryan.org/~bbishop/docs/me302/ | 13:53 |
| bkero | I just have faceless cube. | 13:53 |
| kanzure | cube? | 13:53 |
| bkero | Cubicle | 13:53 |
| kanzure | there were one or two cubes in Andy's lab | 13:53 |
| Phreedom | kanzure, fenn, nsh: I wonder if any of you use jabber? | 13:53 |
| bkero | Coworkers are made out of cardboard. | 13:53 |
| kanzure | they had the Holy Post Docs that No One Must Ever Disturb. | 13:53 |
| kanzure | Phreedom: yes | 13:53 |
| kanzure | Phreedom: kanzure@gmail.com | 13:53 |
| * kanzure also knows jer, the guy responsible for xmpp in the first place .. *cough* | 13:54 | |
| kanzure | bkero: Ironically, these cubes were right next to Andy's (the PI's) office | 13:54 |
| kanzure | you'd think they might get some of the most freedom | 13:54 |
| bkero | Cubes are a sterile and uninteresting environment. | 13:54 |
| kanzure | i.e., furthest desks maybe | 13:54 |
| kanzure | Oh no, | 13:55 |
| kanzure | there is no sterility and uninterest in a molecular bio lab | 13:55 |
| kanzure | far from it :) | 13:55 |
| bkero | There is at intel. :P | 13:55 |
| bkero | My cube is J14-JF4-104 | 13:55 |
| kanzure | Isn't that a number from Star Wars? | 13:56 |
| bkero | Not that I can remember. | 13:56 |
| bkero | 3720:1? | 13:56 |
| kanzure | Intel has stormtroopers? | 13:56 |
| kanzure | Are those the DRM goons ? | 13:56 |
| bkero | More or less | 13:57 |
| bkero | Mostly they're overfed downs kids. | 13:57 |
| kanzure | That's unfortunate. | 13:57 |
| kanzure | use case for the automated design prototype with biobricks | 14:17 |
| kanzure | consider Charlie/newgenome | 14:18 |
| kanzure | who has been showing up with his various ideas to use various thingies to do things | 14:18 |
| kanzure | one of his interests is synthetic biology | 14:18 |
| kanzure | How would he, somebody who could learn a techical spec if necessary, address his ooh's and aah's in the right way to let the computer hash out the possible designs via the permutations and scoring and evaluators and so on? | 14:18 |
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| * kanzure doesn't like assuming only one type of variable worth dealing with in these contexts ("gene expression levels, yay we're done") | 14:19 | |
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| kanzure | guess it's dependent on the information available more than anything | 14:19 |
| kanzure | so given a dataset that he selects from, there's certain amount of pre-encoded functionality that could be combined together | 14:19 |
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| kanzure | Daily wtf by way of Damien Broderick: 'David Duchovny has entered a rehabilitation center for sex addiction, The Associated Press reported. Mr. Duchovny, who plays a sex-obsessed character on the Showtime show "Californication," did so voluntarily, according to a statement on Thursday from ... ' | 14:58 |
| kanzure | http://www.neuro.gatech.edu/groups/potter/papers/DagstuhlAIBakkumpreprint.pdf Removing the 'a' from 'ai' | 15:02 |
| kanzure | http://machineslikeus.com/news/thinking-causes-weight-gain <-- studying students and their calorie intake /after/ intellectually daunting tasks | 15:11 |
| kanzure | this sounds like an amazingly awesome excuse for me to head downstairs for a bite to eat right nwo | 15:12 |
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| kanzure | http://austinbrains.org/austin.ics <-- 1.4 MB of events. Not that it's interesting to any of you, of course. | 16:06 |
| kanzure | just had to throw it up there :) | 16:06 |
| kanzure | anybody surprised that Google Calendar can't handle the calendar? | 16:44 |
| * kanzure is downloading 15 GB of data from the UT Solar Vehicle Team server | 16:56 | |
| kanzure | http://utsvt.ece.utexas.edu/wiki/index.php/IT:Quick_Start_Guide | 16:58 |
| kanzure | wtf, somebody on campus uses a bug tracker | 16:58 |
| kanzure | hurray | 16:58 |
| kanzure | argh | 17:07 |
| kanzure | can't escape the bullshit | 17:07 |
| kanzure | just trying to get some cartoons in the background ... | 17:07 |
| kanzure | "A man was dragged over a mile today ... investigation at 10 ... the Autism Conference started today including this ectostatic chamber " -- note that that this was looking like a giant body bag, the thing the Star Trek vessels shoot you out of when you're as dead as you're ever going to be (you have to really worry when even they, the Trekkies, cannot save you) -- "but what did they think about the new vaccine research? Coming up." do'h | 17:08 |
| kanzure | when you're as dead as you're ever going to be (you have to really worry when even they, the Trekkies, cannot save you) -- "but what did they think about the new vaccine research? Coming up." do'h | 17:08 |
| kanzure | 'hyperbaric chamber' | 17:24 |
| kanzure | oh | 17:25 |
| kanzure | sensory deprivation | 17:25 |
| kanzure | ' Portable Hyperbaric Chamber|Hyperbaric Oxygen Chamber|Portable ...Manufacturer of low pressure portable chambers for use in clinics and offices. Includes specifications and distributor locations.!' | 17:25 |
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| bkero | Heh | 20:28 |
| bkero | I need myself a hyperbaric chamber. | 20:28 |
| bkero | Hang out at around 6 BAR all day. | 20:28 |
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| fenn | three years later and this thing still reaches out and grabs me: http://www.positron.org/projects/A51/ | 21:39 |
| kanzure | augh | 22:10 |
| kanzure | so | 22:10 |
| kanzure | of all people | 22:10 |
| kanzure | does anyone remember that I was once dating a blind woman? | 22:10 |
| kanzure | before she knew me she was with someone who turns out to be the 'head sys admin' of the robotics group here | 22:11 |
| kanzure | which is awkward because I think after she knew me she went back to him | 22:11 |
| kanzure | what happened to "there can only be one [programmer per high school]" anyway? | 22:11 |
| fenn | i think that went out of fashion after they stopped playing the Highlander series | 22:12 |
| kanzure | is CentOS worth getting? | 22:15 |
| fenn | no | 22:26 |
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| ybit | anyone speak mandarin? | 22:30 |
| ybit | meh | 22:30 |
| kanzure | it's on my todo list | 22:32 |
| ybit | mine too | 22:37 |
| ybit | after spanish and portuguese | 22:37 |
| ybit | if you learn spanish, you essentially know portuguese | 22:38 |
| ybit | guessing it will take half the time or less to learn compared to spanish | 22:38 |
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| fenn | i would learn mandarin first | 22:50 |
| fenn | spanish is too easy | 22:50 |
| kanzure | agreed | 22:51 |
| kanzure | also, mandarin = more people | 22:51 |
| ybit | spanish = latin america | 22:58 |
| ybit | also, countries with less control if that appeals to anyone | 23:00 |
| ybit | spanish will only take about 2 years to learn anyway, and since i've been studying for about a month now, i'll continue with it :) | 23:01 |
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