| --- Day changed Fri Jun 13 2008 | ||
| -!- percent_ [n=percent@66.158.193.28] has joined #hplusroadmap | 00:58 | |
| percent_ | Howdy. | 00:58 |
|---|---|---|
| wrldpc | hey | 00:59 |
| wrldpc | http://www.flickr.com/photos/worldpeace/ | 00:59 |
| percent_ | Where can I read about gene notation? | 01:00 |
| percent_ | If I wanted to express to you a certain gene and didn't want to do it nucleotide by nucleotide (i.e. AUG UUG CGA) | 01:01 |
| percent_ | say a file format | 01:07 |
| fenn | google fasta, clustal | 01:28 |
| fenn | #bioinformatics is a better channel for that | 01:28 |
| percent_ | What's this channel for, again? | 01:32 |
| fenn | bitching and moaning | 01:33 |
| fenn | fasta is the format, if you didnt catch that | 01:35 |
| percent_ | I didn't. What's gff? | 01:40 |
| fenn | dunno, but it's described here: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml | 01:41 |
| percent_ | In FASTA, I see a lot of things that aren't A,C,G, or T/U. | 01:42 |
| percent_ | What do those mean? | 01:42 |
| fenn | yes, the other letters are where the sequence was ambiguous | 01:42 |
| percent_ | ah, it describes it... | 01:42 |
| fenn | XYW something like that | 01:42 |
| percent_ | GA is purine? Aren't two nucleotides purine-based? | 01:42 |
| fenn | you can also describe genes spread around different organisms with varying sequences, but which are mostly conserved (i.e. no huge deletions or insertions) | 01:44 |
| fenn | re: purine, i dont know what you're asking | 01:45 |
| percent_ | Some organisms have similar sections of conserved DNA? | 01:46 |
| fenn | yeah, of course | 01:46 |
| fenn | havent you heard that chimps and humans are 95% similar? | 01:46 |
| percent_ | Yes. And we keep this sort of information in FASTA files? | 01:47 |
| fenn | um, probably not | 01:47 |
| fenn | i dont know what the genome projects use | 01:47 |
| percent_ | what do we use? | 01:47 |
| fenn | who is we? | 01:47 |
| percent_ | Biohackers in general. | 01:47 |
| fenn | whatever is available? | 01:48 |
| percent_ | I see why kanzure is so obsessed with organization; there appears to be very little of it here. None of us speak the same type of genetic notation, apparently. | 01:48 |
| fenn | honestly the only reason you need to be concerned what format something is, is when you're feeding it into some program that expects that format | 01:49 |
| fenn | wow "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months." | 01:51 |
| percent_ | moore's law | 01:52 |
| fenn | 100 billion bp and climbing | 01:52 |
| fenn | nothing to do with moore | 01:52 |
| percent_ | Purpose thereof? | 01:52 |
| percent_ | No, it's moore's law | 01:52 |
| percent_ | with genes instead of transistors | 01:52 |
| fenn | computer speed has nothing to do with sequencing DNA! | 01:53 |
| fenn | well, ok, it does | 01:53 |
| fenn | but it's not the limiting factor | 01:53 |
| percent_ | I was just making a comparison. | 01:53 |
| fenn | you might say the same thing about the US population | 01:53 |
| fenn | doubles every 25 years | 01:53 |
| percent_ | He said "roughly every two years" | 01:53 |
| percent_ | i.e. about 18 months | 01:54 |
| fenn | silicon fabs have been able to do much finer details than are included in the current generation of chips, they just hold back the development because people expect "moores law" to continue - its a self fulfilling prophecy | 01:55 |
| fenn | this way they get to sell you a new computer every 2 years | 01:55 |
| fenn | look at the data points, not the lines: http://en.wikipedia.org/wiki/Moore's_law | 01:58 |
| fenn | heh 500GHz helium cooled processor | 02:03 |
| fenn | oh, transistor, nevermind | 02:04 |
| percent_ | ebeam litho is amazing. | 02:05 |
| fenn | as useful as they are, i dont think general purpose processors (turing machines) are the future of information processing | 02:11 |
| fenn | i think we'll see more and more reconfigurable FPGA's and ASIC's | 02:12 |
| percent_ | FPGAs are also amazing. | 02:12 |
| percent_ | I really want to work with them. | 02:12 |
| percent_ | Unfortunately, they're not easy to scrounge | 02:12 |
| fenn | they aren't being used properly because Xilinx and Altera are a bunch of fuckheads | 02:12 |
| fenn | you can't change the configuration while running, for example | 02:13 |
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| fenn | and the lack of specifications is the dumbest thing ever | 02:13 |
| percent_ | How would that even be possible? | 02:13 |
| fenn | simple, send a 'change gate' signal | 02:13 |
| percent_ | I don't know how theirs work | 02:13 |
| percent_ | but | 02:13 |
| fenn | its ok, nobody knows | 02:14 |
| percent_ | that may not be possible. | 02:14 |
| fenn | no, xilinx had a set of chips they made for a university study on reconfigurable computing | 02:14 |
| fenn | and then promptly discontinued the line :\ | 02:15 |
| percent_ | i discontinued your mom =\ | 02:15 |
| percent_ | ...sorry, I couldn't tolerate such propriety in this channel. | 02:15 |
| fenn | you should see a psychologist | 02:16 |
| percent_ | no thank you | 02:16 |
| fenn | wow 2 am, where did the day go | 02:20 |
| percent_ | I think it's about time for a your mom joke. | 02:22 |
| fenn | "reported speed-up factors of up to almost four orders of magnitude, as well as a reduction in electricity consumption by more than one order of magnitude" now why dont we see any commercial spinoffs from this eh? | 02:22 |
| percent_ | FPGA? | 02:23 |
| fenn | dunno exactly, its locked up in dead trees :( | 02:23 |
| percent_ | Where are the dead trees? | 02:24 |
| fenn | in a library somewhere | 02:24 |
| fenn | anyway, some sort of reconfigurable computer | 02:24 |
| ybit | Splicer: mind posting a link to your comments? | 02:25 |
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| ybit | i'm guessing here: http://www.metanexus.net/magazine/tabid/166/Default.aspx?id=10543 but it seems to be down atm | 02:26 |
| fenn | bleh. is that the "transhumanist rhetoric" article? | 02:26 |
| ybit | fenn: yep | 02:28 |
| ybit | i've yet to read the log where you guys probably discussed it | 02:29 |
| fenn | sounds like a player-hatin bitch | 02:30 |
| ybit | the article or me not reading the logs? :P | 02:31 |
| fenn | start with the assumption that X is no good, and proceed to use logical fallacies and shoddy research to back up your claims | 02:31 |
| ybit | aha | 02:31 |
| fenn | "polymorphic processor" has a nice ring to it | 02:32 |
| fenn | The TRIPS architecture is composed of many copies of a small number of replicated tiles, | 02:32 |
| fenn | hmm! | 02:32 |
| Splicer | nite | 02:37 |
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| fenn | not exactly: http://www.cs.utexas.edu/users/cart/trips/chip_floorplan.html | 02:39 |
| fenn | i guess i can live with 6 tile types | 02:39 |
| fenn | macrotiles | 02:39 |
| percent_ | What's a dR group? | 03:00 |
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| kanzure | Hrm. | 07:55 |
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| procto | wrldpc: howdy, yeah, I'm Mike | 10:10 |
| procto | kanzure: "ethical" is intended to mean "we will try reeeal hard not to make The White Plague" | 10:14 |
| kanzure | uh? | 10:14 |
| kanzure | funny, considering this is people's chance to *fight* grey goo stuffs :) | 10:15 |
| nsh | the white plague brings back swarths of medieval people from the dead across europe | 10:15 |
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| faceface | kanzure: did you happen to meet wan? | 10:40 |
| kanzure | Not yet. :) | 10:40 |
| faceface | OH... you will be back in the lab? | 10:42 |
| faceface | s/OH/Oh/ | 10:42 |
| kanzure | I'm there now :) | 10:43 |
| faceface | cool :D | 10:44 |
| faceface | wan works late aparently | 10:44 |
| kanzure | This is a pretty neat building. | 10:44 |
| kanzure | Wan's lab has the attic directly above me. | 10:44 |
| kanzure | They have a full yeast knock-out library and giant mechanical arms to fetch entries. | 10:45 |
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| kanzure | nsh: "bring out your dead" | 10:46 |
| percent_ | Are you at u of austin? | 10:48 |
| percent_ | hay kanzure what's a dR group and what does it think it's doing | 10:49 |
| percent_ | on thymine | 10:49 |
| kanzure | dR ? :) | 10:49 |
| kanzure | percent_: Yep. | 10:49 |
| kanzure | http://ellingtonlab.org/ | 10:49 |
| percent_ | yes | 10:49 |
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| kanzure | so, can anybody make some guesses on how factories are made? | 15:25 |
| kanzure | because I've been looking through the literature, through many books an tons of hselves | 15:26 |
| kanzure | and nobody seems to actually *know* | 15:26 |
| kanzure | The closest I have gotten is a list of 'professional societies' that might have people that know what they are doing, /maybe/ | 15:26 |
| fenn | toyota production system was a good attempt at theory of factory-making | 15:33 |
| fenn | most factories these days have a hodgepodge blend of tradition, ad-hoc cruft layering, and imitating toyota/iso9001 crap | 15:34 |
| fenn | its kinda like reading a bunch of books on computer science and then confronting the 30MB of source code with no documentation | 15:35 |
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| kanzure | hrm | 16:07 |
| kanzure | fenn: It seems to me that what would be most helpful would be to just order all of the product catalogs that the factory-builders would use. | 16:07 |
| kanzure | or something | 16:07 |
| kanzure | I'm not even sure who you would hire to build a factory | 16:07 |
| kanzure | maybe figuring that out is a good first step | 16:07 |
| kanzure | and then finding out why they know what they know. | 16:07 |
| kanzure | why/how | 16:07 |
| * kanzure has access to the lab servers :) | 16:08 | |
| * kanzure is downloading the lab servers ;-) | 16:08 | |
| kanzure | Hrm. I should also have pywikipediabot crawl the wiki. | 16:10 |
| --- Log opened Fri Jun 13 16:51:23 2008 | ||
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