--- Day changed Fri Jun 13 2008
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00:58 < percent_> Howdy. 
00:59 < wrldpc> hey
00:59 < wrldpc> http://www.flickr.com/photos/worldpeace/
01:00 < percent_> Where can I read about gene notation?
01:01 < 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)
01:07 < percent_> say a file format
01:28 < fenn> google fasta, clustal
01:28 < fenn> #bioinformatics is a better channel for that
01:32 < percent_> What's this channel for, again?
01:33 < fenn> bitching and moaning
01:35 < fenn> fasta is the format, if you didnt catch that
01:40 < percent_> I didn't. What's gff?
01:41 < fenn> dunno, but it's described here: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
01:42 < 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?
01:44 < 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)
01:45 < fenn> re: purine, i dont know what you're asking
01:46 < 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?
01:47 < 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.
01:48 < 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.
01:49 < 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
01:51 < fenn> wow "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months."
01:52 < 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
01:53 < 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"
01:54 < percent_> i.e. about 18 months
01:55 < 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
01:58 < fenn> look at the data points, not the lines: http://en.wikipedia.org/wiki/Moore's_law
02:03 < fenn> heh 500GHz helium cooled processor
02:04 < fenn> oh, transistor, nevermind
02:05 < percent_> ebeam litho is amazing.
02:11 < fenn> as useful as they are, i dont think general purpose processors (turing machines) are the future of information processing
02:12 < 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
02:13 < fenn> you can't change the configuration while running, for example
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02:13 < 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
02:14 < 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
02:15 < 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. 
02:16 < fenn> you should see a psychologist
02:16 < percent_> no thank you
02:20 < fenn> wow 2 am, where did the day go
02:22 < 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?
02:23 < percent_> FPGA?
02:23 < fenn> dunno exactly, its locked up in dead trees :(
02:24 < percent_> Where are the dead trees?
02:24 < fenn> in a library somewhere
02:24 < fenn> anyway, some sort of reconfigurable computer
02:25 < ybit> Splicer: mind posting a link to your comments?
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02:26 < 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?
02:28 < ybit> fenn: yep
02:29 < ybit> i've yet to read the log where you guys probably discussed it
02:30 < fenn> sounds like a player-hatin bitch
02:31 < 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
02:32 < 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!
02:37 < Splicer> nite
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02:39 < 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
03:00 < percent_> What's a dR group?
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07:55 < kanzure> Hrm.
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10:10 < procto> wrldpc: howdy, yeah, I'm Mike
10:14 < procto> kanzure: "ethical" is intended to mean "we will try reeeal hard not to make The White Plague"
10:14 < kanzure> uh?
10:15 < 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
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10:40 < faceface> kanzure: did you happen to meet wan?
10:40 < kanzure> Not yet. :)
10:42 < faceface> OH... you will be back in the lab?
10:42 < faceface> s/OH/Oh/
10:43 < kanzure> I'm there now :)
10:44 < 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.
10:45 < kanzure> They have a full yeast knock-out library and giant mechanical arms to fetch entries.
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10:46 < kanzure> nsh: "bring out your dead"
10:48 < percent_> Are you at u of austin?
10:49 < 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
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15:25 < kanzure> so, can anybody make some guesses on how factories are made?
15:26 < 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/
15:33 < fenn> toyota production system was a good attempt at theory of factory-making
15:34 < fenn> most factories these days have a hodgepodge blend of tradition, ad-hoc cruft layering, and imitating toyota/iso9001 crap
15:35 < fenn> its kinda like reading a bunch of books on computer science and then confronting the 30MB of source code with no documentation
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16:07 < 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
16:08  * kanzure has access to the lab servers :)
16:08  * kanzure is downloading the lab servers ;-)
16:10 < kanzure> Hrm. I should also have pywikipediabot crawl the wiki.
--- Log opened Fri Jun 13 16:51:23 2008