--- Day changed Tue Oct 28 2008
00:01 < ppk> howdy xp
00:09 < xp_prg> ppk did you finish what is up?
00:54 < ppk> hey xp
01:44 < ppk> hey xp
02:34 < kanzure_> Server froze for a while there.
02:34 < kanzure_> Anything I miss?
02:41 < splicer> na
03:26 < fenn> hmph. pptx2ppt.com errors out with 'The file input type "pptx" is not supported.'
04:02 < fenn> http://www.boston.com/bigpicture/2008/10/enceladus_up_close.html check out the flyby animation
04:06 < splicer> Planet Hoth
04:10 < kanzure_> fenn: maybe it's some sort of political stand. "pptx2ppt: impossible rawr!"
04:11 < fenn> i could think of more direct ways of saying so..
04:12 < kanzure_> yes, but not more annoying
04:30 < xp_prg2> ppk you here man?
04:41 < Sparn> anyone have any experience with GENESIS?
04:41 < kanzure_> Sparn: sort of.
04:42 < kanzure_> I haven't ran many simulations with it.
04:42 < kanzure_> run
04:42 < kanzure_> but it is installed at least :)
04:42 < Sparn> lol
04:48 < ppk> hey xp
05:40 < xp_prg2> ppk you here man?
05:45 < ppk> sup xp
05:59 < ppk> gtg to bed
08:52 -!- jookos is now known as nsh
08:54 < faceface> With regards to the synthesis of DNA I'd like to let you know that this is a multi-step process, of course, which details largely are proprietary of GENEART. The basis is the synthesis of oligonucleotides (http://en.wikipedia.org/wiki/Oligonucleotides) which are subsequently assembled to the full-length sequence. You can learn about the oligo synthesis in relevant biotechnology text books and papers.
08:54 < faceface> I'll reply "WOW THANKS FOR THE INFORMATION!!!!!"
08:55 < nsh> proprietary my arse
08:56 < nsh> you [they] mean "secret"
08:58 < faceface> nsh, yeah
08:58 < faceface> bkero, indeed, PDB is my specialty... kinda
08:59 < faceface> speciality 
09:00 < faceface> I hope this information is useful to you. Please don't hesitate to get in touch again if you have any further queries.
09:00 < faceface> do you think I should send an honest reply?
09:01 < faceface> "Dear sirs, you have done nothing but spew out the measly bit of information that is already on your website. Do you think I can't read? Further more...."
09:01 < faceface> no point I guess... not sure what I hoped to learn... I need to hit the toolkit actually :D
09:02 < faceface> UtopiahGHML, unfortunately I did some work on a presentation instead of the BioCourse thingy... also I watched a show about zombies.
09:02 < faceface> This evening I have some other work to do too... I'll see what I can do during today.
09:19 < nsh> s/during //
09:31 < faceface> not an inclusionist then?
09:31 < faceface> you guys heard of rainbow tables?
09:31 < faceface> http://thelinuxsociety.org.uk/content/rainbow-tables-slides-from-talk
09:31 < faceface> they seem pretty cool (although see WP for the meat).
09:32 < faceface> nsh, ... hmmm... can't think of any redundancies ...
09:42  * nsh smiles
10:49 < UtopiahGHML> faceface: to be completely straight, don't worry I stoped building caste in the sky made out of people's promises ;)
10:50 < UtopiahGHML> if you do something, cool, we use it and move on, if you don't, well that's our lost but I can't complain since I didn't do it either.
11:58 < kanzure_> woah
11:59 < fenn> 'sup neo
11:59 < kanzure_> So on the singularity mailing list, (the one right next to the agi mailing list), there are people now telling me that the 'singularity' is about predicting the financial markets
11:59 < kanzure_> Joshua Fox in particular.
11:59 < fenn> baka darou
11:59 < kanzure_> so he's linking over to Peter Thiels etc.
12:00 < kanzure_> I don't know how they could say these things with a straight face
12:00 < kanzure_> many of the technologies they talk about easily make 'money' irrelevant
12:00 < kanzure_> if you're infinitely intelligent, what does money mean to you ?
12:01 < kanzure_> "Sorry Mr. Jupiter Brain, your bank account has simply run dry."
12:01 < fenn> it is a possibility..
12:01 < fenn> but it has nothing to do with singularity or singularity-ism
12:02 < kanzure_> on the other hand, I should have expected some of this
12:02 < kanzure_> considering that many 'futurists' (*cough* Ray ol' buddy) are in it for predicting the future to make a buck
12:03 < fenn> is that true? i thought ray made keyboards or OCR software
12:03 < kanzure_> he's an "inventor"
12:04 < fenn> a "speak n read" for the blind is one of his latest projects
12:04 < kanzure_> I'm not claiming that he's financially unstable and needs to make a buck predicting what people want to hear or something.
12:05 < kanzure_> remember some of the things from the /fernhout/ notes to kurzweil re: him kind of looking into the future and seeing his own reflection, stock markets, economics of growths and what not
12:05 < fenn> yes of course, simple observer bias
12:05 < fenn> that does not make technological singularity about predicting stock markets
12:07 < fenn> it's about fundamental problem of predicting a system that is more intelligent than yourself
12:07 < fenn> dont whine at me for saying intelligent, you can restate it as "agent with more information"
12:07 < kanzure_> nah, that's just the Anissimovian hijacking of the singularity concepts .. I thought we agreed that even a self-replicating singularity could lead to intelligence/oh-shit-predictability barriers. 
12:08 < fenn> hm. yes.
12:08 < fenn> that's just regular old unpredicability in complex systems though :)
12:08 < kanzure_> whenever PeerInfinity shows up again we should ask him about these things.
12:09 < kanzure_> apparently he contributes money to singinst .. I wonder if it's economically motivated
12:09 < fenn> if what is economically motivated?
12:09 < kanzure_> anywho, did you hear that Hod Lipson is coming to UT?
12:09 < kanzure_> his financial contributions to singinst
12:09 < kanzure_> his 'philanthropy'
12:09 < fenn> um, that doesnt make sense
12:10 < fenn> (tell hod lipson that he should just kill fab@home and switch to reprap)
12:10 < kanzure_> hod is fab@home?
12:10 < fenn> ya
12:10 < kanzure_> I should go back and read up on him :)
12:11 < kanzure_> I sent an email to the ADL doc saying Hod was showing up, and he had a two minute turn around to get an email out to all of his lab-students something like "most important lecture of the year if you don't go head on a stick rawr"
12:12  * kanzure_ goes down to eat.
12:12 < fenn> lol
12:38 < kanzure_>  http;//open-innovation-projects.org/ <-- yet another HTTP-HTML-only directory interface.
12:38 < fenn> i thought it was a pretty good start
12:39 < fenn> the "browse" kinda sucks
12:40  * fenn waits on slow computer..
12:40 < fenn> but look at the metadata fields! http://open-innovation-projects.org/projects/show/66/bug-labs
12:41 < fenn> (too bad they are mostly empty)
12:42 < fenn> ew @ http://open-innovation-projects.org/terms-of-use
12:44 < fenn> "Please check "Outsourced" whenver an external party is paid for supplying components."
12:46 < kanzure_>  what's wrong with 'outsourced'? sounds like debian's "free vs. nonfree" distinctions
12:47 < fenn> i just thought it was interesting because they are considering supply chain closure
12:49 < fenn> is there some kind of FOSS javascript thingy that will display a table and let you sort by columns?
12:50 < kanzure_> No. userscripts.org might have it if it did exist.
12:52 < fenn> i dont really understand why people release things this way: http://www.mattkruse.com/javascript/sorttable/source.html
12:52 < fenn> "you may not redistribute in any way except through use"
12:52 < fenn> like that even means anything?
12:52 < kanzure_> maybe there's some weird situation where your ignorance of the existence of the item causes it to proliferate more
16:47 < UtopiahGHML> anybody did stats on his Firefox SQL data?
16:47 < UtopiahGHML> or anything useful based on personal data basically
16:47 < UtopiahGHML> like top sites, top time spent, patterns, etc?
16:48 < UtopiahGHML> eventually use it to suggest new patterns based on good practices?
16:48 < UtopiahGHML> (like transforming your FF to a teacher ;)
16:48 < kanzure_> Hi UtopiahGHML.
16:48 < UtopiahGHML> hey kanzure_ 
16:48 < kanzure_> Yes, so, as to what you're looking for, that's, optimally, what I should have been doing for the past three or four years
16:48 < fenn> what are you hoping to learn from the data? "i spend too much time trolling on slashdot"?
16:48 < kanzure_> Instead I just have this crappy ADR file of all bookmarks (2.8 MB at this point)
16:49 < kanzure_> http://heybryan.org/bookmarks/
16:49 < kanzure_> fenn: that's about all that you'd get
16:49 < kanzure_> I'd be less interested in personal stats
16:49 < kanzure_> and more interested in pathways / patterns like that
16:49 < kanzure_> i.e., down the fifth branch and to the left, becomes a pattern and then maybe compartmentalize that as a 'command' or something.
16:49 < kanzure_> i.e. so that I don't loose track in my tabbing sessions
16:49 < kanzure_> *lose
16:49  * kanzure_ just got back
16:50 < kanzure_> guess this isn't what UtopiahGHML is wanting .. but I figure it'd be somewhat more usable than just timewastegraphs
16:50 < fenn> i've got three years of timewastegraphs if anyone is interested
16:50 < kanzure_> sleeplogs?
16:50 < kanzure_> or are you actually timing how long you look at a webpage?
16:50 < fenn> http://fennetic.net/sleep/
16:50 < kanzure_> heh
16:50 < fenn> both
16:51 < kanzure_> :)
16:51 < fenn> and other stuff, like what i eat
16:51 < kanzure_> how complete?
16:51 < fenn> chronologically complete, lacking in some resolution of course (to avoid the diary dilemma)
16:51 < faceface> UtopiahGHML, yup
16:51 < kanzure_> fenn: do you go wild if you can't log what you ate for the da y, or some such?
16:51 < kanzure_> *day
16:52 < UtopiahGHML> :)
16:52 < kanzure_> "Today, we all vow to change the galaxy, and indeed the galaxy will one day be free."
16:52 < fenn> go wild? no i just get sort of anxious about having to keep track of bits of paper
16:52 < kanzure_> hrm
16:52 < UtopiahGHML> kanzure_: well bookmark data is cool but Im more interested in behavior and as you said patterns
16:52 < fenn> instead of second-naturedly writing in my familiar text console
16:52 < kanzure_> right
16:53 < fenn> or if i'm being chased through the woods by a swamp monster and have no time to keep logs, then yeah i guess i'd go wild
16:53 < kanzure_> I gthe issue I have with this is that I'd be anxious about "starting late", i.e. "Randomly, one day in October, Bryan decided to start keeping track."  wtf?
16:53 < fenn> and that your data is incomplete for previous years?
16:53 < kanzure_> right. 
16:54 < kanzure_> would need some sort of formal metadata for expressing known incompleteness maybe?
16:54 < UtopiahGHML> guess you can start with sth imprecise/vague then refine it based on needs
16:54 < UtopiahGHML> and eventually an adapted tool for notation.
16:54 < kanzure_> I guess if I keep track of incompleteness, that's not bad
16:54 < UtopiahGHML> Bit by bit you improve it.
16:54 < fenn> i should have been more explicit about energy levels/ moods but they're hard to quantify
16:54 < kanzure_> but incompleteness, by nature, is incomplete
16:54 < kanzure_> fenn: I like the stats that ICUs in hospitals do.
16:54 < fenn> so i will just try to infer from what i did instead
16:54 < kanzure_> erm, not stats, but the beeping and the graphing etc.
16:55 < kanzure_> what the hell.
16:55 < kanzure_> I accidentally missed a few seconds of a cut scene
16:55 < kanzure_> some integral, important part of the story
16:55 < kanzure_> and there's no way to go back
16:55 < kanzure_> yay "autosave"
16:55 < fenn> always burning ahead on the razor's edge of the present
16:56 < kanzure_> poetry?
16:56 < fenn> can you feel the angst?
16:57 < kanzure_> I wonder what they were thinking.
16:59 < fenn> it takes about a minute to parse the logs and output images, so its too slow for a casual grep 'foo' | ./logparse.py
16:59 < fenn> i'm wondering if writing a gtk frontend is worth the effort
17:00 < UtopiahGHML> Suggesting for going further based on the personal data your browser daily collects : http://seedea.free.fr/wiki/index.php?n=Utopiahanalysis.Pim#pimderivedidea
17:00 < kanzure_> "Quick! A massive space station still under construction! Plot a course for the outer rim!"
17:00 < fenn> is "pim" your tachikoma thing?
17:00 < kanzure_> "okay."
17:01 < kanzure_> yay understanding of geometry
17:01 < fenn> what's "outer rim"?
17:01 < kanzure_> of the galaxy
17:01 < fenn> oh
17:01 < UtopiahGHML> nop I just use PIM for "Personal Internet Memory" locally
17:01 < fenn> kanzure_: i suppose they have FTL then
17:01 < kanzure_> hrm.
17:01 < kanzure_> oh, Star Wars? yes
17:02 < UtopiahGHML> fenn: but... I guess it could also use the tachikoma as a visual way to represent the teacher, right.
17:02  * fenn notes that the degree of FTL technology is inversely proportional to the amount of melancholic poetry
17:03 < fenn> UtopiahGHML: too bad surfraw never quite made it..
17:04 < kanzure_> yeah :(
17:04 < UtopiahGHML> surfraw?
17:04 < kanzure_> the most awesome thing ever
17:04 < fenn> UtopiahGHML: you could do stuff like 'google foobar' and it would dump the results to stdout
17:04 < kanzure_> As everything should.
17:04 < fenn> or 'define squidgyboo'
17:05 < UtopiahGHML> hmmm like some Webdav thing?
17:05 < kanzure_> Hey, what is the definition of squidyboo anyway? I hear it mentioned in these contexts often.
17:05 < kanzure_> No.
17:05 < kanzure_> It's just a scrape.r
17:05 < kanzure_> *scraper.
17:05 < kanzure_> Not even SOAP.
17:05 < fenn> i use youtubedl.py instead of in a browser because it works so much better in mplayer than flash plugin
17:05 < fenn> kanzure_: simpsons reference, they're playing scrabble
17:06 < kanzure_> originated there too? Huh.
17:06 < UtopiahGHML> so it would be like a command line API to the web?
17:06 < UtopiahGHML> like wget but "just for data"?
17:06 < fenn> am spelling it wrong and google isnt helping
17:07 < fenn>        Surfraw  provides  a  fast  unix command line interface to a variety of
17:07 < fenn>        popular WWW search engines and other artifacts of power.   It  reclaims
17:07 < UtopiahGHML> hard to see how this could be faster than Vimperator though.
17:07 < fenn>        google,  altavista,  dejanews,  freshmeat, research index, slashdot and
17:07 < fenn>        many others from  the  false-prophet,  pox-infested  heathen  lands  of
17:07 < fenn>        html-forms,  placing  these  wonders  where  they  belong, deep in unix
17:07 < kanzure_> Terrible paste.
17:07 < fenn>        heartland, as god loving extensions to the shell.
17:08 < fenn> when firefox takes 2 minutes to start you start to hate it
17:08 < kanzure_> Vimperator sucks because firefox sucks
17:08 < kanzure_> otherwise vimperator is fine
17:08 < fenn> i wish i could use ubiquity from the shell and just tell FF to fuck off
17:08 < kanzure_> ubiquity?
17:08 < fenn> ff commandline plugin
17:09 < fenn> sorta like hyperwords (?)
17:09 < xp_prg2> ppk u here?
17:10 < kanzure_> ugh
17:10 < faceface> bkero, PDB question?
17:11 < UtopiahGHML> well then I guess you could build a local GET meta-API that would be an abstraction for all the APIs of the websites you like (eventually with scrappers for websites that don't provide APIs) you like then query it with wget, no?
17:11 < xp_prg2> kanzure_ I did some work on the script last night man!
17:11 < UtopiahGHML> eventually make it community based to have faster adoption rate of new innovate websites
17:11 < fenn> UtopiahGHML: that was the idea behind surfraw
17:11 < xp_prg2> kanzure_ quick question what os do we want to target for this?
17:11 < UtopiahGHML> fenn: oh. ok, well then it was a cool idea :P
17:11 < fenn> problem was that the websites changed faster than coders could keep up
17:11 < xp_prg2> windows, linux?
17:12 < UtopiahGHML> hmmm yes but since then we have wider RSS adoptions, more public APIs and sometimes webservices, no?
17:12 < fenn> i guess :\
17:12 < kanzure_> xp_prg2: Target operating systme?
17:12 < kanzure_> *system?
17:12 < kanzure_> libsbml compiles on all systems known to man as far as I can tell
17:13  * fenn drags out the mac plus "it doesnt have a compiler! yay"
17:13 < kanzure_> gcc cross compiling?
17:13 < fenn> damn, i guess that would work
17:14 < UtopiahGHML> hmmm Im adding surfraw to my PIM article, pretty cool, thanks
17:14 < xp_prg2> kanzure_ well, the problem is you have to install libsmbl so its not "easy" to setup 
17:14 < xp_prg2> then you have to set the dynamic library path
17:14 < kanzure_> guess this isn't for flash then huh
17:14 < kanzure_> geeze
17:15 < xp_prg2> well the back end is not in flash and never was going to be
17:15 < UtopiahGHML> (talking of which I still didn't write the API for my website so no LINK>>PIMarticle<CR> possibility, damn
17:15 < xp_prg2> just wondering if you want the back end to be easily setup is all
17:15 < UtopiahGHML> fuck lazyness)
17:15 < xp_prg2> what os do you use kanzure_ ?
17:15 < kanzure_> debian
17:15 < xp_prg2> awsome ok
17:15 < kanzure_> look, all I need is the mapping between the element names and the API calls
17:15 < bkero> faceface: Just wondering what a good PDB viewer was
17:15 < kanzure_> I'll figure out everything else, okay?
17:16 < xp_prg2> kanzure_ ok, I am working on that
17:16 < kanzure_> at this point I don't really trust you for anything more than that heh'
17:16 < xp_prg2> heh
17:16 < xp_prg2> well, remember things are a compromise, you want what you want, I want what I want, we meet in the middle and get what we both want
17:16 < xp_prg2> I am learning a huge amount!!!
17:16 < kanzure_> there's nothing to learn really .
17:16 < xp_prg2> there is for me!
17:16 < kanzure_> nothing to compromise either .. either it's there or it isn't
17:17 < kanzure_> it's not like this requires specialized domain knowledge
17:18 < faceface> bkero, oh
17:18 < faceface> I wrote the FAQ on that one ;-)
17:18 < bkero> Haha
17:18 < bkero> There doesn't seem to be much in the portage tree--at least that I can see.
17:18 < faceface> http://pdbwiki.org/index.php/PDB_FAQ
17:18 < xp_prg2> kanzure_ you have to be able to understand the input/output to make a program man, without that you mine as well give it to a blind person and say draw me castle
17:19 < faceface> bkero, the best viewer imho is rasmol, because its so simple
17:19 < kanzure_> I did tell her to draw me a castle, and it was beautiful. What do you know of being blind?
17:19 < faceface> you should ask on #bioinformatics too
17:19  * kanzure_ grumbles about people talking about the blind.
17:19 < UtopiahGHML> "Please.please understand thoroughly about this artificial, virtual money market in western world and then you will realize you are part of booby trap laid by certain western capitalists to retain their hegemony." http://renjithmn.wordpress.com/2008/10/25/global-economic-downturn-and-indian-reality/
17:19 < bkero> faceface: Thanks, rasmol is in the portage tree too. :)
17:20 < faceface> what is the portage tree?
17:20 < fenn> bkero: ghemical maybe?
17:21 < faceface> l8r dudes
17:21 < bkero> Are thos compatible with 2.3 and 3.0 specs?
17:22 -!- xp_prg2 is now known as xp_prg
17:22 < fenn> UtopiahGHML: if people are feeling uptight because they realize their "financial instrument" is a sack of shit, that's a real phenomenon
17:23 < fenn> it affects how generous they are with resource allocation
17:25 < UtopiahGHML> well, doesn't being serious with resource allocation usually result in optimizations?
17:25 < fenn> renjithm is a whiny bitch, tell him to go study some math
17:25 < UtopiahGHML> well you tell him yourself Im just skimming through his writting
17:26 < UtopiahGHML> gather other PoW.
17:26 < xp_prg> kanzure_ you here?
17:26 < xp_prg> can I get a login to your debian box?
17:26 < kanzure_> yes
17:26 < kanzure_> I'm on it
17:30 < ppk> hey xp
17:30 < xp_prg> ppk!
17:31 < xp_prg> ppk I have questions about what you sent me got a sec?
17:32 < ppk> yeah
17:33 < fenn> bah - "Access to PyMOL Documentation (Paid Subscribers Only)"
17:33 < xp_prg> I am writing it to pastebin one sec
17:35 < xp_prg> http://pastebin.com/d14301512
17:36 < ppk> ok
17:37 < fenn> that's going to be a lot of menus
17:37 < fenn> arent there a couple thousand biobricks?
17:37 < xp_prg> ppk wow you know what you did do this right, my bad
17:38 < xp_prg> didn't understand cuz you didn't indent
17:38 < ppk> I couldn't in gmail
17:38 < ppk> it was annoying
17:38 < xp_prg> now did you do terminators?
17:38 < ppk> no
17:38 < ppk> I don't really know the difference between them
17:38 < xp_prg> dude I need terminators!
17:38 < ppk> and the purpose of having diff terminators
17:38 < kanzure_> what the hell are you doing, anyway, xp_prg ?
17:38 < ppk> so I can't choose cool/popular ones
17:38 < xp_prg> well ask questions, I don't know either :>
17:39 < xp_prg> kanzure_ working on my interface, I need a login to your debian box to work on the back end, is that cosure?
17:39 < kanzure_> what the fuck/
17:39 < kanzure_> ?
17:39 < kanzure_> no?
17:39 < xp_prg> why not?
17:39 < kanzure_> because you have a computer yourself?
17:40 < xp_prg> sbml is being a bitch to setup on my mac :(
17:40 < xp_prg> I know how to do it on linux though
17:40 < kanzure_> know how to do what
17:41 < xp_prg> get libsbml compiled and integrated with python to make the backend script
17:41 < kanzure_> just tell me what API functions to call
17:41 < kanzure_> that's all you have to do
17:41 < kanzure_> I'll take care of the rest
17:41 < kanzure_> there's already a python module anyway
17:43 < xp_prg> I don't know the answer to that without working with the code I need a place to work with the code
17:43 < kanzure_> How could you not know the answer to that?
17:43 < kanzure_> I even gave you the link to the API docs
17:44 < kanzure_> really at this point it's me being lazy and that's why you're (supposedly) doing it instead of me.;
17:44 < xp_prg> well, I want to do it, anyway, I will work on setting it up on my mac no big deal
17:44 < kanzure_> uh, why?
17:45 < xp_prg> why what?
17:45 < kanzure_> why set it up?
17:45 < kanzure_> when you just have to give me the list? :)
17:45 < fenn> kanzure_: i need to login to your debian box to browse your porn collection, is that cool?
17:45 < xp_prg> kanzure_ I don't understand your method of coding, I don't code that way, I don't understand api docs that way, I work with code to understand api's etc...
17:45 < kanzure_> fenn: yeah
17:45 < xp_prg> ppk you here man?
17:45 < kanzure_> you don't have to code xp_prg 
17:46 < ppk> I'm here
17:46 < kanzure_> I don't trust you to code anything any more
17:46 < xp_prg> ok
17:46 < kanzure_> just give me teh lists
17:46 < xp_prg> ppk, lets talk about those terminators man
17:46 < ppk> if I can find out why there are so many different kinds
17:47 < xp_prg> can anyone help ppk for a sec?
17:47 < kanzure_> ppk: that's the sort of things that biobricks are supposed to contain
17:47 < kanzure_> since that information isn't presently maintained in their information set, we're going to ignore it for now
17:47 < kanzure_> and maybe also go yell at them while we're at it :)
17:48 < ppk> well I mean I see different terminators in pre-made completed parts
17:48 < ppk> on partsregistry.org
17:48 < kanzure_> that's because they were done by hand
17:48 < ppk> termination seems like a simple task to me
17:48 < procto> kanzure_: see my gelbox-o-matic?
17:48 < ppk> which is why I don't understand why there are so many different kinds
17:48 < kanzure_> procto: I commented on it yesterday btw :) I like.
17:49 < ppk> you made the gel box laser cutting schematics?
17:49 < procto> yah
17:49 < ppk> that's cool
17:50 < ppk> I don't know how to view the file
17:50 < procto> well, the generator for the schematics
17:50 < procto> it's a .py file
17:50 < procto> you run it
17:50 < ppk> but I intend on using those, soon
17:50 < kanzure_> ppk: SVG? firefox or opera
17:50 < procto> run electrophoresis.py --help if you need help
17:50 < kanzure_> heh
17:50 < fenn> procto: where?
17:50 < procto> if you're on windows and have inkscape installed in its default location, it should open it in inkscape by default
17:50 < procto> fenn: http://logarchy.org/electrophoresis.py
17:51 < fenn> hm i was close
17:51 < procto> you can use the -d parameter to specify path to alternative viewer
17:51 < kanzure_> fenn: you're not on diybio?
17:51 < procto> for example, you can put in -d display, if you have imagemagick installed on a linux machine
17:51 < kanzure_> procto: ew, automatic viewer opening?
17:51 < procto> if you don't like it, put -s or --silent
17:51 < kanzure_> and by default?
17:52 < procto> yes. the default user story has the user converting it to DXF in inkscape right away
17:54 < fenn> why must length >= 16*thickness ?
17:55 < procto> because of the way it needs to fit with it
17:55 < procto> when you are setting the gel, the inner box is turned sideways, and the walls of the big one maintain edges
17:56 < procto> then it slides into the center of the big one
17:56 < procto> in order for the hooks that make it hang to fit into the big box
17:56 < procto> that's the minimum size
17:56 < fenn> i keep getting sh: /home/fenn/sandbox/electrophoresis.svg: Permission denied
17:57 < procto> hm, at what stage?
17:58 < procto> try running it with -s
17:58 < fenn> after it dumps the struct
17:59 < fenn> -s silenced the error, seems to work fine either way 
17:59 < xp_prg> ok ppk, I put in your changes, I need those terminators, got any?
17:59 < procto> I think it's mostly that you're not on windows :>
17:59 < procto> fenn: I'll modify the next version
18:00  * kanzure_ still doesn't understand what xp_prg is doing.
18:00 < xp_prg> creating an input front end to make an sbml interface
18:00 < fenn> and the resulting box is massively huge in inkscape relative to the page
18:00 < xp_prg> based on interface1.php, I need Promoter, RBS, Coding DNA, and Terminators
18:00 < kanzure_> then why ask for a list of specific terminators
18:00 < kanzure_> yes, so why ask for a list?
18:01 < kanzure_> you jnuyst need a single line of input\
18:01 < xp_prg> to make it easy on the user
18:01 < kanzure_> no, don't bother with that
18:01 < procto> xp_prg is correct
18:01 < kanzure_> I'll handle that bullshit ok?
18:01 < procto> but the list needs to be loaded dynamically
18:01 < kanzure_> correct
18:01 < kanzure_> but in fact
18:01 < kanzure_> if any of you asshats had been listening yesterday,
18:01 < xp_prg> hahah
18:01 < kanzure_> one thing that we can do is make it abstract so that the user doesn't have to see them at all
18:02 < xp_prg> ppk where are you man?!
18:02 < xp_prg> what are you doing?
18:02 < xp_prg> I need this last part!
18:14 < xp_prg> is anyone alive in here, what happened?
18:15 < fenn> our satellite uplink is being jammed by KGB agents
18:15 < xp_prg> ppk you still here, someone give me some good terminators real quick
18:15 < xp_prg> that is the last thing I need right now
18:18 < xp_prg> fenn anyone, hello?
18:19 < kanzure_> we already gave you the lists
18:24 < xp_prg> well which ones would specifically apply to the ones in my menu for now?
18:24 < xp_prg> http://pastebin.com/d14301512
18:25 < kanzure_> what menu
18:25 < kanzure_> why is there a menu
18:25 < ppk> back
18:26 < ppk> so xp_prg, why don't you mock up a pre-made plasmid
18:26 < ppk> from partsregistry.org
18:26 < kanzure_> why 
18:26 < kanzure_> ppk: what does that have to do with his task?
18:26 < ppk> if you want to get non-working stuff in there asap
18:27 < ppk> I'm guessing it's easier for him to do stuff if he has tangible examples of parts in biobench
18:27 < kanzure_> but you see, he already does
18:27 < ppk> ./shrug
18:27 < kanzure_> do you do any programming?
18:27 < ppk> not really
18:27 < kanzure_> aha
18:28 < kanzure_> that explains all of this ..
18:28 < fenn> ./shrug.py > /dev/null
18:28 < xp_prg> ppk what?
18:29 < xp_prg> we can't just terminator parts?
18:29 < xp_prg> just use?
18:29 < ppk> nevermind
18:30 < xp_prg> ppk, dude explain to me where we are on the terminator parts menu please?
18:30 < ppk> there are plasmids in partsregistry.org
18:30 < kanzure_> this is so stupid..
18:30 < ppk> you could mock up an actual one
18:30 < kanzure_> fenn: help me :(
18:30 < ppk> with the graph::easy stuff
18:30 < kanzure_> fenn: like, even if it's yelling at me for feeding the troll
18:30 < kanzure_> Why oh why did I feed the troll?
18:30 < fenn> kanzure_: please provide me complete specifications on how to help you
18:30 < kanzure_> Heh.
18:30 < xp_prg> ppk, I don't understand what your saying, can you help me to understand?
18:31 < fenn> you must state the answer in the form of a question
18:31 < fenn> or was it the other way around?
18:32 < fenn> kanzure_: i really think someone, maybe me, should try to get the data from open-innovation-projects.org or whatever
18:32 < kanzure_>  write a crawler?
18:33 < kanzure_> or go knocking?
18:35 < kanzure_> Well this is a disappoint. The game is over already?
18:35 < kanzure_> *disappointment
18:35 < kanzure_> "Do you want to restart the game now with all your powers, costumes and upgrades unlocked? This will overwrite your saved game."
18:36  * kanzure_ suddenly remembers why arcade games are the win
18:39  * bkero wins.
18:39 < kanzure_> You're an arcade game?
18:39 < bkero> Just win
18:40 < kanzure_> "{Your dad} is now following you on twitter!" <- Crap.
18:41 < bkero> haha
18:41 < bkero> AnandTech started following me the other day
18:41 < kanzure_> Who now?
18:42  * kanzure_ goes for lunch
18:43 < bkero> Me
18:43 < bkero> The winner
18:43 < UtopiahGHML> "{Your dad} is now following you on twitter!" :)
18:43 < UtopiahGHML> technology, yeah! 
18:44 < UtopiahGHML> does he also twitt?
18:44 < fenn> is your dad a twitt?
18:45  * xp_prg is stuck and ppk won't talk to him anymore :(
18:46 < xp_prg> anyone want to help me with the terminator question please?
18:47 < UtopiahGHML> Sarah Connor?
18:47 < xp_prg> the terminators for a biobrick part
18:47 < fenn> "TwoWayMirroringWithRsync : How to keep identical copies of a wiki on two systems, one hosted and the other local,"
18:48 < UtopiahGHML> well, at least I tried.
18:48  * fenn grumbles about ikiwiki
18:49 < xp_prg> how do you pick the terminator for a bio brick part?
18:50 < fenn> UtopiahGHML: instead of Rsync you might want to use Unison (or even dump the wiki backend into git somehow, then merge changes)
18:50 < fenn> instead of overwriting local changes
18:51 < UtopiahGHML> fenn: http://seedea.free.fr/wiki/index.php?n=Seedea.RemoteInstall
18:51 < UtopiahGHML> Rsync was a bad idea, I just added it because it was an already existing pmwiki module
18:51 < UtopiahGHML> problem is, it's not just the backend though
18:52 < UtopiahGHML> but yes Ill soon start to use a real *VS soon for the modules and packaging it
18:52 < UtopiahGHML> still dunno on what though, GIT, Trac, etc... :/
18:53 < UtopiahGHML> (checking Unison)
18:53 < fenn> there are a lot of ~meaningless choices, and they will all become interoperable eventually
18:53 < UtopiahGHML> yep, especially since ideally I want the whole thing to be self contained anway
18:53 < fenn> except for backwater sludge like svn of course
18:54 < UtopiahGHML> but bit by bit I should just go first a working option and move on.
18:54 < fenn> yes
18:55 < UtopiahGHML> (updated with Unison)
19:00 < UtopiahGHML> uhhh... I started to think about the API and changes propagation over several installs based on different underlying wiki and... Id rather not think about it and go cook sth really :/
19:02 < fenn> this is why a real RCS like git is better than unison/rsync
19:02 < bkero> git++
19:03 < bkero> There's a trac-git plugin
19:04 < UtopiahGHML> thanks for the tip, Ill think about it, bbl
19:09 < ppk> any of you know what the following parameters are and how they're useful for measuring terminators?
19:09 < ppk> forward_efficiency	0.309[CC]	
19:09 < ppk> reverse_efficiency	-0.368[CC]	
19:28 < kanzure_> Games aren't very much fun anymore. I'll just sit down and "teh win" and then be sad.
19:29 < kanzure_> ppk: Context? Where did you find those parameters?
19:29 < ppk> partsregistry.org, on terminators
19:30 < kanzure_> Is it in the biobrick XML format?
19:30 < ppk> it's just on the terminator part description page
19:30 < kanzure_> *expressed in the
19:30 < ppk> http://partsregistry.org/wiki/index.php?title=Part:BBa_B0012
19:34 < ppk> what do you think?
19:35 < kanzure_> That doesn't answer my question.
19:35 < kanzure_> Here, look here:
19:35 < kanzure_> http://heybryan.org/books/biobricks/
19:36 < kanzure_> I downloaded all biobrick information.
19:37 < bkero> You got all of it?
19:38 < bkero> Snazzy
19:38 < kanzure_> Yes.
19:38 < kanzure_> Also, you should see the scripts there too. I don't actually expect anybody to ever read them, so I might have my SSN in there or something.
19:39 < ppk> I don't see anything on forward/reverse efficiency in here
19:40 < kanzure_> Then the biobrick people suck. So ignore that information for now.
19:41 < ppk> I'd still like to know what that means
19:41 < kanzure_> efficiency?
19:41 < ppk> google only finds MIT affiliated sites when searching for those terms though
19:41 < fenn> i think a terminator works because the polymerase falls off the strand, so it probably falls off more reliably when going in one particular direction
19:42 < ppk> hmm
19:42 < fenn> http://en.wikipedia.org/wiki/Terminator_sequence
19:43 < fenn> polyadenylation is what i'm remembering
19:44 < ppk> still not sure about this
19:44 < fenn> what are you doing?
19:45 < ppk> I guess I'd have to ask somebody who's worked with the parts before
19:45 < ppk> nothing in particular, just want to learn what those parameters mean
19:45 < ppk> your explanation seems plausible
19:45 < fenn> ah. well, perhaps you can convince whoever made them to add some more info
19:45 < ppk> yeah
19:46 < kanzure_> "HOPE: it hasn't killed Apple [yet]"
19:46 < fenn> wasnt Linux supposed to kill Apple?
19:47 < fenn> i mean, the only thing keeping them going was that they were the microsoft alternative
19:47 < kanzure_> huh
19:48 < bkero> what
19:59 < procto> hm, the dow is up over 800 and holding
20:11 < bkero> Over 8000?
20:21 < kanzure_> Hi ppk, Nade, splicer
20:22 < splicer> hi kanz
20:27 < kanzure_> "You may call it a dungeon, but to me it's a giant mazetoilet."
20:30 < bkero> wtf
21:30 < UtopiahGHML> Programming Bits and Atoms http://www.youtube.com/watch?v=w8ubXgXM7kk
21:46 < xp_prg> ok I have biobench .003 who wants it?!
21:47 < UtopiahGHML> what can I do with it?
21:49 < xp_prg> use biobricks in a graphical way
21:50 < xp_prg> give me your email if you want it!
21:52 < xp_prg> I am about to send it so let me know now
21:53 < xp_prg> too late
21:55 < UtopiahGHML> what could I do using biobricks in a graphical way?
21:55 < xp_prg> you could design e-coli or yeast organisms to do novel things
21:56 < UtopiahGHML> once the design is done how can I test the result?
21:57 < xp_prg> with the compile/simulation abilities
21:58 < UtopiahGHML> and when it's ready?
21:58 < xp_prg> what do you mean?
21:59 < UtopiahGHML> compiled and tested? what do I d with the result?
22:00 < xp_prg> you can simulate it, then you could create it physically by either doing it yourself or sending it to company like blue heron to make it for you:http://www.blueheronbio.com/index.html
22:00 < UtopiahGHML> how could I do it myself?
22:01 < xp_prg> with centrifuges, chemicals, cells, petri dishes etc...
22:02 < UtopiahGHML> what have you personnaly done with it so far?
22:03 < xp_prg> I am creating the software only right now, but we have successfully built an e-coli plasmid that will generate a flourescent protein
22:03 < UtopiahGHML> nice
22:05 < UtopiahGHML> is your result public too? let's imagine that Id like BlueheronBio to make it for me, what would I need?
22:05 < xp_prg> this is opensource software gpl'd free
22:05 < xp_prg> just send them the dna :>
22:05 < xp_prg> and the cell you want it in
22:06 < UtopiahGHML> have you tried it yet? the whole process
22:06 < xp_prg> no, still learning how it works
22:06 < xp_prg> I want to though
22:06 < UtopiahGHML> to do what ultimately?
22:07 < UtopiahGHML> your wild long term goal let's say :)
22:07 < xp_prg> create a biologically based cpu similar to a retina
22:08 < UtopiahGHML> a retina?
22:09 < xp_prg> http://thalamus.wustl.edu/course/eyeret.html
22:09 < xp_prg> F. Signal processing in the retina - the center-surround receptive field.
22:10 < UtopiahGHML> ok so similar in what sense?
22:10 < xp_prg> a retina behaves like a silicon based cpu
22:10 < xp_prg> but biologically based
22:12 < UtopiahGHML> what similarities? it can compute? it can schedule? it can access memory?
22:12 < xp_prg> yes all of the above
22:13 < UtopiahGHML> isn't it connected neurones behind it that do that? connected to the optical nerve?
22:13 < xp_prg> yes the neuronal structures that do the signal processing are in the retina
22:14 < UtopiahGHML> and why do you want it for? replace a normal eye but with embeded augmented reality functionalities?
22:17 < xp_prg> to create cheap cpus
22:19 < UtopiahGHML> and why are you especially interested in the retina instead of classical neural networks?
22:20 < xp_prg> because the retina does not re-configure itself, it is static neuronal structures
22:22 < UtopiahGHML> nice, so when will I be able to try it?
22:25 < kanzure_> sense when the fuck is biobench about a retina? 
22:25 < kanzure_> *since
22:25 < kanzure_> Argh.
22:25 < kanzure_> This is like a bad horror story.
22:27 < xp_prg> UtophiahGHML you can try it now but it is not complete :>
22:27 < xp_prg> kanzure I just released biobench .003!
22:27 < xp_prg> do you want it?
22:27 < kanzure_> I read the backlog.
22:27 < kanzure_> yes
22:27 < kanzure_> I thought you were sending it to me anyway ??
22:27 < xp_prg> kanzure_ I wasn't sure you wanted it anymore you seem upset and stuff
22:28 < kanzure_> I am very upset. Doesn't mean I don't rabbidly archive  .. even the shitstuff. :(
22:28 < xp_prg> UtophiahGHML what is your email?
22:28 < UtopiahGHML> Id rather check it on your website/wiki if you don't mind
22:29 < xp_prg> ok
22:29 < xp_prg> maybe kanzure_ will post it
22:29 < UtopiahGHML> you don't have a website?
22:29 < kanzure_> he's on a mac
22:29 < kanzure_> and apparently doesn't have server software
22:29 < xp_prg> ok sent it!
22:30 < UtopiahGHML> eh... so what? you don't have to host your own website locally
22:30 < kanzure_> :)
22:30 < kanzure_> "You are what you cache."
22:30 < UtopiahGHML> (dunno how I feel about Dojo...)
22:31 < kanzure_> Dojo the js thingy?
22:31 < UtopiahGHML> yep
22:31 < xp_prg> post it kanzure_ so UtopiaGHML can see it!
22:31 < UtopiahGHML> xp_prg: did you make some in-use screenshots?
22:31 < xp_prg> no
22:32 < UtopiahGHML> are you doing some right now?
22:32 < kanzure_> xp_prg: I haven't received the email.
22:32 < xp_prg> I sent it
22:33 < kanzure_> That does not mean I have received it.
22:36 < UtopiahGHML> maybe both of you lied...
22:36 < kanzure_> ?
22:37 < UtopiahGHML> maybe he didn't send it and maybe you did receive it.
22:40 < UtopiahGHML> That will be my conclusion for tonight, bye guys.
22:54 < gene_> are you there Kanzure?
22:54 < kanzure_> yes
23:06 < xp_prg> hi ppk!!!
23:06 < xp_prg> ppk did you try it yet?
23:06 < ppk> yeah
23:06 < xp_prg> what do you think?
23:08 < xp_prg> http://www.umassigem.org/biobench/biobench.html
23:08 < xp_prg> check it out everyone!
23:09 < kanzure_> we don't have flash
23:09 < kanzure_> we've been telling you.
23:09 < xp_prg> so get it
23:09 < kanzure_> uh, it doesn't work on the terminal
23:09 < xp_prg> you can get codeweaver for free for year today
23:09 < kanzure_> I'm not interested in commercial systems
23:09 < xp_prg> well there is osflash
23:10 < xp_prg> it fully opensourced
23:10 < kanzure_> does it work in the terminal?
23:10 < xp_prg> no
23:10 < xp_prg> works in a web page though
23:10 < kanzure_> uh?
23:10 < kanzure_> not necessarily
23:10 < kanzure_> for instance, I have elinks, links, links2, w3m, and lynx
23:10 < kanzure_> and flash does not work in these.
23:10 < xp_prg> kanzure_ your cool, never met anyone who doesn't use X
23:11 < xp_prg> your missing out but ok
23:11 < kanzure_> I use X when it's convenient :) running X on the server is a bad idea
23:11 < xp_prg> kanzure_ can you help me to understand more about what an effector is, I think I saw it on interface2.php
23:13 < kanzure_> What difference would it make whether it was X or Y?
23:15 < xp_prg> cuz it will help me to understand how they relate to the SBML modeling file
23:15 < kanzure_> Really? How?
23:15 < xp_prg> so I can understand the output correctly
23:15 < kanzure_> You don't see "effectors" already in the pregenerated SBML examples from the synbioss designer?
23:16 < xp_prg> yes the example does have an effector in it
23:16 < kanzure_> Okay, then what's so hard about that?
23:16 < kanzure_> Now you know.
23:16 < xp_prg> I don't know what it does
23:16 < kanzure_> You don't have to.
23:21 < xp_prg> well I want to, you won't tell me why?