--- Day changed Wed Oct 08 2008 00:01 < fenn> china is pretty darn industrialized if you ask me 00:20 < kanzure> http://www.cs.utexas.edu/~porter/ "our research focuses on explanation generation" 00:20 < kanzure> "could you explain?" 00:20 < kanzure> "if I could, I wouldn't have a job" 00:20 < ybit> heh 00:21 < ybit> nice to have that on campus 00:41 < ybit> UtopiahGHML: i see what you mean now 00:41 < ybit> http://en.wikipedia.org/wiki/Image:2005education_spending.PNG 00:42 < ybit> concerning where biotech or anything related may be n brazil 00:42 < ybit> damn the "i" key 00:48 < ybit> it's a terribly rough graph of where the money is going for public education in each country 01:01 < kanzure> huh, six million emails were sent to the presidential debate nonsense 01:01 < kanzure> wonder how they sorted through that 01:01 < kanzure> they probably didn't. 01:07 < kanzure> where'd I recently see Collis' name? 01:08 < kanzure> ah, nevermind 01:25 < kanzure> "I posit that the service economy is actually hiding the fact that the majority of people in the west are now unemployable in any productive sense. That the economy is structured such that we can still consume massive amounts of products, while contributing nothing of substance, is probably what underlies the current financial crisis, and implies deep sustained crisis." 01:25 < kanzure> heh 01:26 < kanzure> aka people are useless. 01:41 < kanzure> I'm sure we could convert them into food 01:42 < kanzure> as president, or evil genius overlord, I propose all people get a solyency license, good for 2 pounds of their own flesh redeemable at the butchery. 01:47 < kanzure> http://en.wikipedia.org/wiki/Mining#Mining_industry 'An event at a mine which causes death or bodily injury to an individual not at the mine at the time the event occurs.' what? 01:47 < kanzure> telekenetic rocks? 01:47 < kanzure> *telekinetic 02:30 < bkero> Hm. How difficult would it be to build a centrifuge? 02:33 < kanzure_> ROPE + KNOT + BUCKET AT END. SWING. 02:34 < bkero> I was thinking cone + soldering iron + bolt + elecric motor 02:35 < kanzure_> Supermassive electric motor? pleeease please please? 02:38 < willPow3r> get one of those that people put on electric motorcycles 02:45 < gene> anyone watch the debate? 02:45 < willPow3r> what debate 02:51 < kanzure> ? 03:19 < bkero> I did. 03:19 < bkero> You don't need a massive electric motor for a centriuge. 03:19 < bkero> You can use a rather tiny motor for it. 03:19 < kanzure_> you do for a massive centrifuge. 03:20 < bkero> I've got a $60 motor on ebay. It could spin a centrifuge the size of a small room. 03:20 < kanzure_> What mass is this small room? 03:21 < bkero> The masses in vials that go in centrifuges are usually negligable. 03:21 < kanzure_> Vials? 03:21 < kanzure_> They were talking about large nuclear warheads. Presumably the core materials would be the size of the original nukes, I'm guessing. 03:21 < bkero> Or whatever you're spinning 03:21 < kanzure_> That's far more than vials. 03:22 < bkero> Who was talking about it?d 03:22 < bkero> Oh, you mean the debates. 03:22 < kanzure_> Presidential debates. 03:22 < bkero> Yea, you could set something like that up for a couple hundred dollars. 03:22 < willPow3r> what the hell is a "presidential debate" 03:22 < kanzure_> I don't care about the price, we were talking about the ratio between size of the motor and the mass of the object to be spun. 03:22 < kanzure_> willPow3r: A load of shit. Ignore it. 03:23 < willPow3r> thats what i thought. thanks for thinking for me kanzure_ 03:23 < kanzure_> No problem. 03:23 < kanzure_> Seriously, that's an hour of my life that I want back. 03:23 < kanzure_> I could have been doing something more productive .. like watching House. 03:23 < bkero> Size doesn't have much to do with it. Wattage, advancing of the brushes, and RPM are the right criterions. 03:24 < bkero> Criteria, whatever 03:25 < bkero> They were referring to separating uranium out of things by using a centrifuge, right? 03:25 < kanzure_> I'm not entirely sure. 03:25 < kanzure_> Does it worry you too that neither of us know what they were talking about? 03:25 < bkero> Probably 03:25 < kanzure_> Huh. 03:26 < bkero> They're politicians. You can't expect them to know what they're talking about. 03:26 < kanzure_> Maybe it was just lab terminology they've picked up before. 03:26 < bkero> They appoint other people who appoint others who might have taken a class in that in community college 05:15 < emlyn> hey there 05:22 < bkero> Good evening. 05:22 * mindspillage waves 05:34 < gene> hello 05:36 < ybit> hi gene 05:36 < ybit> and goodnight to all 05:36 < willPow3r> nite 05:43 < bkero> Adieu. 06:43 -!- mindspillage is now known as mind|wandering 07:56 < faceface> I emailed GeneArt, but they seem to be on to me 07:56 < faceface> http://pastebin.com/d11c5f8a9 07:57 < faceface> i.e. fuck off you nozy bastard 14:17 < kanzure> grr, where are my glasses? 14:18 < kanzure> if they end up being on my face again I'm going to be so pissed. 14:19 < fenn> uranium comes in two isotopes, 235 and 238. you centrifuge solutions of uranium salts to separate the isotopes 14:19 < fenn> because one is heavier and denser 15:15 < bkero> Making some high grade uranium? 15:16 < bkero> faceface: company or institution? This man, Gunnar, has a rather narrow mind. Knowledge background? WHERE DID YOU GO TO SCHOOL SON, LETS SEE HOW SMART YOU ARE 15:23 < faceface> bkero, ? 15:23 < faceface> oh yeah 15:23 < faceface> sorry 15:23 < faceface> yeah... and lets see which company you work for!!! 15:24 < faceface> (but he has my number) 15:24 < bkero> I wonder how he would react if you said you were on your own. 15:26 < bkero> This guy is giving a talk today at GOogle. http://en.wikipedia.org/wiki/Prusiner 17:37 < xp_prg> hi all! 17:41 < xp_prg> anyone here? 17:41 < xp_prg> hi gene! 17:41 < gene> hello 17:41 < xp_prg> how are you today? 17:41 < gene> fine why do you ask? 17:42 < xp_prg> cuz I am new to this room and excited to be here :> 17:42 < gene> oh yeah 17:42 < kanzure___> ok, I need to run out, but could somebody link drop to the git repository, link drop to biobricks.zip, link drop to matweb.zip and newparts.zip or the small 600 KB part repository? There's some coding that has to be done that xp_prg might be interested in 17:42 < gene> you want to build a validator 17:42 * kanzure___ runs 17:42 < xp_prg> kanzure___ awsome I am here to help! 17:42 < gene> Shoot I don't know 17:43 < gene> but hey why use biobricks 17:43 < xp_prg> help to know the specifications of the desired script/program please 17:43 < gene> when you can use the NCBI protein database 17:44 < gene> and use parts from working replicators 17:44 < xp_prg> gene share your wonderful knowledge with me :> 17:44 < xp_prg> I have studied synthetic biology intently 17:44 < gene> I know some but not that much 17:44 < xp_prg> well share with me what you know :> 17:45 < gene> http://www.ncbi.nlm.nih.gov/ 17:45 < gene> type in whatever protein, dna sequence, paper, or function into search 17:46 < gene> and it will bring up many things 17:47 < fenn> some links 17:47 < fenn> http://heybryan.org/~bbishop/docs/matweb.zip 17:48 < fenn> http://heybryan.org/~bbishop/docs/prettyrepo.zip 17:50 < fenn> http://heybryan.org/gitweb.cgi 17:51 < fenn> i dunno about the rest 17:52 < fenn> gene: screw home depot, why not just dig around in a junkyard and get parts from working machines? 17:54 < gene> what do you mean? 17:54 < gene> you mean like sequence organisms to steal their dna? 17:55 < fenn> that's basically what you just said "why use biobricks when there's NCBI pdb" 17:55 < fenn> i wouldnt call it stealing though, unless you're a patent troll 17:55 < gene> heh 17:56 < gene> or you could go gene mining 17:56 < gene> go search caves and stuff for billion dollar bacteria 17:56 < fenn> why bother 17:57 < gene> Do you know what taq polymerase is? 17:57 < fenn> it's like going to the moon to get raw materials to build your shed 17:57 < gene> it's one of the best damn polymerases out there 17:57 < gene> it made PCR practical 17:57 < gene> before taq 17:57 < fenn> yes and soon the patent will expire 17:57 < fenn> and we will have a taq biobrick 17:57 < gene> you had to add polymerase after going through a thermal cycle 17:58 < gene> polymerases are expensive 17:58 < gene> this made PCR astronomically expensive 17:58 < fenn> bullshit.. it's bloodsucking patent lawyers that made them expensive 17:58 < gene> no 17:58 < gene> dude 17:58 < fenn> polymerases grow in sludge, on trees 17:58 < fenn> i've purified proteins, it's not that hard 17:59 < fenn> especially recombinant proteins 17:59 < gene> you need a lot of VERY FUCKING PURE polymerase for old PCR 18:00 < gene> PCR can amplify the DNA from a piece of paper that has been breathed on 18:01 < gene> so you don't want contamination 18:01 < gene> so someone gets the bright idea of using a polymerase from a microbe that lives in hot springs 18:01 < gene> in yellowstone 18:01 < gene> and made lots of money 18:01 < gene> so much now 18:02 < gene> that yellowstone doesn't let you take free samples anymore 18:02 < gene> so do you know how to purify taq? 18:03 < xp_prg> gene I wish I understood what your saying :( 18:03 < gene> DNA polymerase is a protein that copies DNA 18:03 < gene> polymerase chain reaction or PCR 18:04 < xp_prg> ok 18:04 < gene> is a technique for amplifying sequences of DNA 18:04 < fenn> he's just being contrary about biobricks, that's all 18:04 < xp_prg> it creates copies of certain sequences of DNA or the entire DNA? 18:04 < gene> entire DNA 18:04 < fenn> it falls off after a couple thousand kbase 18:04 < xp_prg> and how did tag polymerase help? 18:05 < xp_prg> fenn falls off? 18:05 < fenn> it can withstand high temperatures you need to separate the strands of dna for PCR 18:05 < gene> taq polymerase made PCR a lot cheaper 18:05 < fenn> falls off the strand of DNA 18:05 < fenn> and stops copying 18:05 < gene> you don't have to add new polymerase every cycle for the 100s of cycles that PCR goes through 18:06 < xp_prg> why does it take high temperatures to seperate stands of dna for PCR? 18:06 < xp_prg> stands = strands? 18:06 < fenn> that's how it works 18:06 < gene> I have no idea ask a chemist 18:06 < xp_prg> our bodies seperate strands of dna all the time and not at high temperatures right? 18:07 < gene> with unzipping proteins 18:07 < xp_prg> anyway so tag polymerase can do it at the high temperature without denaturing? 18:07 < fenn> they only separate a tiny length of dna 18:07 < fenn> for pcr you need to separate the whole molecule 18:07 < gene> yup 18:07 < xp_prg> nice 18:07 < gene> that's what taq is good for 18:09 < gene> it comes from Thermus aquaticus which can survive at up to 80 deg c 18:09 < xp_prg> nice man! 18:10 < fenn> so xp what do you do? 18:10 < nsh> retrobseletes vista, mostly 18:11 < fenn> thought that was 2k 18:11 < bkero> What's XP? Vista? 2k? What are all these things? 18:11 < bkero> Are you guys taking about software or something nerdy like that? 18:12 < fenn> bkero: voodoo curses 18:12 < bkero> Ew. I wouldn't want anything like that. 18:12 < fenn> me either 18:12 < bkero> So are they just to punish people or something? 18:13 < gene> what vista 18:13 < gene> ? 18:13 < gene> yes 18:13 < fenn> the are sort of like succubi that control the people who succumb to them 18:13 < gene> I run it, I can't stop running it 18:13 < fenn> and then spread to family members and co-workers like a plague 18:13 < xp_prg> I am a software engineer 18:13 < xp_prg> BSCE, MSCS, and MB A 18:14 < fenn> yes but what do you _do_ 18:14 < xp_prg> web development with python, postgres, javascript, html etc... right now 18:14 < fenn> ever worked with django? 18:14 < xp_prg> no not yet 18:15 < gene> can you reverse engineer code with lots and lots of goto statements? 18:15 < fenn> one thing i'd like is a "thing" that is sort of a combination of wiki, cad DB, and git repo 18:15 < fenn> i was looking at django for building it 18:16 < xp_prg> gene reverse engineer it how, if you have the goto statements do you not have the code? 18:16 < gene> it was a figurative question 18:16 < fenn> the only reverse engineering we do around here is file formats 18:17 < fenn> well, and some pesky javascript 18:17 < gene> genetic code tends to have lots of "goto" statements 18:17 < gene> if you could call them that 18:17 < fenn> i wouldnt call it that 18:18 < gene> I am not that familiar with programming 18:18 < gene> AFK 18:18 < fenn> "spaghetti code" is definitely applicable however 18:19 < fenn> (biobricks are much better in this sense of course) 18:23 * nsh makes nondescript noises 18:24 < xp_prg> hi nsh :> 18:25 < nsh> hey 18:26 < nsh> i'm trying to figure out how to make this university webmail save sent messages 18:26 < nsh> why the fuck would it have a sent messages folder but not save them by default?! 18:29 < fenn> why are you using webmail? 18:39 < nsh> couldn't be bothered to set up a mail client 18:39 < nsh> been waiting for a new external so i can backup my data and install a decent OS 18:40 < nsh> "Mendelsohn et al.’s study is important because it demonstrates that hypnotic suggestions influence brain activity, not just behavior and experience." --http://www.sciam.com/article.cfm?id=hypnosis-memory-brain&print=true 18:40 < nsh> wtf is that shit!? 18:40 < nsh> how the fuck do you influence behavior and experience without influencing brain activity!? 18:40 < nsh> they need to not let idiots write for scientific american 18:41 < nsh> (next sentence: "Hypnotic effects are real!") 18:41 < nsh> idiot. 18:45 < fenn> i guess someone didnt get the memo back in 1920 18:46 * nsh smiles 18:52 < xp_prg> so can anyone tell me more synthetic biology stuff that will help me to make my program etc.. ? 19:14 < kanzure_> xp_prg: fenn already mentioned it to you 19:14 < kanzure_> you seem to have ignored him. 19:19 < xp_prg> you mean the pcr stuff? 19:19 < fenn> well, not really. the biohack.sf.net is mostly technical "how to" info, but he wants more theoretical overview i think 19:19 < fenn> also it's 500MB download :{ 19:20 < fenn> xp_prg: i guess wikipedia is a good place to start 19:20 < xp_prg> I don't beleive I have concrete requirements for the scripts you want me to create, can anyone be specific? 19:21 < fenn> i dont know what scripts you're talking about 19:21 < kanzure> fenn: ikiwiki + git + package/repo analysis stuff 19:21 < kanzure> i guess 19:21 < kanzure> you were mentioning it above 19:22 < kanzure> (2008-10-08 13:19:09) fenn: one thing i'd like is a "thing" that is sort of a combination of wiki, cad DB, and git repo 19:22 < kanzure> (2008-10-08 13:19:24) fenn: i was looking at django for building it 19:22 < fenn> well, it's sorta dependent on the skdb file format 19:22 < kanzure> (and I was also looking at django - I have some logs of talking with ##django and ##python people about it, and they suggested django wasn't really fit for this yet) 19:22 < xp_prg> kanzure are you bryan bishop? 19:22 < kanzure> yes, this is true 19:22 < kanzure> xp_prg: yes 19:22 < kanzure> for the moment we can laugh at the dot repo file format 19:22 < kanzure> there's obvious improvements to be made there, no? 19:23 < kanzure> like it hardly allows for multiple connections between artifacts and other cyclic or acyclic graphs :( 19:23 < fenn> or quantitative descriptions of 'flows' 19:23 < kanzure> ugh 19:23 < fenn> i hate the whole flow concept anyway 19:23 < kanzure> I just had a query that I was using today 19:23 < kanzure> it turned out that the 'flows' table in the mysql db was not filled in 19:24 < kanzure> because of a typo in my perl script that was processing my 'all.repo' file 19:24 < xp_prg> kanzure I am still not clear exactly what you want me to work on, can you possibly give me a small project to get started, on, the one you just mentioned seems immense 19:24 < kanzure> (all.repo is really just the 600 KB newrepo.zip thingy cat * > all.repo ) 19:24 < xp_prg> I want to work up to the immense projects as I go :> 19:24 < fenn> xp_prg: we've been using ikiwiki to provide a web frontend for git, but ikiwiki kinda sucks in general 19:24 < kanzure> ikiwiki is hitting pretty close to the mark though :) 19:24 < fenn> so it'd be nice to have some script that updates a git repo via wiki-ish interface 19:25 < kanzure> k, I need to run again 19:25 < kanzure> was just back for a few seconds. 19:26 < xp_prg> kanzure so can you tell me what you want me to code please? 19:26 < fenn> for example i might edit a text file from the web, save it, then edit a local copy in my text editor and push that to the git repo, and the edit should show up on the web interface 19:26 < fenn> (actually i'd have to merge the edit somehow) 19:26 < fenn> do you see what we're going at? 19:27 < xp_prg> you want me to assist with a wiki front end for git? 19:27 < fenn> this way i can easily fork the whole wiki 19:27 < fenn> yes 19:27 < xp_prg> I hate to say it but that doesn't interest me, I want to do synthetic biology type code like with bio perl etc... 19:27 < kanzure> but don't make it sound so crude. it has direct applications to the synthetic biology project 19:27 < kanzure> how do you think it's NOT for the synthetic biology stuff? 19:27 < kanzure> would you rather do the synthetic biology circuit creator ajax frontend? 19:27 < xp_prg> ya 19:27 < kanzure> that has to link up to the ikiwiki+git repo interface stuff though 19:28 < xp_prg> what is ikiwiki written in? 19:28 < fenn> as long as it can push to a git repo it doesnt matter if the wiki stuff is done yet 19:28 < fenn> ikiwiki is perl and uses markdown format (no way to switch wiki formatting or use other file types) 19:28 < xp_prg> nice so it is perl! 19:30 < kanzure> there's even repo files already made 19:30 < kanzure> including biobrick files too 19:30 < kanzure> so there's some starting material to work from 19:30 < kanzure> insert link here to the graph-easy or graph-demo link from the bloodgate link or something as an example of what it might look like 19:30 < kanzure> or fenn's mockup screenshot 19:31 < fenn> honestly if you arent already familiar with bioinformatics, the biobrick stuff will just be confusing 19:31 < xp_prg> fenn I am familiar with biobrick stuff 19:31 < fenn> but you dont even know how PCR works 19:31 < xp_prg> they are polypeptide sequences that do novel things inside of a cell 19:32 < xp_prg> actually I do, just needed a refresher was all 19:32 < fenn> hrm 19:33 < fenn> lol @ my mockup: http://fennetic.net/pub/irc/skdb-mockup/select-icon.png http://fennetic.net/pub/irc/skdb-mockup/select-edge.png 19:34 < fenn> is that the 'ajax circuit creator'? 19:35 < xp_prg> cool fenn! 19:36 * bkero just sat through a tech talk from this guy: http://en.wikipedia.org/wiki/Prusiner 19:42 < xp_prg> feen can you give me a simple use case scenario I can work on for the ajax circuit creator please? 19:46 < xp_prg> fenn do you have a perference for the ajax libraries, such as jquery, dojo, scriptaculous etc... ? 19:47 < fenn> no i generally hate java equally in all its incarnations 19:47 < xp_prg> ajax uses javascript fenn :> 19:47 < fenn> yes i am aware of that 19:47 < xp_prg> unless you want me to write in flash which is not opensource nor free 19:47 < fenn> and java is preferable to flash 19:48 < xp_prg> so I have to use javascript and I would prefer to use one of the ajax toolkits that are opensource/free, which one would you like me to use? 19:48 < xp_prg> my preference initially is jquery 19:48 < fenn> ok, i'm pretty ignorant of java libraries so whatever you think is best 19:49 < xp_prg> ok, fenn, may I ask what you do etc... ? 19:49 < fenn> i whine on the internet 19:49 < xp_prg> I would like to get a better feel for who my project manager/knowledge expert is :> 19:50 < fenn> i'm dismayed at the primitive state of industrial technology and working on my own to fix it 19:50 < xp_prg> what do you do for a living? 19:50 < fenn> with various open source cad and robotics projects 19:50 < fenn> i'm trying to figure that out right now :) 19:51 < fenn> i've done some linux sysadmin stuff in the past but it's bad for my mental health 19:51 < xp_prg> so you don't have a job currently? 19:52 < fenn> and there's not much in the way of employment around here except for university teaching and restaurants 19:52 < fenn> no, i'm thinking about working at the local coop grocery 19:52 < xp_prg> well that is cool, I don't care, just wondering :) 19:52 < xp_prg> how old are you fenn? 19:52 < fenn> 26 19:52 < xp_prg> do you have a degree? 19:52 < fenn> yes, BS microbiology at indiana university 19:52 < xp_prg> cool man 19:52 < fenn> but they didnt teach me what i wanted to know :( 19:53 < xp_prg> I know the feeling for sure 19:53 < xp_prg> fenn, can you please help me to know where to start a wiki for my project? 19:53 < fenn> i dont understand the question? 19:53 < fenn> you want web hosting? 19:53 < xp_prg> well, don't we have a wiki page for the project somewhere? 19:55 < fenn> i'd say make a new wiki page and link to it from here: http://heybryan.org/mediawiki/index.php/Skdb 19:55 < xp_prg> where do we make the wiki page exactly? 19:55 < fenn> a page with the name as your project 19:56 < xp_prg> what shall we call the project I am working on wiki notation? 19:57 < fenn> how bout 'biobench' 19:57 < fenn> BioBench if you prefer camel case :) 19:57 < xp_prg> fenn go ahead and make it :> 19:58 < fenn> make a wiki page for you? 19:58 < xp_prg> ya 19:58 < fenn> why? 19:58 < xp_prg> so we can get started :> 19:58 < xp_prg> I don't know where to place it on that big big page 19:58 < fenn> ugh 19:58 < fenn> that page needs split up anyway 20:01 < fenn> ok bullet point Connect the pieces... http://heybryan.org/mediawiki/index.php/Societal_engineering_knowledge_database#Getting_started 20:01 < procto> xp_prg: I forget, you're william heath, right? 20:02 < xp_prg> yes 20:02 < procto> xp_prg: also, how do you get "tim" out of "william"? is it your middle name? 20:02 < xp_prg> no it is a nick name 20:02 < procto> <-- Mike K 20:02 < procto> not to sound prejudiced, but nicknames aren't usually completely ordinary names 20:02 < procto> I believe you, but is there a circumstance/story? 20:03 < procto> you know, like, someone might be nicknamed "limpy" 20:03 < procto> usually though, people aren't nicknamed "stephen" 20:03 < xp_prg> cool man! 20:03 < procto> I'm just curious :> 20:05 < xp_prg> procto what do you do? 20:05 < xp_prg> fenn did you make the wiki page yet? 20:06 < fenn> yep just click on biobench 20:06 < fenn> an uncreated wiki page will just prompt you to add some content 20:08 < xp_prg> awsome fenn! 20:08 < xp_prg> fenn, one last thing I really, really need your help with, a simple use case scenario I can try to implement using biobench 20:09 < bkero> xp_prg: write it using openlazlo 20:09 < xp_prg> openlazlo is what exactly, php? 20:09 < bkero> It's own language 20:09 < bkero> fenn: Hey man, are you still in IN? 20:10 < fenn> yes 20:10 < procto> xp_prg: for work or in general? 20:10 < xp_prg> all of the above :> 20:11 < procto> xp_prg: I'm a software engineer, working in the hedge fund industry. I'm also finishing up my undergrad degrees in linguistics and computer science 20:11 < fenn> xp_prg: i'm probably not the best person to ask about bio circuit stuff.. that's more of kanzure's area 20:11 < xp_prg> nice procto 20:11 < xp_prg> kanzure you here? 20:14 < bkero> fenn: What city? 20:14 < bkero> xp_prg: openlazlo is a programming language that generates flash output 20:14 < xp_prg> wow really? 20:14 < bkero> Yea 20:14 < xp_prg> that sounds cool 20:15 < fenn> bkero: bloomington 20:15 < xp_prg> is it free and opensource? 20:15 < bkero> We use it for the huge monitor systems at work 20:15 < bkero> fenn: I know the guy who runs the huge supercomputer up there. 20:15 < bkero> Do you want me to ask him if he has any positions available? 20:15 < fenn> i probably know him too :) 20:15 < bkero> Corey Shields 20:15 < fenn> hmm nope 20:15 < bkero> Apparently he's pretty high up 20:15 < bkero> He used to be my boss at the OSU Open Source Lab. 20:15 < bkero> He graduated from IU, and went back there for work. 20:16 < fenn> i wonder if they'd want a scruffy hacker like me 20:16 < bkero> YES 20:16 < fenn> alrighty then 20:16 < fenn> yes please put in a word for me 20:16 < bkero> Corey's the guy who would come in at 2AM after all the servers are down, carrying a 6 pack of red bull and start DigitallyImported 20:16 < bkero> He's on freenode. :P 20:16 < fenn> i have a sort of resume thingy around here tailored for computer jobs 20:18 < bkero> fenn: He msg you? 20:18 < bkero> http://www.indiana.edu/~uitshr/services/jobs/IUBhourly.html 20:19 < bkero> Are you hot shit at databaess? :P 20:20 < fenn> uh, i can use the mysql command line :) 20:20 < fenn> i know what "select" does 20:20 < fenn> he didnt msg 20:20 < bkero> I don't think that's going to be enough 20:20 < bkero> I guess he just wanted to point you at that. 20:22 < fenn> $8.75 and a commitment for 1 year? why bother 20:22 < fenn> at least the grocery store gives me free food 20:23 < bkero> So you don't have to work at a grocery store. :P 20:23 < fenn> how am i supposed to be 'hot shit' at databases when everyone wants an "experienced senior database developer" 20:24 < bkero> Gain experience outside of work? 20:25 < fenn> databases are so stupid and simple, so why does experience matter so much 20:26 < bkero> It's not designing the database that's the problem. It's making relational table structures and writing an application around them. 20:26 < fenn> experience is much more important with programming languages because there are vast numbers of application specific libraries to get acquainted with 20:27 < fenn> database is just tables and more tables 20:28 < fenn> did you know the US spends $750 billion on education? 20:28 < fenn> that's more than the military budget 20:29 < bkero> Uh 20:29 < bkero> That doesn't sound right. 20:29 < fenn> i was surprised too 20:29 < bkero> Military spending is roughly half of our federal budget 20:29 < bkero> It can't be more 20:30 < fenn> military budget is about $650B including the iraq war 20:33 < fenn> here is my source: http://en.wikipedia.org/wiki/Image:2005education_spending.PNG 20:34 < fenn> apparently americans spend a lot of money: http://en.wikipedia.org/wiki/Image:2005military_spending.PNG 20:34 < fenn> (spent) 20:34 < bkero> Seems the budget 2009 numbers are $515.4 billion military 20:35 < bkero> 2004 education was $827 billion 20:35 < fenn> they usually leave off the iraq war addition for some reason 20:36 < fenn> maybe it will be over by then eh? :) 20:36 < fenn> anyway not a huge dent in the beast 20:36 < xp_prg> where is kanzure? 20:36 < fenn> probably in class 20:37 < bkero> iraq is $10 billion per week 20:37 < bkero> fenn: Are you still in school? 20:37 < fenn> no 20:38 < fenn> i was just wondering why IU pays their employees so badly 20:38 < bkero> Don't want to work for a lab? 20:38 < bkero> If you feel like moving to montana I could get you a job in a university pharmsci lab. 20:38 < bkero> Because those are student jobs :P 20:39 < fenn> i feel like moving to iceland or thailand 20:39 < fenn> but i dont really have that planned out yet 20:39 < fenn> so, montana is a bit of a step backward 20:39 < fenn> cold, uncultured 20:40 < bkero> uncultured? 20:40 < fenn> relatively 20:40 < bkero> In what ways? 20:40 < bkero> The only time I've heard somebody calling something uncultured was some of these snobs in New York calling everything outside of New York uncultured. 20:41 < fenn> montana is mainly based on ranching 20:41 < fenn> any sort of movement towards automation, vegetarianism, or liberal politics, generally goes against what ranchers believe in 20:41 < bkero> Er 20:42 < bkero> I didn't say rural montana. 20:42 < fenn> feel free to correct me 20:42 < bkero> http://en.wikipedia.org/wiki/Missoula liberal bastion 20:42 < fenn> we have the same problem in indiana, more or less 20:43 < fenn> furthermore, the cold environment makes it difficult to live, encouraging monogamy and conservative politics 20:43 < fenn> why is missoula liberal do you think? 20:43 < bkero> I grew up there 20:44 < bkero> Jeannette Rankin's politics. She's got a small nonprofit there that lobbies against city hall. There's also a well respected liberal arts college, and a relatively large amount of people. 20:45 < fenn> there are these islands of liberality, austin, bloomington, missoula 20:45 < fenn> i havent really figured out why they exist 20:45 < xp_prg> fenn what is your name for the wiki? 20:45 < bkero> Population fluxuates up to around 120,000 when school is in session. 20:45 < fenn> xp_prg: i didnt log in 20:45 < bkero> fenn: Try ann arbor. I've researched it, and realy want to visit. 20:45 < xp_prg> no I need it for the participants area 20:45 < fenn> minneapolis is another one 20:46 < xp_prg> Fenn? 20:46 < fenn> yes? 20:46 < xp_prg> What is your name? 20:46 < fenn> my legal name? 20:46 < xp_prg> ya 20:47 < fenn> may i ask why? 20:47 < bkero> Sir Bender Bending Rodriguez 20:48 < xp_prg> http://heybryan.org/mediawiki/index.php/BioBench 20:49 < fenn> ok, it's a start 20:50 < bkero> My name is Bender Karma Ego Rodriguez Orange 20:50 < fenn> no relation :) 20:50 < fenn> we're 47th cousins 20:51 < xp_prg> fenn can you please add your name to it? 20:51 < fenn> i'm suspicious when someone wants to put my name on their project 20:51 < xp_prg> I don't care, its ok if you don't want to :> 20:51 < fenn> i have enough unfinished projects as is 20:52 < bkero> ajax spice? 20:52 < fenn> spice is an electrical circuit simulator 20:52 < xp_prg> pretty much bkero :> 20:52 < xp_prg> right 20:52 < bkero> Have you ever used spice? 20:52 < xp_prg> yes in my undergrad 20:52 < fenn> i thought it was command line, or batch oriented or something 20:52 < fenn> i.e. no interface 20:52 < xp_prg> ajax != command line 20:53 < bkero> SPICE is a giant application for circuit design 20:53 < bkero> IIRC 20:53 < bkero> Or else it's a standard that applications model around 20:58 < kanzure___> hm. I think I know a good first step. maybe I'll write a quick black box diagram generator. dynamic generator, at least, something in php to export to the dot/dia library routines, since the database is otherwise kind of difficult to understand properly at the moment. 20:59 < xp_prg> Kanzure did you see my project wiki?! 21:00 < kanzure___> procto: scriptalicous works ok for javascript/ajax crap 21:00 < xp_prg> kanzure___ do you like my wiki page? 21:01 < kanzure___> use case scenario: a user has a project that he wants to make out of biobricks. so the circuit creator app has to let him draw up a black box, it has to fill in the gaps and connect how things are going to connect, and then it has to fill in with actual parts from the biobrick repository. 21:01 < kanzure___> which is given on the server 21:01 < fenn> that's a rather vague use case 21:01 < xp_prg> ya I need a real use case, like a real project but extremely simple for the first one etc... 21:02 < kanzure___> you have the files. 21:02 < kanzure___> it's a drop down menu more or less 21:02 < kanzure___> or a list of things to select from 21:03 < kanzure___> drawn from reading the on-server directory of possible parts or components that they can select from 21:03 < kanzure___> *ideally* it shows them all possible components that satisfy some given constraints ... like 'it needs to be given xyz' and then all parts that match 'takes xyz input' will be turned up in the list 21:03 < kanzure___> the user would then proceed to select something from the list, and that should be added to the circuit 21:04 < xp_prg> kanzure___ I wish we had a blog to put these ideas in, or this channel logged? 21:04 < kanzure___> channel is logged 21:05 < xp_prg> kanzure___ what your describing is ideal for prolog on the back end 21:05 < kanzure___> no it's not. 21:05 < xp_prg> why not? 21:05 < kanzure___> because you wanted to do the frontend. 21:06 < xp_prg> oh ok, right, but it will required back end invocations for the different steps your talking about 21:06 < xp_prg> I don't think you want all data existing in javascript do you? 21:06 < xp_prg> ajax by definition communicates with the server 21:07 < kanzure___> correct 21:07 < kanzure___> but I'm not about to do the backend in prolog 21:08 < xp_prg> why not?! ;) 21:08 < kanzure___> prejudice. 21:09 < xp_prg> well it will use ajax json, so the back end can be implemented in any way since it is loosley coupled :) 21:12 < xp_prg> kanzure___ what is your preference on the back end? ruby on rails or something? 21:20 < kanzure___> no, I'll do some perl, it's okay 21:21 < xp_prg> kanzure___ you going to use catalyst or jifty? 21:21 < fenn> hey we could even have multiple constrain engines as long as the file format is well specified 21:22 < kanzure___> sure 21:22 < kanzure___> I haven't heard of catalyst/jifty yet 21:22 < kanzure___> uhh 21:22 < kanzure___> question 21:22 < kanzure___> why in the all.repo file is there the subfunction element that has inputartifact and outputartifact? 21:23 < kanzure___> I ask because the subfunction element is a child to the artifact element 21:23 < kanzure___> the inputartifact and outputartifact variables are properties to the subfunction element. 21:23 < kanzure___> this doesn't really make much sense to me. since I'm figuring which variables to select for in the db to make the black box generator. kinda important. 21:24 < kanzure___> it'd make sense if the subfunction inputartifact was its parent 'artifact' element in the XML, that would make (some) sense, but the fact that the inputartifact ID is not its parent ID is cause for concern 21:27 < fenn> whois cshields 21:27 < fenn> oops 21:27 < kanzure___> in fact, in one case, look at the subfunctions with SubInputArtifact='counter wheel' .. it's not until a few products down in the all.repo file do you see an artifact with the name 'counter wheel' 21:27 < kanzure___> so that 'counter wheel' artifact isn't even in the friggin' product 21:27 < kanzure___> what's going on? 21:29 < fenn> where is this all.repo file? 21:30 < kanzure___> oh wait, I'm wrong. yay. the 'counter wheel' is in fact in the same 'system'/product. yay. 21:30 < kanzure___> uh 21:30 < fenn> counter wheel is a subfunction of the camera.repo 21:31 < kanzure___> don't need subfunction .. apparently there is an artifact with property ArtifactName="counter wheel" in that same system / that single file, so it's a moot point now 21:31 < kanzure___> panic attack over. 21:31 < kanzure___> all.repo is uh, nonexistent 21:31 < kanzure___> just do cat *.repo > all.repo 21:32 < kanzure___> only with the repo files from prettyrepo.zip 21:32 < xp_prg> http://courses.ece.uiuc.edu/ece442/PSPICE%20Tutorial.htm 21:32 < kanzure___> don't bother with the massivei mage files 21:32 < kanzure___> *massive image files 21:32 < xp_prg> check this out kanzure____ this is kind of what I envision for the interface etc... 21:32 < kanzure___> okay, that's one lab meeting down 21:32 < kanzure___> another one to go 21:32 < kanzure___> xp_prg: ask fenn. I trust him on this one .. 21:32 < kanzure___> I'll be back 21:32 < kanzure___> eventually? 21:32 < fenn> counter wheel is also an artifact 21:33 < fenn> lol dont try to pass the buck 21:34 < ybit> bkero: what did stanley prusiner speak about? 21:35 < fenn> xp_prg: the problem is that electrical components are all easily classified and you can use symbols and a small set of parameters to describe them 21:35 < xp_prg> kanzure___ I need a concrete use case scenario please!!!!! 21:35 < fenn> xp_prg: ok here's a use scenario, you want to hook up an environmental toxin sensor to a firefly luciferase gene 21:36 < fenn> but also you want it to NOT light up when in the presence of some other chemical, and you also want a 'test' mode so it lights up in the presence of your test chemical 21:36 < fenn> this is an e. coli cell with a plasmid in it probably 21:37 < fenn> make sense? 21:37 < xp_prg> ya but is that the simplest use case scenario you can come up with, that sounds extremely complex :( 21:37 < fenn> well i don't want it to just be a->b 21:38 < xp_prg> why not for the first scenario? 21:38 < xp_prg> the first scenario is extremely simple for now 21:38 < fenn> because that's too easy and you won't be thinking about it right 21:38 < xp_prg> then it gets more complex 21:38 < xp_prg> ok 21:38 < fenn> we dont want notepad 21:38 < xp_prg> fenn can you please document the use case senario on the wiki page you want me to implement? 21:39 < fenn> god this is starting to sound like work 21:39 < xp_prg> fenn well I need you to at document it :) 21:40 < xp_prg> at least 21:43 < fenn> malaysia? 21:44 < xp_prg> fenn did you document it? 21:44 < fenn> no i am slow (i hate mediawiki because it is so slow to use) 21:45 < xp_prg> well red1 can you assist? 21:45 < xp_prg> red1 can you add the scenario 1 requirements to the projec tpage wiki? 21:45 < red1> scenario 1.. ? 21:46 < red1> i m watching the youtube... to get a slice of spice or whatever u guys do :> 21:47 < xp_prg> http://heybryan.org/mediawiki/index.php/BioBench 21:47 < xp_prg> red1 please reformat that 21:47 < red1> to what? 21:47 < xp_prg> some that is not looking like a chat script copy/paste :) 21:48 < xp_prg> fenn can you please elaborate on what he gui will look like to implement scenario I? 21:48 < xp_prg> he - the 21:48 < red1> it looks fine... for a start 21:48 < red1> thats how all things start as 21:49 < red1> a little dot 21:49 < red1> then dots 21:49 < red1> then u join the dots 21:49 < red1> then u paint areas 21:51 < red1> bio as in biology huh? 21:51 < red1> creating life somewhere along the way? 21:52 < xp_prg> ok red1 check it out now! 21:52 < red1> checking.. 21:53 < red1> what does those PNG images mean? Select edge.. 21:54 < red1> frantically looking anywhere... armed with mouse here 21:55 < xp_prg> don't know, need Fenn to explain 21:57 < xp_prg> red1 updated wiki re-check if you want :> 21:58 < fenn> sigh.. merge 21:58 < xp_prg> red1 can you put a link to the bio bricks project on that page? 21:58 < fenn> another reason i hate mediawiki 21:59 < xp_prg> fenn, can you pretty please tell me more about the user interface navigation you would expect to solve scenario I ? 22:01 < red1> hi fenn .. i dont know what to hate... they re just tools, but they get better... when i am older :> 22:01 < fenn> xp_prg: http://heybryan.org/mediawiki/index.php/BioBench 22:01 < xp_prg> sweet dude!!! 22:03 < fenn> nevermind that we just contaminated our well with e. coli 22:05 < xp_prg> fenn I like your ideas for the interface! 22:06 < xp_prg> just out of curiousity, what should be the output in your opinion, is there a standard like dna sequence into a cell file type? 22:07 < fenn> this would call some compiler targeting DNA, and using biobricks "source code" 22:08 < fenn> there's a couple standard DNA file formats, FASTA for example 22:08 < fenn> but that's a sequencing format, not a oligo request format 22:09 < xp_prg> fenn so some where in the interface is like a compile button right? What is the output of that action specifically? A file right? 22:09 < fenn> hmm actually i think biobricks does standard recombinant dna stuff.. sigh 22:09 * fenn feels like he's stuck in the stone age 22:09 < fenn> so it's not so straightforward, you have to specify how to mix vials of liquid and shake them etc 22:10 < fenn> honestly i have no idea what the output is 22:10 < xp_prg> fenn can you please tell how the file should look in this scenario I? 22:10 < fenn> but it's not a DNA sequence 22:11 < ybit> seems that while i was napping, me mum attempted to use this comp. did bkero respond? 22:11 < fenn> probably some special purpose language that hasn't been invented yet 22:11 < fenn> ybit: no 22:11 * ybit is needed at a b-day party, bbl 22:11 < ybit> k thx 22:11 < xp_prg> well its a specification for a lab right? It will have 1 ecoli cell, the tranlucent dna sequence in the plasmid starting at a certain area of the dna rigt? 22:12 < fenn> yeah but there's a lot of other crap that needs to be hooked up in the right order 22:12 < xp_prg> like what? 22:12 < fenn> like promoters and binding sites 22:13 < fenn> um, i forget how sensor proteins are supposed to work 22:14 < fenn> this is the standard example sensor system: http://en.wikipedia.org/wiki/Lac_operon 22:15 < bkero> ybit: I didn't respond. Prusiner talked about how he identified prions, and used their presence as an assay for finding diseases like alzheimers. 22:15 < bkero> and kreutzfeldt-jakobs disease 22:16 < xp_prg> fenn check out the wiki page now 22:16 < xp_prg> under output specifically 22:17 < xp_prg> well I have to go to lunch, feel free to add/change the wiki page! 22:18 < xp_prg> I think we have enough now to at least start the prototype! 22:18 < red1> interesting.. 22:18 < xp_prg> I would love it if you could spell out exactly where I am to get the info I need 22:19 < xp_prg> red1 feel free to pretty up the page too :> 22:19 -!- xp_prg is now known as xp_lunch 22:19 < red1> will do that.. if every1 agrees... if not just revert 22:23 < red1> just edited.. so pls refresh before proceeding 23:02 < xp_lunch> nice red1! 23:02 < xp_lunch> fenn you here? 23:03 < red1> i still have no idea what u re doing here xp_lunch :> 23:03 -!- xp_lunch is now known as xp_prg 23:03 < xp_prg> building cells that do novel things 23:03 < red1> i do like DNA stuff toh... NDR = nano... dna .. robotics 23:03 < red1> as in DNA engineering? 23:04 < xp_prg> yes but more then DNA engineering, DNA engineering with a purpose 23:05 < xp_prg> the DNA is put in the cell and actually funtions and does things! 23:06 < fenn> doesnt all DNA engineering have a purpose? 23:06 < xp_prg> I guess so fenn :> 23:06 < xp_prg> but some are for drugs etc... 23:06 < xp_prg> this is for cells and to do specific things inside of cells etc... 23:06 < fenn> the idea here is a "design compiler" so you dont have to bother with the gritty details over and over again 23:06 < xp_prg> fenn I need your help, help me to understand exactly where I will pull the info to display etc... 23:07 < xp_prg> do I get it from biobricks.zip? 23:07 < fenn> um, i think so 23:07 < fenn> there are multiple places that host the biobricks db i think 23:07 < xp_prg> so you know know exactly where I get the info? 23:07 < fenn> no 23:07 < red1> so what u mean is that this DNA purpose is specific to be progammable at a componentised level? 23:07 < xp_prg> yes red1 23:08 < red1> woooo .. far out! 23:08 < red1> DNA machine 23:08 < xp_prg> it basically turns a cell into a computer 23:08 < fenn> DNA engineering is only a small subset of the whole project though 23:08 < red1> ok ok.. should i go on my knees and bow? :D just joking! 23:08 < fenn> there's all the rest of engineering too 23:08 < xp_prg> fenn I am hurting over here, I can't even begin to code this without knowing where to pull the info 23:09 < red1> now i get it.. biobricks 23:09 < red1> fenn: be patient with xp_prg .. he is like that in our #adempiere ... only at first.. when he grasp it, he becomes one of our supermen 23:10 < red1> thats why i always help him out whenever i can 23:10 * xp_prg bows in honor to red1 23:10 < red1> in return for his favours 23:10 < fenn> xp_prg: i think this is where you can access biobricks API http://heybryan.org/~bbishop/docs/biobricks/notes.txt 23:10 < xp_prg> red1 can you add that to the wiki? 23:10 < red1> xp_prg will definitely do a movie on this soon, i can tell :P 23:10 < xp_prg> indeed I will :> 23:11 < red1> i will revisit later.. i got to finish my rounds... 23:11 < xp_prg> ok 23:11 < red1> helping a hand cannot be intrusive u know 23:11 < red1> its a little a day.. 23:12 < red1> but tell me... is this biobricks thingy dealing with real as in real life cells? 23:12 < kanzure> hi all 23:12 < red1> or just virtual ones? 23:12 < fenn> right now it's in test tubes 23:12 < kanzure> red1: hey there 23:12 < kanzure> let me read the log 23:12 < fenn> real test tubes 23:12 < red1> hola kanzure 23:12 < fenn> getting the DNA into a cell is sort of a pain you see 23:13 < red1> ah .. bioinformatics... heard of that before 23:13 < red1> now i am getting it 23:13 < xp_prg> kanzure please help me, I am almost finished with my first scenario spec! 23:14 < xp_prg> I need to know how to get the information now 23:14 < fenn> bioinformatics is just database mongering really 23:14 < red1> its the tremendous computing power needed in such projects 23:14 < xp_prg> kanzure can you help me to flesh that out? 23:14 < xp_prg> http://heybryan.org/mediawiki/index.php/BioBench 23:14 < xp_prg> check this out! 23:15 < kanzure> xp_prg: you get the info you need from the biobricks repository that fenn has linked to. 23:15 < xp_prg> kanzure but does it have an api, how do I interface with it? 23:16 < kanzure> you have to make up the api 23:16 < kanzure> this is why the biobrick people suck 23:16 < kanzure> you have to go look at the files and determine an api for yourself 23:16 < xp_prg> so I have to use web screen scraping? 23:17 < kanzure> no 23:17 < red1> i would like to be the first to make an API in such a cool project :> 23:17 < kanzure> the files are already on the server 23:17 < kanzure> red1: I suggest you wait a few minutes then 23:17 < xp_prg> please explain the format of these files 23:17 < red1> talking from a person who neve did any 23:17 < kanzure> red1: xp_prg is taking a small chunk of a broader project 23:17 < kanzure> red1: so the API in general is about the parts repository .. not biobricks. but anyway. xp_prg first. 23:17 < red1> xp_prg: firstly... what draws u here? U havent told me yet 23:17 < kanzure> xp_prg: I do not know the format of the files, that's what you'll have to do 23:18 < xp_prg> kanzure can you at least identify the files needed for this first scenario? 23:18 < kanzure> red1: we do crazy things here like do-it-yourself free open source automated manufacturing, kinematic self-replicating machines, ass kicking, brain augmentation, transhuman projects, O'Neill stuff, etc. 23:18 * fenn hasnt seen any ass kicking yet 23:18 < kanzure> xp_prg: it's in the biobricks.zip file. the 'lac operon' that fenn linked to should be on http://partsregistry.org/ which is a web interface to biobricks.zip 23:18 * kanzure kicks fenn's ass 23:18 < fenn> ow! 23:19 < xp_prg> red1 what draws me here is the potential to do computation biologically instead of with silicon 23:19 < red1> yeah .. i seen your previous work... hmm .. was it AI? 23:19 < xp_prg> kanzure can you at least give me some links on the web interface to bio bricks where the info I need is? 23:19 < red1> oh yes YAP 23:19 < kanzure> shit, you guys, have you not even listened to me about how you're not going to be able to do computation with DNA much? 23:20 < kanzure> I was in a lab over the summer exploring that topic 23:20 < red1> what will be their application for our business app , xp_prg ? 23:20 < xp_prg> no kanzure 23:20 < kanzure> silicon is going to be faster 23:20 < kanzure> the only thing that biology is good at computing is *generative* designs/structures/building-shit 23:20 < kanzure> xp_prg: http://partsregistry.org/ I already told you. 23:20 < xp_prg> kanzure the brain is still superior to silicon based computers though :> 23:20 < kanzure> and biobricks.zip has the actual files. 23:20 < kanzure> xp_prg: what for? 23:20 < kanzure> xp_prg: in what sense is it superior, I mean 23:20 < xp_prg> kanzure yes but where on partsregistry.org? 23:20 < fenn> computers just have crappy software imho 23:20 < kanzure> xp_prg: look around and click 23:20 < xp_prg> every way 23:20 < kanzure> xp_prg: what are those ways? 23:21 < kanzure> don't you dare tell me something like 'intelligence' 23:21 < kanzure> I'll just hit you 23:21 < red1> xp_prg: the challenge is to emulate the brain... not just awe at it 23:21 < xp_prg> fault tolerance, speed, contextual understanding 23:21 < red1> its part of the human syndrome 23:21 < xp_prg> power consumption 23:21 < xp_prg> resiliance 23:21 < kanzure> red1: that's one of the projects I'm doing 23:21 < red1> we replicate what we grasp.. (again thru the brain) 23:21 < kanzure> red1: emulation of the cerebellum 23:21 < kanzure> red1: the simulation works faster than the real deal in the lab :) 23:22 < red1> things like the holographic brain... now we can say that its all sensory 23:22 < red1> so i believe that one day we can do just that 23:22 < red1> and move on and on from there 23:22 < red1> if ppl are drawn to this, there is a reason 23:22 < kanzure> holographic brain is bs 23:22 < kanzure> anyway 23:22 < kanzure> back to work. 23:23 < red1> haha 23:23 < red1> that bs gave me some new angle 23:23 < red1> among others 23:24 < kanzure> conceptual leapstone? perhaps 23:24 < kanzure> but anyway, the brain is the brain 23:24 < red1> indeed 23:24 < fenn> memories are distributed throughout the brain, is that bs? 23:24 < xp_prg> kanzure how does biobricks.zip tell me this: 23:24 < xp_prg> There's an error: luciferase must be inside the cell for this to work, so we select location from luciferase's context menu and drag it to the cell icon. This makes a green link showing a satisfied constraint. 23:24 < red1> always amazed by it, the LHC, universe... bla bla 23:25 < xp_prg> how do I know the constraints? 23:25 < kanzure> xp_prg: it doesn't. this is another reason why the biobricks people suck. 23:25 < fenn> whee 23:25 < fenn> we have no chicken, we have no eggs 23:25 < red1> but we have both 23:25 < xp_prg> so how am I going to find out the constraints man?! 23:25 < red1> patience 23:25 < fenn> we have several piles of shit 23:26 < red1> and plants grow well on them 23:26 < xp_prg> fenn are the constraints in that pile somewhere? 23:26 < fenn> not really 23:26 < xp_prg> fenn well how can they be known? 23:26 < fenn> they are in vague human-readable text that assumes you know what you're doing 23:27 < fenn> i.e. incomplete specs 23:27 < fenn> this is a large part of why i'm not following the biobricks thing too closely 23:27 < xp_prg> well I guess we can define them as we go 23:27 < kanzure> or not. just work with what there is in the files already. 23:27 < kanzure> everything else - well - you get to yell at the biobricks people for that later 23:27 < fenn> no, you have to do physical experiments to get these parameters 23:27 < kanzure> this is in part why I was sitting on the biobricks standardization team for a while 23:27 < kanzure> I was talking with them originally about all of this 23:28 < kanzure> trying to get them to define constraints between parts and so on 23:28 < kanzure> and they kind of ignored me it seems 23:28 < kanzure> epigenetic effects too 23:28 < kanzure> sigh 23:28 < red1> yep stds is the way to go , first 23:28 < xp_prg> kanzure one more question please, what is the output of the compile phase exactly? 23:28 < xp_prg> please look at the output area 23:28 < kanzure> xp_prg: two things 23:28 < xp_prg> on the wiki 23:28 < kanzure> xp_prg: first is a strand of DNA representing the plasmid 23:29 < fenn> sequence 23:29 < kanzure> sequence, yes 23:29 < kanzure> or 23:29 < kanzure> secondly, simultaneously, 23:29 < kanzure> I'd also really really like a sort of 'project file format' -- a 'part file format' that represents the aggregation of sub components 23:29 < kanzure> so in other words 23:29 < kanzure> a 'part file' is kind of like a 'tar' file 23:29 < kanzure> except with a standard file inside that has metadata information 23:29 < kanzure> including, but not limited to: 23:29 < kanzure> file format version 23:29 < kanzure> author(s) 23:29 < xp_prg> kanzure I need help understanding these project files formats, I assume we should store in xml format? 23:30 < kanzure> description 23:30 < kanzure> etc. 23:30 < kanzure> xp_prg: well, you could do XML I guess 23:30 < fenn> and all relevant biobrick info 23:30 < fenn> BUT that's not the output of the compiler, it's the input 23:30 < xp_prg> kanzure can you please, please, please, give me the output xml file you would expect for scenario I? 23:30 < xp_prg> it would greatly assist me 23:30 < kanzure> fenn is correct -- the biobricks must be within that 'tar' too .... actually, just a *reference* to those biobricks (by their ID number) 23:30 < fenn> sequence doesn't get you anywhere because we don't have a magic DNA writing machine 23:30 < kanzure> XML output is just all of the variables that you have 23:31 < kanzure> it's a serialization of the information of the design compiler 23:31 < fenn> instead we have to get vials of dna snippets from a freezer and mix and match them and ligate and shake and purify and amplify until we are satisfied 23:31 < xp_prg> kanzure but can you please make the output file for scenario I that has been presented on the wiki? 23:31 < xp_prg> that would greatly, greatly assist me 23:31 < kanzure_> hold on. 23:31 < kanzure_> is my server on? 23:32 < xp_prg> yes 23:33 < kanzure> Hrm. Okay. There it goes. The output section you have isn't very detailed. You should include the need for referencing specific biobricks via their ID number and so on. If you do use XML output, then you should write up a DTD in the end (when you're sure you have everything done) so that we know what data you are aggregating. 23:33 < red1> i always say - who is stopping u? *sniggers* 23:34 < xp_prg> kanzure cool, can you actually make the file? 23:34 < kanzure> xp_prg: Me? 23:34 < xp_prg> it would help me greatly yes 23:34 < kanzure> xp_prg: No, I don't have your specs yet. 23:34 < xp_prg> yes you do they are on the wiki page 23:34 < fenn> heh 23:34 < xp_prg> it is fenn's scenario I 23:34 < fenn> SOMEBODY has to have the spec!!1 23:34 < xp_prg> http://heybryan.org/mediawiki/index.php/BioBench 23:34 < kanzure> somebody set us up the spec 23:34 < kanzure> xp_prg: yeah I'm reading that 23:34 < kanzure> okay, here's another scenario I guess 23:35 < kanzure> http://heybryan.org/genetic-circuits.html at the bottom - the image. 23:35 < kanzure> and the sequence above it. 23:35 < kanzure> ideally the sequence would have metadata with my authoring information, a description (either written by me or generated from a combination of the bricks used in its construction) 23:35 < xp_prg> kanzure cool, can you please put that on the wiki page as Scenario II? 23:36 < fenn> oxytocin seems like perhaps a rather foolish thing to play around with 23:36 < fenn> you might find yourself signing lots of contracts without reading them 23:37 < kanzure> fenn: who said it was for me ? 23:37 < kanzure> :) 23:37 < xp_prg> kanzure are you putting the scenario II on the wiki you just mentioned? 23:37 < kanzure> xp_prg: anyway, that's an example of sequence output I guess, but it's not the metadata too. 23:37 < kanzure> hold on.. 23:37 < kanzure> rawr I hate mediawiki 23:38 < fenn> rawr!! 23:38 < fenn> worse is better 23:39 < fenn> at least usemod never made it to number one 23:39 * kanzure was using usemod wiki meatball thingy for a while 23:39 < kanzure> okay 23:39 < kanzure> I added it to the page, xp_prg 23:40 < bkero> meatball? 23:40 < kanzure> maybe that's what they call their usemod wiki about usemod wiki 23:41 < xp_prg> kanzure can you please supply the actual output xml file you expect for that scenario, it would help me greatly? 23:42 < kanzure_> nope. the design ajax interface thingy will have a lot of variables that it plays around with. the final output is the entire dump of everything really. so remember, the output file has to have the metadata about what the project is, who made it, those descriptions etc, as well as pointers to the files that were used to make it overall -- such as the connectivity of the biobricks or something .. but you can't just make a graph theoretic entry appli 23:42 < kanzure_> lication because the whole synthetic biology thing is more nuanced than that 23:42 < kanzure_> those nuancies are what need to be captured. 23:43 < xp_prg> kanzure_ this is not the project file, it is the output file 23:43 < kanzure_> the project file has output files within it, yes? 23:43 < xp_prg> the ouput file has a generic format does it not? 23:43 < kanzure_> yes 23:43 < kanzure_> so are you talking about a plasmid format? 23:43 < kanzure_> a way to express a plasmid? 23:43 < xp_prg> kanzure_ no not necessarily, the compile phase creates an output file if you get my meaning 23:43 < kanzure_> like a DNA sequence or something? This is what BLAST is for 23:43 < kanzure_> Dan - faceface - if he's around - would have some good ideas here 23:43 < xp_prg> Output 23:43 < xp_prg> 1 e-coli cell 23:43 < xp_prg> translucent dna sequence 23:43 < xp_prg> promoter and binding sites 23:43 < xp_prg> specify how to mix vials of liquid and shake them etc 23:43 < kanzure_> I think BLAST or FASTFA or something does this 23:44 < kanzure_> fenn was talking about this earlier methinks? 23:44 < xp_prg> I am talking about what actually gets output when the compilation phase occurs 23:44 < kanzure_> now I'm confused. 23:44 < xp_prg> ok have you ever made a program? 23:44 < fenn> i think he means the 'mix and shake' recipe 23:44 < xp_prg> you make source code, then you compile it 23:44 < kanzure_> xp_prg: all the time. 23:45 < fenn> so we have two output files, the recipe and the sequence 23:45 < xp_prg> the source code is different then the compiled version 23:45 < xp_prg> help me to understand the compiled version 23:45 < kanzure_> I thought that's what I was talking about 23:45 < fenn> the recipe cites various physical resources such as test tubes full of dna 23:45 < xp_prg> no you were talking about the source code I thought 23:45 < kanzure_> how does BLAST sequence format not answer that question for the 'transluenct DNA sequence' for example? 23:45 < kanzure_> fenn's certainly on to something too 23:46 < kanzure_> the physical recipe is a huge part that I've been neglecting 23:46 < xp_prg> well it does, but that is not the only thing output 23:46 < fenn> this is analogous to CAD design (sequence) and gcode + shop drawing + material specifications (recipe) 23:47 < fenn> and i think the program to go fro design to recipe is beyond the scope of an ajax interface 23:47 < xp_prg> fenn I don't 23:47 < fenn> so let's just stick with getting the sequence for now 23:47 < kanzure_> the recipe is an important aspect, but it comes later sort of 23:47 < xp_prg> we need input and output files 23:48 < kanzure_> xp_prg: yes we do need input and output 23:48 < kanzure_> the recipe for making a synthetic biology structure, for the end-user, is not in this scope 23:48 < fenn> there's the temptation to say 'look a sequence!' and call it finished 23:48 < kanzure_> heh 23:48 < xp_prg> kanzure please help me to define in real xml terms what the input and output files should be 23:49 < kanzure_> god we've been going over this for 20 minutes 23:49 < kanzure_> what part of 'author data' and 'descriptions of the biobricks' is not clear? 23:49 < xp_prg> ok fine, I will just do it, and you can fix it later 23:49 < xp_prg> no worries :> 23:49 < kanzure_> okay then 23:49 < fenn> that's the spirit 23:49 < kanzure_> what's your understanding of the input and output now? 23:50 < xp_prg> well the input is a specification of bio brik parts connected together in a particular cell etc... -> compile -> output is cell, dna seqence, promoter and binding regions 23:51 < kanzure_> so do you know how to connect different biobricks together 23:51 < xp_prg> nope 23:51 < kanzure_> so that's what I was working on last 23:51 < kanzure_> http://heybryan.org/~bbishop/docs/biobricks/ 23:51 < kanzure_> there's some notes in there I think 23:51 < kanzure_> there's also a folder in that directory 23:51 < kanzure_> that has 'categories' of biobricks 23:51 < fenn> most of that is just how to download the files 23:51 < kanzure_> on the partsregistry.org site, there's some 'main categories' from which you can find more biobricks 23:52 < fenn> http://heybryan.org/~bbishop/docs/biobricks/types/ 23:52 < kanzure_> now, the biobrick people don't tell you how to connect the types 23:52 < kanzure_> ah thank you fenn 23:52 < kanzure_> yes, that's the right subdirectory 23:52 < kanzure_> I was going to have a list of all biobricks within each category 23:52 < xp_prg> kanzure_ so do you like my description of input and output files for now? 23:52 < kanzure_> hold on, I'm describing something important 23:52 < xp_prg> ok 23:52 < kanzure_> anyway, the list of biobricks for each 'type' 23:52 < kanzure_> this allows there to be a certain connectivity between each type of biobrick 23:52 < fenn> it would be nice if there were a formal grammar for connecting types 23:53 < kanzure_> the important part is that you have to make up this grammar 23:53 < kanzure_> right 23:53 < kanzure_> there's some basic biological principles that we can assume 23:53 < fenn> (this requires intimate knowledge of molecular bio) 23:53 < kanzure_> like I think one of those categories is for promoters 23:53 < kanzure_> yeha, it does require some intimate knowledge 23:53 < kanzure_> *yeah 23:53 < kanzure_> *promotors? 23:53 < fenn> promoters 23:53 < kanzure_> anyway, yeah, so that connectivity is what the ajax interface is creating 23:53 < kanzure_> given the grammar that fenn is talking about. 23:54 < kanzure_> which allows for certain connectivities. 23:54 < kanzure_> or whatever. 23:54 < fenn> but we dont have the grammar 23:54 < kanzure_> right now I think we're working mostly with linear biobrick constructions. 23:54 < kanzure_> yep 23:54 < kanzure_> so 23:54 < kanzure_> we randomly generate it 23:54 < fenn> whee 23:54 < kanzure_> and then we let somebody yell at us later 23:54 < kanzure_> and give it something more specific in the same general format. 23:54 < kanzure_> right? 23:54 < xp_prg> well a grammer validates sequences which I think is appropriate in this case 23:54 < kanzure_> what the fuck? 23:54 < kanzure_> sort of. 23:55 < xp_prg> like you have a grammar for compilers of programs with key words etc... 23:55 < fenn> the grammar insures a working design mostly 23:55 < kanzure_> fenn: woah, he took your 'design compiler' literally. cool. 23:55 < fenn> it represents physical processes occuring along the dna 23:55 < kanzure_> yeha, so sort of 23:55 < kanzure_> *yeah 23:56 < fenn> think 'paper tape reader' 23:56 < xp_prg> fenn right 23:57 < xp_prg> so I believe we will have 2 phases as well: syntax checker, then binding of sequences to leaf nodes of the syntax tree etc... 23:57 < xp_prg> does that make sense? 23:58 < fenn> kanzure_: this broadened my definition of "grammar" somewhat: http://www.contextfreeart.org/gallery/view.php?by=michael 23:59 < kanzure_> me likes. 23:59 < kanzure_> xp_prg: yep 23:59 < xp_prg> ok 23:59 < kanzure_> looks ok.