| --- Day changed Wed Oct 08 2008 | ||
| fenn | china is pretty darn industrialized if you ask me | 00:01 |
|---|---|---|
| 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 | 00:20 |
| ybit | nice to have that on campus | 00:21 |
| ybit | UtopiahGHML: i see what you mean now | 00:41 |
| ybit | http://en.wikipedia.org/wiki/Image:2005education_spending.PNG | 00:41 |
| ybit | concerning where biotech or anything related may be n brazil | 00:42 |
| ybit | damn the "i" key | 00:42 |
| ybit | it's a terribly rough graph of where the money is going for public education in each country | 00:48 |
| 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. | 01:01 |
| kanzure | where'd I recently see Collis' name? | 01:07 |
| kanzure | ah, nevermind | 01:08 |
| 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 | 01:25 |
| kanzure | aka people are useless. | 01:26 |
| kanzure | I'm sure we could convert them into food | 01:41 |
| 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. | 01:42 |
| 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 | 01:47 |
| bkero | Hm. How difficult would it be to build a centrifuge? | 02:30 |
| kanzure_ | ROPE + KNOT + BUCKET AT END. SWING. | 02:33 |
| bkero | I was thinking cone + soldering iron + bolt + elecric motor | 02:34 |
| kanzure_ | Supermassive electric motor? pleeease please please? | 02:35 |
| willPow3r | get one of those that people put on electric motorcycles | 02:38 |
| gene | anyone watch the debate? | 02:45 |
| willPow3r | what debate | 02:45 |
| kanzure | ? | 02:51 |
| 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. | 03:19 |
| 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? | 03:20 |
| 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. | 03:21 |
| 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. | 03:22 |
| 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. | 03:23 |
| bkero | Criteria, whatever | 03:24 |
| 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. | 03:25 |
| 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 | 03:26 |
| emlyn | hey there | 05:15 |
| bkero | Good evening. | 05:22 |
| * mindspillage waves | 05:22 | |
| gene | hello | 05:34 |
| ybit | hi gene | 05:36 |
| ybit | and goodnight to all | 05:36 |
| willPow3r | nite | 05:36 |
| bkero | Adieu. | 05:43 |
| -!- mindspillage is now known as mind|wandering | 06:43 | |
| faceface | I emailed GeneArt, but they seem to be on to me | 07:56 |
| faceface | http://pastebin.com/d11c5f8a9 | 07:56 |
| faceface | i.e. fuck off you nozy bastard | 07:57 |
| kanzure | grr, where are my glasses? | 14:17 |
| kanzure | if they end up being on my face again I'm going to be so pissed. | 14:18 |
| 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 | 14:19 |
| bkero | Making some high grade uranium? | 15:15 |
| 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 | 15:16 |
| faceface | bkero, ? | 15:23 |
| faceface | oh yeah | 15:23 |
| faceface | sorry | 15:23 |
| faceface | yeah... and lets see which company you work for!!! | 15:23 |
| faceface | (but he has my number) | 15:24 |
| bkero | I wonder how he would react if you said you were on your own. | 15:24 |
| bkero | This guy is giving a talk today at GOogle. http://en.wikipedia.org/wiki/Prusiner | 15:26 |
| xp_prg | hi all! | 17:37 |
| 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? | 17:41 |
| 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 | 17:42 |
| 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 | 17:43 |
| 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 :> | 17:44 |
| gene | http://www.ncbi.nlm.nih.gov/ | 17:45 |
| gene | type in whatever protein, dna sequence, paper, or function into search | 17:45 |
| gene | and it will bring up many things | 17:46 |
| fenn | some links | 17:47 |
| fenn | http://heybryan.org/~bbishop/docs/matweb.zip | 17:47 |
| fenn | http://heybryan.org/~bbishop/docs/prettyrepo.zip | 17:48 |
| fenn | http://heybryan.org/gitweb.cgi | 17:50 |
| fenn | i dunno about the rest | 17:51 |
| fenn | gene: screw home depot, why not just dig around in a junkyard and get parts from working machines? | 17:52 |
| gene | what do you mean? | 17:54 |
| gene | you mean like sequence organisms to steal their dna? | 17:54 |
| 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 | 17:55 |
| gene | or you could go gene mining | 17:56 |
| gene | go search caves and stuff for billion dollar bacteria | 17:56 |
| fenn | why bother | 17:56 |
| 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 | 17:57 |
| 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 | 17:58 |
| fenn | especially recombinant proteins | 17:59 |
| gene | you need a lot of VERY FUCKING PURE polymerase for old PCR | 17:59 |
| gene | PCR can amplify the DNA from a piece of paper that has been breathed on | 18:00 |
| 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 | 18:01 |
| gene | that yellowstone doesn't let you take free samples anymore | 18:02 |
| gene | so do you know how to purify taq? | 18:02 |
| 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 | 18:03 |
| 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? | 18:04 |
| 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 | 18:05 |
| 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? | 18:06 |
| 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 | 18:07 |
| gene | it comes from Thermus aquaticus which can survive at up to 80 deg c | 18:09 |
| xp_prg | nice man! | 18:09 |
| fenn | so xp what do you do? | 18:10 |
| nsh | retrobseletes vista, mostly | 18:10 |
| 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? | 18:11 |
| 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? | 18:12 |
| 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 | 18:13 |
| 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 | 18:14 |
| 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 | 18:15 |
| 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 | 18:16 |
| 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 | 18:17 |
| gene | I am not that familiar with programming | 18:18 |
| gene | AFK | 18:18 |
| fenn | "spaghetti code" is definitely applicable however | 18:18 |
| fenn | (biobricks are much better in this sense of course) | 18:19 |
| * nsh makes nondescript noises | 18:23 | |
| xp_prg | hi nsh :> | 18:24 |
| nsh | hey | 18:25 |
| 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?! | 18:26 |
| fenn | why are you using webmail? | 18:29 |
| 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 | 18:39 |
| 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 | 18:40 |
| nsh | (next sentence: "Hypnotic effects are real!") | 18:41 |
| nsh | idiot. | 18:41 |
| fenn | i guess someone didnt get the memo back in 1920 | 18:45 |
| * nsh smiles | 18:46 | |
| xp_prg | so can anyone tell me more synthetic biology stuff that will help me to make my program etc.. ? | 18:52 |
| kanzure_ | xp_prg: fenn already mentioned it to you | 19:14 |
| kanzure_ | you seem to have ignored him. | 19:14 |
| 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 :{ | 19:19 |
| 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? | 19:20 |
| 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 | 19:21 |
| 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? | 19:22 |
| 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 | 19:23 |
| 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 | 19:24 |
| kanzure | k, I need to run again | 19:25 |
| kanzure | was just back for a few seconds. | 19:25 |
| 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? | 19:26 |
| 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 | 19:27 |
| 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! | 19:28 |
| 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 | 19:30 |
| 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 | 19:31 |
| xp_prg | actually I do, just needed a refresher was all | 19:32 |
| fenn | hrm | 19:32 |
| fenn | lol @ my mockup: http://fennetic.net/pub/irc/skdb-mockup/select-icon.png http://fennetic.net/pub/irc/skdb-mockup/select-edge.png | 19:33 |
| fenn | is that the 'ajax circuit creator'? | 19:34 |
| xp_prg | cool fenn! | 19:35 |
| * bkero just sat through a tech talk from this guy: http://en.wikipedia.org/wiki/Prusiner | 19:36 | |
| xp_prg | feen can you give me a simple use case scenario I can work on for the ajax circuit creator please? | 19:42 |
| xp_prg | fenn do you have a perference for the ajax libraries, such as jquery, dojo, scriptaculous etc... ? | 19:46 |
| 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 | 19:47 |
| 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 | 19:48 |
| 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 :> | 19:49 |
| 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 :) | 19:50 |
| 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? | 19:51 |
| 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 :( | 19:52 |
| 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? | 19:53 |
| 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 | 19:55 |
| xp_prg | what shall we call the project I am working on wiki notation? | 19:56 |
| fenn | how bout 'biobench' | 19:57 |
| fenn | BioBench if you prefer camel case :) | 19:57 |
| xp_prg | fenn go ahead and make it :> | 19:57 |
| 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 | 19:58 |
| 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? | 20:01 |
| 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? | 20:02 |
| 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 :> | 20:03 |
| xp_prg | procto what do you do? | 20:05 |
| xp_prg | fenn did you make the wiki page yet? | 20:05 |
| fenn | yep just click on biobench | 20:06 |
| fenn | an uncreated wiki page will just prompt you to add some content | 20:06 |
| 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 | 20:08 |
| 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? | 20:09 |
| fenn | yes | 20:10 |
| procto | xp_prg: for work or in general? | 20:10 |
| xp_prg | all of the above :> | 20:10 |
| 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? | 20:11 |
| 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 | 20:14 |
| 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. | 20:15 |
| 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 | 20:16 |
| bkero | fenn: He msg you? | 20:18 |
| bkero | http://www.indiana.edu/~uitshr/services/jobs/IUBhourly.html | 20:18 |
| bkero | Are you hot shit at databaess? :P | 20:19 |
| 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. | 20:20 |
| fenn | $8.75 and a commitment for 1 year? why bother | 20:22 |
| fenn | at least the grocery store gives me free food | 20:22 |
| 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" | 20:23 |
| bkero | Gain experience outside of work? | 20:24 |
| fenn | databases are so stupid and simple, so why does experience matter so much | 20:25 |
| 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 | 20:26 |
| fenn | database is just tables and more tables | 20:27 |
| fenn | did you know the US spends $750 billion on education? | 20:28 |
| fenn | that's more than the military budget | 20:28 |
| 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 | 20:29 |
| fenn | military budget is about $650B including the iraq war | 20:30 |
| fenn | here is my source: http://en.wikipedia.org/wiki/Image:2005education_spending.PNG | 20:33 |
| 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 | 20:34 |
| bkero | 2004 education was $827 billion | 20:35 |
| fenn | they usually leave off the iraq war addition for some reason | 20:35 |
| 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 | 20:36 |
| bkero | iraq is $10 billion per week | 20:37 |
| bkero | fenn: Are you still in school? | 20:37 |
| fenn | no | 20:37 |
| 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 | 20:38 |
| 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 | 20:39 |
| 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. | 20:40 |
| 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 | 20:41 |
| 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 | 20:42 |
| 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 | 20:43 |
| 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. | 20:44 |
| 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 | 20:45 |
| 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 | 20:46 |
| fenn | may i ask why? | 20:47 |
| bkero | Sir Bender Bending Rodriguez | 20:47 |
| xp_prg | http://heybryan.org/mediawiki/index.php/BioBench | 20:48 |
| fenn | ok, it's a start | 20:49 |
| bkero | My name is Bender Karma Ego Rodriguez Orange | 20:50 |
| fenn | no relation :) | 20:50 |
| fenn | we're 47th cousins | 20:50 |
| 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 | 20:51 |
| 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 | 20:52 |
| 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 | 20:53 |
| 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. | 20:58 |
| xp_prg | Kanzure did you see my project wiki?! | 20:59 |
| kanzure___ | procto: scriptalicous works ok for javascript/ajax crap | 21:00 |
| xp_prg | kanzure___ do you like my wiki page? | 21:00 |
| 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... | 21:01 |
| 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 | 21:02 |
| 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 | 21:03 |
| xp_prg | kanzure___ I wish we had a blog to put these ideas in, or this channel logged? | 21:04 |
| kanzure___ | channel is logged | 21:04 |
| 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. | 21:05 |
| 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 | 21:06 |
| kanzure___ | correct | 21:07 |
| kanzure___ | but I'm not about to do the backend in prolog | 21:07 |
| xp_prg | why not?! ;) | 21:08 |
| kanzure___ | prejudice. | 21:08 |
| xp_prg | well it will use ajax json, so the back end can be implemented in any way since it is loosley coupled :) | 21:09 |
| xp_prg | kanzure___ what is your preference on the back end? ruby on rails or something? | 21:12 |
| kanzure___ | no, I'll do some perl, it's okay | 21:20 |
| 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 | 21:21 |
| 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? | 21:22 |
| 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. | 21:23 |
| 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 | 21:24 |
| 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? | 21:27 |
| fenn | where is this all.repo file? | 21:29 |
| 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 | 21:30 |
| 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 | 21:31 |
| 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 | 21:32 |
| fenn | lol dont try to pass the buck | 21:33 |
| ybit | bkero: what did stanley prusiner speak about? | 21:34 |
| 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 | 21:35 |
| 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 | 21:36 |
| 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 | 21:37 |
| 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? | 21:38 |
| fenn | god this is starting to sound like work | 21:39 |
| xp_prg | fenn well I need you to at document it :) | 21:39 |
| xp_prg | at least | 21:40 |
| fenn | malaysia? | 21:43 |
| xp_prg | fenn did you document it? | 21:44 |
| fenn | no i am slow (i hate mediawiki because it is so slow to use) | 21:44 |
| 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.. ? | 21:45 |
| red1 | i m watching the youtube... to get a slice of spice or whatever u guys do :> | 21:46 |
| 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 :) | 21:47 |
| 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 | 21:48 |
| red1 | a little dot | 21:49 |
| red1 | then dots | 21:49 |
| red1 | then u join the dots | 21:49 |
| red1 | then u paint areas | 21:49 |
| red1 | bio as in biology huh? | 21:51 |
| red1 | creating life somewhere along the way? | 21:51 |
| xp_prg | ok red1 check it out now! | 21:52 |
| red1 | checking.. | 21:52 |
| red1 | what does those PNG images mean? Select edge.. | 21:53 |
| red1 | frantically looking anywhere... armed with mouse here | 21:54 |
| xp_prg | don't know, need Fenn to explain | 21:55 |
| xp_prg | red1 updated wiki re-check if you want :> | 21:57 |
| 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 | 21:58 |
| xp_prg | fenn, can you pretty please tell me more about the user interface navigation you would expect to solve scenario I ? | 21:59 |
| 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!!! | 22:01 |
| fenn | nevermind that we just contaminated our well with e. coli | 22:03 |
| xp_prg | fenn I like your ideas for the interface! | 22:05 |
| 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? | 22:06 |
| fenn | this would call some compiler targeting DNA, and using biobricks "source code" | 22:07 |
| 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 | 22:08 |
| 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 | 22:09 |
| 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 | 22:10 |
| 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? | 22:11 |
| 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 | 22:12 |
| fenn | um, i forget how sensor proteins are supposed to work | 22:13 |
| fenn | this is the standard example sensor system: http://en.wikipedia.org/wiki/Lac_operon | 22:14 |
| 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 | 22:15 |
| xp_prg | fenn check out the wiki page now | 22:16 |
| xp_prg | under output specifically | 22:16 |
| xp_prg | well I have to go to lunch, feel free to add/change the wiki page! | 22:17 |
| 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 | 22:18 |
| 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 | 22:19 |
| red1 | just edited.. so pls refresh before proceeding | 22:23 |
| xp_lunch | nice red1! | 23:02 |
| xp_lunch | fenn you here? | 23:02 |
| 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? | 23:03 |
| xp_prg | yes but more then DNA engineering, DNA engineering with a purpose | 23:04 |
| xp_prg | the DNA is put in the cell and actually funtions and does things! | 23:05 |
| 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... | 23:06 |
| 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 | 23:07 |
| 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 | 23:08 |
| 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 | 23:09 |
| 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 :> | 23:10 |
| 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.. | 23:11 |
| 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 | 23:12 |
| 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! | 23:13 |
| 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! | 23:14 |
| 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? | 23:15 |
| 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? | 23:16 |
| 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 | 23:17 |
| 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! | 23:18 |
| 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? | 23:19 |
| 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? | 23:20 |
| 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 :) | 23:21 |
| 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. | 23:22 |
| red1 | haha | 23:23 |
| red1 | that bs gave me some new angle | 23:23 |
| red1 | among others | 23:23 |
| 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 | 23:24 |
| 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 | 23:25 |
| 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 | 23:26 |
| 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 | 23:27 |
| 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 | 23:28 |
| 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? | 23:29 |
| 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 | 23:30 |
| 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? | 23:31 |
| xp_prg | yes | 23:32 |
| 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* | 23:33 |
| 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 | 23:34 |
| 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? | 23:35 |
| 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 | 23:36 |
| 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 | 23:37 |
| fenn | rawr!! | 23:38 |
| fenn | worse is better | 23:38 |
| 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 | 23:39 |
| bkero | meatball? | 23:40 |
| kanzure | maybe that's what they call their usemod wiki about usemod wiki | 23:40 |
| xp_prg | kanzure can you please supply the actual output xml file you expect for that scenario, it would help me greatly? | 23:41 |
| 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. | 23:42 |
| 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 | 23:43 |
| 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. | 23:44 |
| 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 | 23:45 |
| 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) | 23:46 |
| 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 | 23:47 |
| 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 | 23:48 |
| 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? | 23:49 |
| 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 | 23:50 |
| 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 | 23:51 |
| 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 | 23:52 |
| 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. | 23:53 |
| 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. | 23:54 |
| 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 | 23:55 |
| fenn | think 'paper tape reader' | 23:56 |
| xp_prg | fenn right | 23:56 |
| 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? | 23:57 |
| fenn | kanzure_: this broadened my definition of "grammar" somewhat: http://www.contextfreeart.org/gallery/view.php?by=michael | 23:58 |
| kanzure_ | me likes. | 23:59 |
| kanzure_ | xp_prg: yep | 23:59 |
| xp_prg | ok | 23:59 |
| kanzure_ | looks ok. | 23:59 |
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