| --- Day changed Mon Oct 27 2008 | ||
| bkero | http://www.rcsb.org/pdb/home/home.do | 00:20 |
|---|---|---|
| ppk | lawl@Tom Knight flipping out in DIYbio | 00:47 |
| * bkero didnt see that | 00:47 | |
| kanzure_ | Me either. | 00:48 |
| bkero | Have any of you guys seen Fringe? | 00:48 |
| ppk | no | 00:49 |
| kanzure_ | Hah. | 00:49 |
| kanzure_ | Toilet strains. | 00:49 |
| kanzure_ | bkero: Yes. | 00:49 |
| bkero | Does it pain you as much as it pains me? | 00:49 |
| kanzure_ | Yep. | 00:49 |
| kanzure_ | Although I have to admit that I like Dr. Bishop. | 00:49 |
| bkero | I just watched the pilot. I couldn't take any more. | 00:49 |
| bkero | Is it all that bad? | 00:50 |
| kanzure_ | Unfortunately, Dr. Bishop is just a Dr. House except less functional, and more delusional. | 00:50 |
| ppk | jj abrams eh | 00:50 |
| ppk | never got into lost much | 00:50 |
| ppk | doubt I'd get into this | 00:50 |
| kanzure_ | There's not much to get into in 'Fringe'. I don't recommend watching it. | 00:50 |
| bkero | After watching regenesis it's just kind of like a shot in the mouth. :/ | 00:50 |
| bkero | Especially since Peter Outerbridge did a cameo in the pilot. | 00:51 |
| kanzure_ | It's like a remake of 'Oddysey Group' or whatever it was that was on HBO. | 00:51 |
| kanzure_ | This was another series with some guys running around trying to uncover "Teh Patternz!" | 00:51 |
| bkero | Fringe: Bullshit <--*---------------------> Science | 00:51 |
| kanzure_ | it was slightly better | 00:51 |
| kanzure_ | i.e., "this week's educational awesomeness is molecular nanotech! yay!" but it was HBO so it was something more like hot nanotech sex or something | 00:52 |
| bkero | lol | 00:52 |
| bkero | Like Eureka nanotech | 00:52 |
| bkero | I found Eureka at least entertaining since it wasn't all FBI BREAK INTO UR HOUSE scare tactic stuff. | 00:52 |
| kanzure_ | I+ | 01:00 |
| kanzure_ | Woah. | 01:00 |
| kanzure_ | Yeah, so re: the Tom Knight post. | 01:00 |
| kanzure_ | I was thinking it might have been me. The first round of flame wars with him, I mean. | 01:00 |
| kanzure_ | Isn't he some sort of ridiculously dignified MIT prof? :( | 01:00 |
| bkero | lol snobbery? | 01:01 |
| kanzure_ | but it's supposed to be snobbery-that-is-really-just-brilliance-manifesting-itself-as-snobbery-to-everyone-who-isn't-in-the-know | 01:01 |
| ppk | ? | 01:14 |
| ppk | first round? | 01:14 |
| ppk | I don't believe I saw that | 01:14 |
| bkero | You mean hubris. | 01:15 |
| kanzure_ | ppk: Tom Knight was telling me that I wasn't made up of cells or something | 01:19 |
| kanzure_ | I had to admit that I had never 'tested myself', but. | 01:20 |
| kanzure_ | Hi Sparn | 01:37 |
| Sparn | Hi | 01:38 |
| kanzure_ | What brings you around these parts? | 01:38 |
| Sparn | Well | 01:39 |
| Sparn | I found this channel on the biopunk forums | 01:39 |
| kanzure_ | Deep in the archives? | 01:40 |
| Sparn | oct 3 | 01:40 |
| Sparn | It is a fairly small forum, so I don't know what qualifies as "deep" lol | 01:41 |
| kanzure_ | There's a few of us in here that visit the forum every now and then, so yeah. | 01:44 |
| Sparn | Any current projects? | 01:51 |
| kanzure_ | Synthetic biology circuit creator | 01:52 |
| kanzure_ | Automated design repository (for more than just biology) | 01:52 |
| kanzure_ | Various musings about rTMS | 01:52 |
| kanzure_ | open source algal bioreactor for biodiesel | 01:52 |
| kanzure_ | various neuron simulators .. | 01:52 |
| kanzure_ | stuff I'm probably forgetting | 01:53 |
| Sparn | cool | 01:54 |
| fenn | is sparn a swedish name? | 01:56 |
| Sparn | nope | 01:56 |
| Sparn | It is just a name I made up. | 01:57 |
| Sparn | Or word. | 01:57 |
| Sparn | It is short and doesn't have any meaning I am aware of. | 01:58 |
| fenn | ah. it just sounded familiar somehow | 01:58 |
| fenn | kanzure why do you need filters for the bioreactor? why not just centrifuge? | 02:00 |
| kanzure_ | right | 02:01 |
| kanzure_ | that's a certainly valid method | 02:01 |
| kanzure_ | I'm a fan of centrifugation here | 02:01 |
| kanzure_ | centrifuge + bioflocculation | 02:01 |
| kanzure_ | but one of the issues I'm seeing is that nobody has taken meticulous care of 'numbahs' here .. i.e., a common variable to keep track of | 02:01 |
| kanzure_ | I would expect concentration would be one of it, for harvesting | 02:01 |
| fenn | heh | 02:02 |
| kanzure_ | uh | 02:02 |
| kanzure_ | I'm slightly distracted re: that random 'it' there | 02:02 |
| * kanzure_ is playing "The Force Unleashed" | 02:02 | |
| bkero | fenn: You ever get a job? | 02:02 |
| fenn | it = numbahs | 02:02 |
| fenn | bkero: no :( | 02:02 |
| bkero | :/ | 02:02 |
| fenn | nobody even replied, and i'm not up in the daytime to telephone | 02:03 |
| bkero | Ouch | 02:03 |
| fenn | i get this total cockblock from academics all the time, i'm wondering if my email is on some galaxy-wide spam blacklist or something | 02:04 |
| bkero | I just use gmail. | 02:04 |
| fenn | ok from now on i'm sending duplicates from both addresses | 02:06 |
| kanzure_ | oh wait | 02:13 |
| kanzure_ | fenn: what's your relayhost? | 02:13 |
| kanzure_ | Are you sending mail from your own mailserver, I mean. | 02:15 |
| fenn | no | 02:16 |
| fenn | sdf.lonestar.org | 02:16 |
| drazak | lonestar :D | 02:52 |
| drazak | fenn: that's where I know you from! | 02:52 |
| -!- splicer_ is now known as splicer | 03:24 | |
| * procto is writing a gel box blueprint generator | 03:43 | |
| procto | I was going just to draw some SVG | 03:46 |
| procto | but then realised that a different thickness of the plastic material | 03:47 |
| procto | would mean I have to use different measurements | 03:49 |
| kanzure_ | procto: What's the input to your generator? | 04:23 |
| kanzure_ | width of plastics? | 04:23 |
| wrldpc | Anyone know any good movies that are comprised entirely of footage taken from the microbiological scale? | 04:44 |
| bkero | lol | 04:49 |
| bkero | Inner Space | 04:49 |
| splicer | It was big in the 30:ies I think | 04:50 |
| splicer | (excuse the pun) | 04:50 |
| fenn | wrldpc: http://www.wehi.edu.au/wehi-tv/index.html http://fennetic.net/pub/irc/drew_berry_urls | 04:53 |
| wrldpc | ty sir | 04:53 |
| fenn | that's all CG, dunno what else you'd do for videos of microbes | 04:53 |
| fenn | more at http://www.molecularmovies.com/showcase/index.html | 04:54 |
| procto | kanzure_: yeah, and you can also tweak other size paramateres | 05:07 |
| procto | kanzure_: like desired depth of gel, etc | 05:07 |
| wrldpc | I hear environmentalists scream all the time "20 species die every minute" but where are the statistics on how many are born? | 05:43 |
| bkero | Ssh | 06:00 |
| bkero | They haven't figured out there are things you can't hug or smoke yet. | 06:00 |
| procto | wrldpc: it's much easier for a species to die than for a new one to come to be | 06:02 |
| procto | I am more familiar with the linguistic analogue | 06:02 |
| procto | i.e. languages dying, versus new ones being created | 06:03 |
| bkero | It's not like we're getting NEW culture or anything | 06:04 |
| procto | we certainly are | 06:06 |
| procto | but not at the same rate | 06:06 |
| procto | this is because there's a reason for languages dying, just like species | 06:06 |
| procto | just like species, the boundaries between languages are VERY unclear | 06:07 |
| procto | languages survive only based on quantity of communication | 06:07 |
| procto | with better and more globalized communication, the isolation which used to cause many many languages to exist is no longer true | 06:07 |
| procto | same with species. the conditions which led to them being well adapted to a niche change | 06:08 |
| procto | and so, they can no longer survivce | 06:08 |
| procto | survive | 06:08 |
| procto | however, adaptation of current species to new niches isn't as fast | 06:08 |
| wrldpc | hm | 06:21 |
| wrldpc | hrm | 06:22 |
| wrldpc | this is a step back but what about the human species? | 06:22 |
| wrldpc | population growth | 06:22 |
| wrldpc | it's just that we are particularly virulent i presume | 06:22 |
| wrldpc | speciation though ... i'm interested in this | 06:22 |
| procto | yay, i'm done writing my generator | 06:26 |
| procto | sorta | 06:26 |
| procto | need to figure out what to do about units... | 06:26 |
| fenn | you shoulda been thinking about units from the start | 06:35 |
| procto | I have been | 06:36 |
| procto | that is, as long as the user is uniform, the resulting SVG will be fine | 06:36 |
| procto | but lets say the sure inputted inches instead of pixels | 06:37 |
| fenn | pixels! that's hardly even a unit | 06:37 |
| procto | with no units specified most svg viewers treat that as pixels | 06:37 |
| procto | with a bit of conversion, you can make it into inches easily | 06:38 |
| procto | but you have to know svg | 06:38 |
| procto | basically, i'm trying to make my script understand that you want to output an inch-aware svg, or whatever | 06:38 |
| procto | the only reason you want such a file is if you're gonna be converting blind to a dxf | 06:38 |
| fenn | or printing the svg | 06:39 |
| procto | well, Ill polish it off | 06:39 |
| procto | tomorrow morning when i'm not as dead tired | 06:39 |
| fenn | why is there no "lcd repair for dummies" book? | 07:00 |
| bkero | Because that's how fuckers die. :) | 07:01 |
| bkero | No, I'm kidding, LCDs aren't nearly as dangerous as CRTs. | 07:01 |
| -!- Irssi: #hplusroadmap: Total of 21 nicks [0 ops, 0 halfops, 0 voices, 21 normal] | 07:01 | |
| fenn | oh come on, it's 1kV and a few mA | 07:01 |
| fenn | i'm suspecting the puffy capacitors on this one... | 07:01 |
| fenn | but they arent shorted out or anything | 07:02 |
| bkero | Caps are kind of a test to pain | 07:02 |
| fenn | i set the meter to 'resistance' and the speed it counts up depends on the capacitance (for big electrolytics) | 07:03 |
| fenn | i guess that doesn't really tell you if the dielectric is busted though | 07:04 |
| bkero | Pass a current through it and see if you get anything out the other end. | 07:07 |
| fenn | it's in-circuit.. not sure it would mean anything | 07:07 |
| bkero | Gotta take it out of circuit first :/ | 07:07 |
| fenn | i'll just desolder them | 07:07 |
| fenn | this guide actually looks pretty good: http://www.lcd-monitor-repair.com/ | 07:29 |
| fenn | judging from the first chapter at least | 07:29 |
| fenn | all-the-schematics-ever.torrent would be better though | 07:29 |
| faceface | garry badder is cool | 08:56 |
| faceface | shame his DB was ethered | 08:56 |
| faceface | although this talk is pretty lame | 08:58 |
| fenn | who what where? | 08:59 |
| faceface | http://uk.youtube.com/watch?v=bVhOntMCmnQ | 08:59 |
| faceface | bind was trashed by funding agencies | 08:59 |
| UtopiahGHML | faceface: h+ degree page=? | 08:59 |
| faceface | UtopiahGHML, I saw bshchool | 08:59 |
| UtopiahGHML | good good but did you integrated all our discussions and links in on virtual-neuron aka wikip-page? ;) | 09:00 |
| faceface | I'll do that this evening | 09:00 |
| faceface | (its morning here) | 09:00 |
| faceface | any wiki in partiki? | 09:01 |
| UtopiahGHML | I really hate to discuss/do things 2 times so writting down things, especially in flexible structures like wikis is a great solution IMHO | 09:01 |
| faceface | yes | 09:01 |
| UtopiahGHML | (I dropped like 9(% of my videogames becaues I had to restart levels, Mario drove me crazy) | 09:01 |
| UtopiahGHML | well if you don't have your own wiki we can put it in mine | 09:02 |
| faceface | Ive got about 150 | 09:02 |
| fenn | heh i have that same problem | 09:02 |
| UtopiahGHML | well the most appropriate one then :) | 09:02 |
| UtopiahGHML | you don't have a meta-wiki "to control them all"? | 09:03 |
| faceface | not really | 09:03 |
| faceface | nor a common login inf. | 09:03 |
| faceface | I was going to work on that for a couple of months this summer, but my boss decided to not let me | 09:03 |
| UtopiahGHML | common login? no OpenID, OAuth, sth? | 09:04 |
| faceface | there are ways | 09:04 |
| UtopiahGHML | but lazyness surpass them all! I know I know ;) | 09:04 |
| fenn | is openID really worth the effort? | 09:05 |
| faceface | OK, UtopiahGHML this one seems apt... http://biocourse.org | 09:05 |
| UtopiahGHML | fenn: I guess if the "effort" is just adding a module with it's config line within your wiki, yes sure. | 09:05 |
| faceface | "HplusDegree" ? | 09:06 |
| UtopiahGHML | yep | 09:06 |
| faceface | HPlusDegreeCourse ? | 09:07 |
| UtopiahGHML | well degree first, the rest will follow based on it's definition and objectives | 09:07 |
| fenn | hm this is weird: http://fenn.blogspot.com/ | 09:07 |
| faceface | just stuck for a winner... Transhumanist degree course | 09:07 |
| fenn | i hope that's not my dissociative personality's blog.. | 09:08 |
| faceface | OK, lets pespone the title | 09:08 |
| UtopiahGHML | fenn: as in AmericanDad recent episode | 09:08 |
| UtopiahGHML | faceface: page with an ok name + edited conversation log, the rest will follow and gradually take place | 09:09 |
| UtopiahGHML | then send back the URL so that I could RSS-subscribe it please | 09:10 |
| fenn | UtopiahGHML: i dont watch TV so you'll have to explain | 09:11 |
| faceface | http://biocourse.org/index.php/H%2B | 09:11 |
| UtopiahGHML | fenn: I don't have TV but I have RSS feeds on series I enjoy like TheBigBangTheory/SouthPark/Gantz/Simpsons/... | 09:12 |
| faceface | http://biocourse.org/index.php/Talk:H%2B | 09:12 |
| UtopiahGHML | need to login to edit :( | 09:12 |
| faceface | UtopiahGHML, the set of wikies is actually administered by a friend of mine | 09:12 |
| faceface | they have had a lot of trouble with spam | 09:13 |
| faceface | but on the other hand, I can give you root access to the server | 09:13 |
| fenn | say.. why "future studies"? | 09:13 |
| faceface | don' tknow | 09:13 |
| faceface | don't know | 09:13 |
| fenn | do you want to train people to be futurists, or to get shit done? | 09:13 |
| faceface | jejej | 09:13 |
| faceface | I mena hehehe | 09:13 |
| faceface | why me ho type | 09:14 |
| faceface | gah! | 09:14 |
| fenn | spanish keyboard | 09:14 |
| UtopiahGHML | faceface: where can we find the logs? | 09:14 |
| faceface | garry badder was in part behind BIND, one of the best protein protein interaction databases around. they pulled the plug thanks to funding politics. | 09:15 |
| faceface | what logs? | 09:15 |
| faceface | UtopiahGHML, click history to get page logs | 09:15 |
| faceface | discussion tab for discussion | 09:15 |
| faceface | IRC logs>? | 09:15 |
| UtopiahGHML | yes irc logs with previous convo+links | 09:15 |
| faceface | there is a command... | 09:15 |
| faceface | UtopiahGHML, I'll do it this evening | 09:16 |
| * fenn sees "BIND" and things DNS server | 09:16 | |
| UtopiahGHML | ok, thanks, if I have any idea Ill edit the wiki then | 09:17 |
| faceface | BioMolecular Interaction Database | 09:17 |
| faceface | :D | 09:17 |
| UtopiahGHML | hmm I can't see the page-specific RSS link | 09:17 |
| UtopiahGHML | http://biocourse.org/index.php?title=H%2B&action=history&feed=rss seems to fail | 09:18 |
| fenn | seems BMID would have been a better acronym, but what do i know.. | 09:42 |
| UtopiahGHML | anybody knows a framework to quickly move from webpage to blackberry/iphone/mobile devices pages? | 10:37 |
| fenn | define "move" | 10:38 |
| UtopiahGHML | url please since it's a common word | 10:38 |
| fenn | ENOPARSE | 10:39 |
| fenn | (A)bort, (R)etry, (F)ail? | 10:39 |
| UtopiahGHML | (is he actually talking to anybody?) | 10:40 |
| fenn | (A)bort, (R)etry, (F)ail? | 10:41 |
| UtopiahGHML | R | 10:43 |
| * UtopiahGHML finds fenn's API pretty basic. | 10:44 | |
| fenn | so, you're trying to get a webpage from some site on the web, right? | 10:44 |
| fenn | (not trying to serve a webpage)? | 10:44 |
| UtopiahGHML | nop, I have my wiki with it's module and I want to be able to use (not just see) on iPhone/Android/Blackberry mobile devices. | 10:45 |
| fenn | seems tough to fit that blob-map onto a cellphone screen | 10:47 |
| fenn | usually this is done with CSS | 10:48 |
| UtopiahGHML | btw Id like to have some virtual devices like that to test it | 10:48 |
| UtopiahGHML | like a www.blackberryvirtualbrowser.com that could open my website to see the result | 10:48 |
| UtopiahGHML | yes the "blob-map" ajax thing would have to be modified | 10:49 |
| fenn | http://mobiforge.com/page/mobile-emulators | 10:53 |
| fenn | i guess "mobile" is the new buzzword, "cell phone" doesnt return crap | 10:55 |
| UtopiahGHML | well the Nokia N810 isn't a cellphone | 10:56 |
| UtopiahGHML | the new buzzword is actually InternetDevice ;) | 10:56 |
| fenn | that's even worse, at least mobile conveys some information | 10:58 |
| UtopiahGHML | they should all be called Navi anyway. | 10:59 |
| fenn | oo wow this is amazing, i take back all snarky comments about "lcd repair for dummies" http://www.wizardanswers.com/liquidvideorepair.html | 11:10 |
| UtopiahGHML | how many miles a normal car can go for 1week of energy of an electrical radiator (the house appliance) because my sister told me I forgot to stop one of those for few days but Im pretty shure that just going to the cinema alone in her car, she wastes more | 11:28 |
| kanzure_ | Why didn't anyone answer fenn's question about the degree? | 11:43 |
| kanzure_ | http://thepiratesdilemma.com/ and there's apparently a wired.com interview "how to profit from piracy: how the youth are reinventing capitalism" | 11:46 |
| fenn | UtopiahGHML: electric car gets about 3mi/kWh and those stupid electric radiator things pull 1450 watts, so 2d*1450W*3mi/kWh = 209 miles | 11:46 |
| fenn | or about 100 miles per day | 11:46 |
| UtopiahGHML | no Im talking about a "normal" car | 11:46 |
| fenn | ok, lemme figure that, one sec | 11:46 |
| fenn | gas = 38.5 MJ/l, car gets 30mi/gal, so 0.205mi/MJ | 11:48 |
| fenn | cars are about 10% efficient, so realistically 0.02mi/MH | 11:49 |
| fenn | so one week is approx 18mi | 11:49 |
| fenn | i dont think it's really a fair comparison though | 11:49 |
| UtopiahGHML | Id like to have a home appliance /per_mile scale :) | 11:50 |
| fenn | because i'm neglecting the efficiency of the entire electricity generation system (which includes burning coal, which isn't terribly efficient (<50%)) | 11:51 |
| fenn | and you could be running a heat pump instead of just dumping the electricity overboard | 11:51 |
| fenn | and coal isn't gasoline | 11:52 |
| UtopiahGHML | hmmk | 11:52 |
| UtopiahGHML | well thanks for the estimate | 11:52 |
| UtopiahGHML | http://seedea.free.fr/wiki/pub/illustrations/projetautonomieenergetique/progrestechno.png ;) | 11:52 |
| fenn | because for some amazingly incomprehensible reason we still can't run cars on coal | 11:52 |
| UtopiahGHML | know any graph with miles per home appliance hour? | 11:53 |
| fenn | or some sort of coal + methane derived liquid | 11:53 |
| fenn | i dont think your comparison is valid for the above stated reasons ^^ | 11:54 |
| UtopiahGHML | well ideally it would recursively include all the waste and negative effect on the chain but... | 11:54 |
| UtopiahGHML | that sounds a bit complex ;) | 11:55 |
| fenn | omg maths | 11:55 |
| fenn | btw my dumpstered LCD works :) | 11:55 |
| UtopiahGHML | (and even... like interactions of effect, now that sounds scary) | 11:55 |
| UtopiahGHML | good job | 11:55 |
| UtopiahGHML | ok, gotta cook with huge waste-energy-home-appliance-devilish modern technology ;) | 11:57 |
| fenn | stove/toaster is not so bad even with the same wattage as a space heater, because it's only on for an hour at most | 12:01 |
| kanzure_ | "The Force Unleashed" feels like a Shadows of the Empire remake. Same sort of TIE-fighter factory. | 12:24 |
| kanzure__ | Hello. | 16:00 |
| bkero | SOTE was pretty cool. | 16:17 |
| kanzure__ | Which game was it where you had the falcon flying through a TIE fighter factory? | 16:28 |
| * bkero shrugs | 16:28 | |
| bkero | I think that was SOTE | 16:28 |
| ybit-school | kanzure_ starfox? | 16:29 |
| ybit-school | oh, star wars, right | 16:29 |
| ybit-school | not literally a falcon flying a ship | 16:29 |
| kanzure__ | bkero: Probably. I do remember it being N64. | 16:34 |
| bkero | Yes, SOTE was the famous N64 one. | 16:37 |
| ybit-school | sote was my first star wars game exp. the software emulation of older games came afterward | 16:37 |
| bkero | My first star wars game was the second SNES one. | 16:38 |
| kanzure__ | http://dhcp-84-253.me.utexas.edu/generaterules.pl.txt <- Search for 'tag'. For some reason, when the function returns to after calling that recursive function, $graph2 is no longer defined and it errors 2 lines below 'tag' or whatever (at the print statement). Any thoughts why? | 16:39 |
| kanzure__ | My first Star Wars game must have been the Macintosh TIE Fighter Simulator. | 16:39 |
| kanzure__ | 1994 or 1995. | 16:39 |
| kanzure__ | erm, wait, that's too early | 16:39 |
| kanzure__ | Yay! Hod Lipson! | 16:40 |
| kanzure__ | Date/Time: Friday, November 7, 2008 11:00 a. | 16:40 |
| kanzure__ | hah hah! | 16:40 |
| * kanzure__ is very happy | 16:42 | |
| bkero | I remember playing X-Wing, then TIE-Fighter, then X-Wing vs TIE-Fighter | 16:43 |
| ybit-school | anyone played moon base one? | 16:44 |
| kanzure__ | Ok. Typo in the pl file. | 16:45 |
| * kanzure__ quickly removes the file so that no one will ever see his error. | 16:45 | |
| kanzure__ | maybe ->copy() is a pointer copy instead of direct copy. | 16:47 |
| ybit-school | "Ubuntu 7.04 was certainly the Feisty Fawn for performance, but based upon these results perhaps it would be better to call Ubuntu 7.10 the Gooey Gibbon, 8.04 the Hungover Heron, and 8.10 the Idling Ibex.'" | 17:20 |
| ybit-school | http://linux.slashdot.org/article.pl?sid=08/10/27/1212214&from=rss | 17:20 |
| ybit-school | i like the names :) | 17:21 |
| bkero | http://en.wikipedia.org/wiki/Rolling_release | 17:23 |
| bkero | So much better, but these don't generate press reports. | 17:23 |
| kanzure__ | http://dhcp-84-253.me.utexas.edu/two.txt <--- Why does the foreach loop run only once? Despite there being 50 nodes in the graph. | 17:34 |
| ppk | heh, everybody wants to hear about Kay's plant experiences | 17:34 |
| kanzure__ | oops | 17:34 |
| ppk | I considered sending an email like the one you sent Bryan | 17:34 |
| kanzure__ | http://dhcp-84-253.me.utexas.edu/two.pl.txt | 17:35 |
| kanzure__ | heh heh | 17:36 |
| kanzure__ | Dr. Campbell got back to me and sent out an email to his goons, "Please try to attend this talk. Hod is a good friend of mine and does very similar research." | 17:36 |
| ppk | bryan do you have anything on synthesizing RNA for RNAi? | 17:37 |
| kanzure__ | Isn't RNAi still up in the air? | 17:38 |
| kanzure__ | Maybe I'm thinking of something else. | 17:38 |
| kanzure__ | There's a type of awesome folding RNA that doesn't survive blood pH, but if it did then we'd all be supersaiyan or something | 17:38 |
| ppk | up in the air as in, unproven? | 17:38 |
| kanzure__ | No, as in, "not yet working" | 17:38 |
| ppk | hmm | 17:38 |
| ppk | well | 17:38 |
| kanzure__ | RNAi is probably not it | 17:38 |
| ppk | it's done a ton | 17:38 |
| kanzure__ | Okay then. I might have some RNAi stuff. Try the /ellingtonia/ dirs. http://heybryan.org/~bbishop/docs/ | 17:39 |
| ppk | one of the best ways to characterize genes | 17:39 |
| ppk | cool | 17:39 |
| kanzure__ | (it will be somewhere in /~bbishop/docs/ellingtonia/ or something) | 17:39 |
| kanzure__ | What's the special sort of RNA that I am thinking of, then? | 17:39 |
| kanzure__ | sRNA? | 17:39 |
| ppk | midichlorians | 17:39 |
| kanzure__ | siRNA? | 17:39 |
| ppk | I'm not sure, tbh | 17:39 |
| kanzure__ | siRNA sounds close enough. | 17:39 |
| * kanzure__ goes off to chem | 17:40 | |
| ppk | yeah so, it sounds like siRNA synthesis is what I'm looking for | 17:41 |
| ppk | cya | 17:41 |
| ppk | Synthetic small interfering RNA (siRNA) and retroviral short hairpin RNA (shRNA) | 17:42 |
| ppk | both apparently trigger RNAi | 17:43 |
| xp_prg | hi ppk! | 17:55 |
| xp_prg | ppk got a sec? | 17:55 |
| bkero | Do any of you guys know a good program for reading PDB files? | 17:55 |
| xp_prg | what is a PDB file? | 17:55 |
| bkero | Protein database | 17:56 |
| bkero | *databank | 17:56 |
| xp_prg | cool | 17:56 |
| xp_prg | bkero can you help me, I want to know all the bio bricks that are "promoters" can this be known? | 17:56 |
| bkero | I'm mirroring the wwpdb. 70gb | 17:56 |
| bkero | xp_prg: I'm not sure, I haven't poke around at biobricks. | 17:56 |
| bkero | I'm a pretty big bionoob. :P | 17:57 |
| xp_prg | ppk you here? | 17:57 |
| ppk | I'm back | 17:58 |
| ppk | hi | 17:58 |
| xp_prg | ppk can you help me to find all bio bricks that are promoters? | 17:58 |
| ppk | should be in here xp_prg | 17:59 |
| ppk | http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Regulatory | 17:59 |
| xp_prg | hi ppk, I am looking at that page but I don't understand the other details, why are they grouped differently? | 18:11 |
| ppk | hm, I'm not sure to be honest | 18:13 |
| ppk | you're referring to the three different sections right? | 18:14 |
| xp_prg | ya | 18:14 |
| ppk | mm, not easy to find info on this stuff | 18:16 |
| xp_prg | ppk want to help me creating an xml file of all the promoters real quick? | 18:16 |
| ppk | yeah ok | 18:16 |
| ppk | what do you need me to do | 18:17 |
| xp_prg | one sec let me get you the format | 18:17 |
| ppk | oh xp_prg, I think I get the diff sectiosn now | 18:18 |
| ppk | so the inducible regulators | 18:18 |
| ppk | that means the gene is not expressed, unless in the presence of a compound, ie AraC | 18:19 |
| ppk | in repressible | 18:19 |
| ppk | the gene is always expressed | 18:19 |
| ppk | EXCEPT in the presence of a compund | 18:19 |
| xp_prg | http://pastebin.com/d748a85bc | 18:19 |
| ppk | ie Lac | 18:19 |
| ppk | do you see what I'm saying? | 18:19 |
| xp_prg | ya kind of | 18:20 |
| xp_prg | do you see my paste link? | 18:20 |
| ppk | yeah I'm on it | 18:20 |
| xp_prg | ok I want you to make the 3 sections under promoters | 18:21 |
| xp_prg | but if you want to further "qualifty" you could do like LAC present only and list those promoters underneath that etc... | 18:21 |
| xp_prg | whatever would help the user | 18:21 |
| xp_prg | do you get what I am saying? | 18:22 |
| ppk | so it would just be repressible, inducible, and other | 18:22 |
| xp_prg | well at its most basic ya, can you think of any sub categories that would be even more useful | 18:23 |
| xp_prg | ? | 18:23 |
| xp_prg | ? | 18:23 |
| xp_prg | perhaps you should sort them by length too | 18:24 |
| xp_prg | I don't know, I leave it to you to decide :> | 18:24 |
| ppk | it would be most useful to people using biobench, I think, to sort by compounds than repress and induce | 18:24 |
| ppk | that* | 18:25 |
| ppk | repress and induce | 18:25 |
| xp_prg | can you explain that to me more, why do you think that? | 18:25 |
| ppk | well they might want a few things to happen | 18:26 |
| ppk | in the presence of one compound | 18:26 |
| xp_prg | ppk lets do this make 2 categories classical and by compound, does that sound good? | 18:26 |
| xp_prg | that way they can have both | 18:26 |
| ppk | sure | 18:27 |
| ppk | but | 18:27 |
| xp_prg | you will repeat biobricks but tha is ok | 18:27 |
| ppk | we ought to get someone who's actually worked with them | 18:27 |
| ppk | too | 18:27 |
| xp_prg | well we have to start somewhere for sure, but I think you get what I am trying to do :> | 18:27 |
| xp_prg | lets get version .004 of this out, go ahead do it as we talked about for now and we can refine it further later | 18:27 |
| ppk | I do, and I mean | 18:27 |
| ppk | you can always sort them later | 18:27 |
| xp_prg | do you understand the xml format etc...? | 18:28 |
| ppk | I think so | 18:28 |
| xp_prg | awsome just paste to pastebin | 18:29 |
| ppk | this is going to be one long-ass file | 18:29 |
| ppk | is there no way to automate this? | 18:30 |
| ppk | then you could periodically check their DB for availability, new parts, and other updated info | 18:30 |
| xp_prg | I wish there was, I don't know of a way, you could do like web screen scraping with perl mechanize | 18:30 |
| xp_prg | do you know perl at all? | 18:30 |
| xp_prg | its pretty straight forward | 18:31 |
| ppk | a little | 18:31 |
| xp_prg | why don't we just do it manually for now and later we will figure out an automated way | 18:31 |
| xp_prg | does that sound good? | 18:31 |
| ppk | sure | 18:32 |
| ppk | the names themselves in biobench isn't going to be very useful | 18:33 |
| ppk | how can you tag the names | 18:33 |
| ppk | with parameters | 18:33 |
| ppk | that allow you to parse through them in different ways? | 18:33 |
| ppk | oh and one other thing | 18:35 |
| xp_prg | well I am just thinking of different sub categories that is all I can think of a way to help | 18:35 |
| ppk | can you make it so if you click on the menu in biobench by accident | 18:35 |
| xp_prg | unless you have another idea | 18:35 |
| ppk | it doesn't close what you just had open? | 18:35 |
| xp_prg | I don't understand what your asking, can you be more specific? | 18:35 |
| ppk | ie, you right click on ecoli | 18:36 |
| ppk | go to promoters | 18:36 |
| ppk | then click on promoters by accident | 18:36 |
| UtopiahGHML | uh.. weird metaphorical idea | 18:36 |
| ppk | you get an error menu | 18:36 |
| UtopiahGHML | you are "the sheepard of your neurones-sheep group/flock" | 18:36 |
| xp_prg | oh ok ya | 18:38 |
| xp_prg | ya I don't like how that works either! | 18:38 |
| xp_prg | I wish I could understand what promoters like only apply to e-coli, do promoters apply to all cells? | 18:38 |
| ppk | yeah | 18:39 |
| ppk | coding DNA (DNA that codes for proteins) is regulated | 18:39 |
| ppk | ok so xp_prg | 18:39 |
| ppk | how does that look | 18:39 |
| ppk | so far | 18:39 |
| xp_prg | ppk I don't mind, whatever you think is best, go ahead and make the xml :> | 18:40 |
| xp_prg | remember this will be the menu drop down when they pick a bio brick | 18:44 |
| ppk | you could definitely automate this | 18:44 |
| xp_prg | if you make the strings too long it will be hard for the people | 18:44 |
| ppk | I know | 18:44 |
| ppk | but | 18:44 |
| xp_prg | ppk we will! Lets just get an initial version though | 18:44 |
| ppk | it makes little sense to label them by biobrick label | 18:45 |
| ppk | then you'd need to know that nomenclature | 18:45 |
| xp_prg | I leave it to you, whatever you think is best for real | 18:45 |
| ppk | which is a block for newbies | 18:45 |
| xp_prg | honestly I am very interested in your opinion, do it how you think is best | 18:45 |
| xp_prg | whatever you think is most intuitive and easy to understand | 18:46 |
| ppk | we need to at least get gfp in there, lawl | 18:53 |
| xp_prg | lawl? | 18:54 |
| xp_prg | ppk you making the xml file? | 18:54 |
| ppk | I'm checking stuff out on partsregistry.org | 18:55 |
| ppk | you know | 18:56 |
| ppk | I bet the MIT people would be open to giving us access | 18:57 |
| ppk | to their db | 18:57 |
| ppk | then we wouldn't need to do as much reverse engineering of the site | 18:57 |
| xp_prg | well lets get something going for now though :> | 18:57 |
| xp_prg | can you pick like a few from each category for now that you think are most important? | 18:58 |
| xp_prg | like GFP? | 18:58 |
| ppk | that's what I'm doing now | 19:01 |
| xp_prg | awsome thanks! | 19:02 |
| kanzure_ | bkero: faceface knows PDB by heart :) | 19:08 |
| kanzure_ | xp_prg: I already gave you a list of all promoter types | 19:08 |
| kanzure_ | http://heybryan.org/books/biobricks/types/ | 19:08 |
| xp_prg | oops sorry :> | 19:08 |
| xp_prg | what on that page are the promoter types? | 19:09 |
| xp_prg | I am confused | 19:09 |
| kanzure_ | xp_prg: Are you using SBML XML format? | 19:10 |
| kanzure_ | ppk: Yes, it's already automated with the scripts in http://heybryan.org/books/biobricks/ | 19:10 |
| ppk | good deal | 19:11 |
| kanzure_ | UtopiahGHML: Shepherding neurons isn't weird. I thought that's the idea of recurisve synaptic plasticity rules/guidaince was amounting to anyway. | 19:11 |
| xp_prg | kanzure it is not SBML, it is the xml necessary for Flash to make a menu display object | 19:11 |
| ppk | they're untagged though | 19:11 |
| xp_prg | ppk do you know what a wiki is and how to use one? | 19:11 |
| ppk | yeah | 19:12 |
| kanzure_ | ppk: So, this is why I don't like xp_prg doing some of these things, :-/ so re: the issue of naming the items. Don't bother. The user doesn't have to see this information. It's a black box. All that matters is that the computer is able to give him candidates for solving a 'black box circuit'. | 19:12 |
| kanzure_ | ppk: I already stole their database, don't bother asking the partsregistry.org people. See the /books/biobricks/ dir that I linked to above. | 19:12 |
| ppk | yeah I see that | 19:13 |
| xp_prg | kanzure the SBML format requires biobricks how is it I don't need to pick one? | 19:13 |
| ppk | but it would be more useful with tags | 19:13 |
| ppk | like a lot of the parts have on partsregistry.org | 19:13 |
| kanzure_ | xp_prg: SBML does not require biobricks. SBML does a lot of General Stuff. | 19:13 |
| kanzure_ | http://sbml.org/ | 19:13 |
| xp_prg | for our purposes though we are going to supply biobricks to SBML are we not? | 19:13 |
| kanzure_ | Yep. | 19:14 |
| xp_prg | ok just making sure | 19:15 |
| UtopiahGHML | kanzure_: well even if it was weird, it's too late, I made http://img227.imageshack.us/img227/9130/neuronsheppardhf8.png ;) | 19:15 |
| xp_prg | ppk can you document what kanzure_ is saying on the project wiki? | 19:15 |
| kanzure_ | Now, as a user, you don't have to pick them. | 19:15 |
| kanzure_ | You could I guess, but for newbies it's not very helpful | 19:15 |
| kanzure_ | In fact, for me it's not very helpful. Like hell I'm going to sit here memorizing the biobricks repository IDing scheme. | 19:16 |
| kanzure_ | That's why I mention the 'black box circuits' example. | 19:16 |
| xp_prg | kanzure_ if you look at the biobench flash app it presents you bio brick parts no memorization required | 19:16 |
| kanzure_ | It's the same work that we were doing with SKDB essentially with the different 'types' and 'flows' and the general 'grammar rules' for the interconnection of components. What does the user care how it is implemented, as long as the requirements are satisfied? | 19:16 |
| kanzure_ | xp_prg: So what? | 19:17 |
| xp_prg | so a user needs to be able to find bio bricks to send to the SBML file | 19:17 |
| ppk | alls I know is, it's going to be a shitload of work to get this up and running and polished | 19:17 |
| xp_prg | ppk, can you just make some initial xml for me to use, I would really appreciate it | 19:18 |
| kanzure_ | ppk: Na. | 19:18 |
| kanzure_ | why not SBML? | 19:18 |
| kanzure_ | That's why we need the SBML generator | 19:18 |
| xp_prg | doesn't have to be lots of stuff or anything | 19:18 |
| kanzure_ | for the past few days that's what we'vebeen talking about .. | 19:18 |
| kanzure_ | http://heybryan.org/graph/ look in here, go into the synbioss dir, then go to the tmp dir | 19:18 |
| kanzure_ | then you will see SBML files that have been generated | 19:18 |
| kanzure_ | (not the .nc files) | 19:18 |
| kanzure_ | Anyway, xp_prg - ideally the user does _not_ have to find biobricks. Your comment about "no memorization required" wasn't talking about the same thing that I was. Two different lines of thought there .. | 19:19 |
| xp_prg | ok, ppk how is that xml coming along? | 19:19 |
| kanzure_ | Heh | 19:19 |
| kanzure_ | Fine, jsut ignore me | 19:20 |
| xp_prg | no, I am not ignoring you, I just want to have a basic proof of concept for my building of the SBML file | 19:20 |
| kanzure_ | What is your script? | 19:20 |
| xp_prg | I must be able to pick biobricks to do that, that is all I am doing | 19:20 |
| xp_prg | I will be leveraging synbioss python scripts | 19:20 |
| xp_prg | but i need to have something to send to them | 19:20 |
| kanzure_ | is this based off of 2008-10-25_sbml_notes.txt? | 19:20 |
| xp_prg | I am not aware of such notes | 19:21 |
| kanzure_ | http://heybryan.org/graph/2008-10-25_sbml_notes.txt | 19:21 |
| xp_prg | no but that is helpful | 19:21 |
| kanzure_ | then what the hell does your script do? | 19:22 |
| xp_prg | kanzure_ I am working on the graphical part right now, it will then build the SBML file from the choices the user makes using the synbyioss python scripts, what is hard to understand? | 19:22 |
| kanzure_ | which scripts. | 19:22 |
| xp_prg | in synybioss? | 19:23 |
| kanzure_ | yes | 19:23 |
| kanzure_ | file names, in particular | 19:23 |
| xp_prg | I don't know yet, I have to find them | 19:23 |
| kanzure_ | How do you know they exist? | 19:23 |
| xp_prg | becuase that is what the designer does | 19:23 |
| kanzure_ | How did you download the designer? | 19:23 |
| xp_prg | it sends input to python modules that build the sbml | 19:23 |
| xp_prg | it is web based, nothing to download | 19:23 |
| xp_prg | interface1.php etc... | 19:24 |
| kanzure_ | so then how do you have the files? | 19:24 |
| kanzure_ | right, you have to have FTP access or something to get the source to the PHP files | 19:24 |
| xp_prg | these files are in subversion on sourceforge on the synbioss project | 19:24 |
| kanzure_ | the interface1.php files etc.? | 19:24 |
| xp_prg | yes, this project is opensource | 19:24 |
| xp_prg | *sigh* | 19:24 |
| kanzure_ | Why weren't these in the main download/ | 19:24 |
| kanzure_ | ? | 19:25 |
| kanzure_ | Grumble grumble. | 19:25 |
| kanzure_ | Let me check. | 19:25 |
| xp_prg | well I don't know for sure, but they should be | 19:25 |
| kanzure_ | There's nothing in the CVS tree on sourceforge. | 19:26 |
| kanzure_ | Aha, so you don't know. | 19:26 |
| kanzure_ | That's what I've been trying to tell you .. | 19:26 |
| kanzure_ | I downloaded synbioss, and it's not there | 19:26 |
| kanzure_ | otherwise I wouldn't be making such a big deal out of it | 19:26 |
| xp_prg | that is a violation of gpl then, you should contact them to release those files | 19:27 |
| kanzure_ | I did. They've ignored my email. :( | 19:27 |
| xp_prg | well I am glad we are doing this project then :> | 19:27 |
| kanzure_ | Kaznessis is the PI of the lab. I emailed him and a few of his students that did the programming. Nothing. | 19:27 |
| xp_prg | ours will be opensource | 19:27 |
| xp_prg | ppk you here? | 19:28 |
| kanzure_ | .. | 19:28 |
| kanzure_ | promotional pep talk doesn't give me my generator. | 19:28 |
| xp_prg | kanzure_ you will have your generator, I like your enthsiasm, keep me on task I agree, but as you have so fondly proven, I must have a gui to supply the parameters to make the sbml file, I am finishing that up as we speak | 19:29 |
| kanzure_ | you don't need a gui | 19:30 |
| kanzure_ | 1) CLI parameter passing | 19:30 |
| kanzure_ | 2) the HTML is already writtenj | 19:30 |
| kanzure_ | so you have two options right there | 19:30 |
| kanzure_ | the second one is a GUI | 19:30 |
| xp_prg | HTML != php, CLI=sucks, either way I need a tool and that is what I am making | 19:30 |
| kanzure_ | HTML is the GUI | 19:30 |
| xp_prg | HTML is not adequate for this applicaiton by itself that is why I am using flash, anyway doesn't matter the ajax will be independent and you can make any gui you would like | 19:31 |
| kanzure_ | who cares about adequacy? | 19:32 |
| kanzure_ | the generator is what matters | 19:32 |
| kanzure_ | it's like putting icing on a cake before you bake the cake | 19:32 |
| xp_prg | kanzure_ you will have it, I must have a way to supply parameters, whether I make in html or cml, I must make one, I am making one relax | 19:32 |
| xp_prg | flash is faster then both of those by the way | 19:32 |
| xp_prg | cml = cli | 19:33 |
| kanzure_ | cml? | 19:33 |
| kanzure_ | eh | 19:33 |
| kanzure_ | flash is faster than both CLI and HTML/ | 19:33 |
| kanzure_ | ?? | 19:33 |
| kanzure_ | 1) you already have the HTML | 19:33 |
| kanzure_ | 2) once you have the generator, the CLI is already done. even faster than #1 | 19:33 |
| xp_prg | yes | 19:33 |
| kanzure_ | so #1 is already done | 19:33 |
| kanzure_ | how is flash faster | 19:33 |
| xp_prg | the html is a program that supplies bio bricks, reactions, effectors, that involves back end coding, flash will encapsulate all of this on the front end, that is faster for this development | 19:34 |
| kanzure_ | HTML is not a program | 19:35 |
| kanzure_ | HTML is already done .. wget http://neptune.cems.umn.edu/designer/interface1.php there you have the first page of HTML | 19:35 |
| xp_prg | HTML is an interface whatever you know what I am saying loops are involved, that involves programming | 19:35 |
| xp_prg | kanzure that html is not enough, back end php code is involved | 19:35 |
| kanzure_ | meh, for ($n = 0; $n < $i; $n++) { print some repeatable part of the HTML } <- done | 19:35 |
| kanzure_ | yes, back end is involved! | 19:36 |
| kanzure_ | go work on the backend! | 19:36 |
| kanzure_ | then the icing on the cake. | 19:36 |
| xp_prg | kanzure_ I am combining the back end in flash relax, I am accomplishing the goal | 19:36 |
| kanzure_ | No you're not. | 19:36 |
| xp_prg | if you want to assist help me finish this gui | 19:36 |
| kanzure_ | No, that's not what we need .. heh' | 19:36 |
| xp_prg | I must have a way to supply the parameters man!!!! | 19:36 |
| xp_prg | stop ignoring that | 19:37 |
| kanzure_ | do you not understand what CLI means? | 19:37 |
| xp_prg | yes I do! | 19:37 |
| xp_prg | the python scripts don't work that way | 19:37 |
| kanzure_ | what python stuff? | 19:37 |
| kanzure_ | it doesn't exist yet | 19:37 |
| kanzure_ | that's why you need to write the backend .. | 19:37 |
| xp_prg | yes it does, its in synbioss! | 19:37 |
| kanzure_ | I thought we just agreed that it's not? | 19:38 |
| kanzure_ | that's why I emailed them, remember? | 19:38 |
| xp_prg | the interface isn't! | 19:38 |
| kanzure_ | the interface is the HTML | 19:38 |
| xp_prg | but the code that generates the sbml from the supplied parameters is! | 19:38 |
| kanzure_ | where? | 19:38 |
| xp_prg | I don't know yet, but it is I can assure you | 19:38 |
| kanzure_ | I've looked, it's not. | 19:38 |
| UtopiahGHML | (I know it's not gonna help but I think you guys are in the Matrix) | 19:38 |
| xp_prg | kanzure_ wow that sucks if it is not | 19:39 |
| kanzure_ | UtopiahGHML: Hm? | 19:39 |
| kanzure_ | That's why you were signed on to do it! | 19:39 |
| xp_prg | ok I was confused regardless to test my code I must have an interface | 19:39 |
| kanzure_ | you have code? | 19:40 |
| xp_prg | kanzure_ I can't make the egg without the chicken man | 19:41 |
| kanzure_ | you already have the icing on the cake .. the HTML .. | 19:41 |
| xp_prg | how will I get the parameters to put in the damn sbml generator? | 19:41 |
| kanzure_ | you know what | 19:41 |
| kanzure_ | new deal | 19:41 |
| kanzure_ | don't worry about that | 19:41 |
| xp_prg | kanzure that HTML is not going to help | 19:41 |
| kanzure_ | just hold them constant | 19:41 |
| xp_prg | constant in what way? | 19:42 |
| kanzure_ | well, instead of input, hold it constant | 19:42 |
| kanzure_ | make it generate a single (known) SBML output of the real designer/interface1,2,3.php scripts | 19:42 |
| kanzure_ | i.e., one of the files in the tmp dir in /graph/synbioss/tmp/ on my server | 19:42 |
| xp_prg | kanzure_ please describe to me the way I will get input into my sbml generator please? | 19:42 |
| kanzure_ | from the previously generated SBML file ;-) | 19:42 |
| kanzure_ | in other words, just hard code it | 19:42 |
| xp_prg | kanzure_ if you have an SBML file, why do you need me to make a generator that makes one? | 19:43 |
| kanzure_ | and then I'll show you how to add parameters to a script | 19:43 |
| kanzure_ | xp_prg: so that I can go make it variablized for you | 19:43 |
| kanzure_ | since you can't seem to do that :( | 19:43 |
| xp_prg | kanzure_ dude I am almost done with the gui, I need 4 things as I see it, biobricks, rates, effectors, and compartments | 19:43 |
| xp_prg | then I can make the sbml, do you disagree? | 19:44 |
| kanzure_ | it's not physically impossibhle, but it's kind of pointless. | 19:44 |
| kanzure_ | you might as well just tell me now how you plan to generate the SBML | 19:44 |
| kanzure_ | in particular, what API calls | 19:44 |
| xp_prg | kanzure_ dude what part of I don't know what api calls I will make without at least first knowing the parameters to use? | 19:45 |
| kanzure_ | the SBML files that were previously generated .. | 19:45 |
| xp_prg | well I would have to write all the code to read in the SBML file, parse them into input parameters, then take those input parameters and create the SBML file, that is more work then writing my own code that makes the input parameters | 19:46 |
| xp_prg | I am working efficiently on this project, please know this | 19:47 |
| kanzure_ | no you wouldn't | 19:47 |
| kanzure_ | you would go physically look at one single file | 19:47 |
| kanzure_ | preferably a small one mind you :) | 19:47 |
| kanzure_ | you would not have to read it in, | 19:47 |
| kanzure_ | you would go eyeball it | 19:48 |
| xp_prg | so you want me to manually type in the input parameters to my sbml generator? | 19:48 |
| kanzure_ | yes | 19:48 |
| kanzure_ | I'll then fix it after that ok? | 19:48 |
| kanzure_ | what's important is that generator. | 19:48 |
| xp_prg | kanzure_ I don't code that way sorry, not trying to be mean, I need you support me in getting a generic good way to get the parameters in, the faster you help me with that, the faster I can make the generator, it won't even take that long! | 19:49 |
| xp_prg | remember this is an ajax app | 19:49 |
| xp_prg | I must pass the paremters in via json | 19:49 |
| kanzure_ | who cares if it is ajax? | 19:49 |
| xp_prg | cuz that is what we agreed on! | 19:49 |
| kanzure_ | the generator is still the generator no matter if it's ajax or not | 19:50 |
| xp_prg | kaznure_ a program takes input man, you must supply that input in a format, I am choosing json, I can't even do a program without input!!! | 19:50 |
| xp_prg | how else would you have me input the parameters? | 19:51 |
| kanzure_ | previous sbml files. | 19:51 |
| kanzure_ | like I said above. | 19:51 |
| xp_prg | kanzure_ dude, you have to read in the data into a data structure | 19:51 |
| xp_prg | then send that as input to the pogram | 19:51 |
| xp_prg | you know this, please don't pretend it is not easier than that | 19:52 |
| xp_prg | how would you store the parameters to input into the pogram? | 19:52 |
| kanzure_ | then why are you wasting so much time with flash? | 19:52 |
| kanzure_ | you'd store it as text on the command line etc. | 19:52 |
| xp_prg | because I can then supply the input in json format easily | 19:52 |
| xp_prg | kanzure please enlighten me on an example cli for sending: biobricks, rates, effectors, compartments to the sbml generator? | 19:53 |
| kanzure_ | example: ./myscript.whateverthefuckthatisn'tflash number_of_biobricks first_biobrick param1 param2 whatever-else-you-need-to-pass-for-each-biobrick biobrick2 param2 ... etc. it's a really dirty simple way of doing it. it requires no thought whatsoever. | 19:54 |
| kanzure_ | no sophistication required | 19:54 |
| kanzure_ | in fact, | 19:55 |
| xp_prg | kanzure_ the devil is in the details man, anyway, dude just help me to do this and we can have this whole thing solved, lets make the simplest sbml file, tell me the inputs you want | 19:55 |
| kanzure_ | strip the SBML from the files and just leave all of the things that were the same as user input and the input to the script should be the file name ("SBML_Stripped") and then the generator's job is to call the set of libsbml API commands that remakes the original file. | 19:55 |
| xp_prg | I will then make the flash to send those inputs *problem solved* | 19:56 |
| kanzure_ | go get the simplest sbml files | 19:56 |
| ppk | xp_prg: you have mail | 19:56 |
| ppk | gotta go run | 19:56 |
| xp_prg | ppk awsome! | 19:56 |
| kanzure_ | already told you, they're over here: http;//heybryan.org/graph/synbioss/tmp/ | 19:56 |
| xp_prg | ok I will look at that, I will do that tonight | 19:57 |
| xp_prg | kanzure_ it would help if you would compromise, projects are a give and take, it would also go faster, just food for thought | 19:58 |
| kanzure_ | there's no compromise here .. either you have the generator or you don't .. it's like somebody saying "hey, can you get me a coke?" and you hand them a Macintosh | 19:59 |
| xp_prg | kanzure_ well we disagree on the best way to supply the parameters to the generator it is a very small point that has been blown out of proportion | 20:00 |
| kanzure_ | you kidding? | 20:00 |
| kanzure_ | you've been on this for a week | 20:00 |
| kanzure_ | it's a friggin' parameter, just make a variable in a script. screw flash and flashy stuff. | 20:01 |
| xp_prg | kanzure_ dude it takes time for me to even learn what is happening, I didn't know what a kinetic reactions was until Satruday | 20:01 |
| kanzure_ | you don't have to know though | 20:01 |
| xp_prg | I can't use an api that I have no idea what it does | 20:01 |
| kanzure_ | (it's nice to know, though, yes) | 20:01 |
| kanzure_ | yeah you can .. | 20:02 |
| xp_prg | I do if I want to make sense of what to pass it | 20:02 |
| kanzure_ | the API is directly correlated to the names of the elements in the SBML | 20:02 |
| xp_prg | dude, that is what I am trying to tell you, I don't know even know the names in the SBML or what they mean | 20:02 |
| kanzure_ | you have to go open up an SBML file to see that information .. | 20:02 |
| xp_prg | if I sent a rate instead of a biobrick the whole thing would not work | 20:02 |
| kanzure_ | http://heybryan.org/graph/synbioss/tmp/ | 20:02 |
| xp_prg | kanzure_ keep in mind, most programmers want to understand what they are doing, it is quite weird and foregin for someone to use an api and they have almost no idea what it is doing | 20:04 |
| kanzure_ | then why focus on flash? | 20:04 |
| kanzure_ | why not focus on understanding the API? | 20:05 |
| kanzure_ | deoxygen even tells you what the variable inputs have to be | 20:05 |
| kanzure_ | i.e., typed inputs (string, int, whatever) | 20:05 |
| xp_prg | kanzure_ cuz originally we decided to make this a web ajax based app | 20:05 |
| xp_prg | that is why | 20:05 |
| kanzure_ | AJAX means that there's a server side component .. | 20:06 |
| kanzure_ | i.e., a 'back end' | 20:06 |
| kanzure_ | the AJAX is just fancy crap frontend stuff that you get to ignore as a programmedr | 20:06 |
| kanzure_ | *programmer | 20:06 |
| xp_prg | yes that is right but you have to have a way to invoke the ajax interface kanzure_ you can't have a cart without a horse | 20:06 |
| kanzure_ | don't worry about that, I'll take care of that | 20:07 |
| xp_prg | kanzure_ I am working on it, I think you understand why I am doing what I am doing, you may not like it, but I must have some kind of program to input parameters | 20:07 |
| kanzure_ | I don't like it because it's wrong./ | 20:08 |
| xp_prg | it is not wrong to have a good way to input parameters | 20:08 |
| kanzure_ | right, as long as you have something that you're inserting it into .. it's like making Windows only to realize that you don't have anything good for your operating system to manage. | 20:10 |
| kanzure_ | i.e., the generator | 20:11 |
| kanzure_ | Ooh. Just defeated the pesky Jedi. Yay. This took way too long. :) (Star Wars game thingy) | 20:12 |
| xp_prg | well cool! | 20:34 |
| xp_prg | anyway, it won't be much longer I am understanding the input parameters etc... | 20:34 |
| kanzure__ | There's nothing to understand .. this doesn't require specialist knowledge. Just allow N of the first kind of inputs, T of the second kind of inputs, etc. | 21:45 |
| xp_prg | I am done arguing kanzure_ if you want it to go faster help me get the basics of my flash input app working | 21:46 |
| xp_prg | otherwise wait | 21:47 |
| bkero | faceface: ping ping | 21:47 |
| kanzure__ | procto: How does one go about converting SVG to DXF? | 21:56 |
| kanzure__ | procto: I like your electrophoresis.py :) /me only wishes there would be some sort of 'metadata usage specification' for piping software together. This would be a good component in SKDB. | 21:59 |
| bkero | There is. It's called xmlrpc. :) | 22:00 |
| kanzure__ | That sounds familiar. I've used it before .. once. | 22:02 |
| bkero | It's for inter-program data passing | 22:16 |
| xp_prg | I know xmlrpc well it is built into python | 22:17 |
| ppk | hey | 22:19 |
| ppk | back | 22:19 |
| ppk | frig, 6-something miler with marathon runners can be demanding | 22:19 |
| ppk | xp_prg: I wasn't sure how to format those sections, but I'll give it a shot now | 22:19 |
| xp_prg | ppk awsome man! | 22:20 |
| xp_prg | ppk you know what the promoters are | 22:20 |
| xp_prg | ppk also I don't see how to link your entries to an actual biobrick can you help me to understand that? | 22:21 |
| ppk | hm | 22:23 |
| ppk | can you have a hidden parameter? | 22:23 |
| ppk | I can give you the part names | 22:23 |
| xp_prg | no, just put them in a list at the top, don't put them in the xml so I can have a way to telling | 22:24 |
| kanzure__ | do you not like my list of bricks? | 22:24 |
| xp_prg | kanzure__ I do and I ask you a question about them and you ignored me | 22:25 |
| xp_prg | anyway I have to go to lunch | 22:25 |
| -!- xp_prg is now known as xp_lunch | 22:25 | |
| kanzure__ | http://www.lightconeinstitute.org/ <- While not awesome, I would love to own lightcone.org | 22:30 |
| kanzure__ | xp_lunch: "what on that page are the promoter types?" <- http://heybryan.org/books/biobricks/types/ <-- ppk answered your question already. "Regulatory". | 22:32 |
| kanzure__ | Added two new presentations to http://heybryan.org/~bbishop/docs/repo/presentations/ (the "Suggestions" pptx files) (nothing hugely important ..) | 22:39 |
| bkero | Shit. Fallout 3 leaked for PC. | 22:43 |
| xp_lunch | ppk you here? | 23:43 |
| -!- xp_lunch is now known as xp_prg | 23:43 | |
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