--- Day changed Mon Oct 27 2008 00:20 < bkero> http://www.rcsb.org/pdb/home/home.do 00:47 < ppk> lawl@Tom Knight flipping out in DIYbio 00:47 * bkero didnt see that 00:48 < kanzure_> Me either. 00:48 < bkero> Have any of you guys seen Fringe? 00:49 < 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. 00:50 < 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. :/ 00:51 < 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 00:52 < 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. 01:00 < 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? :( 01:01 < 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 01:14 < ppk> ? 01:14 < ppk> first round? 01:14 < ppk> I don't believe I saw that 01:15 < bkero> You mean hubris. 01:19 < kanzure_> ppk: Tom Knight was telling me that I wasn't made up of cells or something 01:20 < kanzure_> I had to admit that I had never 'tested myself', but. 01:37 < kanzure_> Hi Sparn 01:38 < Sparn> Hi 01:38 < kanzure_> What brings you around these parts? 01:39 < Sparn> Well 01:39 < Sparn> I found this channel on the biopunk forums 01:40 < kanzure_> Deep in the archives? 01:40 < Sparn> oct 3 01:41 < Sparn> It is a fairly small forum, so I don't know what qualifies as "deep" lol 01:44 < kanzure_> There's a few of us in here that visit the forum every now and then, so yeah. 01:51 < Sparn> Any current projects? 01:52 < 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 .. 01:53 < kanzure_> stuff I'm probably forgetting 01:54 < Sparn> cool 01:56 < fenn> is sparn a swedish name? 01:56 < Sparn> nope 01:57 < Sparn> It is just a name I made up. 01:57 < Sparn> Or word. 01:58 < Sparn> It is short and doesn't have any meaning I am aware of. 01:58 < fenn> ah. it just sounded familiar somehow 02:00 < fenn> kanzure why do you need filters for the bioreactor? why not just centrifuge? 02:01 < 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 02:02 < 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> :/ 02:03 < fenn> nobody even replied, and i'm not up in the daytime to telephone 02:03 < bkero> Ouch 02:04 < 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. 02:06 < fenn> ok from now on i'm sending duplicates from both addresses 02:13 < kanzure_> oh wait 02:13 < kanzure_> fenn: what's your relayhost? 02:15 < kanzure_> Are you sending mail from your own mailserver, I mean. 02:16 < fenn> no 02:16 < fenn> sdf.lonestar.org 02:52 < drazak> lonestar :D 02:52 < drazak> fenn: that's where I know you from! 03:24 -!- splicer_ is now known as splicer 03:43 * procto is writing a gel box blueprint generator 03:46 < procto> I was going just to draw some SVG 03:47 < procto> but then realised that a different thickness of the plastic material 03:49 < procto> would mean I have to use different measurements 04:23 < kanzure_> procto: What's the input to your generator? 04:23 < kanzure_> width of plastics? 04:44 < wrldpc> Anyone know any good movies that are comprised entirely of footage taken from the microbiological scale? 04:49 < bkero> lol 04:49 < bkero> Inner Space 04:50 < splicer> It was big in the 30:ies I think 04:50 < splicer> (excuse the pun) 04:53 < 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 04:54 < fenn> more at http://www.molecularmovies.com/showcase/index.html 05:07 < procto> kanzure_: yeah, and you can also tweak other size paramateres 05:07 < procto> kanzure_: like desired depth of gel, etc 05:43 < wrldpc> I hear environmentalists scream all the time "20 species die every minute" but where are the statistics on how many are born? 06:00 < bkero> Ssh 06:00 < bkero> They haven't figured out there are things you can't hug or smoke yet. 06:02 < 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 06:03 < procto> i.e. languages dying, versus new ones being created 06:04 < bkero> It's not like we're getting NEW culture or anything 06:06 < 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 06:07 < 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 06:08 < 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 06:21 < wrldpc> hm 06:22 < 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 06:26 < procto> yay, i'm done writing my generator 06:26 < procto> sorta 06:26 < procto> need to figure out what to do about units... 06:35 < fenn> you shoulda been thinking about units from the start 06:36 < procto> I have been 06:36 < procto> that is, as long as the user is uniform, the resulting SVG will be fine 06:37 < 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 06:38 < 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 06:39 < 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 07:00 < fenn> why is there no "lcd repair for dummies" book? 07:01 < 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... 07:02 < fenn> but they arent shorted out or anything 07:02 < bkero> Caps are kind of a test to pain 07:03 < fenn> i set the meter to 'resistance' and the speed it counts up depends on the capacitance (for big electrolytics) 07:04 < fenn> i guess that doesn't really tell you if the dielectric is busted though 07:07 < 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 07:29 < 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 08:56 < faceface> garry badder is cool 08:56 < faceface> shame his DB was ethered 08:58 < faceface> although this talk is pretty lame 08:59 < 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 09:00 < 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) 09:01 < 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) 09:02 < 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 :) 09:03 < 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 09:04 < 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 ;) 09:05 < 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. 09:06 < faceface> "HplusDegree" ? 09:06 < UtopiahGHML> yep 09:07 < 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 09:08 < 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 09:09 < UtopiahGHML> faceface: page with an ok name + edited conversation log, the rest will follow and gradually take place 09:10 < UtopiahGHML> then send back the URL so that I could RSS-subscribe it please 09:11 < fenn> UtopiahGHML: i dont watch TV so you'll have to explain 09:11 < faceface> http://biocourse.org/index.php/H%2B 09:12 < 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 09:13 < 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 09:14 < faceface> why me ho type 09:14 < faceface> gah! 09:14 < fenn> spanish keyboard 09:14 < UtopiahGHML> faceface: where can we find the logs? 09:15 < 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... 09:16 < faceface> UtopiahGHML, I'll do it this evening 09:16 * fenn sees "BIND" and things DNS server 09:17 < 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 09:18 < UtopiahGHML> http://biocourse.org/index.php?title=H%2B&action=history&feed=rss seems to fail 09:42 < fenn> seems BMID would have been a better acronym, but what do i know.. 10:37 < UtopiahGHML> anybody knows a framework to quickly move from webpage to blackberry/iphone/mobile devices pages? 10:38 < fenn> define "move" 10:38 < UtopiahGHML> url please since it's a common word 10:39 < fenn> ENOPARSE 10:39 < fenn> (A)bort, (R)etry, (F)ail? 10:40 < UtopiahGHML> (is he actually talking to anybody?) 10:41 < fenn> (A)bort, (R)etry, (F)ail? 10:43 < UtopiahGHML> R 10:44 * 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)? 10:45 < 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. 10:47 < fenn> seems tough to fit that blob-map onto a cellphone screen 10:48 < 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 10:49 < UtopiahGHML> yes the "blob-map" ajax thing would have to be modified 10:53 < fenn> http://mobiforge.com/page/mobile-emulators 10:55 < fenn> i guess "mobile" is the new buzzword, "cell phone" doesnt return crap 10:56 < UtopiahGHML> well the Nokia N810 isn't a cellphone 10:56 < UtopiahGHML> the new buzzword is actually InternetDevice ;) 10:58 < fenn> that's even worse, at least mobile conveys some information 10:59 < UtopiahGHML> they should all be called Navi anyway. 11:10 < fenn> oo wow this is amazing, i take back all snarky comments about "lcd repair for dummies" http://www.wizardanswers.com/liquidvideorepair.html 11:28 < 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 11:43 < kanzure_> Why didn't anyone answer fenn's question about the degree? 11:46 < 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 11:48 < fenn> gas = 38.5 MJ/l, car gets 30mi/gal, so 0.205mi/MJ 11:49 < 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 11:50 < UtopiahGHML> Id like to have a home appliance /per_mile scale :) 11:51 < 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 11:52 < 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 11:53 < UtopiahGHML> know any graph with miles per home appliance hour? 11:53 < fenn> or some sort of coal + methane derived liquid 11:54 < 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... 11:55 < 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 11:57 < UtopiahGHML> ok, gotta cook with huge waste-energy-home-appliance-devilish modern technology ;) 12:01 < 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 12:24 < kanzure_> "The Force Unleashed" feels like a Shadows of the Empire remake. Same sort of TIE-fighter factory. 16:00 < kanzure__> Hello. 16:17 < bkero> SOTE was pretty cool. 16:28 < 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 16:29 < ybit-school> kanzure_ starfox? 16:29 < ybit-school> oh, star wars, right 16:29 < ybit-school> not literally a falcon flying a ship 16:34 < kanzure__> bkero: Probably. I do remember it being N64. 16:37 < 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 16:38 < bkero> My first star wars game was the second SNES one. 16:39 < 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 16:40 < kanzure__> Yay! Hod Lipson! 16:40 < kanzure__> Date/Time: Friday, November 7, 2008 11:00 a. 16:40 < kanzure__> hah hah! 16:42 * kanzure__ is very happy 16:43 < bkero> I remember playing X-Wing, then TIE-Fighter, then X-Wing vs TIE-Fighter 16:44 < ybit-school> anyone played moon base one? 16:45 < kanzure__> Ok. Typo in the pl file. 16:45 * kanzure__ quickly removes the file so that no one will ever see his error. 16:47 < kanzure__> maybe ->copy() is a pointer copy instead of direct copy. 17:20 < 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 17:21 < ybit-school> i like the names :) 17:23 < bkero> http://en.wikipedia.org/wiki/Rolling_release 17:23 < bkero> So much better, but these don't generate press reports. 17:34 < 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 17:35 < kanzure__> http://dhcp-84-253.me.utexas.edu/two.pl.txt 17:36 < 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." 17:37 < ppk> bryan do you have anything on synthesizing RNA for RNAi? 17:38 < 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 17:39 < 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. 17:40 * kanzure__ goes off to chem 17:41 < ppk> yeah so, it sounds like siRNA synthesis is what I'm looking for 17:41 < ppk> cya 17:42 < ppk> Synthetic small interfering RNA (siRNA) and retroviral short hairpin RNA (shRNA) 17:43 < ppk> both apparently trigger RNAi 17:55 < 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? 17:56 < 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. 17:57 < bkero> I'm a pretty big bionoob. :P 17:57 < xp_prg> ppk you here? 17:58 < 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? 17:59 < ppk> should be in here xp_prg 17:59 < ppk> http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=Regulatory 18:11 < xp_prg> hi ppk, I am looking at that page but I don't understand the other details, why are they grouped differently? 18:13 < ppk> hm, I'm not sure to be honest 18:14 < ppk> you're referring to the three different sections right? 18:14 < xp_prg> ya 18:16 < 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 18:17 < ppk> what do you need me to do 18:17 < xp_prg> one sec let me get you the format 18:18 < ppk> oh xp_prg, I think I get the diff sectiosn now 18:18 < ppk> so the inducible regulators 18:19 < 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? 18:20 < xp_prg> ya kind of 18:20 < xp_prg> do you see my paste link? 18:20 < ppk> yeah I'm on it 18:21 < 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 18:22 < xp_prg> do you get what I am saying? 18:22 < ppk> so it would just be repressible, inducible, and other 18:23 < 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> ? 18:24 < 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 18:25 < ppk> that* 18:25 < ppk> repress and induce 18:25 < xp_prg> can you explain that to me more, why do you think that? 18:26 < 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 18:27 < 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 18:28 < xp_prg> do you understand the xml format etc...? 18:28 < ppk> I think so 18:29 < xp_prg> awsome just paste to pastebin 18:29 < ppk> this is going to be one long-ass file 18:30 < 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? 18:31 < 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? 18:32 < ppk> sure 18:33 < 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? 18:35 < 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? 18:36 < 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" 18:38 < 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? 18:39 < 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 18:40 < xp_prg> ppk I don't mind, whatever you think is best, go ahead and make the xml :> 18:44 < 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 18:45 < 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 18:46 < xp_prg> whatever you think is most intuitive and easy to understand 18:53 < ppk> we need to at least get gfp in there, lawl 18:54 < xp_prg> lawl? 18:54 < xp_prg> ppk you making the xml file? 18:55 < ppk> I'm checking stuff out on partsregistry.org 18:56 < ppk> you know 18:57 < 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 :> 18:58 < 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? 19:01 < ppk> that's what I'm doing now 19:02 < xp_prg> awsome thanks! 19:08 < 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 :> 19:09 < xp_prg> what on that page are the promoter types? 19:09 < xp_prg> I am confused 19:10 < 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/ 19:11 < 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? 19:12 < 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. 19:13 < 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? 19:14 < kanzure_> Yep. 19:15 < 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 19:16 < 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? 19:17 < 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 19:18 < 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) 19:19 < 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 19:20 < 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? 19:21 < 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 19:22 < 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. 19:23 < 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 19:24 < 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/ 19:25 < 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 19:26 < 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 19:27 < 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 19:28 < xp_prg> ppk you here? 19:28 < kanzure_> .. 19:28 < kanzure_> promotional pep talk doesn't give me my generator. 19:29 < 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 19:30 < 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 19:31 < 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 19:32 < 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 19:33 < 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 19:34 < 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 19:35 < 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 19:36 < 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!!!! 19:37 < 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! 19:38 < 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) 19:39 < 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 19:40 < kanzure_> you have code? 19:41 < 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 19:42 < 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 19:43 < 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 19:44 < 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 19:45 < 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 .. 19:46 < 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 19:47 < 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, 19:48 < 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. 19:49 < 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! 19:50 < 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!!! 19:51 < 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 19:52 < 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 19:53 < xp_prg> kanzure please enlighten me on an example cli for sending: biobricks, rates, effectors, compartments to the sbml generator? 19:54 < 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 19:55 < 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. 19:56 < 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/ 19:57 < xp_prg> ok I will look at that, I will do that tonight 19:58 < 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 19:59 < 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 20:00 < 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 20:01 < 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) 20:02 < 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/ 20:04 < 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? 20:05 < 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 20:06 < 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 20:07 < 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 20:08 < 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 20:10 < 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. 20:11 < kanzure_> i.e., the generator 20:12 < kanzure_> Ooh. Just defeated the pesky Jedi. Yay. This took way too long. :) (Star Wars game thingy) 20:34 < xp_prg> well cool! 20:34 < xp_prg> anyway, it won't be much longer I am understanding the input parameters etc... 21:45 < 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. 21:46 < 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 21:47 < xp_prg> otherwise wait 21:47 < bkero> faceface: ping ping 21:56 < kanzure__> procto: How does one go about converting SVG to DXF? 21:59 < 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. 22:00 < bkero> There is. It's called xmlrpc. :) 22:02 < kanzure__> That sounds familiar. I've used it before .. once. 22:16 < bkero> It's for inter-program data passing 22:17 < xp_prg> I know xmlrpc well it is built into python 22:19 < 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 22:20 < xp_prg> ppk awsome man! 22:20 < xp_prg> ppk you know what the promoters are 22:21 < xp_prg> ppk also I don't see how to link your entries to an actual biobrick can you help me to understand that? 22:23 < ppk> hm 22:23 < ppk> can you have a hidden parameter? 22:23 < ppk> I can give you the part names 22:24 < 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? 22:25 < 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 22:30 < kanzure__> http://www.lightconeinstitute.org/ <- While not awesome, I would love to own lightcone.org 22:32 < kanzure__> xp_lunch: "what on that page are the promoter types?" <- http://heybryan.org/books/biobricks/types/ <-- ppk answered your question already. "Regulatory". 22:39 < kanzure__> Added two new presentations to http://heybryan.org/~bbishop/docs/repo/presentations/ (the "Suggestions" pptx files) (nothing hugely important ..) 22:43 < bkero> Shit. Fallout 3 leaked for PC. 23:43 < xp_lunch> ppk you here? 23:43 -!- xp_lunch is now known as xp_prg