--- Day changed Tue Oct 14 2008 00:00 < xp_prg> wow cool, what does it do? 00:05 < kanzure> You haven't been listening? I thought we told you about it earlier today. 00:06 < xp_prg> no 00:06 < kanzure> http://synbioss.sf.net/ 00:06 < kanzure> The web interface does what we want to do with 'biobench' except without the AJAX interface. 00:06 < kanzure> Hell, I was talking with you on the mailing list about this .. 00:06 < kanzure> wtf? 00:10 < fenn> ha 00:11 < xp_prg> wow that is cool software! 00:13 < kanzure> I wonder where 'unum' is found. 00:17 < kanzure> .. any hints? 00:17 < bkero> Like E Pluribus unum? 00:17 < kanzure> No, it's a python module. 00:17 < kanzure> For synbioss. 00:18 < xp_prg> kanzure why do we want to re-create synbioss? 00:18 < kanzure> We're not .. 00:18 < fenn> prolly bad path or not installed from src yet 00:18 < kanzure> the module, fenn? 00:18 < fenn> any files called unum in the synbioss release? 00:18 < kanzure> xp_prg: AJAX interface + ikiwiki + git backend for the distribution of those files 00:18 < kanzure> fenn: no. 00:18 < kanzure> "Ecology: The Ascendent Perspective" 00:18 < kanzure> oops 00:18 < kanzure> bad paste 00:19 < kanzure> http://synbioss.sourceforge.net/ 00:19 < kanzure> http://sourceforge.net/project/showfiles.php?group_id=203655&package_id=242861&release_id=625492 00:19 < fenn> anyway, it appears to be here: http://sourceforge.net/projects/unum/ http://home.scarlet.be/be052320/Unum.html 00:19 < kanzure> this being the 'desktop simulator' 00:19 < fenn> and sounds like a great idea to me :) 00:19 < kanzure> hm? 00:19 < kanzure> 'Unum stands for 'unit-numbers'. It is a Python module that allows defining and manipulating true quantities, i.e. numbers with units like volts, hours, meter-per-second. Consistency between units is checked for every operation involving quantities.' 00:19 < fenn> a Python module that allows defining and manipulating true quantities, i.e. numbers with units like volts, hours, meter-per-second. Consistency between units is checked at each expression evaluation; unit conversion and unit output formatting are performed automatically when needed. 00:19 < kanzure> geeze 00:19 < kanzure> hrm 00:20 < xp_prg> how will our project biobench be different then there as far as logic is concerned? 00:20 < kanzure> wonder how they're using it. 00:20 < kanzure> xp_prg: logic? not at all .. 00:20 < kanzure> their code easily serves as backend 00:20 < kanzure> but notice that their wiki is kind of wrong 00:20 < kanzure> it's not git and it's not ikiwiki 00:20 < kanzure> it's on some randomass mediawiki 00:20 < kanzure> whereas those SBML files belong in a repository .. 00:20 < xp_prg> hmm... ok, so basically all we are doing is adding an ajax front end to their program? 00:21 < kanzure> No. 00:21 < kanzure> There's also the backend ikiwiki + git stuff. 00:21 < xp_prg> but how does that affect the logic? 00:21 < kanzure> What? 00:21 < xp_prg> the algoirthms 00:21 < kanzure> It won't. But the codebase has to be manipulated a bit. 00:21 < xp_prg> are we going to use different algoirthms then sybioss or the same ones? 00:22 < kanzure> Same ones. 00:22 < kanzure> Fundamentally they're the same thing, but it's the architecture that matters 00:22 < xp_prg> so what is the real difference besides the ajax front end then? 00:22 < kanzure> ikiwiki + git 00:22 < xp_prg> which offers what exactly? 00:22 < xp_prg> by the way I program python all day :) 00:24 < kanzure> Do you know what a repository is? 00:24 < xp_prg> yes 00:24 < fenn> it offers the ability to edit and massage plain text files without going through some horrible html interface 00:24 < fenn> and also easy forking of the whole project 00:25 < kanzure> "Git is a free distributed revision control, or software source code management project with an emphasis on being fast." "A wiki is a page or collection of files designed to enable anyone who accesses it to contribute or modify content.[1][2] Wikis are often used to create collaborative websites and to power community websites." 00:25 < fenn> and still panders to people who simply must have a pretty html front end 00:25 < kanzure> or pretty ajax frontend 00:25 < xp_prg> ok 00:25 * fenn would prefer plain html 00:26 < kanzure> fenn: I'd disagree. AJAX, or no HTML at all .. just go CLI at that point. 00:26 < fenn> i've seen horrible crimes committed with AJAX 00:26 < fenn> HTML on the other hand is hard to do evil with 00:26 < kanzure> are you kidding :( 00:26 < kanzure> it's all evil 00:26 < fenn> there's only so many ways they can screw up though 00:27 < fenn> so it's a lesser evil :) 00:27 < kanzure> I'm surprised how exactly synbioss matches what I was thinking of 00:27 < fenn> we are shooting for interoperability, that's the whole point 00:28 < kanzure> it's spot-on .. 'unum' is freaky too 00:28 < kanzure> although obvious. 00:28 < fenn> sigh i guess i'll look at synbioss's stupid pd 00:28 < fenn> pdf 00:28 < kanzure> link? 00:28 < fenn> its just the tutorial, closest i could find to a screenshot 00:32 < kanzure> another thing to poke at is the BioModelWiki thing going on there .. don't know how they're storing, generating, or doing anything at all with the downloadable models there 00:32 < kanzure> looks like it's just SBML created from looking through the literature 00:32 < kanzure> which I'm fairly surprised about .. wondering what sort of tie-ins with biobricks they have there 00:34 < kanzure> http://ask.slashdot.org/askslashdot/03/04/25/2054223.shtml?tid=126 open source inventory control software 00:34 < fenn> i thought it was the same people 00:34 < xp_prg> what is SBML ? 00:35 < fenn> synbio modeling language? 00:36 < kanzure> systems biology markup/modeling language 00:36 * kanzure sits on the sbml mailing lists 00:37 < xp_prg> wow cool 00:38 * xp_prg feels excited now that we have a backed already written! 00:38 < fenn> way to go team! 00:38 < kanzure> hah 00:38 < fenn> beer's on me dudes 00:38 < kanzure> get back to work. 00:38 < fenn> i want to celebrate your progress 00:42 < kanzure> a few things; 1) ikiwiki+git+ajax stuff; 2) inventory management, automated procurement for bio materials and eventually equipment / instructions; 3) pulling from giant databases like neurocommons for helping the user to design ridiculous things that they probably don't have the expertise to be designing anyway .. 00:42 < kanzure> but .repo format and the formats used by synbioss should probably be done before #2 00:42 < kanzure> s/done/synchronized/ 00:43 < fenn> what is .repo exactly? 00:44 < kanzure> a load of shit 00:44 < kanzure> have you seen the files? 00:44 < fenn> i mean what you expect to turn it into 00:44 < kanzure> the .tar + yaml metadata 00:44 < kanzure> or no .tar, either way 00:44 < fenn> duh i must be missing something here 00:44 < kanzure> either everything in the same file, like the current .repo files (which I've discovered happens to sucks immensely) or in a tar 00:45 < fenn> yeah files were invented for a reason 00:45 < kanzure> does the duh signify you understand? because the second part of your message suggests you don't 00:45 < kanzure> s/sucks/suck/ 00:45 < fenn> i just feel stupid, writing my resume :( 00:45 < kanzure> "well, I went to school. does that count?" 00:45 < fenn> "should i say tcpdump _and_ tcp/ip knowledge or is the second implied by the first?" 00:46 < kanzure> tcpdump, then cite ISO standards for TCP/IP if you must 00:46 < fenn> ah can wrassle a whole herd o' com pee yoo tars 00:46 < kanzure> o' com pee yoo tars? 00:46 < kanzure> hrm 00:46 < kanzure> deep south? 00:46 < fenn> ken-tucky 00:47 < fenn> or southern indiana, if you prefer 00:48 < fenn> so .repo is basically skdb projects 00:49 < kanzure> except it sucks immensely. it's missing a few important things. 00:49 < kanzure> first of all, all artifacts/subcomponents are _not_ their own repo files which is a failure 00:49 < kanzure> also, there's no metadata specifying their interconnectivity really 00:49 < kanzure> there's some information by having an artifact as a child of the overall system 00:49 < fenn> well, if you hate the ADL stuff then dont try to polish a turd 00:49 < kanzure> and then there's stuff like "ParentArtifact=" and "InputArtifact=" and "OutputArtifact=" 00:50 < kanzure> I really like that it has all of this data already entered 00:50 < fenn> but it's useless 00:50 < kanzure> I'm not entirely sure of that yet 00:50 < kanzure> the format is so terrible that I can't determine that entirely 00:50 < fenn> hm. 00:50 < kanzure> there's input/output artifacts from each artifact, which is *sort of* like interconnectivity 00:51 < kanzure> http://heybryan.org/~bbishop/docs/repo/CFGs/72.png <-- it *looks* useful 00:51 < fenn> you dont need 300 different consumer products to show a proof of concept 00:51 < fenn> shit why did i click on that 00:51 < kanzure> oh crap, you don't like big images, that's right 00:52 < kanzure> have you even seen a part of it yet? or did you use imagemagick to size it down 00:52 < fenn> i've seen it and i think neato/fdm looks way better 00:52 < fenn> and it's not godfuckingawful huge 00:52 < kanzure> I ran it through both of those and it looked the same 00:52 < kanzure> I'll try again Real Soon 00:52 < kanzure> my next run through or something. 00:52 < fenn> what's generating the .dot files/ 00:52 < kanzure> (btw, I have successfully extracted the files from within the .repo files .. but the data format looks peculiar, I think it's encoded) 00:53 < kanzure> well, I exported all of the .repo files into a mysql database 00:53 < kanzure> with about 9 different tables to represent the different types of elements 00:53 < fenn> i ask this because the graphs would be a lot better if the links were colorized by flow type 00:53 < kanzure> instead of labeled by flowtype? 00:54 < fenn> yeah, the labels just get in the way 00:55 < fenn> not that i know what you're going to do with them anyway 00:55 < kanzure> http://dhcp-84-253.me.utexas.edu/phpmyadmin/ if you want to poke at the database 00:55 < kanzure> hrm 00:55 < kanzure> I was thinking this should be obvious 00:55 < kanzure> wouldn't it be a good idea to generate the YAML files that we wanted? 00:55 < kanzure> where the 'units' are going to be very basic such that it's just those flow types that the different parts (apparently) accept 00:56 < kanzure> each part being a new yaml file 00:56 < kanzure> and I guess I want to do it as a system of directories where I'll just tar them up in the end 00:56 < kanzure> or tar+gzip is ok too 00:56 < fenn> as long as you dont start calling 'flow types' units 00:57 < kanzure> 'allowables'. 00:57 < kanzure> but how does this mesh with our previous usage of 'units' ontology? 00:57 < fenn> it's horribly imprecise and has no numerical quantity 00:58 < fenn> like, i cant even guess at what they're talking about for most of the flows 00:58 < kanzure> sometimes it's not even a real flow .. sometimes it's supposed to represent an object leaning against another one 00:58 < fenn> you mean most of the time 00:58 < kanzure> heh 00:58 < kanzure> I haven't ran the stats. 00:58 < fenn> 'force flow' 00:59 < fenn> the force is strong in this bolt 00:59 < kanzure> i wish it told me such. 01:00 < kanzure> okay, so originally I was thinking it would just be a simple variable in the yaml file as one of the first few things that are specified .. 01:01 < kanzure> !!python/thingy/that/I/forget/but/is/necessary/for/specifying/general/type/of/yaml-doc 01:01 < kanzure> inputs: some general specification here 01:01 < kanzure> outputs: some general specification here 01:01 < kanzure> author: 01:01 < kanzure> trulymeta-data-crap here: ... 01:01 < kanzure> what's that "some general specification" if not "50 grams" ? 01:01 < kanzure> (I don't think it was going to be "50 grams" originally anyway) 01:01 < fenn> 50 grams isnt enough info 01:02 < fenn> is that, capacity: 50g? or weight: 50g? 01:02 < fenn> but it gets worse for other units 01:03 < kanzure> terrible problem. 01:04 < kanzure> what if parts had to 'negotiate' their interfaces? 01:05 * fenn flees in panic 01:08 < kanzure> you have a better idea? 01:08 < kanzure> I mean, there's no way for me to figure it all out upfront 01:08 < fenn> standards 01:08 < kanzure> because of the increasingly sophisticated interconnections that will be required 01:08 < kanzure> right 01:08 < kanzure> but right now we don't have those standards 01:08 < fenn> we'll just have to figure them out one by one 01:08 < fenn> or someone will 01:09 < kanzure> and in the mean time 01:09 < fenn> we can get by with a small number of standards to play with 01:09 * fenn has a sense of deja vu 01:10 < kanzure> aren't we right back to where we started 01:10 < fenn> yep 01:11 < fenn> i have NIH syndrome and no motivation, so this tend to lead to pacing in circles 01:11 < kanzure> I tend to pace in straight lines personally 01:11 < kanzure> pacing, by definition, involves going backwards 01:11 < kanzure> or looping etc. 01:11 < kanzure> would you kill me if I do 'allowable flow types' as inputs to the parts? 01:12 < fenn> no, do whatever ou want 01:12 < kanzure> I'll certainly never forgive myself because if it catches on it'll just be al oad of shit 01:12 < kanzure> *a load of shit 01:12 < fenn> yes it will be a load of shit, and already exists as ADL repo, so i dont see why you want to try to continue that 01:12 < kanzure> chicken and egg problem 01:13 < kanzure> ADL repo is an almost-egg 01:13 < fenn> data is easy to make up 01:13 < kanzure> valid data .. 01:13 < fenn> you dont need 300 repo's/projects to start with 01:13 < kanzure> you can't do much with just 1 seed project 01:13 < fenn> we need a word for a thing that a person can sit down and use without having to assemble into other things 01:14 < fenn> but this should also cover standalone nuts and bolts and wires 01:14 < kanzure> connectables? 01:14 < fenn> preferably a word that already exists 01:14 < fenn> like 'artifact' or 'product' or something 01:14 < fenn> a laptop is a: 01:14 < fenn> device? 01:15 < kanzure> tool? 01:15 < fenn> tool is too general 01:15 < fenn> i like device 01:15 < kanzure> you're going all abstract on me 01:15 < kanzure> for the first two variables of the yaml metadata file. 01:16 < kanzure> what the hell do I do .. just use the flow BS? :( 01:16 < kanzure> gaahh 01:16 < fenn> i what are you trying to do? define the skdb file format? 01:16 < kanzure> basically. 01:16 < kanzure> okay, screw it 01:16 < kanzure> no universal catch-all tool 01:16 < kanzure> no universal catch-all format, except for the distribution of furtherly detailed formats 01:17 < kanzure> so the yaml metadata is specifically for sharing data and dependencies 01:17 < kanzure> where dependencies are explicitly defined as other parts in the database 01:17 < kanzure> now, as for interconnectivity with flows and so on, that's specific to something else 01:17 < fenn> no because there could be a range of parts that saisfy the dependencies 01:17 < fenn> hex head bolt, allen head bolt, etc 01:18 < kanzure> can we call that 'dynamic dependencies' ? 01:18 < fenn> sure 01:18 < fenn> feel free to borrow all the computer science terminology 01:18 < kanzure> which is basically where the client checks the dependencies, which causes it to select over the database for things that fall within that range 01:19 < kanzure> still not helping. 01:19 < kanzure> there will have to be scripts that are specifically designed to check if those 'dynamic dependencies' are being satisfied 01:19 < kanzure> it'll be a very lengthy O(n) process 01:20 < kanzure> so it must be domain-specific .. 01:20 < fenn> i dont think its that difficult 01:20 < kanzure> how. 01:20 < fenn> it must be domain specific 01:20 < kanzure> right 01:21 < fenn> no sense comparing bolts and insulation 01:21 < kanzure> you know how we mentioned that the pre-synbioss stuff would require highly specialized knowledge to make the proper grammar and in the mean time we'd use randomly generated stuff? 01:21 < kanzure> isn't this the same? 01:21 < fenn> yes but i never liked the randomly generated grammar because i can't think that abstractly 01:22 < kanzure> the generation step is very simple: you have N components, and then a constraints format according to BNF format, or whatever format the grammar was to be specified in, and just have it fill that in in one swoop step. 01:22 < kanzure> only once that step has been done does the abstraction-thinking-issue crumble. 01:24 < kanzure> so maybe the important factor is the tool used to generate the 'grammars' or the highly specialized domain-dependent formulation of how to express dependencies 01:24 < kanzure> yikes, that's a mouthful 01:24 < fenn> i was just going to use python duck typing 01:25 < fenn> a centralized grammar file is a bad idea 01:25 < fenn> because: restrictions on what you can do with parts is very closely linked to what the part is 01:26 < kanzure> that's why it's domain specific -- so there'd be stuff for synbio, stuff for electronics, for .., etc. compartmentalization. 01:26 < kanzure> anyway, duck typing is fine as long as the methods that the yaml metadata point to actually exist. 01:26 < kanzure> btw, that sounds like 'negotiation' to me. 01:27 < kanzure> radio.skdb __add__ operator to computer.skdb .. one would have to check the other (or something) and if they don't have enough compatabilities between the variables they want to share and constants they want to specify, then failure and sadness. 01:31 < kanzure> beep 01:31 < fenn> ok, sounds fine. "negotiation" sounded like some silly paper about agent-based systems 01:32 < kanzure> ok, so in various langs you use 'hooks' for other functions to throw at various times, like after a timer is done, 01:32 < kanzure> so I imagine a 'hook' for the init method would be a good thing to specify in the metadata 01:32 < fenn> 'init method'? 01:32 < kanzure> and then let one object check its compatability by probing the hook to the init method 01:32 < kanzure> yes 01:32 < fenn> i dont know what that is supposed to mean 01:32 < kanzure> s/to/for/ 01:32 < kanzure> well, how would they have negotiations if they don't know what to call 01:33 < kanzure> I mean, one script has to be the polymerase and the other has to be the thing to be executed/read 01:33 < kanzure> to return variables and information .. right? 01:33 < kanzure> how else will interfacing compatability be determined. 01:33 < fenn> with attributes 01:34 < fenn> polymerase wants a NT-type: ss-DNA sequence-length: >10bp 01:34 < fenn> or something like that 01:35 < kanzure> you're reverting on me. the difference here is that instead of scanning for the first few "inputs" and "outputs" variables in the yaml metadata files, we now have some selected part, and it has a method that lets it check against another given part whether or not its compatible. so it has to go run the metadata scripts and python or whatever for that part. 01:35 < kanzure> guess it's somewhat the same thing. anyway. 01:35 < kanzure> it's amazing that any work gets done with APIs 01:35 < kanzure> I guess the main way it gets done is via the presumption of upstream v. end-users .. "this is the way it is, use it this way or else" 01:35 < kanzure> so the same with parts. there will probably be a central core of important components to mimic in their compatability interfaces. 01:36 < fenn> i am too slow, i can hardly read all this 01:36 < kanzure> sorry. I'll tone down my braindump. I think this is all equating to "there's no difference whatsoever and just do it anyway" 01:36 < fenn> yaml data is numbers and stuff that gets loaded into python class attributes 01:37 < kanzure> you're reverting on me. 01:37 < fenn> am not 01:37 < kanzure> were were discussing some alternatives besides the first few variables 01:37 < kanzure> yeah you are, we were discussing alternatives above 01:38 < fenn> i think your 'init method' is the class name 01:39 < fenn> radio.skdb start out with !python/skdb.radio 01:39 < fenn> then all the attributes of a radio 01:39 < fenn> and all the inherited attributes from electronic devices 01:43 < wrldpc> oi 01:59 -!- xp_prg is now known as xp_gone 03:03 < kanzure_> wtf 03:03 < kanzure_> The machine just turned off on me. 03:03 < kanzure_> I was actively using it .. 03:04 < fenn> overheat 03:04 < fenn> PSU load 03:04 < kanzure_> overheat. 03:04 < kanzure_> it's been doing this increasingly often .. 03:04 < fenn> blow out the dust 03:04 < kanzure_> ` 03:05 < kanzure_> `````````````````,~\ 03:05 < kanzure_> uh, dropped keyboard 03:06 < bkero> flimsy 2lb keyboards are hard not to drop 03:07 < fenn> real steampunkers use solid brass keyboards 03:08 < bkero> You mean these? 03:08 < bkero> http://steampunkworkshop.com/keyboard.shtml 03:08 < bkero> Made from 5lb model M's? 03:08 < kanzure_> bah, my kb is powered on steam 03:09 < kanzure_> it's 200 m tall and it's made out of 34 solid metric tons of brass 03:09 < fenn> bkero: that flimsy plastic thing? 03:11 < fenn> i dont see where you're supposed to put the coal? 03:11 < kanzure_> why, in the laptop! 03:12 < kanzure_> (the steam is wirelessly transported through the aether) 03:13 < fenn> steam doesn't travel in wires anyway 03:13 < fenn> what are they teaching kids in school i wonder 03:13 < kanzure_> see /school 03:13 < fenn> do you even know how to re-babbitt a stopcock? 03:13 < kanzure_> what the hell? 03:13 < kanzure_> No? 03:14 < fenn> trim in an injector? 03:14 < kanzure_> you talk in tongues. 03:14 * fenn shakes head disapprovingly 03:14 < kanzure_> you'll be happy to know that I sat in on a lecture on 'team leadership' today 03:15 < kanzure_> "Start every meeting with a motivating quote." 03:15 < kanzure_> yay education 03:15 < fenn> preferably not something from neverness 03:15 < kanzure_> that's a cold stab. 03:15 < kanzure_> we all know team management talk is bullshit .. 03:16 * fenn focuses on finishing resume before midnight 03:16 < kanzure_> you're still working on that? 03:17 < fenn> fuck i hate this shit so much you dont even know 03:18 < kanzure_> why are you bothering again? 03:20 < fenn> because jobs that pay more than $10/hr generally require them 03:20 < bkero> http://www.engadget.com/2008/10/13/mr-blurrycam-reveals-the-updated-macbook-pro-899-laptop-model/ 03:22 < kanzure_> so far I've never had to actually use my resume in landing me a >$10/hr job 03:22 < fenn> well whoopdeedoo 03:23 < bkero> I had to use my resume to land an $8/hour job, a $12/hour job, 2 $22/hour jobs, and a $35/hour job. 03:23 < kanzure_> I mean, these people aren't really looking at resumes. it's weird. 03:23 < fenn> you should write a book on your success secrets 03:23 < kanzure_> fenn: secrets? you mean, like, falling assbackwards into luck? 03:23 < fenn> ok i'm just going to leave off the whole chronolgy section since it's demeaning 03:58 < fenn> kya! letter sent! 04:00 < fenn> suppose i should like, post this to me website or something now 04:00 < fenn> (as if anyone ever looks at it) 04:00 < kanzure_> i do, i do! 04:00 < fenn> ok lemme hack off the email addy 04:01 < kanzure_> ? keep it on? 04:02 < willPow3r> who was asking yesterday about using a laptop as a 2nd monitor? 04:02 < willPow3r> http://www.maxivista.com/ 04:02 < kanzure_> gene. 04:06 < fenn> http://fennetic.net/ben_lipkowitz_resume.pdf 04:07 < fenn> the thing is, you can learn like 50% of that in under an hour 04:07 < kanzure_> nobody knows that. 04:07 < kanzure_> I mean, if they did, we'd all be out of a job. 04:07 < fenn> *ahem* 04:08 < fenn> ok, maybe more like a day or two 04:08 < fenn> the ol' 5x what you expect it to take rule 04:14 < kanzure_> how much Japanese? 04:53 < bkero> http://www.youtube.com/watch?v=9XQaxIw5y40 06:30 < fenn> enough to confuse some old people at a tea shop in tokyo 09:29 < nsh> what's the chatter? 09:43 < nsh> kanzure might find this interesting: http://www.biologynews.net/archives/2008/10/13/caltech_biologists_spy_on_the_secret_inner_life_of_a_cell.html 09:43 < nsh> wait, wrong article 09:43 < nsh> http://www.biologynews.net/archives/2008/10/11/digital_zebrafish_embryo_provides_the_first_complete_developmental_blueprint_of_a_vertebrate.html 10:26 < nsh> better article from nature: http://www.nature.com/news/2008/081009/full/news.2008.1162.html 10:29 < nsh> journal article: http://www.sciencemag.org/cgi/rapidpdf/1162493.pdf 10:51 < nsh> kanzure_, you should also check out WikiPathways 10:51 < nsh> ( http://www.nature.com/news/2008/080903/full/455022a.html ) 12:46 < kanzure_> digita zebra fish embryo :) heh 12:46 * kanzure_ hasn't actually checked the links yet. 15:35 < willPow3r_> this biology class is teaching me how to hate biology 16:24 -!- Irssi: #hplusroadmap: Total of 18 nicks [0 ops, 0 halfops, 0 voices, 18 normal] 17:22 < kanzure_1_> http://dpatoolkit.sourceforge.net/ design pattern automation toolkit 17:49 < fenn> adelaide sounds great for growing algae 17:49 < fenn> grows in seawater, cover ponds with plastic sheet to catch the evaporated water 18:04 < kanzure_1_> http://doc.trolltech.com/3.1/qbytearray.html#qCompress 18:04 < kanzure_1_> any ideas on what format that compression format that is? 18:04 < fenn> "Few [philosophers] were sufficiently correct that people have forgotten who discovered what they discovered." 18:06 < kanzure_1_> libz yay 18:06 < fenn> qCompress merely uses the same compression algorithm as e.g. gzip, 18:09 < kanzure_1_> the internets says it's "not quite gzip" 18:11 < fenn> probably missing some file formatting 18:12 < fenn> RFC 1952 18:13 * fenn yawns 18:17 < kanzure_1_> gunzip is telling me it's not gz.. 18:17 < kanzure_1_> argh 18:17 < fenn> of course 18:17 < kanzure_1_> forgot to debase64 it 18:17 < fenn> what are you trying to do anyway? 18:18 < fenn> did some fool qcompress() data and then stick it in an xml file? 18:19 < kanzure_1_> yep 18:19 < fenn> "i've got to shrink these files somehow! i know, i'll compress the data!" 18:19 < kanzure_1_> http://function.device.mst.edu/repositoryEntry/doxygen/d8/d12/class_x_m_l_module.html#07e801857b3ca8e1039f415ab27e0e65 18:20 < kanzure_1_> gunzip still hates it, even now after debase64ing it. 18:20 < kanzure_1_> yay for qt being closed source 18:20 < fenn> it's not closed source 18:21 < fenn> it's just unreasonably large 18:21 < kanzure_1_> I can go check the qt sources? 18:21 < ybit> yep 18:22 < kanzure_1_> how is this not open. license crap? 18:23 < fenn> it's dual licensed 18:23 < fenn> so in practice forks are discouraged, although there's no reason one couldnt fork it 18:24 < fenn> too bad their docs dont link to the code 18:25 < kanzure_1_> I was just wondering about that 18:25 < kanzure_1_> it's rather useless to say "it compresses!" without telling me the format 18:26 < kanzure_1_> http://lists.trolltech.com/qt-interest/2007-05/thread01239-0.html 18:27 < kanzure_1_> nope, not zip either. 18:28 < kanzure_1_> ldd /usr/lib/libQtCore.so.4.2.3 | grep libz libz.so.1 => /usr/lib/libz.so.1 (0x00002b6e465ad000) 18:28 < fenn> libz/gzip/zip are all the same algorithm, just different file formats 18:29 < kanzure_1_> so there's a -qt-zip option you can throw at the configure file before the make. 18:29 < kanzure_1_> *-qt-zlib 18:29 < kanzure_1_> which makes it fairly obvious that it's using zlib. 18:29 < nsh> what you trying to recover? 18:29 < kanzure_1_> nsh: http://heybryan.org/~bbishop/docs/repo/CDD/ one of these two zip files. I think the second one has the decoded version. 18:29 < kanzure_1_> (from base64) 18:30 < nsh> no, what are they? 18:30 < kanzure_1_> but for some reason it's also 'compressed' using some mystical qt method that isn't zip, isn't gzip, etc. 18:30 < kanzure_1_> the files are 'CDD' files for ConceptDraw http://conceptdraw.com/ 18:30 < nsh> i meant 18:30 < nsh> WHAT ARE THEY 18:30 < kanzure_1_> black box diagrams in an equivalent of SVG 18:30 < nsh> what is the thing that you want in terms of why you are interested in that particular pattern of ones and zeros 18:30 < fenn> serious ontological crisis 18:31 < fenn> "this is not a pipe" 18:31 < nsh> at the interface between your brain and the external bloody universe 18:31 < nsh> what do they represent?!? 18:31 < kanzure_1_> black box diagrams 18:31 < kanzure_1_> black box diagrams in an equivalent of SVG 18:31 < nsh> hmm 18:31 < fenn> nsh: consumer crap, mostly, and some obscure nasa subsystems 18:31 < nsh> ok, sounds boring 18:31 < kanzure_1_> it is. 18:31 < kanzure_1_> :( 18:32 < nsh> (btw, still can't access heybryan for some reason) 18:32 < kanzure_1_> jaldfjkalfkjal; 18:32 < kanzure_1_> anyone else? 18:32 < kanzure_1_> can somebody whois kanzure_ ? 18:32 < kanzure_1_> I can't because of the stupid alt key config 18:33 < kanzure_1_> http://lists.trolltech.com/qt-interest/2006-07/thread00070-1.html <-- so it's zip but it's not zip 18:33 < nsh> kanzure_ is i=bbishop@66.112.232.108 * Bryan Bishop 18:34 < nsh> you should consider dyndns type arrangement 18:35 < fenn> heybryan.org is up for me 18:35 < kanzure_1_> why did I bother asking for the /whois 18:35 < kanzure_1_> I just uploaded those CDD.zip files 18:36 < nsh> oh 18:36 < nsh> i may have added a hosts entry for heybryan before 18:38 < kanzure_1_> if I have to go write my own qt method to uncompress this stupid data: http://lists.trolltech.com/qt-interest/2006-08/msg00577.html 18:38 < kanzure_1_> what really annoys me is that once I do uncompress all of this, 18:38 < fenn> hmm 5W 1TB disk at newegg.. 18:38 < fenn> $115 18:38 < nsh> better 18:38 < kanzure_1_> I'm going to have to go find the automated Windows XP app-clicker thingies 18:39 < kanzure_1_> and then write a script to use the ConceptDraw software to convert to SVG 18:39 < kanzure_1_> that wouldn't be terrible, normally 18:39 < kanzure_1_> except that those are *SVG* with points and geometries drawing boxes and such 18:39 < kanzure_1_> I'd have to write a script to convert from the SVG to something quantified 18:40 < kanzure_1_> and even then, all of this data was hand-entered, making it mostly useless.. 18:40 < fenn> all of the data was hand entered anyway 18:40 < kanzure_1_> you'd think so 18:40 < kanzure_1_> but there's some products in the repository that do not have CDD files 18:40 < kanzure_1_> thus the data set is incomplete 18:40 < kanzure_1_> I mean to say that this was hand-entered separately, on top of everything else 18:41 < kanzure_1_> there's only 94 out of the 125 products with these CDD files 18:41 < fenn> poor data integration 18:41 < kanzure_1_> this is quickly turning into a nightmare. 18:41 < fenn> i dont know why you bother 18:41 < kanzure_1_> do I get to call trolltech and yell at them? that'd be fun. 18:41 < kanzure_1_> neither do I 18:42 < fenn> what will you do with a diagram anyway? 18:42 < fenn> and why is it not accessible anywhere? 18:42 < kanzure_1_> don't understand the second question. 18:43 < fenn> there should be a web interface to get these diagrams 18:43 < kanzure_1_> with the diagram I will convert it into a quantified, discrete format, and that's basically what we would call a very very basic set of interconnections of components in terms of 'flow type'. it's a black box diagram. so.. 18:43 < fenn> otherwise why did they bother putting them in the repo (if you can't get them back out) 18:43 < kanzure_1_> hrm 18:43 < kanzure_1_> ConceptDraw. 18:44 < fenn> but it's just a black hole 18:44 < kanzure_1_> the entryapp allows you to click a button and save-as the CDD file 18:44 < fenn> ok so just do that 18:44 < kanzure_1_> 94 times? 18:44 < fenn> yeah 18:45 < fenn> sorry if it offends your programmer instincts, but sometimes you have to choose your battles 18:50 < fenn> it's disappointing that i cant even find the qt source code 19:03 < kanzure_1_> No, this is ridiculous. There's about 20 clicks to get to each CDD file. 19:04 < kanzure_1_> This is not including the step where I repetetively translate from CDD to SVG .. 19:04 < kanzure_1_> repetitively. 19:04 < kanzure_1_> Not only 20 clicks but a giant pause in between while the repositoryapp "loads from the database" (AKA my file system ..) 19:04 < fenn> do you have the source for the data entry app? 19:05 < kanzure_1_> I linked you to it 19:05 < kanzure_1_> yeah 19:07 < kanzure_1_> I'd rather just do a quick hack like http://lists.trolltech.com/qt-interest/2006-08/msg00577.html 19:07 < kanzure_1_> I've spent 30 minutes on this? where does time go. 19:10 < fenn> computers are fantabulous devices capable of doing absolutely nothing for hours on end 19:11 < kanzure_1_> s/computers/humans/ 19:11 < fenn> no, i'm sitting here in front of a computer giggling 19:11 < fenn> reading paul graham on philosophy: "There's a market for writing that sounds impressive and can't be disproven." 19:12 < kanzure_1_> evil giggling? 19:13 < fenn> i'm not evil enough, this is more like schoolgirl-ish giggling 19:32 < kanzure_1_> fenn: What was the alternative to dotty that you wanted me to try out for drawing the graphs? 19:32 < kanzure_1_> neato 19:36 < fenn> and fdp 19:36 < fenn> fdp looks more "square" 19:36 < kanzure_1_> fdp looks exactly the same. how weird. 19:38 < fenn> someone should make a map of TLA space 19:38 < fenn> see how many are used in each permutation 19:38 < fenn> 26x26x26 voxel cube 19:39 < kanzure_1_> TLA? 19:39 < fenn> three letter acronym 19:40 < fenn> http://auction.meca.edu/wp-content/uploads/2008/09/goochh_artauctionimage.jpg 19:40 < fenn> a heretofore unconsidered construction material 19:41 < kanzure_1_> I'm doing all of the graphs incorrectly. 19:41 < kanzure_1_> the labels should be the nodes, the current nodes (the "verbs") should be the edges. 19:42 * kanzure_1_ tests. 19:43 < fenn> that would certainly cut down on the number of edges, but it would be totally pointless since you lose interconnectivity information 19:49 < kanzure_1_> input, artifact, output such that i/o specifies another artifact instantation ID, and such that the input flow and output flow is labeled with a 'flow name' which is correlated to a unique artifact instantation ID. 19:50 < kanzure_1_> gah that's hard to say / think about 19:50 < kanzure_1_> yes, it is true that the flows do not connect to one another. the artifacts do however. and the flows are implicitly connected to the 'artifacts'. thus, the flows connect. 19:53 < kanzure_1_> perhaps the biggest piece of evidence is this: 19:54 < fenn> Flows are not like some of the other grammatical modes which express precisely a mode of conception without any reality that corresponds to the conceptual mode, and consequently do not express precisely something in reality by which the intellect could be moved to conceive a thing the way it does, even where that motive is not something in the thing as such. 19:54 < kanzure_1_> in the file where I generate the .dia files, I literally say: "$SubInputArtifact -> $currArtifact [label=flow input flow]" then the next line says "currArtifact -> SubOutputArtifact label outputflow" 19:55 < kanzure_1_> so why not jdo flowinput -> flowoutput 19:55 < kanzure_1_> *just do 19:56 < kanzure_1_> connectivity will be maintained but there will be this ridiculous number of lines going into each of the flows since there's only like 8 types or something 19:58 < kanzure_1_> unless I give each of them a unique ID. Then the problem becomes how to keep the connectivity correct with nodal ID assignments to each of the flows. Ah, the IDs will not be the flow IDs but rather the artifact IDs. This way, connectivity is preserved. 19:59 < kanzure_1_> (there's a way to name a node and hide its name in dia, yes? I seem to recall something like this.) 19:59 < fenn> there will be approximately 8*number of artifacts 19:59 < fenn> edges 20:03 < kanzure_1_> if you count the final graph, yes, but the dia/dot file will have overlapping arcs/edges. 20:20 < kanzure_1_> http://heybryan.org/~bbishop/docs/repo/graphs/2008-10-14_flowgraph_78.png 20:22 * fenn makes a wanking motion 20:29 < wrldpc> what's the plan? 20:38 < kanzure_1_> Context? 20:41 < gene> here's the plan[TM] http://www.geocities.com/SouthBeach/1380/plantxt.html 20:41 < fenn> the south beach diet plan 20:42 < wrldpc> what's the plane? 20:42 < gene> the plan 20:42 < wrldpc> oh 20:42 < gene> [tm] 20:42 < wrldpc> (TM(TM) 20:43 < gene> is to pave the earth flat 20:43 < gene> So that you can drive to wherever you need to go without turning or slowing down 20:49 < fenn> jetpacks for everybody 20:52 < gene> Why jetpacks? 20:53 < gene> can you drink beer and eat burgers while using a jetpack? I think not 20:54 < fenn> you just have a limited imagination 20:55 < gene> Besides you can't go that fast in a jet pack 20:56 < gene> why not join the future and use a rocket powered hypercar to get from place to place 20:58 < gene> besides, rocket powered hypercars use more scarce natural resources and create more pollution than jetpacks 20:59 < gene> Don't you want to be able to look at the sky and say "I made the sky what it is today"? 20:59 < fenn> i do, but dont see what cars have to do with it 21:00 < gene> http://www.geocities.com/SouthBeach/1380/pave.html 21:00 < fenn> it wasn't funny to begin with 21:01 < gene> it's an old meme 21:01 < gene> a very old meme 23:31 < kanzure> fenn: Thanks for the heads up on http://www.newegg.com/Product/Product.aspx?Item=N82E16822152102 that 1 TB $115 hdd. 23:46 < fenn> i'd probably get one but no money 23:46 < fenn> it's not like hard drives are going anywhere 23:50 < willPow3r> you're not cool unless you have one. 23:50 < willPow3r> sorry. 23:51 < kanzure> You're not a man unless you have one. 23:51 < willPow3r> well i have 50 23:51 < willPow3r> so thats a testament to how cool and manly i truly am 23:53 < willPow3r> well, by irc standards anyway 23:53 < willPow3r> which i'm sure will translate to 2nd life 23:54 < willPow3r> wow, 76 F in mid october? its so freaking hot here 23:55 < kanzure> You're not a man unless 80 degrees is abnormally cold where you live. 23:55 < fenn> i always thought colder climates were more manly 23:56 < fenn> need fur and blubber and tusks 23:56 < willPow3r> i think an african zulu tribesman would beat an inuit in a hand-to-hand match 23:57 < fenn> nah zulu get their reputation because of battle tactics 23:57 < willPow3r> then again, i think it would be easier to adapt to a warmer climate than to a colder one 23:57 < kanzure> The warm clients suck. 23:57 < kanzure> Oh, climates? 23:58 < fenn> shaka zulu basically reinvented the phalanx: http://en.wikipedia.org/wiki/Shaka#The_famous_.22buffalo_horns.22_formation 23:58 < willPow3r> so zulu > eskimo 23:59 < willPow3r> at least in physical dominance 23:59 < fenn> no, faggot 23:59 < willPow3r> but give an eskimo and a zulu an education and i'm sure the eskimo would come out on top