--- Day changed Thu Apr 10 2008
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08:50 < kanzure> http://heybryan.org/mediawiki/index.php/2008-04-10 for some news/notes/stuff
08:50 < kanzure> Will somebody please check the http://perlmonk.org/ chatterbox in 20 minutes to see if anybody answered my latest message? I need to run.
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17:41 < kanzure> Hi Aulere.
17:52 < Aulere> hi kanzure
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18:04 < faceface> lets breed baby!
18:09 < faceface> btw, how are you getting on with your BiO.CC account?
18:19 < kanzure> Dan, hey there
18:19 < kanzure> Sorry for my lag
18:19 < kanzure> I've been logging in and checking out some of the folders. Lots of interesting stuff in there.
18:19 < kanzure> I don't understand, though. What's going on there? How many people, who are they, why? etc.
18:21 < faceface> hehe - its confusing I know
18:21 < kanzure> and I checked out the stats, KIGG (the parent govt body) has $100 million in funding
18:21 < kanzure> But it doesn't look like there's much money being used by KOBIC
18:21 < kanzure> what's going on?
18:21 < faceface> basically ... well... perhaps there is no basically.... Jong went to korea to be professor... then he quit and went to another place ... then he quit again I think... now he is the director of KOBIC 
18:22 < faceface> don't know.
18:22 < kanzure> I'm glad I know the director of KOBIC, but I don't know what that *means* - how much influence and push does he have?
18:22 < faceface> Jong is good at leaving a trail of chaos behind him... bio.cc is the center of his chaotic world ;-)
18:22 < kanzure> Could he get some of my bio projects funded? (there's not much in way of costs, of course, just need a lab)
18:23 < faceface> kanzure, not sure... don't know what KOBIC does really... the papers carried a story in korea when he quit his post at KAIST - it was unheard of for a professor to quit and go to 'industry' so KOBIC is kinda like Lion biosciences vs EBI type thing
18:23 < kanzure> hm
18:24 < kanzure> I mean, from his websites and biosophy,
18:24 < kanzure> it really seems like he digs my 'DIY biohacking' ideas
18:24 < faceface> kanzure, you can surely ask about funding / collaboration. He payed for me to visit him in korea some time ago... If I can I would like to go again this summer.
18:24 < kanzure> I see.
18:24 < kanzure> I think he would really enjoy helping me out on the biohacking kit
18:24 < faceface> yeah... biosapien... 
18:24 < kanzure> what I need to do is publish videos and documents that describe the *exact* steps to make the machinery
18:25 < faceface> kanzure, how long would you need / how long a summer holiday do you have / how much would it cost... I am sure Jong would be interested, but he often complains about 'the system' where he is, so his 'push' is a constant struggle
18:26 < faceface> it seems... I don't really know.
18:26 < kanzure> hm
18:26 < kanzure> My summer is June 1st to August 1st (basically)
18:27 < kanzure> and while I know that I would not be able to get everything done within that time, I can focus on a single project - such as DNA sequencing.
18:27 < kanzure> (I am thinking of the STM version of DNA sequencing.)
18:28 < kanzure> it requires some thought obviously
18:28 < kanzure> but I think that the idea of releasing specific videos on doing these things would be a good push
18:28 < kanzure> *show them* how to use the bioinformatics databases (you know, the screen recorders)
18:28 < kanzure> then show them simulations and so on (obviously you cut out the hour-long pauses as you figure out what to do ;))
18:28 < kanzure> and then direct, elegant implementations into wetware
18:31 < faceface> kanzure, jong has always talked about wanting to build a mechanical sequencer (as we discussed) - also he wants to found a company to exploit such a product. I am sure he would be delighted if you proposed such a project... you would need to be very focused though with lots of planning.
18:32 < kanzure> haha
18:32 < kanzure> well, you know me
18:32 < kanzure> <-- intense
18:33 < faceface> cool
18:33 < kanzure> remember my site?
18:33 < kanzure> http://heybryan.org/
18:34 < faceface> indeed
18:39 < faceface> take care. Good luck with your projects. good night.
18:40 < kanzure> g'night
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19:14 < fenn> intense but not focused
19:15 < kanzure> fenn: http://www.w3.org/TR/wsdl
19:15 < kanzure> bah, I'd say I am focused
19:15 < fenn> focused on a broad subject, maybe
19:16 < kanzure> ah, well, I suppose you may mean that in the sense that I don't just isolate myself completely to get a single item done at a time
19:16 < kanzure> but this is mainly because I am working off of a strategy to make sure I don't pick something that doesn't work
19:16 < fenn> um, wsdl, relevant? how?
19:17 < kanzure> the perlmonks told me that wsdl might be my way of doing formalized usage requirements
19:17 < fenn> O-o
19:20 < kanzure> but I don't get it
19:21 < kanzure> let's just do slip
19:21 < kanzure> or xml
19:21 < kanzure> do we want to rip apt-get directly, or write our own client from scratch?
19:23 < kanzure> http://en.wikipedia.org/wiki/Advanced_Packaging_Tool
19:25 < kanzure> looks like we can do autogenix with just bash scripts
19:27 < fenn> i'd rather use python
19:27 < fenn> bash is really hard for anything non-trivial
19:27 < kanzure> I agree
19:28 < kanzure> I'd rather do perl, frankly, because of the larger historical context of packages and so on
19:28 < fenn> oh pff
19:28 < kanzure> wait
19:28 < kanzure> it doesn't matter that much
19:28 < kanzure> we can do bindings back and forth
19:28 < fenn> we can use apt for software packages
19:28 < fenn> right, bindings are a great idea, lets do more of those :)
19:28 < kanzure> sort of - we'd need to hack apt for those meta-files
19:29 < fenn> hmm? apt would be a sub-set of autogenix
19:29 < kanzure> yes
19:29 < fenn> a software package would appear to apt as a leaf node, but in autogenix it would just be part of a tree
19:29 < fenn> or is it a root? i always get confused
19:30  * fenn would like some decent package visualization software
19:30 < fenn> dependency^
19:30 < kanzure> there are a few distinctions to make for software
19:31 < kanzure> some software would do simulations, others would be parsers and generators, converters, etc.,
19:31 < kanzure> in the sense of dependency-loops in the self-replicator design, I doubt software would matter that much; once there's an ability to do software storage, all software can be implemented on it
19:32 < fenn> sure, simulator/test/parse would be specified somehow
19:32 < kanzure> eh
19:33 < kanzure> this sounds like Cantor's mathematics
19:33 < kanzure> that the number of identifiers is the same as the number of possible programs
19:33 < kanzure> or something like that
19:33  * fenn googles
19:33 < kanzure> it's ignorable at the moment
19:33 < kanzure> I haven't thought about whether or not we would specify the structural relationships between the software packages
19:33 < kanzure> I hear that this is a big problem in apt, they only have a few ways to specify dependency
19:34 < kanzure> and dependency-resolution in their system is an even bigger problem
19:34 < kanzure> *dependency-error resolution
19:34 < fenn> lol n*infinity
19:34 < fenn> my math teacher wouldn't have any of it
19:36 < kanzure> okay, so I guess there's only a limited number of relationships that we want to express anyway
19:36 < kanzure> this is just dependency or whatever - "download this at the same time in order to make it run" dependency stuff
19:36 < kanzure> other stuff like "is an alternative to" doesn't have to be specified on the package level ... rather, a larger package would reference all of the packages that are of the same type, and a person would make that package file if they were so inclined
19:36 < kanzure> (plus reverse links of course)
19:37 < kanzure> s/reverse links/backlinks/
19:37 < fenn> you can do aliases for dependencies
19:37 < fenn> in apt
19:38 < fenn> well, dpkg really
19:38 < kanzure> sounds like ##REDIRECT to me
19:38 < fenn> right
19:38 < fenn> why is redirect discouraged?
19:38 < kanzure> which reminds me -- it'd be really nice if we can have CVS integrated into the backend for the wiki ... CVS for mysql or something, and then just make sure that it's editing the wiki tables. That'd be really helpful.
19:38 < kanzure> is it?
19:39 < fenn> yeah you're supposed to send 405 or something
19:39 < kanzure> oh
19:39 < kanzure> it's because redirect is in the HTTP header
19:39 < kanzure> whereas javascript/html redirect is more boggy stuff
19:39 < kanzure> I'm all for 405 :)
19:39 < kanzure> apache mod_rewrite etc
19:39 < fenn> sure
19:39 < kanzure> and mod_redirect IIRC
19:39 < fenn> mod_rewrite is bitchun
19:40 < fenn> (when it works)
19:40 < fenn> CVS is old, but i get your drift
19:40 < fenn> i like git because it can track changes between files
19:40 < kanzure> I refuse to let this be an HTTP-only interface ordeal, where autogenix would have to go through HTTP and HTML to get stuff ... how absurd.
19:40 < fenn> like, if you move code from package a to package b
19:41 < kanzure> I have no preferences for versioning systems, so I'm good for your preferences
19:41 < fenn> what's wrong with http? it gets through firewalls and downloads packages
19:41 < kanzure> wait, http is ok
19:41 < fenn> you mean UI?
19:41 < kanzure> but not html to represent the wiki page only
19:41 < fenn> right
19:41 < kanzure> hm
19:41 < kanzure> I wonder how we would opt to do that
19:41 < kanzure> would we want to dump the package as a wiki-compatable-format
19:42 < kanzure> or would we want the wiki to retrieve the file from another table in the db
19:42 < fenn> wiki is a nebulous concept :)
19:42 < kanzure> and then do its own markup
19:42 < kanzure> true
19:42 < kanzure> I was hoping for mediawiki just to do the status quo thing
19:42 < fenn> it doesnt have to be a markup language
19:42 < fenn> fuck mediawiki
19:42 < kanzure> xml is markup
19:42 < kanzure> although slip isn't
19:42 < fenn> er, uh, i mean a display markup
19:42 < kanzure> ah
19:43 < kanzure> going over it:
19:44 < fenn> ok, the 'wiki' software's job is to take our XML markup and transform it into some pretty HTML
19:44 < kanzure> ohhh
19:44 < fenn> i'm sure there's hundreds of things out there that can do that
19:44 < kanzure> what if our XML is compatable with our standards + wiki at the same time
19:44 < kanzure> or at least we can have a wiki extension to interpret it
19:44 < fenn> yeah, i thought you had come to that conclusion already :)
19:44 < kanzure> for example, in mediawiki you can do <youtube> tags, so same --
19:44 < kanzure> sure, I'll pretend like I did
19:45 < fenn> so.. there's more to it than just xml
19:45 < fenn> also cad files, binaries, assorted nastiness
19:45 < kanzure> xml must reference those files, yes
19:46 < kanzure> i.e., "<dataFile>/path/to/my.cad</dataFile>"
19:46 < fenn> i'm worried about version control systems and large quantities of binary files
19:46 < fenn> it could turn into a mess quickly
19:46 < fenn> but i dont have any suggestions
19:46 < kanzure> are you worried about messy dir structures, or too much used space?
19:46 < fenn> space, inability to track changes
19:47 < fenn> more like, bandwidth for mirroring
19:47 < kanzure> re: space, periodic package pruning? with also backup and mirroring to offsite storage
19:47 < kanzure> hm
19:47 < fenn> we could just say, 'dont do that'
19:48 < fenn> i.e. all illustrations in svg
19:48 < fenn> cad files in ascii
19:48 < fenn> open source cad doesn't exist yet.. wtf are we going to do about that
19:49 < kanzure> are you sure?
19:49 < kanzure> that sounds unlikely
19:49 < fenn> 3d stuff
19:49 < kanzure> http://blender.org/
19:49 < fenn> not cad
19:49 < kanzure> I've never really used CAD
19:49 < fenn> uh, it's hard to tell the difference until you actually try to build something with it
19:49 < fenn> basically, blender is like smooshing modeling clay around
19:49 < kanzure> right
19:50 < fenn> and cad is like, programming a computer
19:50 < fenn> there are various degrees in between too, like rhino
19:50 < kanzure> not working with crappy blender-interfaces?
19:50 < fenn> nothing to do with the interface
19:50 < kanzure> I think blender allows python scripts now though
19:50 < kanzure> so that you can program it to make models 
19:50 < fenn> there have been attempts to create a cad interface for blender, miserable failure
19:51 < kanzure> here's what I am thinking - 
19:51 < kanzure> (1) write up some autogenix code? do we want to steal from apt directly? what do we want it to be able to do? this is dependent on the package definition format; so really we just need a way to bootstrap the downloading of a new version of a script to work with the db
19:51 < kanzure>  this is dependent on the package definition format; so really we just need a way to bootstrap the downloading of a new version of a script to work with the db
19:51 < fenn> basically, a 3d modeler doesn't store high level information, or real-world technological information
19:52 < kanzure> (2) write up the meta-information / file format io specs or DTD (investigate?) ... this is the usage-statement stuff that we were talking about
19:52 < kanzure> (3) wiki/versioning combo investigations
19:53 < fenn> in a first draft, i want autogenix to verify: units, connectors, signal types, software compatibility
19:53 < kanzure> how does apt do it? locally?
19:53 < kanzure> I think apt downloads the overhead database and then does local scanning
19:53 < kanzure> and then only calls the server to get the package
19:53 < fenn> apt downloads the control files, right
19:53 < fenn> actually it downloads diffs which are updated regularly (somehow)
19:54 < kanzure> huh
19:54 < kanzure> well, that would work well with #3
19:54 < fenn> we could do that with git
19:54 < kanzure> since wikis and versioning systems both wrok with diffs
19:54 < fenn> git diff <db root>
19:54 < kanzure> neat
19:55 < kanzure> okay, so you want autogenix to be able to interpret package files
19:55 < kanzure> I wonder if it's worth throwing that into another program
19:55 < kanzure> apt-get = autogenix, apt-check for verification/validation, 
19:55 < fenn> i know you're trying to prod me into writing code, but i gotta do my taxes tonight :\
19:55 < kanzure> I'm trying to prod you into specifications
19:55 < kanzure> I can do code, if I know what I want
19:56 < kanzure> hehe
19:57 < kanzure> there's also the 'usage message' formalization lib - this will come later when we start throwing in some software into the database, I guess, don't think it's that relevant to these bootstrap programs really
19:57 < fenn> apt-check just verifies that the db is consistent
19:58 < fenn> 'lintian' is one program that validates a debian package
19:58 < kanzure> does apt-check actually exist ?
19:58 < fenn> no, i was thinking apt-get check
19:58 < kanzure> ah
19:58 < kanzure> didn't know
19:59 < fenn> usage message? for software or hardware or package management?
20:00 < kanzure> the usage-message stuff is for, say, 
20:00 < fenn> or just documentation in general?
20:00 < kanzure> package re: chairs, references some software that simulates chairs
20:00 < kanzure> chairSimulator requires certain input data
20:00 < kanzure> like a 3d object file
20:00 < fenn> an API?
20:00 < kanzure> yeah, 
20:00 < kanzure> remember the inline code we were discussing?
20:00 < fenn> that's usually too much to pack into a man page
20:00 < kanzure> right
20:00 < kanzure> a man page is plain text anyway
20:01 < kanzure> I'm thinking that this would be like "--help2" -- any program could call this, and get back formal information that says parameter 'testParam' requires file format of type ID 3940141 and then skdb has some information on that format
20:01 < kanzure> *any person could call this
20:01 < kanzure> don't know if programs will, but if they do, they might find a way to use it
20:02 < kanzure> more importantly this xml spec would be available next to the program too
20:02 < kanzure> so that it can be read without executing the program
20:10 < kanzure> we could do away with that idea entirely if we have to
20:10 < kanzure> I'm pretty sure it's useful
20:11 < kanzure> as it is, with apt-get, you could get a physics simulator, but not be able to interpret the results because nobody tells you what the file formats really are
20:16 < fenn> http://en.wikipedia.org/wiki/Table_of_mathematical_symbols
20:17 < fenn> lots of programs dont generate output files
20:18 < fenn> or if they do, its intended as a debug or strictly for hackery
20:18 < fenn> i do like the unix philosophy though
20:18 < fenn> it's almost mandatory for something this large and complex anyway
20:20 < fenn> automated man-page reading would be powerful, but i dont even know where to begin (and it may be beyond the scope of what we're doing)
20:22 < fenn> it's not that hard to tell what kind of file you're reading, as usually there's a limited number of choices anyway
20:23 < fenn> case "slip-xml": parse_slip(); case "stl" parse_stl(); etc
20:23 < fenn> say you had a connector modeled in stl
20:23 < fenn> like a wall plug or something
20:24 < fenn> that stl file would be given a name, and could be referenced as a member of the electricity module
20:25 < fenn> and linked to the autogenix 'unit' describing that interface?
20:25 < fenn> maybe interface needs to be a separate parameter for describing functionality
20:25 < fenn> (instead of being glommed onto units)
20:27 < fenn> 110V 60Hz 15A are the units, but the interface is the familiar 0.o plug
20:27 < fenn> software is another ball game though
20:28 < fenn> hmm. have to get wave-form in there too i guess
20:29 < fenn> sinusoidal is not the same as what most inverters put out, and then there's 'magic sinewaves' and so on
20:30 < fenn> also, all these values want tolerances
20:30 < fenn> we could re-name it 'technological interface database with diagrams included' :)
20:34 < kanzure> automated man page reading *will* be limited. You can only write in terms of text what the parameter is *for*, but you can specify what to give it :)
20:36 < kanzure> for the connector in that case - those units would have to be variablized based off of the material specifications, right?
20:36 < kanzure> think of it like a typical electronics lab
20:36 < kanzure> my high school electronics shop has this huge wall of compartments
20:36 < kanzure> of tens of thousands of components
20:36 < kanzure> in terrible organization, of course
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20:37 < kanzure> specifying the units like that seems kinda weird though
20:38 < kanzure> at first I guess we can have tens of thousands of packages specifying different resistors
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20:38 < kanzure> (of course, we wouldn't do that by hand - we'd eat some digikey.com data sheets or something)
20:38 < kanzure> (or even have an automatic cron job to update based off of digikey.com database queries, as long as we keep up with their HTML format output specs)
20:38 < kanzure> but on the other hand, if we come upon the software to model the materials used to make those resistors
20:38 < kanzure> then that's really, really useful
20:38 < kanzure> so that we can then just have one package that can provide a conventional resistor
20:39 < kanzure> and then we can pass some inputs to it to get the output for a type of resistor that we want
20:39 < kanzure> either way should wrok
20:39 < kanzure> *work
20:40 < fenn_> i got a decent idea; units would be named arguments to the interface class
20:40 < kanzure> define interface class
20:41 < fenn_> a code object that references all the cad files and whatnot
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20:42 < kanzure> oh, interesting
20:42 < fenn> digikey allows parametric search, so you just search for what's specified and get a list of components that match
20:43 < kanzure> cool
20:43 < kanzure> okay, I wasn't expecting your interface class idea
20:43 < kanzure> what I was thinking of was that the package-format could have a way for the programmer to list related files or whatever
20:43 < kanzure> so that you would drop a cad file into a project if it's relevant
20:43 < kanzure> (just link to it, actually, instead of multiple copies)
20:44 < fenn> hmm, i was thinking the class would usually be specified in a standard interface library, like NEMA or some crap, but yeah you could make your own interfaces
20:46 < fenn> i'd like to avoid the scenario where someone thinks they have all the software needed for building a package, but then at (software run) (tech build) time it turns out there's a dangling reference to some file
20:46 < kanzure> that's what the validator and ref-checkers would be for
20:46 < kanzure> or
20:46 < kanzure> we have people devote themselves to making sure a package they throw up really, truly works
20:46 < kanzure> and we can say "this *will* work if you do a full download"
20:47 < fenn> i think i'd rather trust the machine :)
20:47 < kanzure> sure
20:47 < fenn> and devote the energy toward making sure the validator works
20:47 < kanzure> well, how about this
20:47 < kanzure> if the validator finds that there's something missing in the packages, and has to go search the database
20:47 < kanzure> the person using the software doesn't necessarily know what interface is needed to make it work
20:47 < kanzure> they will get a list
20:47 < kanzure> and perhaps there will be only one program that they can choose from, if so that's great
20:47 < kanzure> but otherwise they might be clueless
20:47 < kanzure> they could either do trial and error
20:48 < kanzure> or they could generate a debug report or whatever
20:48 < kanzure> and then go ask somebody who might have a clue
20:48 < kanzure> and if a package *is* chosen, then this should be an auto-generated use case
20:48 < kanzure> and uploaded to the database for analysis/use/whatever
20:48 < fenn> hurr.. the interface should be specified enough so that it truly doesnt matter which one they pick
20:48 < kanzure> well, think about the tools that do different things to files
20:49 < kanzure> for example, html2pdf versus frontpage
20:49 < kanzure> both have html input specs
20:49  * fenn was thinking text editors
20:49 < fenn> uh, lets just leave frontpage out of this okay/
20:49 < kanzure> haha =)
20:49 < kanzure> just trying to think on my feet
20:50 < fenn> you cant say 'look, broken software exists and people use it, so it is a possibility'
20:50 < kanzure> so the solution is not at run-time or download-time
20:50 < kanzure> but rather approval-time
20:50 < kanzure> when we are adding the package into the database
20:50 < fenn> could be both
20:51 < kanzure> with run-time and/or download-time you get into territory where you get ambiguous software suggestions though
20:51 < fenn> the database could get out of whack, then the user unwittingly downloads broken packages and believes they are ok
20:51 < kanzure> yep
20:51 < fenn> why ambiguous?
20:51 < kanzure> like I said: html2pdf v. the unmentionable program
20:51 < kanzure> both take HTML input
20:51 < fenn> html isnt a specification
20:52 < kanzure> stl v. blender
20:52 < fenn> uh, blender isnt a specification :)
20:52 < fenn> its a core dump
20:52 < kanzure> dot blender files
20:52 < kanzure> oh?
20:52 < kanzure> hah
20:52 < fenn> srsly
20:52 < kanzure> what the hell are they smoking?
20:52 < kanzure> I guess it could be sorta easy
20:52 < fenn> i think you cant even load different versions of blender files into blender
20:53 < fenn> ok, so, stl vs. collada
20:53 < fenn> both well defined, and incompatible
20:53 < fenn> so no reason the package should pick the wrong one
20:53 < kanzure> those are file formats
20:53 < fenn> stl 1.0 vs stl 2.0
20:53 < kanzure> nono
20:54 < kanzure> let's suppose we have
20:54 < kanzure> stl-program-1
20:54 < kanzure> stl-program-2
20:54 < kanzure> thus, ambiguity 
20:54 < fenn> ok, stl-program-1 outputs stl version 1.0 file format?
20:54 < kanzure> the cur package does not care what the output of whatever-stl-prog is
20:55 < kanzure> (let's just say)(
20:55 < fenn> it should care what the output is, that's its job
20:55 < kanzure> okay, good point
20:56 < fenn> if it's underspecified, that should be fixed
20:56 < fenn> would like a piece of software to detect that sort of programmer error
20:57 < fenn> i.e. if a program can read stl2.0 then it can read stl1.0, doesnt mean the other way around will work
20:57 < fenn> sounds boring to code though
20:58 < fenn> there really should be some big database describing all the file formats, everywhere
20:59 < fenn> or a language that the people who create file formats can decribe their format with
20:59 < fenn> <.rantD[D[D[D[D/>
21:00  * fenn kicks his wifi
21:03  * fenn grumbles about EXPRESS
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21:31 < kanzure> yep, format db indeed
21:32 < kanzure> we will just keep the format db separate from skdb (even though it is a part of it, yes)
21:32 < kanzure> so that it too can be mirrored and backed up
21:57 < drazak> kanzure: any luck with those books?
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23:19 < kanzure> http://en.wikipedia.org/wiki/Rick_Tumlinson <-- This guy funded the Mars Society and did FINDS. He funds space-tech groups. But the trick is that you don't find him, he finds you, or else he rejects your application. 
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