--- Day changed Sat Oct 25 2008
00:32  * kanzure is back.
00:33 < kanzure> Hi marainein 
00:33 < marainein> hi kanzure
00:33 < marainein> how are your projects going?
00:33 < kanzure> Very well. :)
00:34 < kanzure> Still waiting on interface{1,2,3}.php for the synbioss stuff.
00:34 < marainein> what does it do?
00:34 < kanzure> Think of it as CAD for synthetic biology.
00:35 < marainein> what does it design?
00:35 < kanzure> Biological 'circuits', basically it puts DNA into a strand for you, selected from a repository of pre-constructed parts.
00:35 < kanzure> http://partsregistry.org/
00:35 < kanzure> http://bloodgate.com/graph-easy/
00:36 < kanzure> http://heybryan.org/~bbishop/docs/biobench/001/ 
00:36 < marainein> The requested URL /~bbishop/docs/biobench/001/ was not found on this server.
00:36 < marainein> hmm
00:36 < kanzure> Erm.
00:37 < kanzure> Well.
00:38 < kanzure> I don't know where it's gone.
04:57 < gene_> are you still there?
05:06 < gene_> kanzure can you burn me a ubuntu disk with that free bandwidth you have
05:07 < gene_> I'll even provide you with a disk 
05:08 < gene_> how big is ubuntu
05:22 < xp_prg> kanzure you here man?
05:35 < xp_prg> hi procto!
05:39 < xp_prg> anyone here?
05:39 < xp_prg> ppk you here?
05:39 < kanzure> no
05:39 < xp_prg> hi kanzure
05:40 < xp_prg> kanzure I have my symbioss app open, can you help me to understand how to make it work?
05:41 < kanzure> Oh, so suddenly you're interested in practical things?
05:41 < xp_prg> yes
05:41 < kanzure> No. I need sleep. I just woke up for some fresh air.
05:41 < xp_prg> darn :(
05:41 < xp_prg> not even a little bit of help?
05:41 < kanzure> designer.pdf
05:42 < xp_prg> what is the link?
05:42 < kanzure> http://heybryan.org/graph/synbioss/
05:43 < xp_prg> didn't come up :(
05:47 < kanzure> Retry.
05:49 < xp_prg> so there is a designer and a simulator
05:49 < xp_prg> they are seperated
05:49 < xp_prg> the designer is web based
05:52 < xp_prg> hi PeerInfinity
05:55 < PeerInfinity> hi :)
05:55 < PeerInfinity> it's way past my bedtime :)
05:58 < xp_prg> PeerInfinity do you understand synthetic biology stuff?
06:00 < PeerInfinity> only vaguely.  I haven't actually read much about it.
06:00 < xp_prg> ok, just wondering :>
06:17 < gene_> same with most of us
06:18 < gene_> I have an idea on how to get some funding for research
06:19 < gene_> anyone have access to some GFP?
06:19 < xp_prg> what is GFP?
06:19 < gene_> and a gene gun
06:19 < gene_> green fluourescent protein
06:19 < gene_> it makes stuff glow green under a blacklight
06:20 < gene_> the research on GFP won a nobel prize
06:21 < gene_> step 1: add GFP to something
06:21 < gene_> step 2: ???
06:21 < gene_> step 3: profit
06:21 < gene_> that's the plan
06:21 < xp_prg> awsome man!
06:22 < gene_> adding the GFP and getting it to work is the hard part
06:22 < gene_> so add GFP to cat, dog, guinea pig, or goldfish?
06:23 < gene_> which one would you buy?
06:24 < gene_> or what about rainbow carrots would you buy rainbow carrots
06:25 < gene_> would you buy rainbow carrots?
06:25 < fenn> only if there were a singing midget with green hair pretending to be a carrot to convince me
06:25 < gene_> HAHAHA
06:25 < gene_> you got the reference
06:26 < xp_prg> fenn I need your help man, you got a few secs?
06:26 < fenn> gene_: what a terrible, terrible series that was
06:26 < xp_prg> fenn hello?!
06:26 < fenn> hi
06:26 < xp_prg> fenn did you see my latest biobench?
06:26 < fenn> please state your question in the form of a question
06:27 < fenn> no
06:27 < gene_> I haven't finished watching it yet so I wouldn't know
06:27 < fenn> gene_: airplanes, in OUTER SPACE
06:27 < gene_> I know, I know
06:27 < fenn> they seem to have thrown a lot of money at it :\
06:27 < gene_> I tend to try to ignore physics when I watch anime
06:28 < gene_> or imagine that they invented some magical force generating thruster 
06:28 < fenn> or maybe they're just stuck in the 80's
06:29 < xp_prg> ok fenn, check this out please:  http://www.umassigem.org/biobench/biobench.html
06:29 < xp_prg> I followed your initial outlay
06:29 < fenn> well, i downloaded it for the music by yoko kanno, but it's mostly a disappointment
06:30 < UtopiahGHML> guys, do you know a website that gathers futuristics UI/HUD like ... cool visuals from GITS/Lain/etc?
06:30 < gene_> well at least they have megascale engineered space habitats with self-healing outer walls
06:30 < fenn> xp_prg: seems to be a problem with your DNS, i just get godaddy ads
06:30 < gene_> but on to biobench
06:30 < xp_prg> fenn you don't see Putting Bio Bricks together?
06:30 < xp_prg> do you have flash installed?
06:30 < fenn> hang on, lemme fire up the bloatware..
06:30 < xp_prg> heh
06:31  * fenn yawns
06:31 < fenn> i thought you were doing AJAX
06:31 < xp_prg> I am doing flash with ajax
06:31 < gene_> i don't see any biobricks
06:31 < gene_> if your going to make it visual make it like actual bricks
06:31 < xp_prg> gene_ click file->new
06:32 < gene_> that a two year old could program
06:32 < fenn> ok, i see some pictures, how do i link stuff together?
06:32 < gene_> could you send me the link again?
06:32 < xp_prg> fenn ok file->new
06:32 < xp_prg> http://www.umassigem.org/biobench/biobench.html
06:33 < xp_prg> fenn do you see the cell picture?
06:33 < fenn> yes
06:33 < fenn> now what?
06:33 < xp_prg> right click on the picture
06:33 < xp_prg> and click add bio brick
06:33 < gene_> SWEET
06:33 < gene_> it sorta works now
06:33 < fenn> i can't right click, i just get the adobe menu
06:34 < xp_prg> fenn the first part of the adobe menu if you right click over the picture says new bio brick
06:34 < xp_prg> you don't see that?
06:34 < fenn> oh and it just crashed, whee! i love flash!@
06:34 < xp_prg> fenn are you on linux?
06:34 < fenn> yes
06:34 < xp_prg> oh ok
06:34 < fenn> that's no excuse
06:34 < xp_prg> gene_ do you see it?
06:35 < gene_> yeah
06:35 < gene_> functionality not implemented
06:35 < UtopiahGHML> (Ill look in DeviantArt)
06:35 < xp_prg> fenn can you try again?
06:35 < gene_> so you might want to reconsider umm
06:36 < gene_> the way you approach this project
06:36 < fenn> no, now it just crashes as soon as the page opens
06:36 < gene_> genes and stuff should be thought of more like networks and stuff
06:36 < gene_> but I don't know
06:37 < fenn> yeah the "put in cell" part is not really necessary
06:37 < xp_prg> well I need to figure out the parts I can show under promoter, rbs, coding DNA, and terminator
06:37 < xp_prg> fenn can you help me to understand that?
06:37 < fenn> a lot of things are done in vitro anyway
06:37 < fenn> if it doesn't work in vitro, it probably won't work in a cell either
06:38 < fenn> and then in the end you can just say file->export->to e.coli or whatever
06:38 < xp_prg> so fenn help me to understand the parts I can show for those categorites please
06:38 < fenn> those are the biobrick types i guess
06:39 < gene_> the problem is it is expensive and time consuming to compile and run DNA
06:40 < xp_prg> fenn, I need help understanding those types, can you help me to understand that in relation to promoter, rbs, code dna, and terminator?
06:40 < fenn> this is a list of types; http://heybryan.org/~bbishop/docs/biobricks/types/
06:40 < fenn> unfortunately i dont know precisely what those words are supposed to mean
06:42 < xp_prg> well here are the yeast parts:  http://heybryan.org/~bbishop/docs/biobricks/types/Yeast_Parts.txt
06:42 < xp_prg> I would like to know what parts are a promoter, what are an rbs etc...
06:43 < gene_> please tell me too
06:43 < gene_> I believe the promoter is related to turning on the gene
06:44 < fenn> since i've never used biobricks or even looked at them beyond helping kanzure with some xml crap, i think you should ask on the biobrick mailing list
06:44 < fenn> or whatever the parent organization is called
06:44 < gene_> RBS is ribosome binding site
06:44 < xp_prg> right
06:44 < xp_prg> well ok
06:45 < xp_prg> fenn I wish you could help me more with my gui design :>
06:45 < xp_prg> got any suggestions?
06:45 < fenn> xp_prg: dont use flash
06:45 < fenn> please :)
06:45 < xp_prg> fenn well I probably will only use it to prototype, give me ideas on my gui design man!
06:49 < gene_> use processing it has face recognition libraries
06:49 < gene_> which is entirely useless for what we are doing
06:49 < xp_prg> fenn?
06:50  * fenn hides
06:50 < gene_> a gui isn't all that important for what we are doing
06:50 < gene_> we could have the best damn gui in the world and we still wouldn't be able to do synthetic biology
06:51 < xp_prg> well I must be dumb cuz it seems simple to me
06:51 < gene_> gui's aren't important
06:51 < gene_> knowing what to do with the user's input is more important
06:52 < gene_> which means we have to do some work ie understanding things
06:54 < gene_> our best sources for people like us might be discover magazine or scientific american articles on bio bricks
06:56 < fenn> that's low
06:57 < xp_prg> fenn fundamentally am I not just generated an SBML file?
06:57 < xp_prg> generated = generating
06:57 < fenn> i suppose so
06:58 < gene_> Fenn, a high school student built a nuclear reactor in his garden shed
06:58 < gene_> guess where he learned how to do it?
06:58 < fenn> boy scouts?
06:58 < fenn> discover magazine?
06:58 < gene_> informational packets the department of energy hands out 
06:59 < fenn> was this the guy with americium pellets?
06:59 < UtopiahGHML> do you have UIs of futuristic lab bench?
07:00 < gene_> yeah
07:00 < gene_> but even that large amount of americium wasn't enough to drive his neutron gun
07:00 < gene_> so he ended up using a vial of radium paint
07:01 < fenn> great, now all he needs is large quantities of gadolinium-239 and uranium-235 and he's in business
07:01 < gene_> but my point is that Sciam is a good source for people beginning synth bio
07:01 < gene_> he go u235
07:01 < gene_> extracted it from ore
07:01 < gene_> what's the gadolinium for?
07:02 < fenn> oh bullshit
07:02 < gene_> extracted it from fucking ore
07:02 < fenn> good uranium ore is 1/1000 uranium metal
07:02 < gene_> made yellow cake
07:02 < gene_> read the radioactive boyscout
07:03 < gene_> he was able to obtain MASSIVE amounts of tritium by 'borrowing' ever-glowing gun sights and extracting the tritium
07:03 < gene_> there isn't much tritium in those things
07:04 < gene_> he was very dedicated
07:05 < fenn> so um, what was he trying to do?
07:05 < gene_> make a working breeder reactor
07:05 < fenn> " transform samples of thorium and uranium into fissionable isotopes"
07:06 < fenn> well, alright.. 
07:06 < fenn> this is sort of like those tabletop fusion reactors
07:06 < fenn> except messier
07:06 < gene_> did i mention he extracted the lithium from lithium batteries so he could extract the thorium from burnt up watch mantles
07:06 < gene_> messier does not even come close to describing it
07:07 < xp_prg> fenn can you help me to understand these examples please:  http://hysss.sourceforge.net/examples.shtml ?
07:08  * fenn squints at the words on that page
07:09 < gene_> those look like networks of reactions
07:09 < fenn> xp_prg: why?
07:10 < fenn> it's not even ascii, how am i supposed to read it
07:10 < xp_prg> cuz I need to know this to understand the project that kanzure and I are working on
07:14 < gene_> might this help?
07:14 < gene_> http://partsregistry.org/Assembly:Standard_assembly
07:14 < xp_prg> fenn?
07:15 < fenn> yes?
07:15 < xp_prg> can you help me to understand hysss?
07:16 < fenn> no
07:16 < fenn> it looks to be something like SPICE
07:16 < fenn> and requires matlab, which i dont have
07:16 < xp_prg> A database of
07:16 < xp_prg> kinetic constants, on the other hand, should be easily searchable by participating species,
07:16 < xp_prg> reaction type, etc.
07:16 < xp_prg> what is a species and what are the reaction types?
07:17 < fenn> species are sorta like chemicals but can be less stable
07:17 < fenn> reaction type.. well, figure it out
07:17 < fenn> just chemistry stuff
07:18 < fenn> doesn't seem very applicable to simulating DNA transcription
07:18 < gene_> http://en.wikipedia.org/wiki/Chemical_species
07:19 < gene_> quick question: how much computing power do we all have?
07:19 < gene_> enough to make a supercomputer
07:19 < gene_> ?
07:19 < fenn> there was murmurings about access to a supercomputer
07:20 < gene_> do we have it?
07:20  * fenn shrugs
07:20 < gene_> so we can simulate an E.Coli
07:20 < gene_> cell
07:20 < gene_> or yeast
07:21 < fenn> at what level of abstraction?
07:21 < gene_> all of it
07:21 < gene_> down to atoms
07:21 < fenn> atom by atom ain't gonna happen
07:21 < gene_> they did it with virus
07:21 < fenn> surely you've heard of folding@home
07:21 < gene_> they simulated a whole virus
07:22 < gene_> for acouple of seconds
07:22 < gene_> in other words a long time
07:22 < gene_> so we might want to do a bit of folding
07:24 < gene_> it would be great to see if our code interferes with "system components"
07:24 < gene_> alas
07:24 < gene_> we need to be learning more about biobricks
07:25 < gene_> http://en.wikipedia.org/wiki/Promoter
07:27 < gene_> In order for transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences and response elements which provide a binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase.
07:27 < gene_>     * In bacteria, the promoter is recognized by RNA polymerase and an associated sigma factor, which in turn are brought to the promoter DNA by an activator protein binding to its own DNA sequence nearby.
07:27 < gene_>     * In eukaryotes, the process is more complicated, and at least seven different factors are necessary for the binding of an RNA polymerase II to the promoter.
07:27 < gene_> Promoters represent critical elements that can work in concert with other regulatory regions (enhancers, silencers, boundary elements/insulators) to direct the level of transcription of a given gene.
07:39 < marainein> re: the simulated virus thing - eukaroytic cells are a lot bigger than a puny little virus...it's gonna take a lot more computing power to do an atomic level simulation of them
07:43 < gene_> e.coli ain't a eukaryote
07:44 < marainein> no, although it's still much larger...anyway, simulating a human cell would be much more useful
07:46 < gene_> it would
07:46 < gene_> WE NEED MORE POWER!!!
07:47 < marainein> more than we'll ever have, within any reasonable timeframe
07:48 < gene_> what do you mean?
07:48 < gene_> oh
07:48 < gene_> reasonable timeframe
07:50 < gene_> what would that be?
07:51 < gene_> 2 years? 5 years?
07:51 < gene_> 10 year?
07:54 < marainein> well, think about the sizes involved
07:54 < marainein> say a virus is 100nm across
07:55 < gene_> 1 million moving atoms
07:55 < gene_> in the simvirus
07:55 < marainein> and a eukaryote cell is 10-100um across...between 100 and 1000 times larger in every direction
07:55 < gene_> it's tobacco mosaic
07:56 < marainein> which means the volumes involved would be between a million and a billion times larger
07:56 < gene_> so I can see how they did that
07:56 < gene_> yeah
07:56 < gene_> you do have a point there
07:57 < marainein> how long is it gonna take moore's law to push computing power up by a factor of a million? a billion?
07:59 < marainein> if you say computing power doubles every 18 months, and a billion is 30 doublings (2^30), you're looking at 45 years until we could attempt this with a eukaryotic cell
08:00 < marainein> (I've thought about this before, when I first read about the simulation, and I'd be happy if someone could show me how I'm wrong)
08:01 < UtopiahGHML> maybe because you force a structure on a subtrat that it is not adapted for, no coevolution thus huge waste.
08:18 < gene_> damn
08:18 < gene_> man it's getting late
11:50 < UtopiahGHML> Current Issues in Computational Biology and Bioinformatics http://www.youtube.com/watch?v=bVhOntMCmnQ
13:13 < UtopiahGHML> faceface: BSchool.com could be a good resource for the degree
14:21 < UtopiahGHML> Think faster focus better and remember moreRewiring our brain to stay younger...
14:21 < UtopiahGHML> http://www.youtube.com/watch?v=UyPrL0cmJRs
14:21 < UtopiahGHML> Dr. Michael Merzenich on brain plasticity.
15:09 < kanzure> maranein: No, we actually do have supercomputer access.
15:09 < kanzure> I'm so proud, gene_ maintained a reasonable defense against UI bullshit.
15:10 < kanzure> Anyway, re: learning more about biobricks, what you really need to do is go kill the guy who made http;//neptune.cems.umn.edu/designer/interface1.php and steal the code.
15:10 < kanzure> Re: the virus simulation stuff. That was something like 20 proteins. Probably involved something off of http://heybryan.org/mediawiki/index.php/Computational_chemistry
15:12 < kanzure> Hi codeshepherd, ppk 
15:14 < ppk> hey
17:13 < UtopiahGHML> I need something to use references within videos
17:13 < UtopiahGHML> so far I just use the url plus the timing as text but... not really good ;?
17:13 < UtopiahGHML> Id like people to be able to click and load the video at the moment Im quoting.
17:14 < UtopiahGHML> (like a time #anchor)
17:17 < UtopiahGHML> (I think GoogleVideos support that but others... dunno)
17:27 < kanzure> I am not aware of a standard for representing time-anchors in videos.
17:31 < UtopiahGHML> :/
18:44 < xp_prg> kanzure you here?
18:44 < kanzure> yeah
18:50 < kanzure> What's up?
18:57 < xp_prg> dude I have been studying hy3ss big time
18:57 < xp_prg> I have a couple of questions for you ok?
18:58 < kanzure> Alright.
18:58 < xp_prg> well, it models biochemical reactions
18:59 < xp_prg> I am confused how helpful that is per se, we are composing dna fundamentally, what is you want "reverse engineered" exactly, it seems pretty straight forward
18:59 < kanzure> If it seems pretty straightforward then what's the question?
19:00 < kanzure> http://neptune.cems.umn.edu/designer/interface1.php
19:00 < xp_prg> well, its just building a nc file that goes into hy3ss, hy3ss won't validate that the dna is correct or anything
19:00 < xp_prg> it just doesn't seem "complete" to me
19:01 < xp_prg> you have to know what your doing to make that system work, it doesn't really help you all that much
19:01 < xp_prg> you supply the rate functions etc...
19:01 < xp_prg> the effectors
19:01 < kanzure> Doesn't matter. There's some hidden magic behind interface{1,2,3}.php determining the generation of the files. That's what I need.
19:01 < kanzure> The rest of it can be supplied via wiring up to some other databases that I know of.
19:01 < kanzure> But first things are first, ok?
19:02 < kanzure> Either way it generates NetCDF or SBML files, and that's what I most need to make this work.
19:03 < xp_prg> what I do feel is the real magic is there are rules/constraints they are using that may be very important
19:03 < xp_prg> the composition of SBML/NetCDF files should be relatively straight forward, I will look into that code for you
19:03 < kanzure> The composition of the files given the interface exposed in interface1,2,3.php in particular.
19:03 < xp_prg> it would help me if you gave me more of a big picture idea on the goal of biobench and how you see it working, do you haved a plan sort of speak?
19:04 < xp_prg> my idea is that it will intelligently help create biological organisms to do specific things
19:04 < xp_prg> is that what you see it doing as well?
19:04 < kanzure> What the fuck is intelligence?
19:05 < kanzure> Maybe, but I don't think intelligence has anything to do with it. Most tools are just shortcuts for doing more complicated things anyway.
19:05 < xp_prg> rules based expert system preventing users from making mistakes etc...
19:05 < kanzure> "complicated" / less interesting things I guess.
19:05 < xp_prg> can you give me a better feel for what you see biobench doing?
19:06 < kanzure> Anyway, what I was going to do was plug this into a few repositories of biological modeling information, into partsregistry.org and some inventory systems plus SKDB so as to generate instructions for how to build experimental setups and so on.
19:07 < xp_prg> ok, I am game, just trying to understand it, I was a bit shocked by how simplistic synbioss really is
19:07 < kanzure> For what it's worth, it's also possible to automatically generate all possible networks (up to some certain size) s/networks/circuits/. Done implicitly, i.e. via general rules for grammar rewriting, this could reveal to users possibly interesting things they would have otherwise missed. Somewhat like what I'm doing with mechanical design.
19:07 < xp_prg> so inferring the solution from the goal?
19:07 < kanzure> Hopefully not. 
19:08 < kanzure> In that context, there's a way that you can insert an overall flow diagram and then ask the computer to show specific solutions to it, and then you can select the one you like the most for instance; but this isn't primary.
19:08 < xp_prg> cool, anyway it would help me if you could walk me through a couple of very simple examples with hy3ss that way I can get a better feel for what is going on in the source code of synbioss, can you assist me with that?
19:09 < kanzure> hy3ss isn't what we need to be looking at though
19:09 < kanzure> That's the simulation framework.
19:09 < xp_prg> synbioss is building the netcdf and sbml files that feed into that
19:09 < kanzure> synbioss is a desktop simulator
19:09 < kanzure> the 'synbioss designer' is what we need to have the source code to
19:09 < xp_prg> it would help me to get a feel for what is going on to understand simple scenarios
19:09 < xp_prg> does that not make sense?
19:10 < kanzure> It doesn't make any sense whatsoever because I keep telling you that the simulator isn't what we're looking at here .. the simulator is good and open source, it's usable, yes, but we're not using that here
19:10 < xp_prg> can I tell you what I know so far real quick?
19:10 < kanzure> Yes.
19:10 < xp_prg> dude relax, I am with you
19:10 < kanzure> It doesn't seem like it.
19:11 < xp_prg> ok, it feeds in reactions, effectors, rates of those reactions, degradation type info, proteins that are generated, how many times those proteins can be interacted with etc...  then it simulates what happens creating statistics on those reactions
19:12 < xp_prg> I was up until 2:30 AM studying this, I am definitely "with" you
19:13 < xp_prg> it also specifies gene location as adjust transcription rates as a result of that as well
19:13 < xp_prg> basically your feeding it contraints and initial parameters
19:13 < kanzure> That's right. Now we need a mapping from the constraints and initial parameters to the NetCDF/nc and/or SBML files. (preferably SBML because we like the SBML licensing)
19:13 < xp_prg> it is fundamentally preforming kinetic chemical reactions
19:14 < kanzure> http://heybryan.org/graph/ now has a .tar.gz w/ NetCDF APIs but it's C/C++ only, meaning a nasty CGI script will have to be written to encapsulate its functionality. :(
19:15 < xp_prg> kanzure my hunch is this area of the designer is readily understandible so don't stress, I just need to understand "what" it is doing to make sure I can even begin to understand the code
19:15 < xp_prg> by the way I used to teach c++ :>
19:16 < kanzure> That doesn't mean CGI scripts aren't a hack.
19:16 < kanzure> *terrible hack
19:16 < xp_prg> true
19:16 < xp_prg> I will look into this, I feel I understand the goal now from a concrete level
19:18 < xp_prg> thanks for helping me reach this point
19:42  * kanzure installs libsbml
19:45 < ccc> hello
19:45 < wrldpc2> hello.
19:45 -!- wrldpc2 is now known as wrldpc
19:57 < ccc> <-- despondence -->
19:58 < kanzure> Hey ccc.
20:14 < kanzure> xp_prg: I suppose what you want is http://celldesigner.org/ for the ui .. but meh.
20:55 < UtopiahGHML> how could a desktop widget get noticed when a user is currently visiting a website or not?
20:55 < UtopiahGHML> (knowing that I would code both the website and the widget)
20:55 < UtopiahGHML> (and the user would be warned and agree on it)
20:55 < UtopiahGHML> (but might eventually be behing NAT and such)
20:56 < UtopiahGHML> hmm the widget could periodically request the website using the API... but that's either heavy or slow
20:58 < kanzure> fenn: gitweb.cgi is popping up in top to steal 30% CPU every 5 seconds over here.
20:58 < kanzure> UtopiahGHML: What are you trying to do?
21:00 < UtopiahGHML> kanzure: a virtual mini-tachikoma :P
21:01 < UtopiahGHML> http://seedea.free.fr/wiki/index.php?n=Seedea.Visualization#virtualassistant
21:02 < UtopiahGHML> I know how to make it dive/show up from the website but how to make it by itself... beside repetitive API queries... dunno
21:03 < kanzure> Hrm. I still haven't figured out how to copy URLs in irssi without breaking down and switching into a screen session.
21:03 < UtopiahGHML> hmmm here I just select the text and it's in the clipboard
21:04 < UtopiahGHML> right click and it's pasted in irssi textline
21:04 < kanzure> So you assume I must be using a mouse?
21:04 < UtopiahGHML> well then you can regexp the logs
21:05 < kanzure> Still have the same problem. Once you grep/regexp/etc., you still have to get those variables into some form that you can run links2 on.
21:05 < kanzure> Oh well.
21:05 < UtopiahGHML> dunno, I know that FF can handle remote commands pretty well
21:05 < kanzure> Again with the assumptions
21:06 < UtopiahGHML> Im sure lynx and links can handle urls as parameters
21:06 < UtopiahGHML> remote request, dunno
21:06 < UtopiahGHML> you could just load seedea.org if you want
21:06 < kanzure> Correct, but that'd require some awk skillage on my part or some such ;-) and besides, what about my original request for copy+paste in irssi without screen?
21:07 < UtopiahGHML> without screen?
21:07 < kanzure> You could also tell me what this 'virtual assistant' is supposed to be
21:07 < kanzure> Without screen.
21:07 < UtopiahGHML> what's the relation with the screen command?
21:07 < kanzure> screen allows you to copy and paste and do a number of other useful things
21:07 < kanzure> however, you have to be in screen before that's usable.
21:07 < UtopiahGHML> well Im in screen
21:07 < kanzure> And you're using firefox?
21:07 < UtopiahGHML> Im using screen on a shell
21:08 < UtopiahGHML> to have irssi+bitlbee(IM) 24/7
21:08 < UtopiahGHML> and Im using Firefox locally yes
21:08 < UtopiahGHML> so that I can use Vimperator
21:08 < UtopiahGHML> (never surfed faster)
21:09 < UtopiahGHML> once again, you could see all that on http://seedea.free.fr/wiki/index.php?n=Content.Tools but since you can't open urls... ;)
21:41 < xp_prg> can I ask a dumb question, are biobricks made up of bio parts?
21:43 < kanzure> Can you elaborate on your question? What is a bio part?
21:45 < xp_prg> sure one sec, let me get the link, like when I looked at the synbioss example they entered in bio bricks that seem to compose a larger bio brick, just curious if I was mistaken about that
21:47 < UtopiahGHML> kanzure: a virtual assistant is just a visual interface for my website API + a rssnotifier to pass messages both ways.
21:47 < UtopiahGHML> (eventually with smarter functions later but I don't think so, being able to query the API and communicate is enough)
21:47 < kanzure> UtopiahGHML: I am confused. Are you trying to accomplish XSS?
21:47 < UtopiahGHML> maybe, what is XSS?
21:48 < kanzure> It's where you break the browser security model and let scripts access resources on other servers (or clients)
21:49 < UtopiahGHML> no
21:49 < UtopiahGHML> I don't see the need for that.
21:50 < kanzure> xp_prg: Theoretically there are 'devices' which are made up of multiple biobrick parts, but I don't think this is entirely implemented yet. If it is, then I don't know about it.
21:56 < UtopiahGHML> kanzure:the virtualassistant is only nice if you are a fan of GITS' tachikomas and a heavier user of my website who doesn't keep his browser open 24/7
21:56 < UtopiahGHML> it's more like a cool optional way to interact with the website, nothing more.
21:57 < kanzure> Right, I've done similar things before, such as 'remote controls' for websites, or at one point I had an AIM bot for users to play with their DBZ characters on my old anime website :/
21:59  * kanzure can't believe that he just admitted that.
21:59 < kanzure> *believe
21:59 < UtopiahGHML> yep I have IM/SN hooks too
22:00 < UtopiahGHML> tried ping.fm? can be a good hub and they provide customURL option
22:03 < gene_> so what's this talk about a mini-tachikoma?
22:05 < UtopiahGHML> gene_: http://seedea.free.fr/wiki/index.php?n=Seedea.Visualization#virtualassistant
22:06 < gene_> oh
22:06 < gene_> not the real thing
22:06 < UtopiahGHML> Im not really into real things.
22:07 < UtopiahGHML> but you can buy japanese mini robots with their style
22:07 < UtopiahGHML> (min but still 30cm tall I think)
22:07 < gene_> Kanzure's brainbot thing might be necessary to make the real thing
22:08 < gene_> that and a high density powersource and nice actuators
22:11 < UtopiahGHML> have you seen bigdog and podypedal or other robots with good locomotion?
22:11 < gene_> yeah
22:11 < gene_> they use miniature gasoline generators
22:11 < UtopiahGHML> ?
22:12 < UtopiahGHML> for what bigdog?
22:12 < gene_> for big dog
22:12 < gene_> for power
22:13 < UtopiahGHML> well what impressed me more was the balance and the ability to move on very different surfaces
22:14 < gene_> it is quite impressive
22:15 < gene_> especially kicking it
22:15 < gene_> the kick test should be a standard test for all ambulatory robots
22:16 < UtopiahGHML> :)
22:17 < UtopiahGHML> someone told me that the army tests servers by firing at them on a floating bark for 3 days non-stop (for the servers that can handle it of course)
22:25 < gene_> what is a floating bark?
22:28 < UtopiahGHML> like a container on water
22:28 < UtopiahGHML> a metal cube with servers inside :)
22:28 < UtopiahGHML> and BHAM, they fire and fire and fire at it
22:28 < UtopiahGHML> last one standing wins the contract.
22:34 < kanzure_> I had some troubles there. What was everyone just talking about?
22:34 < gene_> oh
22:34 < gene_> servers
22:34 < gene_> and how the military test them
22:34 < gene_> they shoot at them
22:34 < kanzure_> The military has a "bullet test".
22:34 < kanzure_> Right.
22:34 < kanzure_> NASA does too, as it turns out.
22:35 < kanzure_> There was once a slashdotter who posted about how he had to physically walk outside and down the fiber optics lines that were being installed to his business just to make sure that he was actually getting true redundancy from the ISPs and cablelaying companies .. turns out they were a bunch of morons and the cables just converged to a single provider.
22:37 < gene_> heh
22:37 < gene_> sucks
22:38 < kanzure_> So, Paul Atkinson, one of the Austin Robot Group members, used to consult for NASA. In particular he was working on their launch computer systems. That's how I learned about their "bullet test". They would literally shoot the circuit boards and so on. 
22:43 < gene_> I am surprised nasa would do that
22:44 < bkero> They need redundant systems.
22:46 < kanzure_> Aren't they running low on backup shuttles? ;-)
22:46 < bkero> Maybe if they can make them reusable.
22:57 < gene_> they are running low on shuttles
22:57 < gene_> they need more
22:58 < bkero> How about we privatize space travel? :P
22:58 < bkero> Ala spaceship one
22:59 < gene_> how about instead of giving $700 billion dollar bailouts
22:59 < gene_> we build a $6 billion dollar space elevator
22:59 < bkero> $700,000,000,000 could have bought us a colony on hte moon.
22:59 < gene_> this gives me an idea
23:00  * bkero wonders how hard it is to break atmo.
23:00 < gene_> make bank company
23:00 < gene_> employ lots of people
23:01 < gene_> start building colony on moon
23:01 < gene_> get gov bailout
23:01  * kanzure_ finds a typo in DBZ Budokai Tenkaichi 3.
23:02 < bkero> heh
23:02 < bkero> kanzure_: you should try bt2, I've found the single-player mode to be much better
23:03 < kanzure_> I've been wondering when somebody would sit down to bother with ripping the 3D models from these discs. Isn't it about time?
23:03 < kanzure_> bkero: What's different?
23:04 < bkero> Read the IGN reviews for both games.
23:04 < bkero> It's less like a movie.  There are less characters, but the controls are more fluid.
23:04 < bkero> I downloaded both, and played 2 first, never got around to 3.
23:04 < bkero> 2's story is also more complete.
23:04 < kanzure_> I wonder why the disparity.
23:04 < kanzure_> And were you running it off of an emulator?
23:06 < gene_> ripping the 3d models and textures from dragon ball
23:06 < gene_> heh
23:07 < bkero> kanzure_: We tried it using a quake 3 engine.  Look up DBZ: BFP
23:07 < bkero> Bid for Power
23:08 < gene_> looks like somebody want a meatspace model of vegeta crushing a scouter in his hand
23:08 < gene_> yelling that famous phrase
23:09 < bkero> lol
23:09 < kanzure_> bkero: The quake mod was you?
23:09 < bkero> kanzure_: what was that synthetic biology site on sourceforge you found?
23:09 < bkero> synbioss?
23:09 < kanzure_> bkero: http://synbioss.sf.net/
23:10 < bkero> kanzure_: No, I didn't contribute to it.  I was eagerly awaiting it though, and they got hit with a cease and desist from FUnamation.
23:10 < bkero> Fuckers. :(
23:10 < kanzure_> At the moment I'm busy compiling libsbml .. I'll just do it myself since nobody understands.
23:10 < kanzure_> bkero: Oh please. "Cease and desist" merely means you're being too public about it.
23:11 < kanzure_> I don't recall whether or not the models were ripped.
23:11 < kanzure_> I was checking back in 2002, so my memory is fuzzy.
23:11 < gene_> hmmmm....
23:11 < kanzure_> They looked pretty bad. I think somebody did them by hand.
23:11 < gene_> I wonder if I could get a cease and desist for printing off a 3d model of vegeta
23:24 < kanzure_> "Can't find boot_libsbml in <nasty_path_here>/LibSBML.so". And with python it can't find libsbml.so at all.
23:34 < kanzure_> Heh. Okay. Fixed.
23:35 < kanzure_> Only python. Had to copy the generated library files into /lib/.
23:35 < kanzure_> Looks like I'm using python.
23:38 < xp_prg> hi kanzure_ quick question:  http://partsregistry.org/wiki/index.php/Part_Types:Measurement_Systems
23:39 < xp_prg> I want ot understand what the green arrow, green little circle, lightbulb and red thnig mean
23:39 < xp_prg> is the green arrow a promoter?
23:42 < kanzure_> The green arrow refers to a 'regulatory' component.
23:43 < xp_prg> ok what do the other symbols mean?
23:44 < kanzure_> http://partsregistry.org/Part_Types
23:46 < xp_prg> thanks
23:53 < kanzure_> At this point all that's really needed is to figure out how to correspond the interface{1,2,3}.php files with the libsbml documentation. The XML output has a few features: http://heybryan.org/graph/2008-10-25_sbml_notes.txt and somewhere in the API there's information about generating that information. This is just a matter of reading through the docs really.
23:54 < xp_prg> kanzure ok, just trying to learn a little bit sorry :)
23:55 < kanzure_> in general the information that you're trying to obtain from the partsregistry.org technical docs and so on isn't going to be helpful in the direction that you want to go, this is because it's not really "complete" or "mature" I suppose you could say
23:56 < kanzure_> While there are, in fact, different types, the specialist domain knowledge isn't encoded into the repo, etc.