| --- Day changed Sat Oct 25 2008 | ||
| * kanzure is back. | 00:32 | |
| kanzure | Hi marainein | 00:33 |
|---|---|---|
| marainein | hi kanzure | 00:33 |
| marainein | how are your projects going? | 00:33 |
| kanzure | Very well. :) | 00:33 |
| 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. | 00:34 |
| 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/ | 00:35 |
| 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. | 00:36 |
| kanzure | Well. | 00:37 |
| kanzure | I don't know where it's gone. | 00:38 |
| gene_ | are you still there? | 04:57 |
| gene_ | kanzure can you burn me a ubuntu disk with that free bandwidth you have | 05:06 |
| gene_ | I'll even provide you with a disk | 05:07 |
| gene_ | how big is ubuntu | 05:08 |
| xp_prg | kanzure you here man? | 05:22 |
| xp_prg | hi procto! | 05:35 |
| xp_prg | anyone here? | 05:39 |
| xp_prg | ppk you here? | 05:39 |
| kanzure | no | 05:39 |
| xp_prg | hi kanzure | 05:39 |
| xp_prg | kanzure I have my symbioss app open, can you help me to understand how to make it work? | 05:40 |
| 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 | 05:41 |
| xp_prg | what is the link? | 05:42 |
| kanzure | http://heybryan.org/graph/synbioss/ | 05:42 |
| xp_prg | didn't come up :( | 05:43 |
| kanzure | Retry. | 05:47 |
| 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 | 05:49 |
| xp_prg | hi PeerInfinity | 05:52 |
| PeerInfinity | hi :) | 05:55 |
| PeerInfinity | it's way past my bedtime :) | 05:55 |
| xp_prg | PeerInfinity do you understand synthetic biology stuff? | 05:58 |
| PeerInfinity | only vaguely. I haven't actually read much about it. | 06:00 |
| xp_prg | ok, just wondering :> | 06:00 |
| gene_ | same with most of us | 06:17 |
| gene_ | I have an idea on how to get some funding for research | 06:18 |
| 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 | 06:19 |
| gene_ | the research on GFP won a nobel prize | 06:20 |
| 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! | 06:21 |
| 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? | 06:22 |
| gene_ | which one would you buy? | 06:23 |
| gene_ | or what about rainbow carrots would you buy rainbow carrots | 06:24 |
| 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 | 06:25 |
| 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 | 06:26 |
| 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 | 06:27 |
| gene_ | or imagine that they invented some magical force generating thruster | 06:28 |
| fenn | or maybe they're just stuck in the 80's | 06:28 |
| 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 | 06:29 |
| 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 | 06:30 |
| * 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 | 06:31 |
| 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 | 06:32 |
| 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 | 06:33 |
| 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? | 06:34 |
| 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 | 06:35 |
| 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 | 06:36 |
| 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 | 06:37 |
| 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 | 06:38 |
| gene_ | the problem is it is expensive and time consuming to compile and run DNA | 06:39 |
| 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 | 06:40 |
| 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... | 06:42 |
| gene_ | please tell me too | 06:43 |
| gene_ | I believe the promoter is related to turning on the gene | 06:43 |
| 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 | 06:44 |
| 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! | 06:45 |
| 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? | 06:49 |
| * 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 | 06:50 |
| 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 | 06:51 |
| gene_ | which means we have to do some work ie understanding things | 06:52 |
| gene_ | our best sources for people like us might be discover magazine or scientific american articles on bio bricks | 06:54 |
| fenn | that's low | 06:56 |
| xp_prg | fenn fundamentally am I not just generated an SBML file? | 06:57 |
| xp_prg | generated = generating | 06:57 |
| fenn | i suppose so | 06:57 |
| 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 | 06:58 |
| fenn | was this the guy with americium pellets? | 06:59 |
| UtopiahGHML | do you have UIs of futuristic lab bench? | 06:59 |
| 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 | 07:00 |
| 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? | 07:01 |
| 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 | 07:02 |
| 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 | 07:03 |
| gene_ | he was very dedicated | 07:04 |
| 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" | 07:05 |
| 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 | 07:06 |
| xp_prg | fenn can you help me to understand these examples please: http://hysss.sourceforge.net/examples.shtml ? | 07:07 |
| * fenn squints at the words on that page | 07:08 | |
| gene_ | those look like networks of reactions | 07:09 |
| fenn | xp_prg: why? | 07:09 |
| 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 | 07:10 |
| gene_ | might this help? | 07:14 |
| gene_ | http://partsregistry.org/Assembly:Standard_assembly | 07:14 |
| xp_prg | fenn? | 07:14 |
| fenn | yes? | 07:15 |
| xp_prg | can you help me to understand hysss? | 07:15 |
| 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? | 07:16 |
| 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 | 07:17 |
| fenn | doesn't seem very applicable to simulating DNA transcription | 07:18 |
| gene_ | http://en.wikipedia.org/wiki/Chemical_species | 07:18 |
| 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 | 07:19 |
| 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 | 07:20 |
| 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 | 07:21 |
| 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 | 07:22 |
| 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 | 07:24 |
| gene_ | http://en.wikipedia.org/wiki/Promoter | 07:25 |
| 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. | 07:27 |
| 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 | 07:39 |
| gene_ | e.coli ain't a eukaryote | 07:43 |
| marainein | no, although it's still much larger...anyway, simulating a human cell would be much more useful | 07:44 |
| gene_ | it would | 07:46 |
| gene_ | WE NEED MORE POWER!!! | 07:46 |
| marainein | more than we'll ever have, within any reasonable timeframe | 07:47 |
| gene_ | what do you mean? | 07:48 |
| gene_ | oh | 07:48 |
| gene_ | reasonable timeframe | 07:48 |
| gene_ | what would that be? | 07:50 |
| gene_ | 2 years? 5 years? | 07:51 |
| gene_ | 10 year? | 07:51 |
| marainein | well, think about the sizes involved | 07:54 |
| marainein | say a virus is 100nm across | 07:54 |
| 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 | 07:55 |
| 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 | 07:56 |
| marainein | how long is it gonna take moore's law to push computing power up by a factor of a million? a billion? | 07:57 |
| 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 | 07:59 |
| 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) | 08:00 |
| UtopiahGHML | maybe because you force a structure on a subtrat that it is not adapted for, no coevolution thus huge waste. | 08:01 |
| gene_ | damn | 08:18 |
| gene_ | man it's getting late | 08:18 |
| UtopiahGHML | Current Issues in Computational Biology and Bioinformatics http://www.youtube.com/watch?v=bVhOntMCmnQ | 11:50 |
| UtopiahGHML | faceface: BSchool.com could be a good resource for the degree | 13:13 |
| 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. | 14:21 |
| kanzure | maranein: No, we actually do have supercomputer access. | 15:09 |
| kanzure | I'm so proud, gene_ maintained a reasonable defense against UI bullshit. | 15:09 |
| 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 | 15:10 |
| kanzure | Hi codeshepherd, ppk | 15:12 |
| ppk | hey | 15:14 |
| 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. | 17:13 |
| UtopiahGHML | (like a time #anchor) | 17:14 |
| UtopiahGHML | (I think GoogleVideos support that but others... dunno) | 17:17 |
| kanzure | I am not aware of a standard for representing time-anchors in videos. | 17:27 |
| UtopiahGHML | :/ | 17:31 |
| xp_prg | kanzure you here? | 18:44 |
| kanzure | yeah | 18:44 |
| kanzure | What's up? | 18:50 |
| xp_prg | dude I have been studying hy3ss big time | 18:57 |
| xp_prg | I have a couple of questions for you ok? | 18:57 |
| kanzure | Alright. | 18:58 |
| xp_prg | well, it models biochemical reactions | 18:58 |
| 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? | 18:59 |
| 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 | 19:00 |
| 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? | 19:01 |
| kanzure | Either way it generates NetCDF or SBML files, and that's what I most need to make this work. | 19:02 |
| 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? | 19:03 |
| 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? | 19:04 |
| 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? | 19:05 |
| 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. | 19:06 |
| 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. | 19:07 |
| 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? | 19:08 |
| 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? | 19:09 |
| 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. | 19:10 |
| 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 | 19:11 |
| xp_prg | I was up until 2:30 AM studying this, I am definitely "with" you | 19:12 |
| 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 | 19:13 |
| 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. :( | 19:14 |
| 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++ :> | 19:15 |
| 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 | 19:16 |
| xp_prg | thanks for helping me reach this point | 19:18 |
| * kanzure installs libsbml | 19:42 | |
| ccc | hello | 19:45 |
| wrldpc2 | hello. | 19:45 |
| -!- wrldpc2 is now known as wrldpc | 19:45 | |
| ccc | <-- despondence --> | 19:57 |
| kanzure | Hey ccc. | 19:58 |
| kanzure | xp_prg: I suppose what you want is http://celldesigner.org/ for the ui .. but meh. | 20:14 |
| 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) | 20:55 |
| UtopiahGHML | hmm the widget could periodically request the website using the API... but that's either heavy or slow | 20:56 |
| 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? | 20:58 |
| UtopiahGHML | kanzure: a virtual mini-tachikoma :P | 21:00 |
| UtopiahGHML | http://seedea.free.fr/wiki/index.php?n=Seedea.Visualization#virtualassistant | 21:01 |
| 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 | 21:02 |
| 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 | 21:03 |
| 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 | 21:04 |
| 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 | 21:05 |
| 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? | 21:06 |
| 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 | 21:07 |
| 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) | 21:08 |
| 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... ;) | 21:09 |
| xp_prg | can I ask a dumb question, are biobricks made up of bio parts? | 21:41 |
| kanzure | Can you elaborate on your question? What is a bio part? | 21:43 |
| 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 | 21:45 |
| 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? | 21:47 |
| kanzure | It's where you break the browser security model and let scripts access resources on other servers (or clients) | 21:48 |
| UtopiahGHML | no | 21:49 |
| UtopiahGHML | I don't see the need for that. | 21:49 |
| 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. | 21:50 |
| 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. | 21:56 |
| 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 :/ | 21:57 |
| * kanzure can't believe that he just admitted that. | 21:59 | |
| kanzure | *believe | 21:59 |
| UtopiahGHML | yep I have IM/SN hooks too | 21:59 |
| UtopiahGHML | tried ping.fm? can be a good hub and they provide customURL option | 22:00 |
| gene_ | so what's this talk about a mini-tachikoma? | 22:03 |
| UtopiahGHML | gene_: http://seedea.free.fr/wiki/index.php?n=Seedea.Visualization#virtualassistant | 22:05 |
| gene_ | oh | 22:06 |
| gene_ | not the real thing | 22:06 |
| UtopiahGHML | Im not really into real things. | 22:06 |
| 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 | 22:07 |
| gene_ | that and a high density powersource and nice actuators | 22:08 |
| 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 | ? | 22:11 |
| UtopiahGHML | for what bigdog? | 22:12 |
| gene_ | for big dog | 22:12 |
| gene_ | for power | 22:12 |
| UtopiahGHML | well what impressed me more was the balance and the ability to move on very different surfaces | 22:13 |
| gene_ | it is quite impressive | 22:14 |
| gene_ | especially kicking it | 22:15 |
| gene_ | the kick test should be a standard test for all ambulatory robots | 22:15 |
| UtopiahGHML | :) | 22:16 |
| 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) | 22:17 |
| gene_ | what is a floating bark? | 22:25 |
| 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. | 22:28 |
| 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. | 22:34 |
| 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. | 22:35 |
| gene_ | heh | 22:37 |
| gene_ | sucks | 22:37 |
| 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. | 22:38 |
| gene_ | I am surprised nasa would do that | 22:43 |
| bkero | They need redundant systems. | 22:44 |
| kanzure_ | Aren't they running low on backup shuttles? ;-) | 22:46 |
| bkero | Maybe if they can make them reusable. | 22:46 |
| gene_ | they are running low on shuttles | 22:57 |
| gene_ | they need more | 22:57 |
| bkero | How about we privatize space travel? :P | 22:58 |
| bkero | Ala spaceship one | 22:58 |
| 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 | 22:59 |
| * bkero wonders how hard it is to break atmo. | 23:00 | |
| gene_ | make bank company | 23:00 |
| gene_ | employ lots of people | 23:00 |
| gene_ | start building colony on moon | 23:01 |
| gene_ | get gov bailout | 23:01 |
| * kanzure_ finds a typo in DBZ Budokai Tenkaichi 3. | 23:01 | |
| bkero | heh | 23:02 |
| bkero | kanzure_: you should try bt2, I've found the single-player mode to be much better | 23:02 |
| 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? | 23:03 |
| 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? | 23:04 |
| gene_ | ripping the 3d models and textures from dragon ball | 23:06 |
| gene_ | heh | 23:06 |
| bkero | kanzure_: We tried it using a quake 3 engine. Look up DBZ: BFP | 23:07 |
| bkero | Bid for Power | 23:07 |
| gene_ | looks like somebody want a meatspace model of vegeta crushing a scouter in his hand | 23:08 |
| gene_ | yelling that famous phrase | 23:08 |
| 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/ | 23:09 |
| 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. | 23:10 |
| 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 | 23:11 |
| kanzure_ | "Can't find boot_libsbml in <nasty_path_here>/LibSBML.so". And with python it can't find libsbml.so at all. | 23:24 |
| kanzure_ | Heh. Okay. Fixed. | 23:34 |
| kanzure_ | Only python. Had to copy the generated library files into /lib/. | 23:35 |
| kanzure_ | Looks like I'm using python. | 23:35 |
| xp_prg | hi kanzure_ quick question: http://partsregistry.org/wiki/index.php/Part_Types:Measurement_Systems | 23:38 |
| 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? | 23:39 |
| kanzure_ | The green arrow refers to a 'regulatory' component. | 23:42 |
| xp_prg | ok what do the other symbols mean? | 23:43 |
| kanzure_ | http://partsregistry.org/Part_Types | 23:44 |
| xp_prg | thanks | 23:46 |
| 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. | 23:53 |
| xp_prg | kanzure ok, just trying to learn a little bit sorry :) | 23:54 |
| 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 | 23:55 |
| kanzure_ | While there are, in fact, different types, the specialist domain knowledge isn't encoded into the repo, etc. | 23:56 |
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