| --- Day changed Sat Nov 01 2008 | ||
| xp_prg | kanzure_ do you understand the output of synbioss? | 00:37 |
|---|---|---|
| kanzure_ | I haven't finished converting it to run on linux yet. | 00:38 |
| xp_prg | converting it? | 00:44 |
| kanzure_ | It includes various windows-only libs. | 00:45 |
| kanzure_ | imports. | 00:45 |
| xp_prg | pyGTK is cross platform, I am confused what you mean | 00:46 |
| kanzure_ | Why would they look in C:\GTK for my GTK installation then? | 00:47 |
| kanzure_ | That's clearly a Windows directory. | 00:47 |
| drazak | you did it wrong | 00:47 |
| ybit | it says that its available for linux | 00:54 |
| ybit | btw, who did what in flash? | 00:54 |
| ybit | i went to some link which had flash. | 00:54 |
| ybit | why? you will have to answer to the semantic web gods later | 00:55 |
| ybit | + open source gods = not good for you | 00:55 |
| drazak | http://downloads.sourceforge.net/synbioss/synbioss-1.0.1-src.zip?modtime=1221064192&big_mirror=0 | 00:56 |
| drazak | download that | 00:56 |
| drazak | unzip it | 00:56 |
| drazak | and compile | 00:56 |
| drazak | and it will work in linux | 00:56 |
| drazak | the .exe is windows i386 specific | 00:56 |
| kanzure_ | drazak: Look at setup.py | 00:59 |
| drazak | I'm decently certain that the os module converts c:/ to ~ | 01:01 |
| kanzure_ | I wonder why it failed on my system. | 01:02 |
| drazak | what was the error? | 01:02 |
| kanzure_ | It's been a while. I probably ranted about it in here, though. | 01:03 |
| xp_prg | hi drazak I am using flash because it is more robust for what I need to do | 01:16 |
| drazak | why are you telling me? | 01:16 |
| xp_prg | the back end will be python with django though | 01:16 |
| xp_prg | you asked | 01:16 |
| kanzure_ | Why django? | 01:16 |
| kanzure_ | Who the fuck said anything about django? | 01:16 |
| drazak | no, ybit asked | 01:16 |
| xp_prg | its the best web framework for python | 01:17 |
| xp_prg | do you know a better one? | 01:17 |
| kanzure_ | That doesn't answer my question. | 01:17 |
| xp_prg | kanzure_ what would you have me use? | 01:17 |
| kanzure_ | I'd have you write the dman script you should have written months ago. | 01:18 |
| kanzure_ | *damn | 01:18 |
| xp_prg | I want to use google engine but python needs to use libsbml which is a shared library, google engine can't handle that | 01:18 |
| kanzure_ | Not a web service thing. Not a flash app. Just the script. | 01:18 |
| kanzure_ | I don't care about the google engine. | 01:18 |
| xp_prg | kanzure_ you agreed this would be an ajax app | 01:18 |
| xp_prg | I made my libsbml script | 01:18 |
| xp_prg | what is missing that you want? | 01:18 |
| kanzure_ | No you didn't. | 01:18 |
| kanzure_ | The sbml script is incomplete and doesn't reconstruct the same data. | 01:18 |
| kanzure_ | though it is a step in the right direction | 01:19 |
| xp_prg | I asked you what the next step was and you told me you didn't want my help | 01:19 |
| xp_prg | I would love to know what the next step you want me to do is with that python script | 01:19 |
| kanzure_ | Yeah, I don't need that flash bullshit. | 01:19 |
| kanzure_ | I just told you. | 01:19 |
| kanzure_ | Also, I told you a few days ago as well. | 01:19 |
| xp_prg | kanzure_ please help me to understand what "same" data your referring to, I need an example to attempt to recreate manually, can you supply one please? | 01:20 |
| xp_prg | or is it just reverse engineer the entire functionality of the synbioss designer by myself? | 01:20 |
| kanzure_ | I gave you over 50 MB of examples. What the hell man. | 01:21 |
| xp_prg | just raw xml? | 01:21 |
| kanzure_ | Yep, entire functionality. | 01:21 |
| kanzure_ | Yes, that was the output of the designer-website-thingy on the neptune servers. | 01:21 |
| kanzure_ | http://heybryan.org/graph/synbioss/tmp/ | 01:21 |
| xp_prg | yes, I see that, well I am working on it, I just made one that worked with synbioss, now I have to reverse engineer it | 01:21 |
| kanzure_ | http://neptune.cems.umn.edu/designer/interface1.php | 01:22 |
| kanzure_ | http://neptune.cems.umn.edu/designer/interface2.php | 01:22 |
| xp_prg | yes I know where it is | 01:22 |
| kanzure_ | http://neptune.cems.umn.edu/designer/interface3.php | 01:22 |
| xp_prg | the truth is you don't really need those, you can use the modeler directly in synbioss | 01:22 |
| xp_prg | it is probably more robust anyway | 01:22 |
| kanzure_ | Fuck GUIs. | 01:22 |
| kanzure_ | I just want that script. | 01:23 |
| xp_prg | kanzure_ may I ask how you will supply the inputs to the script? | 01:23 |
| kanzure_ | Do you have a memory problem? | 01:23 |
| kanzure_ | We've gone over this many times before. | 01:23 |
| xp_prg | like how will you supply promoters, effectors, biobricks? | 01:23 |
| kanzure_ | I keep telling you CLI, but maybe you don't understand what a script is? | 01:23 |
| kanzure_ | What a cli-only script is, I mean. | 01:23 |
| xp_prg | you have not gone over the CLI input specification | 01:24 |
| kanzure_ | Same input as on the HTML document. | 01:24 |
| kanzure_ | pages. | 01:24 |
| kanzure_ | *HTML pages. | 01:24 |
| kanzure_ | And yes, I did go over that. | 01:24 |
| xp_prg | kanzure_ that is what goes in, not how, like for example lets say the script is kanzurehy3s.py | 01:24 |
| kanzure_ | What? | 01:24 |
| xp_prg | you would invoke it on the cli with ./kanzurehy3s.py input1 input2 input3 | 01:25 |
| kanzure_ | You could. Another option would be to ask for user input via STDIN. | 01:25 |
| kanzure_ | Either way. | 01:25 |
| xp_prg | oh ok, I didn't know how you wanted that done, that is all I am asking | 01:25 |
| kanzure_ | What? | 01:25 |
| kanzure_ | Parameters are fine. | 01:25 |
| xp_prg | well it would help me to understand the parameters you want it to accept and how you will specify them | 01:25 |
| kanzure_ | The same parameters as on the HTML pages .. I just said this two minutes ago. | 01:26 |
| xp_prg | for example: find . -name "*.py" | 01:26 |
| xp_prg | kanzure_ yes man, but a cli program takes arguments in a certain way, what is that way you want me to use? | 01:26 |
| xp_prg | like -name specifies the name of the files to search for | 01:27 |
| kanzure_ | HTML form elements have a 'name' variable that specifies its name. | 01:27 |
| kanzure_ | *it's | 01:27 |
| kanzure_ | hrm, *their | 01:27 |
| xp_prg | kanzure_ I am not asking what needs to go into the script but how it will be supplied on the command line | 01:29 |
| kanzure_ | You were asking about the name of the parameters. You might as well preserve the same naming scheme of the parameters. | 01:29 |
| kanzure_ | I don't know why you would change it at this point. | 01:30 |
| xp_prg | ok lets try with an example: | 01:30 |
| xp_prg | ./kanzurehy3s.py -biobricks b123, b234, b456 | 01:30 |
| xp_prg | is that how you want to do it? | 01:30 |
| kanzure_ | <input name="thingy" value="user supplied variable"> | 01:30 |
| xp_prg | or like this: | 01:30 |
| kanzure_ | ./program --thingy="user supplied variable" | 01:30 |
| xp_prg | ok | 01:31 |
| xp_prg | that is all I was asking | 01:31 |
| kanzure_ | You can also do STDIN. | 01:41 |
| xp_prg | so prompt the user for input like enter the bio brick:> | 01:42 |
| xp_prg | is that what you mean? | 01:42 |
| kanzure_ | Yes, that's "standard input". | 01:44 |
| kanzure_ | http://heybryan.org/~bbishop/docs/Voltage-controlled_ring_oscillator_for_13_Hz_to_407_MHz.pdf | 02:27 |
| kanzure_ | Ultrasound stimulation of the heart. | 02:35 |
| kanzure_ | fenn: So I was doing a phone conference today with the VOICED people. | 03:53 |
| kanzure_ | It's interesting how literally equivalent their problems are to the ones we were thinking about months ago. | 03:54 |
| kanzure_ | Basically they want better formats and more detail to be packed into it, but everyone is generally clueless. | 03:54 |
| kanzure_ | One character associated with this crowd is apparently surprised how "little detail" all of this work involves, apparently he does finite element analysis and so on, and thus would obviously think much of this 'design' work is pathetic, though I don't see him going through a few million designs with his partial differentials. | 03:55 |
| kanzure_ | +- | 03:56 |
| kanzure_ | For solid (metal) mechanical systems, an algebraic language allowing for 3D geometric primitive subtraction and addition can be used, plus part mating algorithms to make 3D model files for those FEM simulations, I guess. | 04:01 |
| * kanzure_ needs to remember to see if the coffee filters capture the algae. | 04:03 | |
| kanzure_ | I wonder why there's no library for doing that, even in OpenGL or Blender. "Make giant sphere. Take out a triangle on the surface at the pi/2-th coord." <- Isn't subtractive modeling obvious? | 04:07 |
| kanzure_ | or additive. | 04:07 |
| kanzure_ | I suppose it's because it's annoying to have to recalculate the mesh, and calculating collisions between objects given a mesh. | 04:08 |
| kanzure_ | Set of operators (add/del), set of primitives, some way of specifying where on the so-far-constructed-object to perform the action (other than pre-defined based off of the nature of each of the primitives in use) | 04:11 |
| kanzure_ | perhaps also parameters to each of the individual primitive generators | 04:11 |
| kanzure_ | I'm not sure how to relate 'functions' to which primitives to involve. I suppose certain shapes are better/worse for different situations (preferentialism). Hexapods for some scenarios, triangles for ribs/ribbing, .. | 04:18 |
| kanzure_ | bleh | 04:18 |
| * kanzure_ goes off to write about the 'superneuron' simulator | 04:18 | |
| gene_ | kanzure, we have a problem | 04:34 |
| gene_ | a big one | 04:35 |
| kanzure_ | What? | 04:41 |
| -!- Nofairs is now known as SurpriseAbortion | 04:44 | |
| SurpriseAbortion | Me. | 04:44 |
| kanzure_ | Not much of one. | 04:44 |
| * SurpriseAbortion goes back to his corner | 04:47 | |
| * SurpriseAbortion sobs | 04:47 | |
| -!- SurpriseAbortion is now known as Nofaris | 04:47 | |
| kanzure_ | There, there, I'm sure some infertile couple might want you. | 04:47 |
| Nofaris | I'm sorry, I'm in a really silly mood right now | 04:47 |
| Nofaris | More like a pregnant teenager in a religious household | 04:48 |
| kanzure_ | Backstory? | 04:49 |
| Nofaris | More like back alley | 04:49 |
| gene_ | it's with the bioreactor | 04:56 |
| kanzure_ | What? | 04:56 |
| gene_ | the place we have to put the scaled up reactor is near | 04:57 |
| gene_ | a major river | 04:57 |
| kanzure_ | ? | 04:57 |
| gene_ | not only that, but the river is downhill from the bioreactor | 04:57 |
| gene_ | the species we are growing is not native | 04:57 |
| kanzure_ | ? | 04:58 |
| gene_ | we don't want to introduce an invasive species | 04:58 |
| gene_ | especially not into a major river | 04:59 |
| kanzure_ | http://heybryan.org/bioreactor/media/ | 05:01 |
| gene_ | is that a cell | 05:03 |
| gene_ | a lysed cell? | 05:03 |
| kanzure_ | No. | 05:03 |
| gene_ | flocculated cells? | 05:04 |
| kanzure_ | Centrifuged. | 05:04 |
| kanzure_ | I told you, I centrifuged today. | 05:04 |
| gene_ | that's centrifuged | 05:04 |
| gene_ | whoa | 05:04 |
| gene_ | that's really clumpped up | 05:05 |
| kanzure_ | 1.2 to 1.5 mm diameter splotch on the side. | 05:05 |
| kanzure_ | You kidding me? | 05:05 |
| gene_ | that is VERY clumped up | 05:05 |
| kanzure_ | It worked great. | 05:05 |
| gene_ | did you see the sonicator we got? | 05:05 |
| gene_ | when did you show up? | 05:05 |
| kanzure_ | I didn't see. | 05:06 |
| kanzure_ | I was in the lab at 11 and 3. | 05:06 |
| gene_ | I left at 2:30 | 05:06 |
| gene_ | when did you do the centrifuging? | 05:06 |
| kanzure_ | 11 and 3. | 05:06 |
| gene_ | dang | 05:06 |
| gene_ | you know | 05:06 |
| gene_ | I think the centrifuges work in a vacuum | 05:07 |
| gene_ | on 190? | 05:07 |
| gene_ | did you push the coverslip down? | 05:08 |
| gene_ | it looks like cells got flattened | 05:08 |
| kanzure_ | The second batch was a centrifuge->microwave and then another one for microwaving->centrifuging. | 05:09 |
| kanzure_ | The microwaving didn't help. | 05:09 |
| gene_ | you microwaved it? | 05:09 |
| kanzure_ | Got bored. | 05:09 |
| gene_ | hahahahaha | 05:10 |
| kanzure_ | But yeah, the algae clumps up and can be tapped off the side of the tubes. | 05:10 |
| gene_ | it looks like you lysed the cells | 05:10 |
| kanzure_ | Where's me liquid, and why did it still clump? | 05:11 |
| kanzure_ | Or, even, why did the chlorophyll stay? | 05:11 |
| gene_ | what do you mean? | 05:11 |
| gene_ | why wouldn't chrollyphyll say | 05:11 |
| gene_ | stay anyway | 05:11 |
| kanzure_ | No cell walls, so I'd imagine there to be more diffusion instead of uniforn chlorophyll (like with cellular membranes in tact). | 05:12 |
| gene_ | so those flattened cells are the microwaved ones right? | 05:12 |
| kanzure_ | Anyway, on the microwaved algae slides, I noticed rainbow-like colorings, like oil in a parking lot. | 05:12 |
| kanzure_ | Yes. | 05:12 |
| gene_ | YOU DID! | 05:14 |
| gene_ | SWEET | 05:14 |
| kanzure_ | Might have been oils from my fingerprint. | 05:15 |
| gene_ | I think you sintered them bryan | 05:15 |
| gene_ | they melted | 05:15 |
| gene_ | and fused together or something | 05:16 |
| gene_ | what was it like after you microwaved them? | 05:18 |
| gene_ | brittle? | 05:18 |
| kanzure_ | Macroscopically the same. | 05:18 |
| gene_ | huh | 05:18 |
| kanzure_ | No, it was also brittle before. | 05:18 |
| gene_ | weird | 05:18 |
| gene_ | did it look different? | 05:18 |
| kanzure_ | Under the scope, yes. | 05:18 |
| kanzure_ | The first few pictures are the ones that I didn't microwave. The rest is. That's why you don't see distinct cell bodies. | 05:19 |
| gene_ | yeah | 05:19 |
| gene_ | that's very odd | 05:19 |
| gene_ | let's try repeating it? | 05:19 |
| gene_ | anyway what's are the cell walls made out of anyway? | 05:20 |
| kanzure_ | I spent three hours on it. | 05:20 |
| gene_ | on what? | 05:20 |
| kanzure_ | Membranes are lipid bilayers with integral-proteins embedded throughout with a distribution. | 05:20 |
| gene_ | huh | 05:20 |
| gene_ | not silicon dioxide or anything? | 05:21 |
| kanzure_ | You haven't taken a bio class? | 05:21 |
| kanzure_ | But yeah, silicon isn't popular in cells. | 05:21 |
| gene_ | diatoms have SiO2 cell walls | 05:22 |
| kanzure_ | There's no 'cell wall' here. Not plants. | 05:22 |
| gene_ | ok | 05:22 |
| gene_ | congrats bryan | 05:23 |
| gene_ | I believe you've discovered a new lysis method | 05:23 |
| gene_ | microwave disruption | 05:24 |
| kanzure_ | No, it's been in the literature. | 05:25 |
| gene_ | how long did you microwave it for | 05:25 |
| gene_ | damn | 05:25 |
| kanzure_ | A minute. I don't have the wattage rating of the microwave. | 05:26 |
| gene_ | good enough | 05:26 |
| kanzure_ | But it's one of those ancient microwaves with a wood case. | 05:26 |
| kanzure_ | Looks like it belongs in a station wagon. | 05:26 |
| gene_ | so we can't patent it? | 05:26 |
| kanzure_ | What the fuck? | 05:26 |
| kanzure_ | Get out. | 05:26 |
| gene_ | I want to fucking patent it | 05:26 |
| kanzure_ | ? | 05:27 |
| gene_ | so microwave disruption isn't anything new? | 05:27 |
| kanzure_ | Correct. | 05:28 |
| kanzure_ | Studies on microwave disruptions, that lay out specific numbers, would be somewhat new though. | 05:28 |
| gene_ | microwave disruption on a massive massive scale would be new too | 05:29 |
| kanzure_ | How do you know? | 05:30 |
| gene_ | what? | 05:30 |
| gene_ | I guess it's not new | 05:30 |
| gene_ | if you consider certain 'cases' | 05:31 |
| gene_ | microwave cell lysis is patented | 05:34 |
| gene_ | did you add salt to it? | 05:34 |
| kanzure_ | What's with you and patents? | 05:34 |
| gene_ | I need some money | 05:34 |
| kanzure_ | Go get a job? | 05:35 |
| gene_ | why get a job when you can live off patent money | 05:36 |
| kanzure_ | Are you a patent troll? | 05:36 |
| gene_ | or product you sell money | 05:37 |
| gene_ | no | 05:37 |
| kanzure_ | I think you are. | 05:37 |
| gene_ | don't believe in that kind of think | 05:37 |
| kanzure_ | You're the one looking to patent stuff. | 05:37 |
| gene_ | if you patent something you have to sell it | 05:37 |
| gene_ | not leave it patented and not develop it | 05:38 |
| kanzure_ | So what? | 05:38 |
| * kanzure_ is guessing gene_ hasn't read the algamics papers etc. | 05:39 | |
| gene_ | algamics | 05:39 |
| gene_ | never heard of it | 05:39 |
| gene_ | anyway have my own ideas to patent | 05:39 |
| kanzure_ | If you patent and try to sell shit, I'll build it for free. Screw selling. | 05:40 |
| gene_ | heh | 05:40 |
| gene_ | I don't think you'll be able to build it | 05:40 |
| gene_ | I don't think you'd even buy it either | 05:42 |
| kanzure_ | I don't buy much. | 05:42 |
| gene_ | I doubt my product market would even try to build it for free | 05:43 |
| gene_ | so what's algamics? | 05:44 |
| gene_ | how would you build something for free? | 05:45 |
| kanzure_ | Free as in, for no money. Not free energy. | 05:45 |
| gene_ | how? | 05:46 |
| kanzure_ | Money is just icing on a cake, it's not the foundations of physics and reality. | 05:46 |
| gene_ | how | 05:46 |
| gene_ | I know that | 05:46 |
| kanzure_ | The forming of materials into the result. | 05:46 |
| gene_ | how | 05:46 |
| gene_ | so I want to own the Mona Lisa | 05:47 |
| gene_ | what then? | 05:47 |
| kanzure_ | What the hell is ownership? | 05:47 |
| gene_ | the mona lisa | 05:47 |
| kanzure_ | That's a painting. | 05:47 |
| kanzure_ | Not ownership. | 05:47 |
| gene_ | I want to own it | 05:48 |
| gene_ | have ownership of it | 05:48 |
| kanzure_ | What the hell is ownership? | 05:48 |
| gene_ | Ownership is the state or fact of exclusive rights and control over property, which may be an object, land/real estate, intellectual property (arguably) or some other kind of property. It is embodied in an ownership right also referred to as title. | 05:50 |
| gene_ | sauce: wikipedia | 05:50 |
| kanzure_ | "Control is an illusion; order our comforting lie. Through chaos, from chaos, into chaos we fly." | 05:50 |
| gene_ | so | 05:51 |
| Nofaris | lol | 05:51 |
| gene_ | I own this laptop | 05:51 |
| kanzure_ | That was all just a bunch of crap to me. "Rights" are sociology-crap. | 05:52 |
| kanzure_ | According to who? | 05:52 |
| gene_ | ok | 05:52 |
| gene_ | I am going to have your computer ok? | 05:53 |
| kanzure_ | What? | 05:53 |
| gene_ | I am going to have it | 05:53 |
| kanzure_ | It's over here, and it's behind the lock. | 05:53 |
| gene_ | guess I'll have to bring my thermite then | 05:54 |
| gene_ | ok | 05:55 |
| gene_ | I see what you mean by ownership | 05:55 |
| gene_ | now | 05:55 |
| gene_ | so I can have your computer if I can get it? | 05:57 |
| kanzure_ | You basically just asked "if I can get it did I in fact get it" and by the nature of the scenario you're just repeating yourself. | 05:57 |
| Nofaris | lol... | 05:58 |
| gene_ | So I can have your computer in my room and use it if I can move it out of your room without your consent | 05:59 |
| kanzure_ | What does my consent have to do with anything? | 06:00 |
| Nofaris | It removes a possible threat | 06:00 |
| Nofaris | to his plan | 06:00 |
| Nofaris | Silly | 06:00 |
| kanzure_ | Maybe his plan shouldn't be considering stupid threats like that. | 06:01 |
| kanzure_ | I mean to say that perhaps you should be able to plan so that threats aren't even possible within the framework. | 06:01 |
| gene_ | heh | 06:02 |
| gene_ | I can get that tombstone out of your room | 06:02 |
| Nofaris | Some threats cannot be completely eliminated | 06:02 |
| kanzure_ | Nofaris: Fuck death. | 06:02 |
| kanzure_ | http://fuckdeath.org/ | 06:02 |
| Nofaris | LOL | 06:03 |
| Nofaris | BEST WEBSITE EVER | 06:03 |
| Nofaris | <3 | 06:03 |
| kanzure_ | http://sens.org/ | 06:03 |
| kanzure_ | http://mprize.org/ | 06:03 |
| gene_ | no Kanzure I would not like to have sex with death | 06:04 |
| Nofaris | Good websites | 06:04 |
| Nofaris | Already know of them | 06:04 |
| Nofaris | What are you up to kanzure? | 06:04 |
| gene_ | just kidding fuck death | 06:04 |
| kanzure_ | Nofaris: Hm? | 06:04 |
| kanzure_ | Nofaris: Right now? | 06:04 |
| gene_ | world domination | 06:04 |
| gene_ | that's what we're up to | 06:04 |
| Nofaris | Yes | 06:04 |
| kanzure_ | Nofaris: I'm writing up some notes on the superneuron simulator. | 06:04 |
| Nofaris | What is that? | 06:05 |
| kanzure_ | A neuron simulator. | 06:05 |
| Nofaris | that is super | 06:05 |
| kanzure_ | Meh, I got pretentious when I named it. | 06:05 |
| Nofaris | You named it eh? | 06:05 |
| gene_ | you're writing documentation? | 06:06 |
| kanzure_ | 'Superneuron'. | 06:06 |
| kanzure_ | gene_: Not really. | 06:06 |
| gene_ | or code? | 06:06 |
| kanzure_ | gene_: It's just some explanation as to why it's a multicompartment differential-equation-like model rather than a simple array-based ANN. | 06:06 |
| kanzure_ | Nah, it's not code. Just some pseudocode. For the class. | 06:06 |
| gene_ | do you understand diff eq? | 06:06 |
| kanzure_ | I'm rusty on partials. | 06:07 |
| gene_ | damn | 06:07 |
| gene_ | do you dare explain your differential equation | 06:07 |
| kanzure_ | It's just some stuff about rates of change of membrane potentials in relation to ion concentrations etc. | 06:09 |
| gene_ | damn | 06:09 |
| kanzure_ | brb | 06:09 |
| gene_ | I've been thinking about writing something like that for e.coli | 06:10 |
| gene_ | for simulating chemotaxis | 06:10 |
| gene_ | can I see that pseudocode? I am sorta having trouble applying differential equations | 06:11 |
| xp_prg4 | kanzure based on what I can tell, building hy3s takes the intel fortran compiler that costs money, is that what your finding? | 06:13 |
| kanzure_ | xp_prg4: I haven't looked into compiling hy3s yet. | 06:15 |
| kanzure_ | Mostly because I'm still waiting on ahem, a few other things. | 06:15 |
| kanzure_ | Like, uh, that script. | 06:15 |
| xp_prg4 | well I can't even test the script without hy3s | 06:16 |
| kanzure_ | Tell me how you think that's true. | 06:16 |
| kanzure_ | What's the goal of the script? | 06:16 |
| kanzure_ | What's the output of the script? | 06:16 |
| xp_prg4 | because that is the end result, we make a script that makes an sbml file and then it converts to netcdf which then goes to hy3s | 06:16 |
| kanzure_ | Uh, so why does that require hy3s? | 06:16 |
| xp_prg4 | to make sure it will work | 06:17 |
| kanzure_ | Wrong. | 06:17 |
| gene_ | can I see that pseudo code? | 06:17 |
| kanzure_ | You have the examples in http://heybryan.org/graph/synbioss/tmp/ | 06:17 |
| kanzure_ | Remember? | 06:17 |
| kanzure_ | gene_: Give me a few moments. | 06:17 |
| gene_ | did you write the differential equation your self? | 06:17 |
| kanzure_ | http://heybryan.org/school/buildingbrains/superneuron.html | 06:21 |
| kanzure_ | gene_: There you go. | 06:21 |
| gene_ | heh | 06:21 |
| kanzure_ | Hrm. That looks like an older version. Oh well. | 06:21 |
| gene_ | why even have dendrites | 06:21 |
| kanzure_ | It was group work in class, but I had to give them a nudge to understand psuedocode. | 06:22 |
| gene_ | when you can have lots of dendrites | 06:22 |
| kanzure_ | It was restricted to two dendrites. | 06:22 |
| gene_ | or a function that describes dendrite branching | 06:22 |
| kanzure_ | Right, that's the Proper Thing to do. | 06:22 |
| gene_ | anyway | 06:23 |
| gene_ | how do you figure in noise? | 06:23 |
| gene_ | real neurons are noisy am I not correct? | 06:24 |
| kanzure_ | This is not precise. | 06:24 |
| gene_ | due to a whole bunch of things | 06:24 |
| kanzure_ | There's some distortion and degradation in amplitude in the axon that is included in the pseudocode there. | 06:24 |
| gene_ | would your simulated version of a brain diverge with time with the real version of the brain being simulated | 06:25 |
| gene_ | given that both brains are being given equal stimulation | 06:25 |
| kanzure_ | Yep, because this is a simplistic neuron, and it can't be configured to become the types of neurons found in a real brain without some serious modification. | 06:26 |
| gene_ | I know | 06:26 |
| kanzure_ | The mauk.zip stuff doesn't diverge though. | 06:27 |
| gene_ | over the course of how long? | 06:27 |
| kanzure_ | http://heybryan.org/~bbishop/docs/mauksimzip.zip | 06:27 |
| kanzure_ | He sits around in his lab for hours with rabbits strapped up to an oscilloscope. | 06:27 |
| gene_ | what about years? | 06:28 |
| kanzure_ | His software remains consistent. | 06:28 |
| kanzure_ | The rabbit would die by then. ;-) | 06:28 |
| gene_ | I know | 06:28 |
| kanzure_ | It's open-skull for reading the variables. | 06:28 |
| kanzure_ | uh, it might not be open skull. I'm pretty sure it is. | 06:28 |
| gene_ | I bet it is | 06:28 |
| gene_ | would a simulated version of someone actually be them so to say? | 06:29 |
| kanzure_ | What the hell is identity? | 06:29 |
| kanzure_ | ;-) | 06:29 |
| gene_ | as in would divergence ever occur? | 06:30 |
| kanzure_ | Don't you diverge each moment? | 06:30 |
| gene_ | ok | 06:30 |
| gene_ | now your freaking me out | 06:30 |
| gene_ | I mean given the same stimulation would they diverge | 06:31 |
| kanzure_ | ? | 06:31 |
| kanzure_ | Do you mean any general simulation of a neuron, and then comparing it to a real neuron? | 06:31 |
| kanzure_ | Or do you mean a specific neuron simulation that you want to compare to? | 06:31 |
| gene_ | I mean specific neuron simulation | 06:32 |
| kanzure_ | Which one, then? | 06:32 |
| gene_ | no | 06:32 |
| gene_ | as in approximates neuron exactly | 06:33 |
| kanzure_ | If by definition it's exact, then you've already claimed it's exact | 06:33 |
| kanzure_ | If by definition it's only an approximation, then it's by definition just an approximation | 06:33 |
| kanzure_ | I am confused, what do you ask? | 06:33 |
| gene_ | so if I get my brain scanned in, then have it simulated would it be me? | 06:34 |
| kanzure_ | What is "me" though? | 06:34 |
| gene_ | that is what I'd like to define | 06:34 |
| Nofaris | It's too vague a conceptual wrapper to define | 06:34 |
| gene_ | now this is really freaking me out | 06:35 |
| kanzure_ | "Identity" is a folk psych concept. I rank it up (down?) there along with 'money' and 'intelligence'. | 06:35 |
| gene_ | I know | 06:36 |
| Nofaris | Money is a folk psych concept? | 06:36 |
| gene_ | so then Kanzure, can I have your money? | 06:36 |
| gene_ | damn | 06:36 |
| gene_ | I shouldn't think about existentialism stuff | 06:37 |
| kanzure_ | Nofaris: The hypothetical list that I was talking about there is not made up of only folkpsych. | 06:37 |
| kanzure_ | This isn't existentialism. | 06:37 |
| gene_ | I know | 06:37 |
| * Nofaris is confused | 06:38 | |
| gene_ | so the question is am I am who I am from moment to moment? | 06:38 |
| gene_ | man | 06:38 |
| Nofaris | You are constantly changing | 06:38 |
| kanzure_ | gene_: Try http://heybryan.org/quotes.html for some help. | 06:38 |
| gene_ | I really wish they had whole brain maps | 06:38 |
| gene_ | I don't what damn quotes | 06:38 |
| kanzure_ | The map is not the territory. | 06:39 |
| Nofaris | I like quotes | 06:39 |
| gene_ | I want me some fucking data | 06:39 |
| Nofaris | Good quote | 06:39 |
| kanzure_ | "Truly, I cannot know what you are. Conscious or not, aware of your existence or not, I cannot know what you are. But you are only you, you are what you are. Isn't this enough?" | 06:39 |
| gene_ | SYSTEM ERROR | 06:40 |
| Nofaris | not so good a quote | 06:40 |
| kanzure_ | Wrong system. | 06:40 |
| kanzure_ | Nofaris: I'm citing it wrong. It's on the page though. Search for "Truly,". | 06:40 |
| Nofaris | Don't worry about it | 06:41 |
| Nofaris | I think I understand what it amounts to | 06:41 |
| kanzure_ | And what's that? | 06:41 |
| Nofaris | "If mathematical thinking is defective, where are we to find truth and certitude?" | 06:41 |
| Nofaris | I like this a lot | 06:42 |
| Nofaris | Thank you for the quotes. | 06:42 |
| gene_ | now the real question is what is feeling? | 06:42 |
| kanzure_ | What is what? | 06:42 |
| Nofaris | chemicals | 06:42 |
| gene_ | feeling | 06:42 |
| Nofaris | moving in your brain | 06:42 |
| gene_ | yeah | 06:42 |
| gene_ | I know that | 06:42 |
| kanzure_ | No, answer me this: what is what? | 06:42 |
| kanzure_ | (in response to your question) | 06:43 |
| gene_ | feeling | 06:43 |
| kanzure_ | Yes, but what is that? | 06:43 |
| gene_ | you know very well what I am referring to Kanzure | 06:43 |
| gene_ | even if it is a folk psychological concept | 06:43 |
| Nofaris | Gene_ | 06:44 |
| kanzure_ | Heh. | 06:44 |
| Nofaris | What are you referring to? | 06:44 |
| gene_ | it's results can be observed | 06:44 |
| kanzure_ | The map is not the territory. | 06:44 |
| kanzure_ | Results? | 06:44 |
| gene_ | yeah | 06:44 |
| gene_ | I sense the temperature of an object and can act in response to the temperature | 06:45 |
| kanzure_ | "Siren Call of Metaphor: Subverting the proper task of systems neuroscience" | 06:45 |
| gene_ | so how am I able to process information from my hands into what I would call a feeling | 06:46 |
| gene_ | is said information stored in something like a variable? | 06:46 |
| kanzure_ | Not really. | 06:47 |
| gene_ | like a variable | 06:47 |
| kanzure_ | The mapping between experiences, genotypes and phenotypes is not obvious. | 06:47 |
| gene_ | genotypes? | 06:47 |
| kanzure_ | Source code. | 06:47 |
| gene_ | http://en.wikipedia.org/wiki/Surface_structure | 06:48 |
| gene_ | do you mean that? | 06:48 |
| kanzure_ | Not really. | 06:49 |
| gene_ | so then | 06:50 |
| gene_ | how does mri work? | 06:50 |
| gene_ | it just images blood right? | 06:50 |
| kanzure_ | Magnetic resonance is a nuclear physics phenomena that you really should look into. It's because of the alignment of subatomic particles etc. | 06:51 |
| gene_ | ok | 06:51 |
| gene_ | so you are looking for rotating magnetic fields | 06:51 |
| kanzure_ | SciAm had an article this month about a portable MRI unit. | 06:51 |
| gene_ | hmmmm.... | 06:51 |
| kanzure_ | gene_: Assume identity is wrong. Do you know the alternative? | 06:52 |
| kanzure_ | Think of it as a brain teaser. | 06:52 |
| gene_ | what is the alt? | 06:52 |
| gene_ | ok | 06:52 |
| gene_ | so if you introduced small magnetic particles into the brain | 06:52 |
| gene_ | you could see where they are? | 06:52 |
| kanzure_ | What are you trying to do? | 06:53 |
| gene_ | sweet | 06:53 |
| gene_ | they use paramagnetic materials as contrast agents | 06:53 |
| gene_ | make a super contrast agent | 06:54 |
| gene_ | for imaging where neurons are | 06:54 |
| gene_ | and when they are firing | 06:54 |
| kanzure_ | httP;//heybryan.org/mediawiki/index.php/Neuroimaging | 06:54 |
| kanzure_ | Look at EROS. | 06:54 |
| gene_ | I have an idea | 06:54 |
| gene_ | I don't know if it will work | 06:54 |
| kanzure_ | http://heybryan.org/books/mousebrain/ <- "Brain Conqueror" and "Brain Builder", some old stuff I was working on. | 06:55 |
| gene_ | especially because it invloves introducing compounds into neurons | 06:55 |
| gene_ | there are proteins that are paramagnetic | 06:56 |
| kanzure_ | Why do you want to image neurons? | 06:56 |
| gene_ | So I can know how I work | 06:56 |
| gene_ | that's why | 06:56 |
| kanzure_ | Only by writing programs do you learn to program. | 06:57 |
| gene_ | indeed | 06:57 |
| kanzure_ | "I am program, programmer and that which is programmed." | 06:57 |
| kanzure_ | (quotes.html again) | 06:57 |
| gene_ | plus it would be really cool | 06:57 |
| kanzure_ | So, imaging isn't enough. | 06:57 |
| gene_ | and useful for making back ups | 06:57 |
| kanzure_ | Oh, that's certainly true. | 06:57 |
| kanzure_ | Not entirely. | 06:58 |
| kanzure_ | You can't reconstruct from that information. | 06:58 |
| kanzure_ | Anyway, what's important in backups? | 06:58 |
| kanzure_ | What information, what characteristics and what functionality? | 06:58 |
| gene_ | so what do you need? | 06:58 |
| kanzure_ | Many minduploading skinheads think that they want everything, every single detail, | 06:58 |
| kanzure_ | they want "exact identity transferance", whatever the hell that means | 06:59 |
| kanzure_ | I'm not going for that. | 06:59 |
| kanzure_ | I'd rather do what works. | 06:59 |
| gene_ | well if you don't capture everything | 06:59 |
| xp_prg4 | kanzure__ your going to be so proud of me! | 06:59 |
| gene_ | you end up diverging from yourself | 07:00 |
| kanzure_ | YOu end up diverging anyway. | 07:00 |
| kanzure_ | *You end up diverging anyway. | 07:00 |
| kanzure_ | "How do you capture a beautiful bird without killing its spirit?" (also quotes.html) | 07:00 |
| kanzure_ | (an answer is found in the Neverness books, btw.) | 07:00 |
| gene_ | ok so you have real and simulated system | 07:01 |
| gene_ | denoted r and s | 07:01 |
| gene_ | initially system r and s start out in the same state | 07:02 |
| kanzure_ | How do you know? | 07:02 |
| gene_ | given the exact same stimulating | 07:02 |
| gene_ | this is a hypothetical case | 07:02 |
| gene_ | system s might go down a decision path that results in it receiving different stimulation than system r | 07:03 |
| kanzure_ | What's a decision? | 07:04 |
| gene_ | ie whether a system looks left or right | 07:04 |
| kanzure_ | How do you define left and right in a brain? | 07:05 |
| kanzure_ | That makes no sense. | 07:05 |
| gene_ | this is a hypothetical situation | 07:05 |
| gene_ | if you look right you receive different stimulation than if you looked left resulting a path of changes that leads to more changes | 07:06 |
| gene_ | so the question is, are systems r and s the same? | 07:07 |
| kanzure_ | What is sameness? | 07:07 |
| gene_ | if they diverge no? | 07:07 |
| gene_ | going down the same decision path | 07:08 |
| kanzure_ | Didn't you just answer your own question then? | 07:08 |
| gene_ | performing all the same actions in the same order | 07:08 |
| gene_ | as the other system | 07:08 |
| gene_ | if the systems perform different actions they receive different stimulus which results in different actions | 07:12 |
| gene_ | ERROR: STUCK IN INFINITE LOOP | 07:13 |
| kanzure_ | xp_prg4: are you ever going to tell me or not? | 07:13 |
| xp_prg4 | I have roughly 50% duplication of generates sbmlfile of that created with designer | 07:14 |
| xp_prg4 | I clearly understand what they are doing | 07:14 |
| kanzure_ | What's the other 50%? | 07:14 |
| xp_prg4 | just still coding it, wat me to send you the comparison files? | 07:14 |
| kanzure_ | Sure. | 07:14 |
| xp_prg4 | ok | 07:15 |
| xp_prg4 | sent | 07:17 |
| xp_prg4 | look at lacl in particular | 07:18 |
| xp_prg4 | added reactants! | 07:32 |
| xp_prg4 | want to see it now kazure__ ? | 07:32 |
| kanzure_ | Sure. | 07:33 |
| xp_prg4 | sent | 07:34 |
| xp_prg4 | added products | 07:38 |
| kanzure_ | Are you allowing for a variable number of these elements per the HTML forms did? (The dynamically generated forms with the help of the PHP scripting.) | 07:38 |
| xp_prg4 | yes they are stored as variables | 07:43 |
| kanzure_ | No, a variable number of them. | 07:44 |
| xp_prg4 | yes | 07:44 |
| xp_prg4 | that is not difficult | 07:44 |
| xp_prg4 | this is actually exremely easy | 07:44 |
| kanzure_ | I know. | 07:44 |
| kanzure_ | I wasn't sure if you were doing it though. | 07:44 |
| kanzure_ | If you're doing the parameter version, then it's simply a pre-specified number in one instance, or if the STDIN version then that's the simple ask-if-the-user-wants-to-do-blah version. | 07:45 |
| xp_prg4 | just added Reactions | 07:45 |
| xp_prg4 | well it is a little late, I must go to bed | 07:45 |
| -!- xp_prg4 is now known as xp_bed | 07:46 | |
| fenn | "if you patent something you have to sell it" <- wrong | 10:14 |
| UtopiahGHML | lots of patents are defensive | 10:15 |
| UtopiahGHML | 01:03:00 -=> http://quicksilverscreen.com/watch?video=52571 | 13:59 |
| UtopiahGHML | (little part on Citizen/P2P R&D as "Politics" from Zeitgeist Addendum) | 14:00 |
| willPow3r | http://sandiego.craigslist.org/csd/sci/900879701.html | 15:10 |
| willPow3r | too bad i dont have any of those quals | 15:12 |
| willPow3r | or even a Ph.D. that would be nice. | 15:15 |
| kanzure_ | UtopiahGHML: I read "CItizen/P2P R&D" as "Citizen-P2P Radio" | 16:06 |
| kanzure_ | Technically there's enough content to do a radio show. | 16:06 |
| kanzure_ | webcast, I mean. | 16:06 |
| UtopiahGHML | faceface: Is IT ready for the Dreaded DNA Data Deluge? by Andras Pellionisz http://www.youtube.com/watch?v=WJMFuc75V_w | 21:41 |
| kanzure-_ | http://heybryan.org/~bbishop/docs/neuro/Design_of_a_wearable_ultrasound_system.pdf <- See pg 44. | 23:13 |
| kanzure-_ | fig 23 | 23:13 |
| kanzure-_ | also pg 66 fig 44 | 23:14 |
| fenn | now there's a science fair winner | 23:23 |
| fenn | haha 'make the embedded computer more "medical" in appearance" | 23:27 |
| fenn | x86 processors generate so much heat that they're hard to waterproof | 23:29 |
| fenn | one would think that embedded computers would take this into account, such that one could simply bolt the board to a suitable heatsink | 23:35 |
| kanzure-_ | http://heybryan.org/~bbishop/docs/neuro/Auditory responses in cats produced by pulsed ultrasound.pdf | 23:42 |
| kanzure-_ | making cats hear things :) | 23:42 |
| kanzure-_ | if you can figure out the mapping between which ultrasound frequencies lead to which "phantom sounds" in the auditory nerve, you have another science faire winner. | 23:43 |
| kanzure-_ | *faire | 23:43 |
| kanzure-_ | **fair | 23:43 |
| kanzure-_ | Ok, so Ms. Majestic is recommending 600 to 700 kHz. | 23:47 |
| kanzure-_ | This one does 12 to 50. http://web.archive.org/web/20060602085215/circuitos.cl.tripod.com/schem/r72.gif | 23:47 |
| kanzure-_ | I'm not sure which variables would have to be modified. | 23:47 |
| kanzure-_ | Should I just go get a few variable-capacitors and variable resistors and plug them up to that 555 timer? | 23:47 |
| kanzure-_ | I wouldn't be doing any of the waveforms and sinewave generation that the Ultrasound_brain.pdf paper does, but I have seen schematics before showing sinewave generators and other functions. | 23:48 |
| kanzure-_ | http://www.reconnsworld.com/audio_tonegenerate.html <- suggests using an ultrasonic transducer for frequencies over 30 kHz. :-/ | 23:49 |
| fenn | 600-700kHz is doable with hardware PWM on an AVR | 23:53 |
| fenn | uh i think :) | 23:54 |
| kanzure-_ | While technically a dog whistle is an ultrasonic transducer that converts mechanical energy in the form of air pressure into ultrasonic sound waves, | 23:54 |
| kanzure-_ | PWM? | 23:54 |
| fenn | there are two pins which toggle based on the contents of a register and a clock w/divider | 23:54 |
| fenn | so you can run a program and not be constantly worrying about i/o | 23:55 |
| kanzure-_ | http://www.explorecircuits.com/circuit/schematic/3.jpg and its explanation http://www.explorecircuits.com/circuit/cir_ultrasonic_transmitter_receiver.htm | 23:55 |
| kanzure-_ | hm | 23:55 |
| fenn | 555 might not be fast enough.. dunno | 23:55 |
| kanzure-_ | hrm, these schematics say 40 kHz speakers. | 23:56 |
| kanzure-_ | blah | 23:56 |
| fenn | yeah i think you need piezo transducers | 23:56 |
| kanzure-_ | There should be a simple formula for how the capacitors and resistors need to change with respect to the expected frequency. | 23:56 |
| fenn | it's not that simple | 23:56 |
| kanzure-_ | I don't know anything about piezo transducers. Is there a circuit component I can pick up at Radioshack? | 23:57 |
| fenn | the wires in the circuit act as inductors and capacitors (and radio antennae) | 23:57 |
| fenn | forget radioshack | 23:57 |
| fenn | pretend it doesn't exist | 23:57 |
| kanzure-_ | I don't have many other options :) | 23:57 |
| kanzure-_ | I suppose I can order a few things, but I was hoping to pick up a bag of goodies tonight. | 23:57 |
| fenn | unless you have a real electronics company nearby, it's mail order | 23:58 |
| fenn | jameco is probably easiest to figure out | 23:58 |
| kanzure-_ | mouser/digikey/jameco, right | 23:58 |
| kanzure-_ | digikey can burn in hell, yes yes, I know | 23:58 |
| kanzure-_ | anyway | 23:58 |
| fenn | digikey is actually pretty good, but it's hard to sort through the 9 million options | 23:58 |
| kanzure-_ | I'm still not understanding. If I picked up a piezo transducer, let's call it part XYZ, then what? How do I know which capacitors and resistors to use? | 23:59 |
| kanzure-_ | I suppose I can go with variable resistors/capacitors and just keep it within the ranges I'm seeing on these schematics? | 23:59 |
| fenn | ur... uh.. the 555 stuff? | 23:59 |
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