--- Day changed Fri Sep 19 2008 00:39 < procto> kanzure: hmm, what? 00:40 < procto> about #diybio 00:40 < procto> kanzure: I got my 23andme kit in the mail today. 00:40 < procto> kanzure: checked on the site, and though they don't give you the snp csv, they do give you a raw data dump. I was afraid they might not. 00:40 < procto> kanzure: I'm trying to figure out Vector NTI, so I can maybe import some of my DNA into it 04:15 < kanzure> procto: What's Vector NTI? 04:15 < kanzure> Glad that they dump the data to you. 04:15 < kanzure> It would be worth a refund if they didn't. 04:32 < procto> kanzure: vector nti is a fancy-ass bioinformatics package from invitrogen 04:32 < procto> nice and polished 04:32 < kanzure> What does it do? 04:32 < procto> and pretty for demos since it comes with a large library 04:33 < procto> well, you can edit sequences 04:33 < procto> s 04:33 < procto> so you car download a biobrick or a biopart 04:33 < procto> and drag and drop, and look at the graphical cad dispaly 04:33 < kanzure> Crap. 04:33 < kanzure> Really? 04:33 < procto> it can also simulate electrophoresis cells 04:33 < procto> gells 04:33 < kanzure> Screenshot it please. 04:33 < kanzure> Also, does it really work with biobricks? 04:33 < procto> http://tools.invitrogen.com/imgLibrary/VNTI_Gateway_Fig3.jpg 04:34 < procto> I haven't seen it used with biobricks 04:34 < procto> I've seen it with parts 04:34 < procto> jason kelly showed it in a slide show 04:34 < procto> (he's one of the gingko folks) 04:34 < procto> you really drag the text of the biopart into the text area 04:34 < kanzure> me knows of jkelly 04:34 < procto> but you can do it right out of a browsser 04:35 < kanzure> the text of? 04:35 < procto> into the software 04:35 < kanzure> what does that do? 04:35 < procto> the code, GATC 04:35 < kanzure> text analysis bullshit? 04:35 < kanzure> oh 04:35 < kanzure> that's not much 04:35 < procto> and just drop it into where it goes 04:35 < procto> sure, but that's just one example 04:35 < kanzure> that's just stupid Windows GDI bullshit 04:35 < procto> anyways, it has a lot of various fancy features 04:35 < kanzure> like drag/drop? 04:35 < procto> haha, that's really not the major thing it's about 04:36 < procto> the reason invitrogen provides this for free to nonsenterprise users 04:36 < procto> is that there's a little order button on the toolbar. so you've just designed something 04:36 < procto> you can click on it, and the order goes straight to their site 04:36 < procto> a few weeks later, and you've got some DNA or a protein in the mail 04:36 < kanzure> right 04:37 < procto> my bioinformatics-fu is quite so-so at this stage 04:37 < procto> but if you have a windows or mac machine around 04:37 < procto> I recommend giving it a try 04:37 < procto> it's very feature rich, but learning curve is less steep than other things 04:37 < kanzure> Linkage? 04:38 < kanzure> oh 04:38 * kanzure missed http://tools.invitrogen.com/imgLibrary/VNTI_Gateway_Fig3.jpg 04:38 < procto> http://www.basic.northwestern.edu/VectorNTI/Documentation/VectorNTI/images/10_3.gif 04:38 < procto> here it is running a gel 04:38 < procto> old version 04:38 < procto> ah well, there ya go 04:39 < procto> obviously it can handle both circular and linear dna, etc 04:39 < procto> http://www.invitrogen.com/site/us/en/home/LINNEA-Online-Guides/LINNEA-Communities/Vector-NTI-Community/Vector-NTI/Download.html 04:39 < kanzure> I don't get it, this just looks like annotation 04:39 < kanzure> how much bioinformatics do you know? 04:39 < procto> there's the downlad link 04:39 < kanzure> are you aware of how to use the databases and such? click click click 04:39 < procto> like I said, fairly intro stuff 04:40 < procto> not so much, but i've seen folks who know much much more than me use this to nice effect :) 04:42 < procto> so you can give it a whirl, and then let me know what you think 04:42 < kanzure> sure 05:19 < ybit> http://www.collegehumor.com/video:1830262 05:19 < ybit> sorry, couldn't help 05:24 < ybit> genre: comedy, title: "professor wikipedia" 05:25 < ybit> language: english, subtitles: none 05:25 < ybit> just thought i would give info required to post a video link ;) 05:28 < kanzure> Hah. :) 05:47 < kanzure> http://search.cpan.org/~ewilhelm/CAD-Drawing-0.26/ 05:47 < kanzure> Hrm, what's YAML doing there? 05:50 < kanzure> Wilhelm's data dump: http://scratchcomputing.com/svn/ 06:32 < kanzure> Hey Depucelator. 06:33 < Depucelator> Hello yes I am Depucelator 06:34 < Depucelator> someone on another channel said you guys were giving away free girls gone wild tapes how do i get them 06:34 < kanzure> Which channel? 06:34 < Depucelator> #linux????? 06:34 < Depucelator> i already email kanzure@gmail.com but guy not answer yet 06:35 < Depucelator> nobody else get an answer either i think 06:35 < kanzure> Huh? 06:35 < kanzure> What's up? 06:35 < Depucelator> well i neverf got my free girls gone while yet 06:35 < Depucelator> nobody else either 06:36 < Depucelator> this is a very disappointment to me 06:37 < Depucelator> well if i cant get girls gone wild does anyone know where i can get a server for groups, representations and cohomology preprints? 06:38 < Depucelator> no dudes tho 06:39 < kanzure> Cohomology? Yeah, arxiv. 06:39 < Depucelator> thanks fellow! 06:39 < kanzure> Depucelator: http://www.math.uga.edu/archive.html 06:39 < kanzure> Group, representations and cohomology preprint server 06:40 < Depucelator> nice i like how the 404 makes a bold statement 06:40 < Depucelator> perhaps about the futility of human existence 06:40 < Depucelator> Bryan why do you stay up so late 06:41 < willPow3r> he's a robot 06:41 < Depucelator> are you an insomniac 06:41 < willPow3r> sorry, wasn't supposed to tell you that 06:42 < Depucelator> Robots can have peachfuzz moustaches? 07:05 < willPow3r> once they evolve that ability, yes 09:09 < kanzure> Hm, so Phreedom is at least alive. 09:10 < marainein> how do you make that deduction? 09:11 < kanzure> I use life/death to describe login/logout of the otherworld. 09:32 < willPow3r> kanzure, your idea of life/death then is not valid if you compare it to login/logout 09:32 < kanzure> willPow3r: Valid? 09:32 < kanzure> Sir, vitalism is a thing of the past. 09:32 < willPow3r> link 09:33 < kanzure> oh shit :) 09:33 < kanzure> http://en.wikipedia.org/wiki/Vitalism 09:33 < willPow3r> the word "login" isn't anywhere on that page 09:33 < willPow3r> nor is logout 09:34 < kanzure> You're claiming that my idea of life/death is wrong, 09:34 < kanzure> I'm telling you that life/death strikes me as vitalism 09:34 < willPow3r> if you compare it to logging in and logging out 09:34 < willPow3r> it strikes another friend of mine as vitalism too 09:34 < willPow3r> oddly enough 09:35 < kanzure> that's the architecture of IRC 09:35 < willPow3r> i hold that logging out and logging back in does not equate to dieing and being reborn 09:37 < bkero> kanzure: The otherworld is known as meatspace. 09:38 < kanzure> Meat .. space? 09:38 < bkero> Yes 09:38 < kanzure> There is none other than the digital. 09:38 < bkero> This spae...not IRC 09:38 < bkero> It's full of meat 09:38 < bkero> In strange sacs. 09:38 < kanzure> Clearly years of Lain should have taught you this by now. 09:41 < bkero> Bossy meat creature. 09:41 * bkero enters his protocomotose state. 09:42 < bkero> *protocomatose 09:42 < bkero> ;) 09:42 < kanzure> Ho hum, 09:43 < kanzure> Geschke is coming, Geschke is coming! 09:43 < kanzure> I get to yell at him for PDF. Yay! 09:44 < kanzure> so glad that it conflicts with the president of bank of america 09:51 < kanzure> 'Sep 18, 2008 Designed to create complex turbine components requiring 5-axis machining, Turbomachinery Application Library (TAL) addresses manufacturing of complex rotary parts such as impellers, blisks, airfoils, and inducers. It includes toolpath strategies for efficient machining of hard materials such as stainless steel and titanium. Strategies are designed to provide long tool life and create optimum finishes.' 09:51 < kanzure> how specific 09:51 < kanzure> ' Used to manufacture components for dental industry, DentMILL v4 offers 5-axis machining options as well as abutment production module. It offers functionality based on PowerMILL CAM system and can produce copings and bridges in ceramics and titanium with minimal material waste. In addition to accepting data from any dental design system or any scanner capable of exporting data in STL format, knowledge-based solution can output machining toolpaths t 09:51 < kanzure> hah 09:51 < kanzure> DentMILL 12:36 * kanzure needs to look up engineering mechanic calculations for metals in general, to play around with the matweb dataset 16:25 < kanzure> http://arxiv.org/abs/0807.3697 Stellar structures with different fundamental constants 16:32 < kanzure> http://www.pnas.org/content/105/37.cover-expansion <- Visualization of the web. Highest concentration at some central 'singularity' point, everything scattered out around it. Don't know the algorithm, but it looks suspiciously like an atom. 16:43 < kanzure> wtf argh 16:43 < kanzure> DIY Maxam-Gilbert sequencer just brings up my site :( 16:49 < kanzure> http://blog.wired.com/wiredscience/2008/09/making-open-sou.html 16:49 < kanzure> open source nanotech 16:49 < kanzure> ugh 16:49 * kanzure clicks 16:50 < kanzure> http://www.aerogel.org/?p=3&page=2 16:51 < kanzure> http://opensourcenano.net 17:15 < kanzure> hrm? http://www.time.com/time/magazine/article/0,9171,1673265,00.html "In TIME magazine, Michael Kinsley Thursday, Oct. 18, 2007 wrote: The computer revolution has bred a generation of smart loners, many of them rich and some of them complacently Darwinian, convinced that they don't need society--nor should anyone else." 17:15 < kanzure> oh, it's political 17:15 < kanzure> nevermnd 19:41 < kanzure> Hi all. 19:53 < kanzure> Does anyone know of a paper that consists of an overview of the modeling of biological devices, tools, instruments, circuits, networks, reactions, pathways, cascading anythings, etc.? Specifically, an overview of the variables, unit dimensions and equations for working with those variables. 19:54 * kanzure picked up a copy of Mathematica today 19:58 < spookact> student edition or insanely high priced edition? 20:02 < kanzure> Uhm. 20:02 < kanzure> The disc says "For network and single machine" 20:02 < kanzure> Mathematica 6 20:02 < kanzure> So it doesn't say student. This is a Good Sign. 20:42 < kanzure> http://www.dna20.com/tools.php 'Gene Designer from DNA2.0 Inc. is the design tool for molecular biologists and synthetic biologists.' 20:42 < kanzure> ' Drag-and-drop sequence elements from a pre-compiled library, add new sequence elements to a user-created library and rearrange elements within a project and much more for designing functional DNA molecules.' 20:43 < kanzure> Precompiled library? 20:52 < kanzure> http://www.icsb-2007.org/proceedings/abstracts/C15.pdf CAD/CAM for synthetic biology 21:53 < kanzure> Hm. What to code, what to code. 21:53 < kanzure> It's when I'm away from the computer that I figure I should be doing something more productive with my time, like writing code, but then I end up back in front of a terminal forgetting the majority of my todo list. 21:56 < kanzure> 'Dynamics and control of synthetic bio-molecular networks - delvecchio_sontag_07acc_tutorial_21mar07.pdf' seems to have some of what I'm looking for re: circuit-creator 22:04 < kanzure> numerical computation package - http://www.scilab.org/ 105 MB for linux - must have missed this one when I was doing my searching way back when 22:05 < willPow3r_> its modeled after matlab 22:05 < willPow3r_> pretty useful 22:20 < ybit> kanzure, oh how i can relate to your comment 22:22 < ybit> comment on scilab: http://science.slashdot.org/comments.pl?sid=383631&cid=21624601 22:37 < kanzure> ybit: yeah, the situations are pretty bad 22:37 < kanzure> Aren't you glad to know that your nuclear reactor is running on Windows? 22:42 < willPow3r_> WinME? 22:45 < kanzure> That's even worse.