| --- Day changed Fri Sep 19 2008 | ||
| procto | kanzure: hmm, what? | 00:39 |
|---|---|---|
| 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 | 00:40 |
| 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. | 04:15 |
| 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 | 04:32 |
| 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 | 04:33 |
| 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 | 04:34 |
| 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 | 04:35 |
| 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 | 04:36 |
| 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? | 04:37 |
| 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 | 04:38 |
| 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 | 04:39 |
| procto | not so much, but i've seen folks who know much much more than me use this to nice effect :) | 04:40 |
| procto | so you can give it a whirl, and then let me know what you think | 04:42 |
| kanzure | sure | 04:42 |
| ybit | http://www.collegehumor.com/video:1830262 | 05:19 |
| ybit | sorry, couldn't help | 05:19 |
| ybit | genre: comedy, title: "professor wikipedia" | 05:24 |
| ybit | language: english, subtitles: none | 05:25 |
| ybit | just thought i would give info required to post a video link ;) | 05:25 |
| kanzure | Hah. :) | 05:28 |
| kanzure | http://search.cpan.org/~ewilhelm/CAD-Drawing-0.26/ | 05:47 |
| kanzure | Hrm, what's YAML doing there? | 05:47 |
| kanzure | Wilhelm's data dump: http://scratchcomputing.com/svn/ | 05:50 |
| kanzure | Hey Depucelator. | 06:32 |
| Depucelator | Hello yes I am Depucelator | 06:33 |
| 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 | 06:34 |
| 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 | 06:35 |
| Depucelator | this is a very disappointment to me | 06:36 |
| Depucelator | well if i cant get girls gone wild does anyone know where i can get a server for groups, representations and cohomology preprints? | 06:37 |
| Depucelator | no dudes tho | 06:38 |
| 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 | 06:39 |
| 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 | 06:40 |
| willPow3r | he's a robot | 06:41 |
| Depucelator | are you an insomniac | 06:41 |
| willPow3r | sorry, wasn't supposed to tell you that | 06:41 |
| Depucelator | Robots can have peachfuzz moustaches? | 06:42 |
| willPow3r | once they evolve that ability, yes | 07:05 |
| kanzure | Hm, so Phreedom is at least alive. | 09:09 |
| marainein | how do you make that deduction? | 09:10 |
| kanzure | I use life/death to describe login/logout of the otherworld. | 09:11 |
| 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 | 09:32 |
| 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 | 09:33 |
| 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 | 09:34 |
| 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 | 09:35 |
| bkero | kanzure: The otherworld is known as meatspace. | 09:37 |
| 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. | 09:38 |
| bkero | Bossy meat creature. | 09:41 |
| * bkero enters his protocomotose state. | 09:41 | |
| bkero | *protocomatose | 09:42 |
| bkero | ;) | 09:42 |
| kanzure | Ho hum, | 09:42 |
| kanzure | Geschke is coming, Geschke is coming! | 09:43 |
| kanzure | I get to yell at him for PDF. Yay! | 09:43 |
| kanzure | so glad that it conflicts with the president of bank of america | 09:44 |
| 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 | 09:51 |
| * kanzure needs to look up engineering mechanic calculations for metals in general, to play around with the matweb dataset | 12:36 | |
| kanzure | http://arxiv.org/abs/0807.3697 Stellar structures with different fundamental constants | 16:25 |
| 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. | 16:32 |
| kanzure | wtf argh | 16:43 |
| kanzure | DIY Maxam-Gilbert sequencer just brings up my site :( | 16:43 |
| 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 | 16:49 | |
| kanzure | http://www.aerogel.org/?p=3&page=2 | 16:50 |
| kanzure | http://opensourcenano.net | 16:51 |
| 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 | 17:15 |
| kanzure | Hi all. | 19:41 |
| 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. | 19:53 |
| * kanzure picked up a copy of Mathematica today | 19:54 | |
| spookact | student edition or insanely high priced edition? | 19:58 |
| 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. | 20:02 |
| 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.' | 20:42 |
| kanzure | Precompiled library? | 20:43 |
| kanzure | http://www.icsb-2007.org/proceedings/abstracts/C15.pdf CAD/CAM for synthetic biology | 20:52 |
| 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. | 21:53 |
| 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 | 21:56 |
| 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 | 22:04 |
| willPow3r_ | its modeled after matlab | 22:05 |
| willPow3r_ | pretty useful | 22:05 |
| ybit | kanzure, oh how i can relate to your comment | 22:20 |
| ybit | comment on scilab: http://science.slashdot.org/comments.pl?sid=383631&cid=21624601 | 22:22 |
| 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? | 22:37 |
| willPow3r_ | WinME? | 22:42 |
| kanzure | That's even worse. | 22:45 |
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