| --- Day changed Sat Feb 14 2009 | ||
| fenn | 3 bathrooms?? | 00:00 |
|---|---|---|
| kanzure | yes | 00:00 |
| fenn | i've been picturing this place as like a steel barn with concrete floors and no interior walls | 00:00 |
| kanzure | yes | 00:00 |
| fenn | but it has 3 bathrooms | 00:00 |
| kanzure | but we're going to be putting in some walls for that renting space apparently. | 00:00 |
| kanzure | well, there's also some interior walls though I guess | 00:01 |
| kanzure | for the front office (entry room) | 00:01 |
| kanzure | and then the three bathrooms on one wall there | 00:01 |
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| kanzure | and then a giant conference room | 00:01 |
| fenn | ricecake failed :( | 00:01 |
| kanzure | conference room is 271x192 | 00:01 |
| fenn | inches? | 00:01 |
| kanzure | what would that be in feet? | 00:01 |
| fenn | 22x16 | 00:01 |
| kanzure | yes, it would have to be in inches | 00:02 |
| fenn | was the 10 inch bandsaw for wood or metal? | 00:04 |
| kanzure | probably wood | 00:04 |
| fenn | i'm thinking i should bring the gingery lathe and the metal bandsaw | 00:05 |
| kanzure | well, definitely those two things | 00:05 |
| kanzure | although 50 qty ethernet cables always comes in handy | 00:06 |
| fenn | well i have 50 qty a bunch of other stuff too | 00:06 |
| kanzure | I used to carry around ethernet back when I was smarter than I am now | 00:06 |
| fenn | like ethernet switches and thin clients | 00:06 |
| kanzure | yay | 00:06 |
| fenn | but i cant take everything | 00:06 |
| fenn | there is somewhat a mass limit in addition to a volume limit | 00:07 |
| fenn | with "normal people stuff" it wouldnt be an issue, but i tend to optimize things for packing | 00:07 |
| kanzure | "20 years of playing tetris have finally paid off!" | 00:07 |
| fenn | and metal blocks weigh a lot | 00:07 |
| fenn | heh | 00:07 |
| fenn | 20 years of tetris have finally destroyed my suspension! | 00:07 |
| kanzure | I don't imagine you can sue Atari for that eh? | 00:08 |
| fenn | so, he has a lot of stuff.. | 00:08 |
| kanzure | so les was learning how to weld a few days ago | 00:08 |
| kanzure | apparently he picked it up pretty fast | 00:09 |
| kanzure | anyway, I told him that he looked like Keanu Reeves | 00:09 |
| kanzure | ("I know kung-fu.") | 00:09 |
| kanzure | "I know welding." | 00:09 |
| kanzure | "you think that is steel you are welding? huh." | 00:09 |
| kanzure | anyway. | 00:09 |
| fenn | woah. | 00:10 |
| kanzure | right | 00:10 |
| fenn | i'd like to add a GC-MS to that list.. | 00:10 |
| kanzure | a what? | 00:10 |
| fenn | gas chromatography mass spectrometer | 00:10 |
| fenn | or at least a microscope or something | 00:11 |
| kanzure | heh | 00:11 |
| kanzure | yeah, we're definitely going to have to do the diybio hardware dance thingy | 00:11 |
| kanzure | at least a box of straws :( | 00:11 |
| fenn | ah i've got the straws on the "take" pile | 00:12 |
| fenn | three boxes even :) | 00:12 |
| fenn | wrong kind for agarose though | 00:12 |
| fenn | tea bubblers and stiff oblique-ended yellow straws | 00:13 |
| fenn | why doeshe want a 20 inch disk sander? | 00:13 |
| kanzure | want? | 00:14 |
| kanzure | is that in the want list? | 00:14 |
| kanzure | oh, you mean why does he have it / want it in the first place | 00:14 |
| fenn | its in the 'build' list | 00:14 |
| kanzure | huh. | 00:14 |
| kanzure | well, no clue | 00:15 |
| kanzure | it might be something he already has, I kind of screwed up on the build list at one point, but I might have fixed with a copy-and-paste (I will double check in a bit) | 00:15 |
| kanzure | oh, you're right | 00:17 |
| kanzure | huh. | 00:17 |
| fenn | 396 lbs 2HP | 00:18 |
| fenn | those are electrical ponies | 00:18 |
| kanzure | ponies? so not a horse? | 00:18 |
| fenn | like a horse but more compact | 00:19 |
| fenn | so.. this is really closer to "techshop" than "fablab" | 00:21 |
| kanzure | remember, it was originally going to be the austin techshop | 00:21 |
| fenn | which shouldnt be surprising i guess | 00:21 |
| kanzure | me wants more big equipment involved | 00:21 |
| fenn | why? | 00:23 |
| kanzure | sorry, size doesn't matter | 00:23 |
| kanzure | nevermind | 00:23 |
| kanzure | just fabricational capacity | 00:23 |
| fenn | the way i see it, if you have humongous equipment available, you're going to design stuff to be made on that equipment | 00:24 |
| fenn | but that's not really what we're aiming for is it? | 00:24 |
| kanzure | no | 00:24 |
| fenn | on the other hand, huge stuff gets the job done quicker | 00:25 |
| fenn | and i'd rather have one cnc that gets the job done 20x faster than 20 little cnc's | 00:25 |
| fenn | but if there's more than one person they can't use the cnc at the same time | 00:25 |
| fenn | and for non-factory stuff most of the time is setup and dicking around | 00:26 |
| fenn | so.. yeah. topic for future meeting i guess | 00:26 |
| fenn | guess i should bring the little TIG welder too | 00:29 |
| kanzure | oh, I have a freshman that will be working on the CFD analysis with me | 00:30 |
| kanzure | he doesn't know anything, but at least it let me pretends I have somebody to work with | 00:31 |
| kanzure | *lets me | 00:31 |
| kanzure | I was shing him the openfoam "water breaking a dam" demo. that was actually a neat 2D demo, looking back on it. | 00:31 |
| fenn | CFD for the algae thing? | 00:31 |
| kanzure | yes | 00:31 |
| kanzure | but also for hydrocyclones and other things | 00:31 |
| kanzure | basically I just want him to get openfoam running, that would be a freaking miracle | 00:32 |
| fenn | isnt that what i just said? | 00:32 |
| kanzure | well, the spiral filter is not a hydroclone necessarily | 00:32 |
| kanzure | they are different designs. | 00:32 |
| kanzure | supposedly. | 00:32 |
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| fenn | i think the cone shaped cyclone cavity will work a lot better than your spiral :) | 00:32 |
| kanzure | yeah, I want to try that. | 00:32 |
| kanzure | btw, it's not my spiral. is gene's. | 00:33 |
| fenn | i guess i should have said something earlier | 00:33 |
| kanzure | ? | 00:33 |
| kanzure | well it's pretty obvious though | 00:33 |
| fenn | about the spiral not working | 00:33 |
| kanzure | I mean, we're doing this all wrong | 00:33 |
| kanzure | first of all, who the hell manufactures before simulations | 00:33 |
| fenn | people who are comfortable manufacturing things | 00:34 |
| kanzure | secondly, finding only a signle reference to a design idea, and running with it ? without simulations or any history? | 00:34 |
| fenn | often it's easier to just try something than set up a simulation which is probably going to be wrong anyway | 00:34 |
| kanzure | perhaps | 00:34 |
| fenn | it's one of those dark ages things | 00:35 |
| kanzure | gah. | 00:35 |
| fenn | like drawing on paper | 00:35 |
| kanzure | but this is *wrong* | 00:35 |
| fenn | or talking to people in person | 00:35 |
| fenn | what did the tool carts look like? were they like this? http://toolmonger.com/wp-content/uploads/2006/12/post-toolcart.jpg | 00:38 |
| kanzure3_ | hrm, maybe, but that might be referring to the giant rolling red toolboxes instead. | 00:39 |
| fenn | like this? http://images.netshops.com/mgen/master:WTR034.jpg | 00:39 |
| kanzure3_ | there's definitely one of those rolling around the place | 00:40 |
| fenn | i dont see that coming apart into "parts" | 00:40 |
| fenn | i really like these http://www.ontarioindustrial.com/user_files/images/wire.jpg | 00:41 |
| fenn | debating whether to bring mine, since i won't have very many fish tubs there anyway (mine are perfect size for 8 tubs) | 00:42 |
| kanzure3_ | you should certainly ask. maybe. | 00:43 |
| fenn | there's just not enough space in the car | 00:44 |
| fenn | maybe | 00:44 |
| fenn | they do compact very nicely, which is why i like them | 00:44 |
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| wrldpc | http://www.youtube.com/watch?v=ZWurBuI_3fM | 05:56 |
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| kanzure3_ | argh. http://ftp.utexas.edu/pub/debian/ | 08:30 |
| kanzure3_ | you mean I've been missing out on this? | 08:30 |
| kanzure | paraview conflicts with mplayer? | 08:44 |
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| kanzure3_ | http://grail.cs.washington.edu/projects/videoenhancement/videoEnhancement.htm Using Photographs to Enhance Videos of a Static Scene | 09:46 |
| jm | 35 million $ for Twitter Inc., 6 million for the Methuselah Foundation. This is ridiculous. | 10:36 |
| kanzure3_ | http://dvlabs.tippingpoint.com/blog/2009/02/12/python-interfacing-a-usb-missile-launcher heh, wonder if once I get a USB port cad'd up if I should go add it to the pig launcher design (plus a few other mechanisms) | 12:00 |
| kanzure3_ | Can anyone give me the name of a handcraft / fine motor skill that is ridiculously obscure? | 12:16 |
| kanzure3_ | origami might count | 12:17 |
| kanzure3_ | but it's not that obscure | 12:17 |
| kanzure3_ | nevermind, lost my train of thought | 12:18 |
| kanzure3_ | http://heybryan.org/legal/lee_kottner.txt that export-blog-posts-to-blosxom feature has caused me more legal trouble than anything I've ever done | 12:55 |
| fenn | they have no shame, it says it right there on their blog | 13:27 |
| fenn | writing teacher, no wonder | 13:33 |
| fenn | We are using an original development method we've dubbed "Toy Driven Development". Under this process graphical toys are implemented which allow playing with the features of the library. | 13:44 |
| kanzure | what is this? | 13:44 |
| kanzure3_ | http://wiki.inkscape.org/wiki/index.php/Lib2geom_Goals | 13:44 |
| fenn | from lib2geom, part of inkscape | 13:44 |
| fenn | good for CAM stuff possibly | 13:44 |
| fenn | http://lib2geom.sourceforge.net/ | 13:45 |
| kanzure | David Cary and Alec Resnick have finally subscribed to openmanufacturing | 13:47 |
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| samrose | fenn: bugs everywhere is awesome, thanks for the reference | 16:06 |
| fenn | cool | 16:06 |
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| kanzure | hey xp_prg, I have something related to diybio for you to do if you're interested | 16:20 |
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| xp_prg | what is it kanzure? | 16:46 |
| kanzure | did you see pcr.xml the other day? | 16:47 |
| xp_prg | no what is that? | 16:47 |
| kanzure | a molecular biology protocol (PCR) marked up in CLP-ML, an XML format. | 16:47 |
| xp_prg | wow cool! | 16:47 |
| xp_prg | what do you want me to do with it? | 16:47 |
| kanzure | there's a post on the diybio mailing list about it btw | 16:48 |
| xp_prg | oh ok let me look | 16:48 |
| kanzure | well, I was wondering if you might want to write up gel electrophoresis using the same DTD | 16:48 |
| kanzure | or some other protocol of your choice. | 16:48 |
| kanzure | there are many: http://protocol-online.org/ | 16:48 |
| xp_prg | can you help me to understand what you mean by mapping a protocol to a dtd? | 16:48 |
| kanzure | when did I say mapping? | 16:49 |
| xp_prg | you are saying to describe a protocol with a dtd? | 16:49 |
| kanzure | do you know what a dtd is? | 16:49 |
| xp_prg | yes it is a grammar for validating xml | 16:50 |
| kanzure | a DTD for protocols has already been defined (see the email) | 16:50 |
| kanzure | so I made an example, pcr.xml | 16:50 |
| xp_prg | awsome | 16:50 |
| kanzure | PCR is a molecular biology protocol | 16:50 |
| xp_prg | let me see if I can find it | 16:50 |
| kanzure | so, I was wondering if you want to write up gel electrophoresis using that same DTD. | 16:51 |
| kanzure | or some other protocol of your choice. | 16:51 |
| xp_prg | ok :> | 16:51 |
| xp_prg | I definitely do! | 16:51 |
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| kanzure3_ | http://reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379391 dopamine synthesis pathway | 17:13 |
| kanzure3_ | does it make sense to want to be able to identify a 'target compound' from these bioinformatics databases, and want to unravel all relevant genomic information that is required to manufacture that item? | 17:15 |
| kanzure3_ | would it work if I wrote a program to do that? | 17:15 |
| kanzure3_ | http://reactome.org/cgi-bin/svgexporter?DB=gk_current&ID=379391 | 17:16 |
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| gene | how's the fablab coming along? | 18:30 |
| kanzure | http://reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379391 Synthesis of Dopamine [Homo sapiens] | 18:30 |
| kanzure | gene: did you see the inventory? | 18:30 |
| gene | I believe so | 18:30 |
| kanzure | http://heybryan.org/austin_fablab_2009-02-13.txt | 18:31 |
| gene | hey I bet ten dollars we could make to sponsor us | 18:31 |
| gene | vacuum pump? | 18:31 |
| gene | SWEET | 18:32 |
| kanzure | are you missing a verb in that sentence? | 18:32 |
| gene | I've always wanted a good vacuum pump | 18:32 |
| gene | screw grammar, I'm on the internet | 18:32 |
| gene | imacs might be useful | 18:33 |
| kanzure | but I don't know what the bet is | 18:33 |
| gene | that we could have Make Magazine sponsor our fablab | 18:33 |
| kanzure | oh | 18:34 |
| gene | no internet? | 18:34 |
| gene | selling food? | 18:34 |
| kanzure | luke iseman is the local Austin make magazine editor | 18:34 |
| gene | interesting way to fund a fablab | 18:34 |
| gene | that's how the anime club is funded | 18:35 |
| kanzure | gene: so far it looks like the business model is that some of the space is going to be rented out | 18:35 |
| kanzure | for $225/mo | 18:35 |
| gene | ok | 18:35 |
| kanzure | and that this would then pay for the maintenance costs | 18:35 |
| kanzure | there's already a few people signed up for slots | 18:35 |
| kanzure | somebody took the double space, and then there's two more people that I don't quite remember | 18:35 |
| gene | what are people going to be living there? | 18:36 |
| kanzure | no | 18:36 |
| gene | or just run a business or something | 18:36 |
| kanzure | just some shop space for their own work | 18:36 |
| kanzure | separate rooms on the side of two of the walls | 18:36 |
| gene | ah | 18:37 |
| kanzure | then there'd be an "open to the public" day each week (once things start rolling) | 18:37 |
| gene | what is reverse kinesthetics? | 18:37 |
| kanzure | something about human motion and software | 18:37 |
| kanzure | and probably also video editing. | 18:37 |
| gene | reverse kinematics? | 18:37 |
| gene | thing used to figure how to move ragdolls and robot arms? | 18:38 |
| gene | got me some algae samples | 18:38 |
| kanzure | sort of- like how to make a 2D character animation look like it is actually walking | 18:38 |
| gene | why would we need that? | 18:39 |
| kanzure | it was just something that les and I were talking about | 18:39 |
| kanzure | so I jotted it down | 18:39 |
| gene | ah | 18:39 |
| gene | any chance I can visit? | 18:39 |
| kanzure | yes | 18:39 |
| gene | see how much vacuum that vacuum pump will do | 18:39 |
| kanzure | I don't know when. it will probably be a few weeks though. | 18:39 |
| gene | that's fine | 18:40 |
| fenn | how big is the "big" air compressor? | 18:41 |
| gene | hehehe, we have an air compressor | 18:42 |
| kanzure | you know what, I don't know, but I'm pretty sure we were walking around with the air compressor nozzle all over the shop | 18:42 |
| kanzure | does it make sense if it was wired up to through the whole shop? | 18:42 |
| kanzure | because I think that's the case | 18:42 |
| fenn | yes | 18:42 |
| gene | so the shop has amish electricity? | 18:42 |
| fenn | was it like this/ http://www.epowerrail.com/Product pages/air compressors.htm | 18:43 |
| fenn | gene: i think i'm going to be making quite a few "amish" items | 18:43 |
| gene | heh, me too fenn | 18:43 |
| kanzure | fenn: don't know. sorry. | 18:43 |
| fenn | algae butter churn :) | 18:43 |
| gene | hmmm... | 18:43 |
| gene | what's butter made of again? | 18:43 |
| gene | cream and what not? | 18:44 |
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| fenn | ghee and whey? | 18:44 |
| kanzure | fenn: can you throw a rock at my scheme to splice dopamine synthesis into yeast? | 18:44 |
| fenn | no, i think it would work | 18:44 |
| kanzure | I've found the synthesis pathway, but maybe something like the amino acid receptors would be a stumbling block? | 18:44 |
| kanzure | hrm | 18:44 |
| gene | no it's made by centrifuging milk or something | 18:45 |
| fenn | apparently there's an "alkaloid" synthesis pathway that covers a lot of interesting chemicals with a small number of genes | 18:45 |
| fenn | gene: you can make butter by putting whipping cream in the blender for too long | 18:45 |
| gene | dopamine? why the heck are you trying to make dopamine ? | 18:45 |
| fenn | omgwtf dopamine | 18:46 |
| kanzure | a biology teacher once told me that nobody knew how to synthesize neurotransmitters in bulk | 18:46 |
| gene | depressed or trying to start a new drug ring? | 18:46 |
| fenn | uh, that's bunk | 18:46 |
| fenn | CO and NO are neurotransmitters | 18:47 |
| kanzure | well, you could grow neuron cultures I guess | 18:47 |
| kanzure | oh. | 18:47 |
| gene | hmmm... I guess they get em from cow brains | 18:47 |
| gene | you can get a whole bunch of useful stuff from cow brains | 18:47 |
| kanzure | anyway, it would be nice to be able to synthesize a variety of neurotransmitters | 18:47 |
| fenn | like beta amyloid plaques? | 18:47 |
| gene | I guess so | 18:47 |
| gene | you want you some alzheimers? | 18:48 |
| fenn | hrm wrong disease | 18:48 |
| gene | oops | 18:48 |
| fenn | i'm thinking mad cow disease | 18:48 |
| gene | what's PPAR used for and why do we have one? | 18:49 |
| gene | ah | 18:49 |
| fenn | for the spray booth | 18:49 |
| gene | fenn, we don't do bioterror here, ok? | 18:49 |
| fenn | define 'bioterror' | 18:50 |
| gene | recreational explosive use is ok, but using explosive for terrorism is not | 18:50 |
| fenn | pig launcher = bioterror? | 18:50 |
| gene | bioterror, using biological agents to kill people | 18:50 |
| gene | yup | 18:50 |
| fenn | ok, i won't kill anyone on purpose | 18:50 |
| kanzure | "micro-capsule destruction by pulse waves for drug delivery systems" | 18:52 |
| kanzure | + micro-encapsulated neurotransmitters | 18:52 |
| kanzure | + ultrasound head setup thingy. | 18:52 |
| gene | remember kids, if you accidently synthesize ebola, you can easily destroy it with household bleach | 18:52 |
| gene | interesting | 18:52 |
| kanzure | (for targeted neurotransmitter release in certain regions of the brain) | 18:52 |
| gene | I am not a big fan of bombarding my brain with ultrasound capable of breaking microcapsules | 18:53 |
| fenn | ..yeah | 18:53 |
| kanzure | wait, what? make it something sensitive to vibrations, isn't that what the trick is supposed to be? | 18:54 |
| fenn | and the blood/brain barrier thing | 18:54 |
| gene | or use resonance | 18:54 |
| fenn | what happens to the capsule pieces? | 18:55 |
| kanzure | ideally you piss them out, but I'm just making this up | 18:56 |
| fenn | yeah, that won't happen | 18:56 |
| fenn | kidneys only pass small molecules | 18:56 |
| gene | how do you get microcapsules in your blood in the first place | 18:56 |
| fenn | syringe | 18:57 |
| kanzure | right. | 18:57 |
| kanzure | this is probably not one of my better ideas | 18:57 |
| kanzure | best you ignore it | 18:57 |
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| kanzure | I keep forgetting that my neighbor is a comp sci monkey | 19:20 |
| kanzure | over dinner, he asked me for a way to do line-by-line debugging in vim | 19:20 |
| kanzure | presumably there's a vim plugin related to gdb | 19:21 |
| kanzure3_ | http://www.volny.cz/zellerin/gdbvim/ | 19:22 |
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| kanzure3_ | hm | 19:34 |
| kanzure3_ | smallest synthesis pathway of dopamine is in neurospora crassa | 19:34 |
| kanzure3_ | http://en.wikipedia.org/wiki/Neurospora_crassa | 19:34 |
| kanzure3_ | http://reactome.org/cgi-bin/eventbrowser?DB=gk_current&FOCUS_SPECIES=Homo%20sapiens&ID=492508& | 19:34 |
| kanzure3_ | "N. crassa is used as a model organism because it is easy to grow and has a haploid life cycle that makes genetic analysis simple since recessive traits will show up in the offspring. Analysis of genetic recombination is facilitated by the ordered arrangement of the products of meiosis in Neurospora ascospores. Its entire genome of seven chromosomes has been sequenced.[1]" | 19:34 |
| kanzure3_ | "Strains and other materials for working with Neurospora are available from the Fungal Genetics Stock Center" | 19:35 |
| kanzure3_ | http://www.fgsc.net/ | 19:35 |
| kanzure3_ | http://www.nih.gov/science/models/neurospora/resources.html | 19:35 |
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| kanzure3_ | this is fishy. | 19:39 |
| kanzure3_ | http://www.genome.jp/dbget-bin/www_bget?md+M00075 <-- this looks better. | 19:45 |
| kanzure3_ | l-dopa + 3,4-Dihydroxy-L-phenylalanine carboxy-lyase => dopamine | 19:45 |
| kanzure3_ | 1,2-Benzenediol:oxygen oxidoreductase + L-Tyrosine:oxygen oxidoreductase + L-Tyrosine,tetrahydrobiopterin:oxygen oxidoreductase | 19:45 |
| kanzure3_ | (3-hydroxylating) + L-Tyrosine | 19:46 |
| kanzure3_ | => l-dopa | 19:46 |
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| kanzure | this is stupid, a computer should be doing this for me | 19:48 |
| kanzure | why isn't this program written yet? | 19:48 |
| kanzure | this ideal program would (1) recursively find all dependencies in the synthesis pathway of whatever compound you're looking to grow, (2) search through a database of available model organisms, and (3) find the one that meets the most number of dependencies in terms of what genes it already has. Of course, it would just find a typical neuron in this case, which isn't too helpful since neurons need smoe more care than mold. | 20:03 |
| kanzure3_ | http://biocyc.org/ECOLI/NEW-IMAGE?object=PREPHENATE | 20:05 |
| kanzure3_ | oh yay, I'm so much in luck | 20:05 |
| kanzure3_ | huh, tyrosine is synthesized in ecoli? | 20:05 |
| kanzure | oh shit. of course it is. it's an amino acid. | 20:07 |
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| fenn | is there a central library of genome sequences somewhere | 20:32 |
| fenn | the sequences themselves can't take up that much space | 20:32 |
| kanzure3_ | yeah, ncbi | 20:33 |
| kanzure3_ | hold on a sec, there's an ftp link | 20:33 |
| fenn | so, why are there all these other genome databases? | 20:33 |
| kanzure3_ | ftp://ftp.ncbi.nih.gov/pub/ | 20:34 |
| * fenn sees a lot of usernames | 20:34 | |
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| fenn | too bad i can't sort by directory content size | 20:35 |
| kanzure3_ | ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/ | 20:36 |
| kanzure3_ | (by chromosome) | 20:36 |
| fenn | there's only 40 genomes there | 20:38 |
| fenn | neurospora is missing for example | 20:38 |
| fenn | can you copyright a genome? | 20:39 |
| kanzure | does a pirate still sail when the sea is stormy? | 20:39 |
| fenn | uh, does he? | 20:40 |
| kanzure | hrm. | 20:40 |
| fenn | Results 1 - 3 of 3 for "copyright a genome" | 20:40 |
| fenn | perhaps i should write a dear lazyweb article | 20:41 |
| kanzure | so, I've narrowed it down to 4 enzymes that I need to add to ecoli. | 20:41 |
| kanzure | but each enzyme has about four homologous structures that I need to go select from PDB. | 20:42 |
| kanzure | (and apparently they dislike wget. oops.) | 20:42 |
| kanzure | (pdb, that is) | 20:42 |
| fenn | -U "not wget" | 20:42 |
| fenn | ah what happened to my nefarious plans to have google index my misc directory | 20:44 |
| fenn | "The recipient of the produce contained in this package agrees not to propagate or reproduce any portion of the produce, including (but not limited to) seeds, stems, tissue and fruit." | 20:46 |
| kanzure3_ | 3F9T, 1JS3, 1JS6 | 20:50 |
| kanzure3_ | 1BT1, 1BT2, 1BT3, 1BUG, 2P3X | 20:50 |
| kanzure3_ | 1WX2, 1WX3, 1WX4, 1WX5, 1WXC, 2AHK, 2AHL | 20:50 |
| kanzure3_ | 1TOH, 2TOH | 20:50 |
| kanzure3_ | which one do I want from each line? | 20:50 |
| kanzure3_ | they are supposedly all the same. | 20:51 |
| kanzure3_ | (erm, per line) | 20:51 |
| fenn | what is that? | 20:52 |
| kanzure | list of proteins in pdb's naming scheme. | 20:52 |
| gene | oh damn how did I miss this | 20:52 |
| gene | damn a lot of proteins still arent .pdb yet | 20:52 |
| kanzure | there's a .pdb file format? | 20:53 |
| kanzure | because I just renamed all of these files to .pdb, and they are just FASTFA sequences | 20:53 |
| kanzure | so I don't want to lie | 20:53 |
| kanzure | *FASTA | 20:53 |
| gene | what you don't know? | 20:53 |
| fenn | yes there is; i'd just name them .fasta | 20:54 |
| kanzure | blah, okay | 20:54 |
| kanzure | I guess .pdb is what pdb serves up eh? | 20:54 |
| gene | FASTA FORMAT FUCK YEAH | 20:54 |
| fenn | The Protein Data Bank (PDB) format provides a standard representation for macromolecular structure data derived from X-ray diffraction and NMR studies. | 20:54 |
| gene | .pdb is a datafile for 3d models of proteins | 20:54 |
| fenn | it's what you build those ribbon diagrams from | 20:54 |
| kanzure | yeah yeah I know (sort of :)) | 20:54 |
| kanzure | okay, it's all .fasta now | 20:55 |
| kanzure | happy? :p | 20:55 |
| kanzure | http://heybryan.org/~bbishop/docs/dopamine/ | 20:55 |
| gene | I love fasta is so much easier to understand | 20:55 |
| fenn | vs what? | 20:55 |
| gene | what do you want to use the dopamine for anyway? | 20:55 |
| kanzure | fenn: nick taylor is full of shit | 20:57 |
| kanzure | he was otherwise promising before his latest email | 20:58 |
| fenn | when i was in school there was this meme that everything we were being taught would be wrong in five years anyway.. i think it was actually that the professors didn't understand the computer tools | 20:58 |
| fenn | "miraculous healing-power of the human-touch" i wonder if that's in aleister crowley :P | 20:58 |
| gene | What I was told fenn, was that you need to know how to use word and type fast, because that's what you should learn in computer class | 20:59 |
| kanzure | quick! smash the keys! make it look like work! | 20:59 |
| kanzure3_ | kndfkjl;ads;jlksalkj;fsa | 21:00 |
| gene | yes, that was exactly it | 21:00 |
| gene | now back to dopamine | 21:00 |
| gene | much more interesting | 21:00 |
| fenn | kanzure: you'll love his post to diybio then | 21:01 |
| kanzure | I don't even know how to respond to this first one | 21:01 |
| kanzure | there's the typical spiell about videos not being searchable, but then procto will pipe up I'm sure | 21:01 |
| kanzure | but that's not the real crux of the matter | 21:02 |
| kanzure | gene: I don't know why I want dopamine | 21:02 |
| kanzure | I guess I'm just rather attached to my neurotransmitters | 21:02 |
| fenn | i understand what he's saying, i just dont think it's important because video doesn't provide social support even if it appears to | 21:02 |
| gene | I know why you want dopamine | 21:02 |
| fenn | curse of the television | 21:02 |
| kanzure | why do I want dopamine? | 21:02 |
| gene | lot's of people want it | 21:02 |
| kanzure | why? | 21:02 |
| gene | you want to be happy | 21:02 |
| fenn | because | 21:02 |
| fenn | you want it because you want it | 21:02 |
| gene | dopamine makes you happy | 21:02 |
| kanzure | dopamine makes you what? | 21:02 |
| gene | WARNING PHILOSOPHY DETECTED | 21:03 |
| gene | back to topic | 21:03 |
| kanzure | WARNING BULLSHIT DETECTED | 21:03 |
| fenn | in hplusroadmap line 119041: | 21:03 |
| fenn | TypeError: function does not accept tautology as argument | 21:04 |
| gene | how is dopamine synthesized? | 21:05 |
| kanzure | did you see the reactome.org link? | 21:05 |
| fenn | why does my high school diploma get this fancy red embossed leather case, and they send my uni diploma in a cardboard envelope? | 21:05 |
| kanzure | because the world hates you | 21:05 |
| kanzure3_ | http://reactome.org/cgi-bin/eventbrowser?DB=gk_current&FOCUS_SPECIES=Homo%20sapiens&ID=530163& | 21:05 |
| kanzure | hm, that's not homo sapiens, sorry | 21:06 |
| kanzure3_ | http://reactome.org/cgi-bin/eventbrowser?DB=gk_current&FOCUS_SPECIES=Oryza%20sativa&ID=379391& | 21:06 |
| kanzure3_ | try that one. | 21:06 |
| fenn | huh oryza has dopamine? | 21:06 |
| kanzure | well there's a catch here | 21:06 |
| kanzure | some of this is done by an inference engine | 21:07 |
| kanzure | it's in the disclaimer on the neurospora link for instance | 21:07 |
| fenn | i guess it's not a very complicated molecule | 21:07 |
| kanzure | (thus why I'm not sure about neurospora. especially since nowhere else on the net mentions it and dopamine, except reactome) | 21:08 |
| fenn | dihydroxy phenyl ethyl amine | 21:08 |
| fenn | your bio teacher was definitely full of shit | 21:08 |
| kanzure | :) | 21:08 |
| gene | but neurospora looks like nerve cells or something | 21:08 |
| kanzure | so I think I'll just convert the compressed protein data to DNA and go with that | 21:08 |
| kanzure | and then tell people "hey look, drop this into e. coli and you've got a dopamine fountain! (please don't drink from it)" | 21:09 |
| fenn | it might be tasty | 21:09 |
| gene | the proteins from the reactome? | 21:09 |
| kanzure | what, gene? | 21:09 |
| gene | you are getting the proteins from the reactome and putting them in Ecoli? | 21:10 |
| kanzure | the proteins are from pdb | 21:10 |
| kanzure | I tracked down the pathway via KEGG actually, not reactome.org | 21:10 |
| kanzure3_ | my notes: http://heybryan.org/~bbishop/docs/dopamine/synthesis_of_dopamine.txt | 21:10 |
| gene | hmmm... | 21:11 |
| gene | I need to find that research they're doing here on putting eukaryotic genes into e.coli here | 21:12 |
| gene | they talked about making e.coli into somesort of super protein factory | 21:12 |
| kanzure | isn't that standard procedure? | 21:12 |
| gene | no | 21:13 |
| gene | it had something to do with eukaryotic gene expression or something | 21:13 |
| kanzure3_ | "Expression of mouse tyrosine hydroxylase in Escherichia coli." | 21:13 |
| kanzure3_ | http://www.ncbi.nlm.nih.gov/pubmed/1677565?dopt=Abstract | 21:13 |
| kanzure3_ | looks fairly standard to me though.. I see these studies all the time | 21:13 |
| kanzure3_ | "Expression of human tyrosine hydroxylase type I in Escherichia coli as a protease-cleavable fusion protein" | 21:14 |
| kanzure3_ | http://www.springerlink.com/content/65dbvjukm9m30e51/ | 21:14 |
| gene | no no no no no | 21:14 |
| gene | nothing like that | 21:14 |
| gene | I need to find the paper | 21:14 |
| gene | oh wait, they aren't even finished yet there is no paper | 21:14 |
| kanzure3_ | "Expression of human tyrosine hydroxylase type I in Escherichia coli as a protease-cleavable fusion protein" | 21:14 |
| fenn | is this a biobricks thing? | 21:14 |
| gene | they're still compiling it | 21:14 |
| gene | yes fenn it is | 21:14 |
| kanzure | fenn: who are you asking? | 21:14 |
| fenn | gene: to make strawberry flavor and such? | 21:15 |
| gene | saw it at the undergraduate research fair | 21:15 |
| gene | sure if you wanted to fenn | 21:15 |
| kanzure | http://heybryan.org/genetic-circuits.html <- my previous work with regulary circuits and biobricks | 21:15 |
| kanzure | *regulatory | 21:15 |
| gene | dangit forgot which lab | 21:17 |
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| kanzure3_ | http://www.bioinformatics.org/sms2/rev_trans.html <-- need to plug in the fasta sequences into here next. | 21:22 |
| gene | why not find the originals? | 21:26 |
| kanzure3_ | do you know how to translate pdb IDs to genbank/entrez IDs? | 21:27 |
| gene | I heard that different codons for the same protein get translated at different speeds | 21:27 |
| gene | try google | 21:27 |
| gene | try pasting the name into NCBI | 21:27 |
| kanzure3_ | http://www.ncbi.nlm.nih.gov/sites/gquery?term=3F9T | 21:28 |
| gene | don't you have the name for it? | 21:28 |
| kanzure3_ | there's like 20 names for everything.. | 21:29 |
| gene | tell me the name | 21:29 |
| kanzure3_ | L-Tyrosine Decarboxylase | 21:29 |
| gene | http://www.ncbi.nlm.nih.gov/sites/entrez | 21:32 |
| kanzure3_ | yes, I know the link to entrez | 21:32 |
| gene | have fun finding L-Tyrosine Decarboxxylase | 21:32 |
| kanzure3_ | http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=1644&ordinalpos=2&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum | 21:33 |
| kanzure3_ | I think that might be it. | 21:34 |
| kanzure3_ | hm, nope, that's dopa decarboxylase | 21:34 |
| gene | I think that's it too | 21:34 |
| gene | but you're trying to make dopamine | 21:34 |
| gene | The encoded protein catalyzes the decarboxylation of L-3,4-dihydroxyphenylalanine (DOPA) to dopamine, L-5-hydroxytryptophan to serotonin and L-tryptophan to tryptamine. Defects in this gene are the cause of aromatic L-amino-acid decarboxylase deficiency (AADCD). AADCD deficiency is an inborn error in neurotransmitter metabolism that leads to combined serotonin and catecholamine deficiency.... | 21:34 |
| gene | ...Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq] | 21:34 |
| kanzure3_ | http://www.genome.ad.jp/dbget-bin/www_bget?enzyme+4.1.1.25 | 21:35 |
| kanzure3_ | odd, that organism is Streptococcus | 21:35 |
| kanzure3_ | 9002-09-9 | 21:36 |
| gene | I wonder if streptococcus makes you feel better so you go out and spread it more | 21:39 |
| kanzure3_ | Drosophila melanogaster tyrosine decarboxylase 2 (Tdc2), mRNA. | 21:41 |
| kanzure3_ | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=24586043 | 21:41 |
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| gene | maybe you could grow a bunch of fruit flies and harvest their brains | 21:43 |
| fenn | or find some grad students and harvest their brains | 21:47 |
| gene | but grad students are useful and relatively expensive these days | 21:48 |
| kanzure3_ | haha useful haha | 21:48 |
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| kanzure3_ | http://www.genome.jp/dbget-bin/www_bget?rn+R00031 | 21:56 |
| kanzure3_ | http://www.genome.jp/dbget-bin/www_bget?rn+R00731 | 21:56 |
| kanzure3_ | what's the difference between these two? | 21:56 |
| kanzure3_ | they are both called tyrosinase | 21:57 |
| kanzure3_ | but are apparently different? | 21:57 |
| fenn | one of those has to be wrong | 21:59 |
| fenn | probably the first one | 21:59 |
| kanzure3_ | the first one is found in the human genome | 22:00 |
| kanzure3_ | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&qty=1&c_start=1&list_uids=NG_008748.1&uids=&dopt=gb&dispmax=5&sendto=&fmt_mask=0&from=end&to=begin&extrafeatpresent=1&ef_STS=64&ef_MGC=16&ef_HPRD=32&ef_tRNA=128&ef_microRNA=256&ef_Exon=512 | 22:00 |
| kanzure3_ | (it just happens to be the one I looked up first, and the second one I stopped and scratched my head) | 22:00 |
| kanzure3_ | anyway, if that's true, then there's really only 3 genes that need to be inserted for dopamine synthesis | 22:00 |
| kanzure3_ | (well, 3 main new genes) | 22:00 |
| fenn | that's not surprising | 22:04 |
| kanzure3_ | http://heybryan.org/~bbishop/docs/dopamine/synthesis_of_dopamine.txt | 22:05 |
| kanzure3_ | updated. | 22:05 |
| fenn | heh | 22:07 |
| fenn | "done" | 22:07 |
| kanzure | now to patent and hold the world hostage for one hundred billion dollars | 22:09 |
| kanzure | or something like that | 22:09 |
| fenn | "give me money or i'll make everyone really happy!" | 22:11 |
| kanzure | hey, we have a business plan now. | 22:11 |
| kanzure | p | 22:11 |
| kanzure | :p | 22:12 |
| fenn | in larry niven's books there's a fictional weapon called a "tasp" which acts like those pleasure center stimulators (but wireless) | 22:12 |
| kanzure | right | 22:12 |
| kanzure | I haven't read his books, but somehow I know that | 22:12 |
| kanzure | (maybe I started to read The Ringworld Engineers book) | 22:12 |
| fenn | yeah that's where I read it | 22:12 |
| kanzure | so it's my understanding now that if I was to have some ecoli with these genes under expression, | 22:15 |
| kanzure | that bursting the cells and running it through gel electrophoresis would allow me to separate the proteins by mass? | 22:15 |
| kanzure | and then I'd just need some way to figure out what the relative mass of dopamine is, right? | 22:15 |
| fenn | 137kbase is that right? | 22:16 |
| kanzure | hm? | 22:16 |
| fenn | seems awfully long for 3 enzymes | 22:16 |
| kanzure | hm | 22:16 |
| kanzure | that second one is the painfully long one | 22:16 |
| fenn | less is choking on that preponderously long line | 22:16 |
| kanzure | (tyrosinase) | 22:16 |
| kanzure | which is also the one that you suggested might be wrong | 22:17 |
| kanzure | say, I detect a pattern. heh' | 22:17 |
| kanzure | that may be the entirety of chromosome 11 | 22:18 |
| kanzure3_ | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&qty=1&c_start=1&list_uids=NG_008748.1&uids=&dopt=gb&dispmax=5&sendto=&fmt_mask=0&from=end&to=begin&extrafeatpresent=1&ef_STS=64&ef_MGC=16&ef_HPRD=32&ef_tRNA=128&ef_microRNA=256&ef_Exon=512 | 22:18 |
| kanzure3_ | though this says that it's indeed tyrosinase | 22:18 |
| fenn | nah chromosome is way biggre | 22:19 |
| fenn | 134MB | 22:20 |
| kanzure | ? | 22:20 |
| fenn | chromosome 11 is 134 million base pairs | 22:21 |
| kanzure | mrgene.com does $0.50 for up to 3k bp. | 22:22 |
| kanzure | I wonder what the normal price on dopamine is | 22:23 |
| fenn | Yeast proteins are on average 466 amino acids long and 53 kDa in mass | 22:23 |
| fenn | your ridiculously large gene would be about 45000 amino acids | 22:23 |
| kanzure | well, what's the max yeast gene size :/ | 22:24 |
| kanzure3_ | http://www.sigmaaldrich.com/catalog/ProductDetail.do?N4=H8502|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC | 22:25 |
| fenn | i'm guessing around 20kbase | 22:25 |
| kanzure3_ | $5/gram | 22:25 |
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| gene | I think you can seperate proteins by electrophoresis | 22:26 |
| kanzure3_ | http://www.haque.co.uk/papers/hardsp-softsp-open-so-arch.PDF | 22:27 |
| kanzure3_ | Hardspace, Softspace and the possibilities of open source architecture - Usman Haque | 22:27 |
| fenn | hm it probably has a bunch of introns and crap | 22:27 |
| gene | relative mass of dopamine = easy | 22:27 |
| fenn | you should find the protein sequence and reverse translate it | 22:27 |
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| kanzure3_ | fenn: is that going to be reliable? | 22:27 |
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| kanzure3_ | it will take the crud out, yes, but | 22:27 |
| gene | well it depends | 22:27 |
| gene | if there is something that weight the same as dopamien | 22:28 |
| kanzure3_ | fenn was talking about something else. | 22:28 |
| fenn | well, what are you trying to do? | 22:28 |
| fenn | make dopamine right? | 22:28 |
| kanzure3_ | right? | 22:28 |
| fenn | first of all, why use yeast and not organic synthesis techniques | 22:28 |
| gene | because this is texas and anyone with organic synthesis in their garage is a Terrorist | 22:29 |
| fenn | or just buy it from sigma aldrich | 22:29 |
| kanzure3_ | buy what from sigma aldrich? | 22:29 |
| fenn | dopamine | 22:29 |
| kanzure3_ | "just because" | 22:30 |
| kanzure3_ | really there is no point to this | 22:30 |
| fenn | ok fine | 22:30 |
| kanzure3_ | sorry to disappoint, think of it more like an exercise | 22:30 |
| gene | we're doing for the lulz | 22:30 |
| kanzure3_ | although I probably should look into organic chem instead :/ | 22:30 |
| fenn | i wanted to splice the genes for GFP and THC production into pesticide resistant dandelions, then spread them on courthouse lawns throughout the world | 22:31 |
| fenn | now that's bio terrorism :P | 22:31 |
| gene | hahahaha | 22:32 |
| gene | well fenn | 22:32 |
| gene | there was this guy | 22:32 |
| kanzure3_ | fenn: dave asks about caelinux | 22:32 |
| gene | who made some oranges that expressed the THC gene | 22:32 |
| fenn | haven't tried caelinux | 22:32 |
| kanzure3_ | http://www.caelinux.com/CMS/ | 22:32 |
| gene | he spread them, he spread them far and wide | 22:32 |
| kanzure3_ | hm, it seems to be packaged with salome, code aster, code saturne, and openfoam | 22:32 |
| fenn | gene are you making this up as you go along? | 22:32 |
| gene | the police arrested him, and we don't know what happened to oranges | 22:33 |
| gene | no | 22:33 |
| gene | I am not | 22:33 |
| gene | this is all very much real | 22:33 |
| fenn | arrested him for what? | 22:33 |
| gene | for making THC oranges of course! | 22:33 |
| fenn | is it a crime? | 22:33 |
| gene | I guess so | 22:33 |
| fenn | somehow i doubt it | 22:33 |
| fenn | not yet at least | 22:34 |
| kanzure3_ | http://twitter.com/elevenarms | 22:34 |
| kanzure3_ | why would anyone communicate with me via twitter? | 22:34 |
| kanzure3_ | argh | 22:34 |
| gene | DATELINE--Tallahassee, Fla. | 22:34 |
| gene | Oranges that get you high | 22:34 |
| gene | A Florida Biochemist designs a citrus tree with THC. | 22:34 |
| gene | In the summer of 1984, 10th-grader Irwin Nanofsky and a friend were driving down the Apalachee Parkway on the way home from baseball practice when they were pulled over by a police officer for a minor traffic infraction. | 22:34 |
| gene | After Nanofsky produced his driver's license the police officer asked permission to search the vehicle. In less than two minutes, the officer found a homemade pipe underneath the passenger's seat of the Ford Aerostar belonging to the teenage driver's parents. The minivan was seized, and the two youths were taken into custody on suspicion of drug possession. | 22:34 |
| gene | Illegal possession of drug paraphernalia ranks second only to open container violations on the crime blotter of this Florida college town. And yet the routine arrest of 16 year-old Nanofsky and the seizure of his family's minivan would inspire one of the most controversial drug-related scientific discoveries of the century. | 22:34 |
| gene | Meet Hugo Nanofsky, biochemist, Florida State University tenured professor, and the parental authority who posted bail for Irwin Nanofsky the night of July 8, 1984. The elder Nanofsky wasn't pleased that his son had been arrested for possession of drug paraphernalia, and he became livid when Tallahassee police informed him that the Aerostar minivan would be permanently remanded to police custody. | 22:34 |
| gene | Over the course of the next three weeks, Nanofsky penned dozens of irate letters to the local police chief, the Tallahassee City Council, the State District Attorney and, finally, even to area newspapers. But it was all to no avail. | 22:34 |
| gene | Under advisement of the family lawyer, Irwin Nanofsky pled guilty to possession of drug paraphernalia in order to receive a suspended sentence and have his juvenile court record sealed. But in doing so, the family minivan became "an accessory to the crime." According to Florida State law, it also became the property of the Tallahassee Police Department Drug Task Force. In time, the adult... | 22:34 |
| gene | ...Nanofsky would learn that there was nothing he could do legally to wrest the vehicle from the hands of the state. | 22:34 |
| gene | sorry big post | 22:34 |
| gene | all I could find | 22:34 |
| gene | can't find like | 22:34 |
| gene | can't find link | 22:34 |
| fenn | the “Pot Orange” story is a product of South to the Future, a phony news service that’s somewhat Onionesque. | 22:35 |
| fenn | according to snopes | 22:35 |
| gene | oops | 22:35 |
| gene | shit | 22:35 |
| gene | well then we should make some, not for the drugs, but to cause lot's of interesting things to happen | 22:38 |
| fenn | right | 22:38 |
| gene | haha gfp dandelions | 22:39 |
| fenn | i really wonder what the hippies will think of it | 22:39 |
| kanzure3_ | you know what, my mom's twin is a hippie | 22:39 |
| kanzure3_ | I could totally arrange something. | 22:39 |
| gene | so we could make them the main distributor | 22:39 |
| kanzure3_ | she travels the world, so yes. | 22:40 |
| gene | I for one will not partake in the consumption of THC dandelions though | 22:40 |
| gene | I just won't | 22:40 |
| fenn | hah from the same article "The idea of nicotine tomatoes would actually be much more viable than THC oranges, since the tomato plant and tobacco are related" | 22:41 |
| fenn | http://www.nisr.or.jp/englishHP/report2004/NISR04taura.pdf THC yeast | 22:41 |
| gene | tomacco? | 22:41 |
| gene | hahahahah | 22:42 |
| fenn | and tobacco. neat | 22:42 |
| gene | WTF, srsly WTF, living in a dorm is weird | 22:43 |
| fenn | weirdo | 22:44 |
| gene | indeed | 22:44 |
| fenn | why are you living in a dorm? | 22:44 |
| gene | because I'm at school | 22:44 |
| gene | I do not understand why someone would voluntarily have a green bed sheet duct taped too them | 22:47 |
| fenn | so they can pretend to be a spinach tortilla? | 22:47 |
| gene | screw humanity | 22:48 |
| gene | I'm going transhuman | 22:48 |
| fenn | you're going to turn into a spinach tortilla? | 22:48 |
| gene | no | 22:48 |
| gene | I'm starting to begin to think humanity needs to be replaced | 22:51 |
| kanzure3_ | I've heard that line before | 22:51 |
| kanzure3_ | in a movie | 22:51 |
| kanzure3_ | it was followed by a swift punch in the face. | 22:51 |
| gene | why are transhumans always the bad guys? | 22:52 |
| -!- mindspillage [n=kat@wikimedia/KatWalsh/x-0001] has joined #hplusroadmap | 22:54 | |
| fenn | gene: because people who are satisfied (harmless) don't want to change? | 23:06 |
| gene | they get to survive | 23:06 |
| fenn | perhaps harmless is the wrong word | 23:07 |
| kanzure3_ | " | 23:32 |
| kanzure3_ | Shortest Perl Script to Find [Government] Corruption" | 23:32 |
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