--- Day changed Sat Feb 14 2009 00:00 < 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. 00:01 < 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 -!- RiceCake [i=RiceCake@static24-72-67-166.regina.accesscomm.ca] has quit ["Leaving"] 00:01 < 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 00:02 < kanzure> yes, it would have to be in inches 00:04 < fenn> was the 10 inch bandsaw for wood or metal? 00:04 < kanzure> probably wood 00:05 < fenn> i'm thinking i should bring the gingery lathe and the metal bandsaw 00:05 < kanzure> well, definitely those two things 00:06 < 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 00:07 < 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! 00:08 < 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 00:09 < 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. 00:10 < 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 00:11 < 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 :( 00:12 < 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 00:13 < fenn> tea bubblers and stiff oblique-ended yellow straws 00:13 < fenn> why doeshe want a 20 inch disk sander? 00:14 < 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. 00:15 < 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) 00:17 < kanzure> oh, you're right 00:17 < kanzure> huh. 00:18 < fenn> 396 lbs 2HP 00:18 < fenn> those are electrical ponies 00:18 < kanzure> ponies? so not a horse? 00:19 < fenn> like a horse but more compact 00:21 < 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 00:23 < fenn> why? 00:23 < kanzure> sorry, size doesn't matter 00:23 < kanzure> nevermind 00:23 < kanzure> just fabricational capacity 00:24 < 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 00:25 < 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 00:26 < 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 00:29 < fenn> guess i should bring the little TIG welder too 00:30 < kanzure> oh, I have a freshman that will be working on the CFD analysis with me 00:31 < 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 00:32 < 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 -!- PeerInfinity [n=someone@216.36.180.162] has quit [] 00:32 < 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. 00:33 < 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 00:34 < 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 00:35 < 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 00:38 < fenn> what did the tool carts look like? were they like this? http://toolmonger.com/wp-content/uploads/2006/12/post-toolcart.jpg 00:39 < 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 00:40 < kanzure3_> there's definitely one of those rolling around the place 00:40 < fenn> i dont see that coming apart into "parts" 00:41 < fenn> i really like these http://www.ontarioindustrial.com/user_files/images/wire.jpg 00:42 < fenn> debating whether to bring mine, since i won't have very many fish tubs there anyway (mine are perfect size for 8 tubs) 00:43 < kanzure3_> you should certainly ask. maybe. 00:44 < 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 04:48 -!- davidnunez [n=davidnun@209-6-203-217.c3-0.smr-ubr1.sbo-smr.ma.cable.rcn.com] has joined #hplusroadmap 04:56 -!- elias` [n=me@unaffiliated/elias/x-342423] has joined #hplusroadmap 05:56 < wrldpc> http://www.youtube.com/watch?v=ZWurBuI_3fM 08:00 -!- Netsplit hubbard.freenode.net <-> irc.freenode.net quits: UtopiahGHML, chizu, Overand, fenn, tarbo2, elias`, davidnunez, kanzure--, bkero, boogles, (+3 more, use /NETSPLIT to show all of them) 08:01 -!- Netsplit over, joins: elias`, davidnunez, fenn, wrldpc, bkero, Overand, chizu, boogles, kanzure--, UtopiahGHML (+3 more) 08:30 < kanzure3_> argh. http://ftp.utexas.edu/pub/debian/ 08:30 < kanzure3_> you mean I've been missing out on this? 08:44 < kanzure> paraview conflicts with mplayer? 08:53 -!- davidnunez [n=davidnun@209-6-203-217.c3-0.smr-ubr1.sbo-smr.ma.cable.rcn.com] has quit [] 09:45 -!- jm [n=jm@p57B9BDA1.dip.t-dialin.net] has joined #hplusroadmap 09:46 < kanzure3_> http://grail.cs.washington.edu/projects/videoenhancement/videoEnhancement.htm Using Photographs to Enhance Videos of a Static Scene 10:36 < jm> 35 million $ for Twitter Inc., 6 million for the Methuselah Foundation. This is ridiculous. 12:00 < 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) 12:16 < kanzure3_> Can anyone give me the name of a handcraft / fine motor skill that is ridiculously obscure? 12:17 < kanzure3_> origami might count 12:17 < kanzure3_> but it's not that obscure 12:18 < kanzure3_> nevermind, lost my train of thought 12:55 < 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 13:27 < fenn> they have no shame, it says it right there on their blog 13:33 < fenn> writing teacher, no wonder 13:44 < 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 13:45 < fenn> http://lib2geom.sourceforge.net/ 13:47 < kanzure> David Cary and Alec Resnick have finally subscribed to openmanufacturing 14:43 -!- h2i [n=heath@unaffiliated/ybit] has joined #hplusroadmap 14:44 -!- ybit [n=heath@unaffiliated/ybit] has quit [Read error: 104 (Connection reset by peer)] 15:43 -!- elias` [n=me@unaffiliated/elias/x-342423] has quit ["leaving"] 15:49 -!- samrose [n=samrose@c-24-11-214-181.hsd1.mi.comcast.net] has joined #hplusroadmap 16:06 < samrose> fenn: bugs everywhere is awesome, thanks for the reference 16:06 < fenn> cool 16:20 -!- xp_prg [n=xp_prg3@dsl092-008-180.sfo1.dsl.speakeasy.net] has joined #hplusroadmap 16:20 < kanzure> hey xp_prg, I have something related to diybio for you to do if you're interested 16:25 -!- xp_prg [n=xp_prg3@dsl092-008-180.sfo1.dsl.speakeasy.net] has quit ["This computer has gone to sleep"] 16:39 -!- xp_prg [n=xp_prg3@dsl092-008-180.sfo1.dsl.speakeasy.net] has joined #hplusroadmap 16:46 < xp_prg> what is it kanzure? 16:47 < 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? 16:48 < 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? 16:49 < 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? 16:50 < 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 16:51 < 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! 16:59 -!- samrose [n=samrose@c-24-11-214-181.hsd1.mi.comcast.net] has quit [Remote closed the connection] 17:13 < kanzure3_> http://reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379391 dopamine synthesis pathway 17:15 < 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? 17:16 < kanzure3_> http://reactome.org/cgi-bin/svgexporter?DB=gk_current&ID=379391 18:15 -!- jk4930 [n=jk@p54BCD8EF.dip.t-dialin.net] has joined #hplusroadmap 18:30 -!- gene [n=chatzill@wireless-128-62-91-63.public.utexas.edu] has joined #hplusroadmap 18:30 < 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 18:31 < 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? 18:32 < 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 18:33 < 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 18:34 < 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 18:35 < 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 18:36 < 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 18:37 < 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? 18:38 < 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 18:39 < 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. 18:40 < gene> that's fine 18:41 < fenn> how big is the "big" air compressor? 18:42 < 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? 18:43 < 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? 18:44 < gene> cream and what not? 18:44 -!- xp_prg [n=xp_prg3@dsl092-008-180.sfo1.dsl.speakeasy.net] has quit ["This computer has gone to sleep"] 18:44 < 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 18:45 < 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 ? 18:46 < 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 18:47 < 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 18:48 < 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 18:49 < 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? 18:50 < 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 18:52 < 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) 18:53 < gene> I am not a big fan of bombarding my brain with ultrasound capable of breaking microcapsules 18:53 < fenn> ..yeah 18:54 < 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 18:55 < fenn> what happens to the capsule pieces? 18:56 < 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 18:57 < 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 19:04 -!- elias` [n=me@unaffiliated/elias/x-342423] has joined #hplusroadmap 19:20 < 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 19:21 < kanzure> presumably there's a vim plugin related to gdb 19:22 < kanzure3_> http://www.volny.cz/zellerin/gdbvim/ 19:30 -!- elias` [n=me@unaffiliated/elias/x-342423] has quit ["leaving"] 19:34 < 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]" 19:35 < 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 19:39 -!- wrldpc [n=ben@173.48.207.37] has quit [] 19:39 < kanzure3_> this is fishy. 19:45 < 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 19:46 < kanzure3_> (3-hydroxylating) + L-Tyrosine 19:46 < kanzure3_> => l-dopa 19:47 -!- jm [n=jm@p57B9BDA1.dip.t-dialin.net] has quit ["quit"] 19:48 < kanzure> this is stupid, a computer should be doing this for me 19:48 < kanzure> why isn't this program written yet? 20:03 < 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. 20:05 < 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? 20:07 < kanzure> oh shit. of course it is. it's an amino acid. 20:21 -!- jk4930 [n=jk@p54BCD8EF.dip.t-dialin.net] has left #hplusroadmap ["Konversation terminated!"] 20:32 < fenn> is there a central library of genome sequences somewhere 20:32 < fenn> the sequences themselves can't take up that much space 20:33 < 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? 20:34 < kanzure3_> ftp://ftp.ncbi.nih.gov/pub/ 20:34 * fenn sees a lot of usernames 20:35 -!- jm|earth [n=jm@p57B9BDA1.dip.t-dialin.net] has joined #hplusroadmap 20:35 < fenn> too bad i can't sort by directory content size 20:36 < kanzure3_> ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/ 20:36 < kanzure3_> (by chromosome) 20:38 < fenn> there's only 40 genomes there 20:38 < fenn> neurospora is missing for example 20:39 < fenn> can you copyright a genome? 20:39 < kanzure> does a pirate still sail when the sea is stormy? 20:40 < fenn> uh, does he? 20:40 < kanzure> hrm. 20:40 < fenn> Results 1 - 3 of 3 for "copyright a genome" 20:41 < 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. 20:42 < 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" 20:44 < fenn> ah what happened to my nefarious plans to have google index my misc directory 20:46 < 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." 20:50 < 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? 20:51 < kanzure3_> they are supposedly all the same. 20:51 < kanzure3_> (erm, per line) 20:52 < 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 20:53 < 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? 20:54 < 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 :)) 20:55 < 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? 20:57 < kanzure> fenn: nick taylor is full of shit 20:58 < 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 20:59 < 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! 21:00 < 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 21:01 < 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 21:02 < 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? 21:03 < gene> WARNING PHILOSOPHY DETECTED 21:03 < gene> back to topic 21:03 < kanzure> WARNING BULLSHIT DETECTED 21:03 < fenn> in hplusroadmap line 119041: 21:04 < fenn> TypeError: function does not accept tautology as argument 21:05 < 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& 21:06 < 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 21:07 < 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 21:08 < 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 21:09 < 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? 21:10 < 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 21:11 < gene> hmmm... 21:12 < 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? 21:13 < 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 21:14 < 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? 21:15 < 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 21:17 < gene> dangit forgot which lab 21:22 -!- mindspillage [n=kat@wikimedia/KatWalsh/x-0001] has joined #hplusroadmap 21:22 < kanzure3_> http://www.bioinformatics.org/sms2/rev_trans.html <-- need to plug in the fasta sequences into here next. 21:26 < gene> why not find the originals? 21:27 < 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 21:28 < kanzure3_> http://www.ncbi.nlm.nih.gov/sites/gquery?term=3F9T 21:28 < gene> don't you have the name for it? 21:29 < kanzure3_> there's like 20 names for everything.. 21:29 < gene> tell me the name 21:29 < kanzure3_> L-Tyrosine Decarboxylase 21:32 < 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 21:33 < 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 21:34 < 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] 21:35 < kanzure3_> http://www.genome.ad.jp/dbget-bin/www_bget?enzyme+4.1.1.25 21:35 < kanzure3_> odd, that organism is Streptococcus 21:36 < kanzure3_> 9002-09-9 21:39 < gene> I wonder if streptococcus makes you feel better so you go out and spread it more 21:41 < kanzure3_> Drosophila melanogaster tyrosine decarboxylase 2 (Tdc2), mRNA. 21:41 < kanzure3_> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=24586043 21:42 -!- mindspillage [n=kat@wikimedia/KatWalsh/x-0001] has quit ["Leaving"] 21:43 < gene> maybe you could grow a bunch of fruit flies and harvest their brains 21:47 < fenn> or find some grad students and harvest their brains 21:48 < gene> but grad students are useful and relatively expensive these days 21:48 < kanzure3_> haha useful haha 21:49 -!- splicer [n=patrik@h71n1c1o261.bredband.skanova.com] has left #hplusroadmap ["Ex-Chat"] 21:56 < 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? 21:57 < kanzure3_> they are both called tyrosinase 21:57 < kanzure3_> but are apparently different? 21:59 < fenn> one of those has to be wrong 21:59 < fenn> probably the first one 22:00 < 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) 22:04 < fenn> that's not surprising 22:05 < kanzure3_> http://heybryan.org/~bbishop/docs/dopamine/synthesis_of_dopamine.txt 22:05 < kanzure3_> updated. 22:07 < fenn> heh 22:07 < fenn> "done" 22:09 < kanzure> now to patent and hold the world hostage for one hundred billion dollars 22:09 < kanzure> or something like that 22:11 < 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 22:12 < 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 22:15 < 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? 22:16 < 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) 22:17 < kanzure> which is also the one that you suggested might be wrong 22:17 < kanzure> say, I detect a pattern. heh' 22:18 < 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 22:19 < fenn> nah chromosome is way biggre 22:20 < fenn> 134MB 22:20 < kanzure> ? 22:21 < fenn> chromosome 11 is 134 million base pairs 22:22 < kanzure> mrgene.com does $0.50 for up to 3k bp. 22:23 < 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 22:24 < kanzure> well, what's the max yeast gene size :/ 22:25 < 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 -!- ferrouswheel [n=jp@203-109-203-98.static.ihug.net] has joined #hplusroadmap 22:26 -!- ferrouswheel_ [n=jp@203-109-203-98.static.ihug.net] has joined #hplusroadmap 22:26 -!- ferrouswheel__ [n=jp@203-109-203-98.static.ihug.net] has joined #hplusroadmap 22:26 < gene> I think you can seperate proteins by electrophoresis 22:27 < 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 -!- ferrouswheel_ [n=jp@203-109-203-98.static.ihug.net] has quit [Client Quit] 22:27 < kanzure3_> fenn: is that going to be reliable? 22:27 -!- ferrouswheel__ [n=jp@203-109-203-98.static.ihug.net] has quit [Client Quit] 22:27 < kanzure3_> it will take the crud out, yes, but 22:27 < gene> well it depends 22:28 < 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 22:29 < 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 22:30 < 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 :/ 22:31 < 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 22:32 < 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? 22:33 < 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 22:34 < 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 22:35 < 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 22:38 < 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 22:39 < 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 22:40 < 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 22:41 < 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? 22:42 < gene> hahahahah 22:42 < fenn> and tobacco. neat 22:43 < gene> WTF, srsly WTF, living in a dorm is weird 22:44 < fenn> weirdo 22:44 < gene> indeed 22:44 < fenn> why are you living in a dorm? 22:44 < gene> because I'm at school 22:47 < 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? 22:48 < 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 22:51 < 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. 22:52 < gene> why are transhumans always the bad guys? 22:54 -!- mindspillage [n=kat@wikimedia/KatWalsh/x-0001] has joined #hplusroadmap 23:06 < fenn> gene: because people who are satisfied (harmless) don't want to change? 23:06 < gene> they get to survive 23:07 < fenn> perhaps harmless is the wrong word 23:32 < kanzure3_> " 23:32 < kanzure3_> Shortest Perl Script to Find [Government] Corruption"