--- Day changed Fri Oct 10 2008 00:03 * drazak waes 00:03 < kanzure_> wae to you too :) 00:03 < drazak> hehe 00:03 < drazak> I'm going through some of those books you gave me 00:04 < drazak> I read the stuff for ochem 1 and 2, and I'm reading stryer's bichemistry 01:07 < kanzure_> http://senselab.med.yale.edu/ModelDb/ShowModel.asp?model=83562 Basal ganglia-thalamocortical loop model of action selection. 01:12 < fenn> hm. so it's not just me: http://xkcd.com/448/ 01:13 < kanzure_> you wake up knowing what international time zone your clock happens to be in? :) 01:18 < kanzure_> ".. might be described as a type of _kinesia paradoxa_, where the individual who typically experiences severe difficulties with the most simple of movements may suddenly perform complex, skilled movements ..'. 01:23 < kanzure_> http://en.wikipedia.org/wiki/User:Skysmith/Missing_topics_about_Neurology <- don't we all love lists? 01:28 < willPow3r> lists are sexy 01:30 < xp_prg> missing topics, they are listed how are they missing? 01:48 < kanzure_> hrm http://wexler.free.fr/library/files/annett%20(1996)%20on%20knowing%20how%20to%20do%20things.%20a%20theory%20of%20motor%20imagery.pdf 02:40 < drazak> kanzure_: reading your diy at home stuff 02:40 < kanzure_> I have lots of stuff :) which stuff? 02:43 < drazak> the zip file 02:43 < drazak> how good is the PCR at home? 02:43 < kanzure_> Sorry, which zip file? 02:43 < kanzure_> Are you talking about the git repository? 02:43 < kanzure_> http://heybryan.org/gitweb.cgi and such? 02:43 < drazak> http://biohack.sourceforge.net/ 02:44 < kanzure_> k, ignore that site and just go to the gitweb.cgi link 02:44 < kanzure_> that 40 MB zip file is the old version 02:44 < kanzure_> anyway, there were some guys in Boston trying the PCR :) 02:44 < kanzure_> actually, just the gel 02:44 < kanzure_> I remember them saying something about wanting to do PCR soon though. 02:44 < kanzure_> http://heybryan.org/~bbishop/docs/thermocycler.pdf for a simple thermocycler 02:47 < drazak> right 03:00 < ybit> procto: you live in s.f. or visiting there for the convergence conf.? 03:07 < kanzure_> http://ponoko.com/ laser-cutting-print-on-demand-from-the-web service. 03:07 < kanzure_> input: CAD, output: metal trincket in your mailbox. 03:08 < kanzure_> Wonder what their resolution is. 03:12 < drazak> if it's a decent machine, almost perfect 03:37 < kanzure_> http://graphviz.org/Gallery.php Any recommendations or favorites? 03:38 < drazak> kanzure_: do you have a link for making a home made centrifuge? 03:38 < kanzure_> yes 03:38 < kanzure_> do you need it right now? 03:38 < drazak> well it's cool if you could link me, but I don't need it 03:38 < kanzure_> The laptop isn't working well - would take me 15 or 20 minutes to get Opera and pidgin up 03:39 < kanzure_> I'll get it to you Real Soon 03:39 < drazak> I'll look for it myself then 03:39 < kanzure_> but yes, there are homemade centrifuges all the time 03:39 < kanzure_> small-time centrifuges are just computer case fans + magnets 03:39 < kanzure_> bkero was talking about room-sized centrifuges with brushless electric motors from motorcycles or something yesterday :p 03:40 < drazak> way too big 03:40 < drazak> I'll just grab a case fan or something 03:40 < drazak> I saw something for a blender centrifuge 03:41 < kanzure_> I'm pretty sure a blender works like a centrifuge. 03:41 < kanzure_> Motor + sit a blade on top of it. 03:41 < drazak> right 03:41 < drazak> you'd just have to replace the blade with something else 03:41 < kanzure_> except the blade is within the mixed contents, instead of spinning the whole vial/case 03:42 < drazak> well 03:42 < drazak> kind of 03:42 < kanzure_> wtf "Autism Speaks walk". rawr. I'll cure you with a foot up your ass. 03:43 * kanzure_ has a few televisions on 04:14 < kanzure_> huh. overlap=false doesn't make overlap false in 'dot'. 04:24 < bkero> what? 04:24 < bkero> Centrifuges are easy 04:25 < bkero> It's just a motor with a cone on it. The cone has holes drilled for vials 04:26 < drazak> yeah 04:55 * ybit likes http://graphviz.org/Gallery/directed/psg.html 04:56 < ybit> and http://graphviz.org/Gallery/directed/Genetic_Programming.html 04:56 < ybit> kanzure_ ^ kanzure_ 04:56 < kanzure_> mm 04:56 * kanzure_ watches some pokemon 04:56 < ybit> grr, i meant the second nick 04:56 < ybit> hehe, pokemon 04:57 < ybit> did anyone here play the card game? 04:57 < kanzure_> yes but no 04:57 < ybit> i was the only one to own pokemon cards in my town it seems :P 04:57 < kanzure_> It turns out I wasn't really playing the game 04:57 < kanzure_> but instead "haha, this looks cooler" 04:57 < kanzure_> Nobody knew the rules anyway. 04:58 < splicer> they weren´t printed on the package? 04:58 < ybit> i knew how to play... by myself 04:58 < ybit> luckily i would always win 04:58 < splicer> magic was big here 04:59 < ybit> ah, same 04:59 * ybit needs some rest since... 04:59 < ybit> i'll be getting up @ 4am to drive my mum somewhere far, far away 05:00 < ybit> gn (good night) 05:00 < splicer> nite 05:00 < kanzure_> in context, 'gn' makes sense here 05:00 < kanzure_> but not just randomly :) 05:00 < kanzure_> anyway. 05:01 < ybit> :P 05:01 < kanzure_> Covering my tail and all. 05:01 < splicer> won't help, bend over 05:02 < splicer> do people listen to ACDC? 05:02 < kanzure_> Yes. 05:02 < kanzure_> <-- Metalhead. 05:02 < splicer> me to 05:02 < splicer> I'm a bit fascinated by the Walmart thing 05:02 < kanzure_> ? 05:03 < splicer> ACDC apparently makes release their new album exclusively on walmart 05:03 < kanzure_> That's unfortunate. 05:03 < splicer> the idea being that there is a walmart anywhere, but not always a record store 05:04 < splicer> The thing is.. the release is in 10 days and the torrent is out now... 05:05 < splicer> so much for being proactive by choosing walmart 05:07 < splicer> The recordindustry have been amazingly slow in understanding what's going on... It's been like this for 10 years now... and they still don't completely get it. 05:08 < splicer> An ACDC album peole are waiting for will be on the trackers about 10 days before the release date. 05:09 < splicer> It's like death and taxes 05:10 < kanzure_> I hear my musician friends sometimes joking that their albums appear on torrents before they're even post-production, they listen and say "Damn, this is good shit" and use it anyway. 05:10 < splicer> hehe 05:12 < splicer> In a few years I think the industry maybe understands that the release date is the date the music hits the torrents... People could actually be buying ACDC albums now. 05:35 < xp_prg2> hi all! 05:45 < gene> hello 05:55 < gene> I accidentally the whole thing 06:08 < xp_prg2> you accidentally what? 07:13 -!- xp_prg2 is now known as xp_bed 08:51 < faceface> the app I was looking for yesterday is called vsound 08:51 < faceface> http://www.vsound.org/ 08:51 < faceface> fyi 09:34 < faceface> but I can't make it work 10:35 -!- marcel_inuse is now known as hjkl 11:14 -!- ybit2 is now known as ybt 11:14 -!- ybt is now known as ybit 14:20 < fenn> now this is some pretty documentation: http://www.python.org/doc/2.6/tutorial/introduction.html 14:21 < fenn> apparently that is ReStructuredText output 15:45 < school_ybit> did you guys see this? http://www.youtube.com/watch?v=ynL8BCXih8U 15:45 < school_ybit> probably already commented on it when my laptop was down 16:07 < kanzure___> Hello 16:28 < faceface> hi 16:29 * faceface goes to conference 16:29 * bkero remains at work 16:29 < faceface> I was working on a pdf downloader from JMB, what shall I do with the bundle? 16:29 < faceface> so far I need a list of 'toc' pages 16:29 < faceface> I'm sure I can find one 16:30 < faceface> I was going to call my blog "decode this" - a pun on "decode me" 16:31 < faceface> I'm sure you can tell me what to do with my PDF's when I get back 16:31 < faceface> I named the files with a random file name... do we have a tool to look up a pdf in pubmed? 16:31 < faceface> I figure its easier to apply the metadata afterwards rather than try to capture it from the journal site 16:32 < faceface> any opinion? 16:32 < faceface> put opinions @ the discussion group 16:34 < nsh> pun does not mean what you think it does. 17:28 -!- xp_bed is now known as xp_prg 18:43 < xp_prg> fenn you here? 18:47 -!- zybit is now known as ybit 20:38 < kanzure___> Hrm. So this is unfortunate. 20:38 < bkero> Drop your gum on the floor? 20:39 < fenn> bkero: i semi-randomly met corey shields at iu linux fest today 20:39 < kanzure___> The designs in the repository are ambiguous. The subcomponents and artifacts (and so on) don't have explicit connections between each other; one of the things that I was going to do was remove the input and output artifacts entirely and just focus on the functions, but as it turns out this introduces problems into the graph. 20:39 < kanzure___> I'm still trying to figure out how wrong everything is 20:39 < kanzure___> my gut tells me "very wrong" 20:40 < fenn> a graph with no vertices? 20:40 < fenn> yeah i'd call that a problem 20:40 < kanzure___> nope, allow me to explain 20:40 < kanzure___> apparently in the repository there are supposed to be 3 graphs 20:40 < kanzure___> an assembly graph, a 'CFG' (component function graph?), and a 'function structure' 20:41 < kanzure___> the CFG is what I already have successfully generated from the database 20:41 < kanzure___> edges and arcs are labeled with flows - like "electrical" - between components 20:41 < kanzure___> the 'function structure' is supposed to be like a black box diagram 20:41 < kanzure___> http://heybryan.org/~bbishop/docs/repo/cdd/supermax%20hair%20dryer.png 20:41 < fenn> what's the diff between cfg and function structure? 20:42 < kanzure___> that last link is what a function structure would look like for the hair dryer. here's my attempt at the output: http://heybryan.org/~bbishop/docs/repo/cdd/78.png 20:42 < kanzure___> cfg and function structure diff, please hold 20:42 < drazak> so I'm definitely going to setup some stuff form home PCR/electrophoresis 20:43 < kanzure___> http://heybryan.org/~bbishop/docs/repo/cdd/78_CFG.png <-- CFG. 20:43 < kanzure___> drazak: Avoid ethidium bromide. 20:43 < fenn> and dont electrocute yourself either :) 20:44 < kanzure___> what do they run at these days, 200 V? 20:44 < fenn> dunno, agarose is much lower thann acrylaamide of course 20:44 < kanzure___> acrylamide is the way to go as far as I'm concerned 20:44 < fenn> higher volage = faster 20:44 < kanzure___> Anyway, 20:44 < fenn> youur god damn ggiant png's are messing up my computer 20:45 < kanzure___> why is it loading the whole PNG at once 20:45 < fenn> it's cranking away, i assume out of ram 20:46 < drazak> kanzure___: I'm not worried about ethidium bromide 20:46 < kanzure___> drazak: just use something else. 20:47 < drazak> are other stains as good? 20:47 < kanzure___> yeah 20:47 < kanzure___> labs down here really love sybergold 20:47 < kanzure___> or cybergold 20:47 < kanzure___> but it's commercial :( 20:48 < drazak> I don't mind commercial stuff 20:48 < drazak> I'm going to have to buy commercial primers 20:48 < kanzure___> Traitor. You'll be shot. 20:48 * kanzure___ queries the primerfarm for a new batch 20:49 < kanzure___> fenn: If you have any bright ideas on getting that "function structure" / black box diagram version from the messy 78_CFG.png data set, I'm all ears. 20:49 < fenn> hair dryer diagram was done by hand? 20:50 < kanzure___> yes. in a stupid program called 'conceptdraw pro' 20:50 < kanzure___> $300 pricetag .. so, yeah, hax0red that. 20:50 < kanzure___> in the XML repo, the CDD (ConceptDraw Diagram) files are inclued in the .repo files apparently 20:50 < kanzure___> but only for some of them 20:51 < kanzure___> it's done by hand and thus, yes, doesn't actually have a correlate necessarily to the xml.. 20:51 < kanzure___> certainly no specified correlate. 20:56 < fenn> so that PNG is only 400k, so it's not that big 20:57 < fenn> konqueror gqview and convert all take forever to load it, lots of kernel-level cpu usage? 21:09 < fenn> 16000 pixels wide, no wonder 21:09 < drazak> fenn: use feh to view it 21:09 < fenn> convert wanted a gig of ram, so that's probably why it wasnt working (256MB on my old lappy) 21:25 < fenn> feh dies repeating: libpng error: IDAT: CRC error 21:26 < fenn> oo and a snow crash even 21:26 < kanzure___> wtf? 21:26 < fenn> a zoomed out snow crash 21:27 < fenn> feh is very fast but it crashes if i look at it wrong 21:29 < fenn> anyway i can see the output as a jpeg, but it just looks like a bunch of spaghetti 21:36 < bkero> fenn: What did you say to him? 21:36 < bkero> fenn: Did you tell him you know me? :P 21:37 < fenn> yeah i said "hi bkero mentioned me yesterday, here i am whee" 21:37 < bkero> What did he say? 21:37 < fenn> then he poked at the employment website for like 20 minutes talking about the way iu hires people 21:37 < bkero> Was it pretty casual? 21:38 < fenn> and eventually i mentioned i have a degree in microbiology and so he explained that each department had their own it specialist staff 21:38 < fenn> it was a convention with tables and cookies and stuff, so yeah i guess it was casual 21:38 < bkero> Heh 21:38 < bkero> His nickname is C-Money 21:39 < bkero> He's a bandwidth pimip 21:39 < bkero> pimp 21:39 < fenn> also he had this gigantic monitor showing the status of all their nodes 21:39 < bkero> Hehe he probably stole that from bigscreen. 21:39 < fenn> so i was sort of hypnotized by that 21:40 < fenn> i also asked what the big deal was with database developers 21:41 < fenn> apparently they have this database to keep track of tera grid usage, and whoever developed it left, so there's a big mess nobody understands 21:41 < bkero> Hehe 21:42 < bkero> So in the end was he able to help you out or point you in the right direction? 21:43 < fenn> dunno, i will look at the biology department now i guess 21:54 < fenn> hmm @ http://cgb.indiana.edu/employment/details/15 21:55 < fenn> i can do all that, but i bet they will ignore me because i dont have a degree in CS 21:55 < bkero> Do you know anybody over ther? 21:55 < fenn> no 21:55 < bkero> no dude 21:55 < bkero> Sysadmins don't need degrees. 21:56 < bkero> Because a CS degree does not equal sysadmin. 21:56 < fenn> maybe i can weasel microbiology as 'related discipline' LP 21:56 < fenn> s/LP/:P/ 21:56 < kanzure___> argh 21:57 * kanzure___ whines 21:57 < bkero> Do you know what RAID, LVM, NFS, SAMBA, DNS, and processes are? 21:57 < kanzure___> I don't wanna do data entry 21:57 < fenn> ya 21:57 < bkero> Can you code small bash/python? 21:57 < kanzure___> bkero: uh, I think everyone here knows those :) 21:57 < bkero> And can you use svn? 21:57 < kanzure___> except maybe LVM. Is that llvm? 21:57 < fenn> i can do big bash/python. oog 21:57 < bkero> That's all that should be required for that job. :P 21:57 < bkero> No. LVM is Logical Volume Management. 21:57 < kanzure___> Corporate shit? 21:57 < fenn> its like MD0 21:57 < bkero> kanzure___: Have you ever set up a RAID56 array? ;) 21:58 < kanzure___> or hdd boot sector stuff? 21:58 < bkero> Yes, md? devices are lvm 21:58 < bkero> er no 21:58 < bkero> md? devices are software raid 21:58 < fenn> why would anyone use hardware raid? it's so unreliable :) 21:58 < bkero> No, LVM is what is used to make partitions resizable and encryptable. 21:58 < bkero> Hardware raid performs much better than software raid. 21:59 < kanzure___> Anyway. I'm pretty sure the repository is more or less useless. Their turtles aren't uniform anyway. Bad turtles. 22:00 < kanzure___> but I'm sure as hell not going to do the reverse engineering and data entry of 150 products to seed the repositories 22:00 < kanzure___> :/ 22:00 < fenn> i guess i dont know what LVM's are used for then 22:01 < bkero> To logically split a disk into resizable and joinable parts. 22:01 < fenn> how does it "Stripe whole or parts of logical volumes across multiple PVs, in a fashion similar to RAID0." without using /dev/md0? 22:01 < bkero> LVM is split into 3 pieces. Physical volumes, (physical) volume groups, and logical volumes. 22:02 < bkero> Volume groups are made of physical volumes, and logical volumes are made of volume groups. 22:03 < bkero> So if I have 2 hard drives, I make them into 'physical volumes'. Then I make a volume group, and the physical volumes to it. Then, for example, I just want one big logical disk. I allocate all of the volume groups space into 1 big logical volume. 22:03 < fenn> and this is not raid0? 22:03 < bkero> No 22:03 < drazak> fenn: hardware rade is 1000x more reliable than software 22:03 < bkero> This is just LVM doing what LVM does. 22:04 < fenn> drazak: i was just trolling 22:04 < drazak> s/rade/raid/ 22:04 < drazak> :P 22:04 < fenn> drazak: lots of people have nightmares when their hardware raid card dies and they can't do shit until they get another identical one 22:04 < drazak> it's because they're using subpart cards to begin with 22:07 < bkero> Same case with software raid though 22:07 < bkero> If your motherboard dies you can't get shit until you get another. Given, it doesn't have to be ientical. 22:08 < bkero> fenn: Apply for the job. You can do it. 22:08 < bkero> Sysadmin work is cake. 22:10 < kanzure___> oh 22:10 < kanzure___> Bad turtles => just means that more information has to be filled in really 22:10 < kanzure___> not that the turtles have to be exterminated 22:11 < kanzure___> Hard to fill in that extra data without actually looking at the original products though. 22:11 * kanzure___ soldiers home. 22:24 < fenn> hmm could i do LVM with a spool of DVD-R's? 22:28 < bkero> uh 22:28 < bkero> If you've got the drives 22:28 < bkero> alla t once 22:28 < fenn> that's no good 22:29 < fenn> my mac plus used to say 'please insert floppy disk 23' 22:29 < fenn> we seem to have lost that ability 22:33 < kanzure_> fenn: consider multi-CD installation apps 22:33 < fenn> basically i want to keep track of my DVD collection without having to make some spreadsheet that doesn't directly represent the data 22:34 < kanzure_> fenn: oh my. that'd be nice :) 22:34 < kanzure_> I see what you mean with the use of LVM there. 22:34 < kanzure_> that's a simple /mnt/ hack, isn't it? 22:34 < fenn> except apparently that's not what LVM does, so i still dont know what LVM does 22:35 < fenn> kanzure_: have to unmount dvd to mount another one, and it wouldnt be persistent anyway (would have to cycle through all of them every boot) 22:35 < kanzure_> why would you have to cycle every boot? 22:36 < kanzure_> I'd be okay with broken file system mounts, as long as I in fact have a system for umounting and giving it to another friend for mounting 22:36 < fenn> how would this mount hack work? 22:37 < fenn> i'm picturing just overlapping everything on the same directory 22:37 < kanzure_> I wouldn't care if it has multiple dirs really .. as long as you have the 'direct representation of the medium' in kernel space somehow 22:37 < kanzure_> that's what your message clued me in to. 22:38 < kanzure_> everybody has lists but we all know the problem with these lists.. 22:38 < fenn> lists get out of sync and require maintenance 22:39 < kanzure_> worse, it sometimes requires O(n) or O(something greater than n) maintenance 22:39 < kanzure_> hrm 22:39 < kanzure_> I need a way to distinguish O of the kernel/boxen versus O of me brain 22:41 < fenn> weird this is an hourly job: I am recruiting a laboratory assistant to contribute to several epigenetic research projects investigating the role of tumor suppressor gene silencing in the pathogenesis of human gastrointestinal cancers. 22:42 < kanzure_> technically I'm working as an 'assistant' as well. 22:42 < kanzure_> in wet/bio labs, this seems to imply dish washing or standard routines, like gels over and over again 22:42 < kanzure_> in engineering labs this means just be awesome evidently