--- Day changed Wed Sep 17 2008
00:02 < kanzure> Where's fenn?
00:03 < ybit> i need a wearable computer
00:04 < kanzure> eee pc is wearable
00:04 < ybit> the dilemma of being physically active or sitting on my ass comes up too often
00:04 < kanzure> then use the Private Eye that I linked to a few weeks back
00:04 < ybit> heh, how so?
00:04 < kanzure> eee pc? seriously? just strap it on to your back
00:05 < ybit> heh
00:05 < kanzure> wire usb output to some microcontroller + pcb and then wire that pcb over to the Private Eye or a cell phone screen thingy
00:05 < ybit> i can strap my lappy on my back, but i have to read it.. so it doesn't seem much usable 
00:05 < kanzure> and then for a keyboard walk around with one tied to your belt loops
00:05 < kanzure> right, I said cell phone screen :)
00:05 < ybit> hehe
02:01 < kanzure> http://www.osdd.net/ open source drug discovery
02:03  * bkero wonders how people afford labs without big fat pharma budgets.
02:03 < bkero> Or university budgets :P
02:07 < kanzure> It's India: chances are, one of their 10019401414810498140184018501285032589 people have already mutated into an entire lab.
02:07 < bkero> lol
02:07 < kanzure> But seriously, this must be what they're doing with their overflow of CS students
02:08 < bkero> I thought their overflow of CS students just turned into excess Java programmers
02:08 < kanzure> Oh god.
02:09 < kanzure> Open source java bean discovery
02:11 < bkero> More like a bunch of useless progammers
02:12 < kanzure> At least they're putting them to a possibly good cause
02:12 < kanzure> If they had all of their programmers seriously doing 'open source' ?
02:12 < kanzure> You have any idea what would happen?
02:12 < kanzure> World explodes.
02:13 < bkero> The US would be on it's way to the third world?
02:13 < bkero> Oh wait...
02:13 < kanzure> Hrm. Sounds familiar.
02:15 < bkero> How's that entire texas being shitty thing going?
02:15 < kanzure> Lots of traffic.
02:15 < bkero> Want a place to stay in oregon while the whole thing blows over? :P
02:15 < kanzure> A few dead bodies. Nothing to report.
02:15 < kanzure> Yes.
02:15 < bkero> ok
02:15 < bkero> gtfup
02:15 < kanzure> up?
02:15 < bkero> oregon
02:16 < kanzure> Oh, you want me to provide transportation?
02:16 < kanzure> I see.
02:16 < bkero> lol yea
02:16 < bkero> I can't pay for your bills, I'm poor.
02:16 < kanzure> Aren't we all?
02:16 < kanzure> Hrm.
02:18 < ybit> why the hrming?
02:19 < kanzure> Well, he works at Intel.
02:19 < kanzure> If intel has no money, then
02:20 < kanzure> question mark question mark question mark question mark
02:20 < bkero> I'm an intern
02:20 < bkero> and I only work there until friday.
02:25 < kanzure> WTF
02:25 < kanzure> http://sysborgtb.osdd.net/bin/view/Main/TWikiUsers
02:25 < kanzure> You can count this list on your fingers
02:27 < bkero> DUDE
02:27 < bkero> Look at the dates
02:27 < bkero> That's not too bad for less than a month
02:28 < kanzure> for 150 million USD ? You kidding?
02:28 < bkero> oh this got sank $150m?
02:28 < bkero> I thought they were running off nothing
02:28 < kanzure> NOpe
02:29 < kanzure> They have the Indian government shelling out significant cash
02:29 < bkero> It's impossible to do anything with science without "significant cash". :P
02:31 < ybit> http://arxiv.org/abs/0809.1634
02:31 < ybit> can't remember where i got this link now
02:31 < kanzure> ybit: title first please
02:32 < ybit> printer graphene circuits
02:32 < kanzure> oh crap
02:33 < bkero> http://oregonstate.edu/dept/ncs/newsarch/2006/Mar06/circuit.htm :P
02:38 < kanzure> hm
02:38 < kanzure> so
02:38 < kanzure> I have reached a new level of laziness
02:38 < kanzure> Since a buddy wahoo'd me about this link - http://www.physorg.com/news140787110.html - saying they are doing graphene research in the mechanical engineering department here
02:38 < kanzure> and ybit has also wahoo'd me about that arxiv paper, possibly,
02:39 < kanzure> then I'm going to just start guessing
02:39 < kanzure> :)
02:39 < kanzure> Wait. Crap.
02:39 < kanzure> I fail.
02:39 < kanzure> the physorg news is graphene energy storage
02:45 < kanzure> anybody want to buy me a cray supercomputer on a credit card? http://blog.wired.com/gadgets/2008/09/impulse-buyers.html but apparently it runs only windows, so it's not worth it
02:48 < ybit> i have a linux live cd if you would like to use it ;)
02:49 < kanzure> of what?
02:49 < kanzure> the architecture might be off, that's what I mean
02:49 < bkero> http://www.gentoo.org/images/gwn/20060320_cover.png
02:49 < bkero> The architecture on that is just amd64
02:50 < kanzure> The Singularity is Far - http://scottaaronson.com/blog/?p=346 - somebody give this man a damn link to http://heybryan.org/fernhout/ before he goes ape on us
02:50 < bkero> kanzure: Have you ever looked into agalmics?
02:50 < kanzure> dlfajdlkaaqioewriqj
02:50 < kanzure> sort of
02:50 < kanzure> Post-Scarcity stuff
02:50 < kanzure> neurons firing .. uh ..
02:51 < bkero> Post-scarcity economics
02:51 < bkero> It makes economists shit themselves :)
02:51 < kanzure> People genuinely can't imagine not working
02:51 < kanzure> on the contrary .. I have just the opposite problem
02:52 < bkero> Are you sure you're not a liberal arts major?
02:53 < kanzure> I do have a ridiculously broad range of interests
02:53 < kanzure> Yes, I am a liberal arts major .. in the sense of liberation, not liberalism.
02:53  * kanzure offed a Gershenfeld quote :)
02:53 < kanzure> http://heybryan.org/exp.html
02:54 < kanzure> ' From this combination of passion and inventiveness I began to get a sense that what these students are really doing is reinventing literacy. Literacy in the modern sense emerged in the Renaissance as mastery of the liberal arts. This is liberal in the sense of liberation, not politically liberal. 
'
02:55 < kanzure> Argh. I need to fork my brain.
02:55 < bkero> They're still sharing the same resources.
02:55 < bkero> http://fuse.sourceforge.net/wiki/index.php/FileSystems
02:57 < kanzure> http://arxiv.org/abs/0809.0339
02:57 < kanzure> The Cepheid Galactic Internet
02:57 < kanzure> Authors: John G. Learned, R-P. Kudritzki, Sandip Pakvasa, A. Zee
02:57 < kanzure> Abstract: We propose that a sufficiently advanced civilization may
02:57 < kanzure> employ Cepheid variable stars as beacons to transmit all-call
02:57 < kanzure> information throughout the galaxy and beyond. One can construct
02:57 < kanzure> many scenarios wherein it would be desirable for such a civilization
02:57 < kanzure> of star ticklers to transmit data to anyone else within viewing
02:57 < kanzure> range. The beauty of employing Cepheids is that these stars can be
02:57 < kanzure> seen from afar (we monitor them out through the Virgo cluster), and
02:57 < kanzure> any developing technological society would seem to be likely to
02:57 < kanzure> closely observe them as distance markers. Records exist of Cepheids
02:57 < kanzure> for well over one hundred years. We propose that these (and other
02:57 < kanzure> regularly variable types of stars) be searched for signs of phase
02:57 < kanzure> modulation (in the regime of short pulse duration) and patterns,
02:57 < kanzure> which could be indicative of intentional signaling.
02:57 < kanzure> Crap. Pasting.
03:00 < kanzure> hey, wait a sec
03:01 < kanzure> fuck this
03:01 < bkero> lol
03:01 < kanzure> Anybody remember my work on autozen 2008?
03:01 < kanzure> it's my paper reader app for using a monitor to just flip up damn papers
03:01 < kanzure> let's throw this in to an apt-get system
03:01 < kanzure> and then upload papers for communal reading/sharing
03:01 < kanzure> big problem was that my stupid perl script kept on opening up processes 
03:01 < kanzure> leaving zombies
03:02 < bkero> zombify
03:02 < kanzure> What?
03:03 < kanzure> oh, cool, I already had autoreader/autozen reading from a list of files to be read
03:03 < kanzure> But the zombies. Anybody know how to kill zombies?
03:05 < kanzure> http://heybryan.org/projects/autoscholar/autoreader.pl.txt
03:54 < kanzure> Bah.
04:57 < kanzure> '   Two postdoctoral positions are available in the lab of Nathan Urban at Carnegie Mellon University to work as part of a DARPA-funded project (REALNOSE http://www.darpa.mil/dso/solicitations/baa07-21mod11.htm) on analysis of data from arrays of biologically-based chemical sensors. This position is part of a large multi-investigator project involving collaboration with biologists, engineers and computer scientists at several institutions. The ideal 
04:57 < bkero> kanzure: Do they want to give me a job?
04:57 < bkero> I'll only work for them if all my code can be GPL'd.
04:58 < kanzure> Postdoctoral positions.
04:58 < bkero> bah
04:58 < bkero> I'm basically postdoctoral
05:00 < kanzure> Huh?
05:00 < kanzure> You don't even have an undergrad degree, I thought :) 
05:01 < bkero> Sshh
05:01 < bkero> I can fake it though. ;)
05:01 < kanzure> Don't they check references or something?
05:01 < bkero> lol nobody checks references
05:02 < kanzure> hrm
05:02 < kanzure> really?
05:02 < bkero> I guess they'll call someone and ask them if I'm awesome.
05:02 < bkero> And everyone will invariably say yes.
05:02 < kanzure> I mean, right now I have like four professors of references
05:02 < kanzure> guess I'm kinda overkilling it
05:02 < bkero> Heh
05:02 < bkero> I have one professor, a CTO, leader in 2 open source projects, and my boss. :)
12:45 -!- johnhitt is now known as new_nickname_her
12:45 -!- new_nickname_her is now known as JohnH
16:35 < kanzure__> Hi all.
16:45 < Nofaris> Hi kanzure
16:45 < Nofaris> What are you thinking about?
16:46 < kanzure__> I wrote some quick code in class today to make a 'perceptron'. Just checking some email until I head off into chemistry.
16:46 < kanzure__> Has anybody downloaded matweb yet?
16:48 < kanzure__> Rogers Aerospace has released their software for aerodynamic analysis - free download - http://www.rasaero.com/ - not sure if it's better than OpenFOAM or anything, though.
17:02 < kanzure__> "Extensive involvement of social actors and perspectives is an increasing trend in foresight. Simultaneously, however, the theoretical literature suggests that there is a trade-off between increasing variety and productive convergence. The paper examines, through a sample of recent foresight exercises, how European foresight balances between variety and convergence. The findings support the existence of a trade-off, and suggest that it can be clas
17:03 < kanzure__> 'Foresight ? balancing between increasing variety and productive convergence'
17:03 < kanzure__> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V71-4RR82VN-1&_user=108429&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=108429&md5=801604eaedbf5a96693539105273cffc
17:05 < kanzure__> Formal studies of 'mental toughness' - http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V9F-4T832Y2-1&_user=108429&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059713&_version=1&_urlVersion=0&_userid=108429&md5=2b8be8751fbd56e8f1438065af522aa3
17:09 < kanzure__> Hm. gcc is coming up with a new plugin architecture
17:11 < kanzure__> http://immigration.gov.ph  uses debian :)
17:12 < kanzure__> http://www.dailymail.co.uk/sciencetech/article-1056482/Returning-roots-Scientists-claim-grow-tree-homes-decade.html
17:12 < kanzure__> plantware - growing trees for homes
17:16 < kanzure__> md5 reverse lookup http://benramsey.com/code/source.php?file=md5.php
19:04 < kanzure> Hi all.
19:10 < bkero> Afternoon
19:10 < kanzure> Anything new?
19:11 < kanzure> Hm. Looks like there's a meeting with the local bioreactor professor at 430. 
19:12 < kanzure> Apparently the purification process that he uses is via histamines.
19:12 < kanzure> I completely forgot how common a technique antibodies are for purification and filtering :-) (as opposed to column chromatography)
19:56 < kanzure> ASM mirror complete. Downloaded 2.03 GB in 207553 files.
20:05 < kanzure> http://heybryan.org/~bbishop/docs/matweb/wtf.html Search the source code for 'WTF' to see something interesting.
20:16 < kanzure> Hey ybit. Anything new?
20:20 < kanzure> Heh, somebody in #biology is trying to identify some cryoelectroscopy images. IIRC, it's kind of like freeze fracture but more awesome.
20:22 < kanzure> http://img47.imageshack.us/my.php?image=imageqm0.jpg
20:26 < kanzure> Hey elias`.
20:27 < ybit> ?? kanzuer.. hmm, not much
20:27 < ybit> oh.. well..
20:27 < ybit> i get to work on a research project 
20:27 < ybit> yay
20:28 < kanzure> details?
20:28 < ybit> psh, i wish, i know nothing
20:28 < ybit> i had to install this behemoth of a monster: http://en.wikipedia.org/wiki/IRAF
20:29 < ybit> it's nothing interesting
20:29 < ybit> i get to work with some bio professor next semester studying tardigrades
20:30 < ybit> maybe we will shift into discovering just what the mysterious object in the sky is that every news outlet keeps blabbing about
20:31 < ybit> i'm essentially taking any research i can get
20:31 < kanzure> Sky?
20:31 < kanzure> Tardigrades and water bears might be fun to look at.
20:31 < ybit> there's not much to be given on campus, atleast with my status
20:32 < kanzure> I know that I would sometimes spend many hours back in the bio lab in high school looking under a microscope. 
20:32 < kanzure> Ask your professor for his video stash on microbiology. And when he denies its existence, there's your clue to go in for the kill. 
20:32 < kanzure> From what I've seen, these videos are pretty entertaining.
20:33 < ybit> i'm trying to get him to look at species similar to tardigrades, because there are, after all, species that can survive extremes just as well
20:33 < ybit> hehe, he has a youtube account :)
20:33 < ybit> one sec...
20:35 < kanzure> link?
20:37 < ybit> http://www.youtube.com/user/pgdavison8
20:40 < kanzure> ybit: I have some videos on my server if you want to take a look.
20:41 < ybit> yeah, and i hope you don't mind me retreiving every pdf in http://heybryan.org/~bbishop/docs/manufacturing/ :)
20:41 < kanzure> Yes, I do mind. Ask me for a zip next time :-p.
20:42 < kanzure> Unless you didn't do it manually .. i.e., wget -m -np would work I guess.
20:42 < ybit> it's not quite as much as the diybio kit, so it shouldn't have as much of an effect on the server
20:42 < kanzure> Effect on the server isn't what I'm worried about :-p
20:42 < kanzure> I imagine people going through and clicking each link. :(
20:42 < kanzure> And that's just silly.
20:42 < ybit> heh, indeed
20:43 < kanzure> Hm. I'm having trouble remembering what the date was for my microbiology divings in the bio class.
20:43 < kanzure> 2006-12-07 ?
20:43 < kanzure> Hrm.
20:44 < kanzure> http://heybryan.org/school/Biology/
20:44 < kanzure> Once I remember that I can link over to the videos.
20:45 < kanzure> Aha
20:45 < kanzure> http://heybryan.org/school/Biology/3-25-06,%20Protozoa%20Expedition%20Plan%20-%20real.html
20:46 < kanzure> Those aren't my images. Crap.
20:48 < ybit> going back to dr. davison, he invented something recently where all you do is: take two slides of glass, hot glue the glass together on two parallel sides, and then rubberband the plates onto plastic. the plastic should cover one open end. then, grab some specimen such as a baby dragon fly and place it in
20:48 < ybit> i figure everyone could do this, especially aspiring general bio students
20:49 < ybit> i'll draw the designs for it to make it much simple to understand than the description :)
20:49 < ybit> simpler*
20:49 < kanzure> What?
20:50 < kanzure> Diagram?
20:50 < ybit> yeah, i figured
20:50 < kanzure> Seriously though, that's confusing :)
20:50 < ybit> :P
20:54 < kanzure> diy bio group just made boingboing - http://www.boingboing.net/2008/09/17/diy-biohacking-in-th.html
20:59 < ybit> oi willPow3r
21:00 < willPow3r> ello there
21:00 < ybit> hmm, haven't seen Phreedom in a few days, last we talked, he was off to work on circuit boards for his EDM project
21:04 < kanzure> ybit: I haven't seen fenn either
21:04 < kanzure> Are they dead?
21:04 < kanzure> Storm and such?
21:04 < willPow3r> they come on late @ night usually
21:05 < willPow3r> i saw them yesterday
21:05 < kanzure> Yeah, but fenn usually idles.
21:05 < kanzure> Oh well.
21:07 < kanzure> Okay, I need to run. I'm trying to figure where OnNodeClick is specified on matweb.com (particularly I found it on the 'category' listing page). I guess I'll get back to that later.
21:07  * ybit tries to get ahead in chem
21:08 < willPow3r> which chem are you taking?
21:08 < ybit> chem 111 :)
21:09 < willPow3r> general?
21:09 < ybit> indeed
21:09 < ybit> not much catching up to do really
21:10 < willPow3r> i would hope not
21:10 < willPow3r> even though the concepts are easy, theres a lot of them
21:19 < xp_prg> hi all
21:20 < willPow3r> whast up
21:20 < xp_prg> anyone know bioperl stuff here?
21:25 < bkero> oh hey bioperl
21:25 < bkero> I've done some research into biosql, which is part of bioperl/biopython
21:30 < ybit> what do you need help with xp_prg?
21:32 < ybit> if nobody in here can help you, there's always #bioperl 
21:32 < willPow3r> timmy
21:49 < xp_prg> timmy?
21:49 < xp_prg> hahah
21:49 < xp_prg> who are you?
21:51 < willPow3r> master of the known universe
21:52 < willPow3r> you can call me will though
21:52 < xp_prg> oh ok
21:52 < xp_prg> want to teach me some bioperl, I want to learn it bad!
21:52 < xp_prg> I know perl well
21:52 < willPow3r> bkero is your man
21:52 < willPow3r> try #bioperl
21:53 < bkero> yea that
21:53 < xp_prg> bkero want to teach me some bioperl man?
21:54 -!- xp_prg is now known as xp_lunch
21:55 < bkero> xp_lunch: Sorry man, I don't really know that much
21:55 < bkero> Plus I'm at work. O_o
21:56 < xp_lunch> well who does man! :(
21:56 < xp_lunch> ok bbl
22:28 -!- marcel_away is now known as marcel_sleep
22:56 -!- xp_lunch is now known as xp_prg
22:57 < kanzure> Rawr.
22:57 < xp_prg> hi kanzure!
22:57 < kanzure> xp_prg: I've been around bioperl a bit.
22:57 < xp_prg> I liked your post today in diybio
22:57 < kanzure> There's #bioperl? Since when?
22:57 < xp_prg> tell me some stuff please
22:57 < xp_prg> I don't know kanzure
22:58 < kanzure> xp_prg: Which post in diybio?
22:58 < xp_prg> ya
22:58 < kanzure> Which one?
22:58 < kanzure> Btw, I just got back from the bioreactor group meeting. 
22:58 < xp_prg> about lightning talks
22:58 < xp_prg> what is that?
22:58 < xp_prg> where is that?
22:59 < kanzure> Oh, lightning talks happen at the perl user groups.
22:59 < kanzure> http://pm.org/
22:59 < kanzure> http://perl.org/ 
22:59 < kanzure> http://cpan.org/
22:59 < kanzure> More the first than the other two.
22:59 < xp_prg> where you at kanzure?
23:01 < kanzure> UT Austin, Texas
23:15 < kanzure> xp_prg: yeah, so I'll be using git
23:15 < xp_prg> kanzure please help me to brainstorm more synthetic biology problems I can solve with bioperl
23:17 < kanzure> maybe some biofeedback to monitor the chemical contents of a fish tank
23:17 < kanzure> get some electrodes going or something 
23:17 < kanzure> for electrochemistry
23:17 < xp_prg> you would use bioperl for that?
23:18 < xp_prg> lets stick to more software related problems please
23:18 < kanzure> xp_prg: Why software though?
23:18 < xp_prg> cuz I don't have a lab
23:18 < kanzure> ende: I just suggested to xp_prg to make some software to do online monitoring of a fish tank of chemical contents etc. for feedback control systems.
23:18 < kanzure> xp_prg: A fish tank is hardly a whole lab :)
23:18 < xp_prg> well lets brainstorm more software problems please :>
23:18 < kanzure> it's a huge software problem though
23:19 < xp_prg> so finding the best way/place to insert a gene in a plasmide though
23:19 < kanzure> you have to figure out the equivalency of waveforms to chemical contents
23:19 < kanzure> What do you mean the best place?
23:19 < ende> xp_prg, are you just looking for software solutions "for the hell of it" ?
23:19 < xp_prg> ende no to understand synth bio and bio perl so I can do more complex things later
23:19 < ende> xp_prg: generally speaking you can splice a gene anywhere you want into a plasmid 
23:20 < ende> You should take a course in recombinant dna if you can
23:20 < xp_prg> well how about reverse engineering the gene associated with a protein?
23:20 < kanzure> You just need to find a strand in the plasmid's sequence that you can cut out with an endonuclease or exonuclease.
23:20 < kanzure> Reverse engineering what?
23:20 < kanzure> Anyway, that's one of the uses of the synthetic biology circuit creator
23:20 < kanzure> Since it's designing 10,000,000 circuits all at once, it can help fill in the gaps ;-)
23:21 < kanzure> the Marcotte lab that I was working under (by "under" I mean physically - one floor down) was doing whole genome analyses on yeast GRNs
23:21 < kanzure> so what they were doing was figuring out the entire network
23:21 < kanzure> since they could computationally contain the entire genome at once anyway, they could look for the patterns in reactivity and expression and the like
23:21 < xp_prg> kanzure explain to me the concept of network please
23:21 < kanzure> to decypher the reaction pathways
23:21 < kanzure> xp_prg: X triggers Y, Y triggers ...
23:21 < kanzure> Not necessarily linear.
23:21 < xp_prg> via proteins and gene expression?
23:21 < kanzure> Sometimes in tree/bush form where stuff branches
23:21 < kanzure> yeah
23:22 < xp_prg> wow cool!
23:22 < kanzure> http://heybryan.org/genetic-circuits.html has a very simple circuit at the bottom
23:22 < kanzure> But that's something I was making, not something from nature. 
23:22 < xp_prg> cool man!
23:22 < kanzure> gah, where's fenn?
23:23 < willPow3r> yeah bro
23:23 < kanzure> He'll like this one ..
23:23 < kanzure> just got back from the bioreactor subgroup meeting
23:23 < kanzure> I've been tasked with the scale up from a 5 gallon growth chamber to 10,000 gallon bioreactor system
23:23 < ende> more like a network graph i'd imagine
23:23 < kanzure> ende: yep
23:23 < kanzure> ende: especially since specifity isn't ever 100%
23:23 < kanzure> ende: Graphs are some of my favorite mathematical objects as it turns out .. :)
23:24 < kanzure> in one of the, what, three labs that I'm working in, we're doing graph grammars
23:24 < kanzure> for the design of networks or other structures related to manufacturing and design of systems
23:24 < kanzure> in very broad/general terms .. although specifically it's in the mechanical engineering department :p
23:26 < kanzure> Oops, did I kill both of you? :(
23:32 < xp_prg> no, just trying to understand good uses for bioperl with synth bio and not getting specifc answers on that
23:32 < xp_prg> can you assist more with that?
23:35 < kanzure> Assist more on what though?
23:35 < kanzure> Your questions are vague, unfortunately :(
23:35 < kanzure> I mean, go look at the bioperl api, right?
23:40 < xp_prg> no, what practical problems can I solve in synthetic biology with bio perl?
23:40 < xp_prg> help me to think up some please
23:41 < ende> xp_prg, unfortunately I don't think you're going to get very far with this line of questioning.  
23:42 < ende> What is your background?
23:42 < ende> biology?  comp sci?
23:42 < xp_prg> comp sci
23:42 < ende> you have a degree?
23:42 < ende> working on one?  
23:42 < xp_prg> several
23:42 < xp_prg> already done
23:42 < kanzure> Sorry for my lag.
23:43 < ende> um, ok
23:43 < ende> so
23:43 < ende> synthetic biology is no simple domain
23:43 < xp_prg> right
23:43 < ende> it's actually a supergroup of several disciplines
23:43 < ende> bioperl is just a bunch of tools that make the more mundane aspects of bioinformatics computing a bit easier
23:44 < kanzure> :)
23:44 < ende> things like parsing result files, format conversion, etc
23:44 < ende> it's not going to give you the cure to cancer
23:44 < ende> and it's certainly not the first place to be looking for questions to answer
23:45 < ende> in fact I think the wisest among scientists would agree that finding the right questions -is- the hard part.  the answers are easy to come by, once you know what the questions are.
23:45 < kanzure> ende: re: the cure to cancer. You need to do it on an individual level .. so go get a biopsy, blood sample, etc. from the /real/ patient, and then start sequencing the genotype of the cancer - that's the definition of a cancer - so you might be wrong. You might cure (a single) cancer. 
23:45 < ende> I think you're coming at this from the completely wrong direction.
23:45 < xp_prg> actually I know the cure to cancer anyone want to know it?
23:45 < ende> can't wait
23:46 < xp_prg> it has been proven that like 90% of the population is immune to cancer.  A simple blood transfusion will immunize someone who is not immune by transferring over the immune proteins that kill cancer
23:47 < ende> I believe there are a lot of oncologists and immunologists that would look at you weird if they heard you say that
23:48 < xp_prg> this is in the current literature, they are spinning blood to just transfer these immune proteins now
23:48 < ende> for certain kinds of cancers, perhaps
23:48 < ende> but cancer is a plural word
23:48 < ende> or should be considered as such
23:49 < ende> anyway I thought you wanted to talk about synth-bio
23:49 < xp_prg> I do
23:49 < xp_prg> talk way, tell me some common problems I can solve with bio perl please
23:49 < ende> I'm not really sure what you're objective here is, but I think you should first figure that out before asking around for solutions
23:49 < ende> bioperl doesn't really solve anything, I've said this
23:49 < kanzure> on the contrary
23:49 < xp_prg> my objective is to use bio perl for synthetic biology
23:50 < kanzure> it's some useful tools for people to not do hard work any more
23:50 < ende> ok, yes, that is solving something ;)
23:50 < kanzure> I mean, I've seen some people in labs doing some pretty crazy informatics stuffs
23:50 < kanzure> in very hard ways
23:50 < ende> It has helped me solve the problem of wasting my time writing parsers
23:50 < kanzure> how so ?
23:50 < kanzure> What were you writing parsers for?
23:50 < xp_prg> kanzure tell me some of these ways it is being used to reduce labor please
23:50 < ende> 99% of the bioinformatics applications out there
23:50 < kanzure> xp_prg: I believe there's some functions in the bioperl api that help with BLASt searches
23:51 < kanzure> Also, some other connections to databases and the like
23:51 < ybit> i believe xp_prg, you are referencing zheng cui's work, he's been popular lately
23:51 < kanzure> It's been used in the human genome project too. I remember that article on the bioperl.org wiki. Something about integrating the dna sequencer tools together to save it.
23:51 < kanzure> ybit: link?
23:51 < ybit> http://en.wikipedia.org/wiki/Zheng_Cui
23:51 < kanzure> bah
23:51 < kanzure> I should have guessed as much :)
23:51 < ende> anyway, it's been emotional.  peace
23:55 < kanzure> xp_prg: Does that answer your question?
23:55 < kanzure> I think faceface has used it frequently before. Let me see if he's on.
23:55 < kanzure> Apparently he's not.
23:55 < xp_prg> it is not specific enough
23:55 < xp_prg> can you give me some examples of problems that are solved?
23:58 < ybit> xp_prg: this is a good example of what you would be using bioperl for: http://www.bioperl.org/wiki/How_Perl_saved_human_genome
23:58 < xp_prg> cool thanks!
23:59 < kanzure> ybit: Yep, that's the article I was thinking.
23:59 < kanzure> Hm. John left>