| --- Day changed Wed Sep 17 2008 | ||
| kanzure | Where's fenn? | 00:02 |
|---|---|---|
| ybit | i need a wearable computer | 00:03 |
| 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 | 00:04 |
| 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 | 00:05 |
| kanzure | http://www.osdd.net/ open source drug discovery | 02:01 |
| * bkero wonders how people afford labs without big fat pharma budgets. | 02:03 | |
| bkero | Or university budgets :P | 02:03 |
| 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 | 02:07 |
| bkero | I thought their overflow of CS students just turned into excess Java programmers | 02:08 |
| kanzure | Oh god. | 02:08 |
| kanzure | Open source java bean discovery | 02:09 |
| bkero | More like a bunch of useless progammers | 02:11 |
| 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. | 02:12 |
| bkero | The US would be on it's way to the third world? | 02:13 |
| bkero | Oh wait... | 02:13 |
| kanzure | Hrm. Sounds familiar. | 02:13 |
| 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 | 02:15 |
| 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. | 02:16 |
| ybit | why the hrming? | 02:18 |
| kanzure | Well, he works at Intel. | 02:19 |
| kanzure | If intel has no money, then | 02:19 |
| 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. | 02:20 |
| kanzure | WTF | 02:25 |
| kanzure | http://sysborgtb.osdd.net/bin/view/Main/TWikiUsers | 02:25 |
| kanzure | You can count this list on your fingers | 02:25 |
| bkero | DUDE | 02:27 |
| bkero | Look at the dates | 02:27 |
| bkero | That's not too bad for less than a month | 02:27 |
| 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 | 02:28 |
| 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 | 02:29 |
| 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 | 02:31 |
| ybit | printer graphene circuits | 02:32 |
| kanzure | oh crap | 02:32 |
| bkero | http://oregonstate.edu/dept/ncs/newsarch/2006/Mar06/circuit.htm :P | 02:33 |
| 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, | 02:38 |
| 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 | 02:39 |
| 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 | 02:45 |
| ybit | i have a linux live cd if you would like to use it ;) | 02:48 |
| 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 | 02:49 |
| 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 .. | 02:50 |
| 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 | 02:51 |
| bkero | Are you sure you're not a liberal arts major? | 02:52 |
| 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 | 02:53 |
| 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. ' | 02:54 |
| 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 | 02:55 |
| 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. | 02:57 |
| kanzure | hey, wait a sec | 03:00 |
| 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 | 03:01 |
| bkero | zombify | 03:02 |
| kanzure | What? | 03:02 |
| 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? | 03:03 |
| kanzure | http://heybryan.org/projects/autoscholar/autoreader.pl.txt | 03:05 |
| kanzure | Bah. | 03:54 |
| 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. | 04:57 |
| kanzure | Postdoctoral positions. | 04:58 |
| bkero | bah | 04:58 |
| bkero | I'm basically postdoctoral | 04:58 |
| kanzure | Huh? | 05:00 |
| kanzure | You don't even have an undergrad degree, I thought :) | 05:00 |
| 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 | 05:01 |
| 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. :) | 05:02 |
| -!- johnhitt is now known as new_nickname_her | 12:45 | |
| -!- new_nickname_her is now known as JohnH | 12:45 | |
| kanzure__ | Hi all. | 16:35 |
| Nofaris | Hi kanzure | 16:45 |
| Nofaris | What are you thinking about? | 16:45 |
| 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? | 16:46 |
| 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. | 16:48 |
| 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 | 17:02 |
| 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 | 17:03 |
| 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 | 17:05 |
| kanzure__ | Hm. gcc is coming up with a new plugin architecture | 17:09 |
| kanzure__ | http://immigration.gov.ph uses debian :) | 17:11 |
| 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 | 17:12 |
| kanzure__ | md5 reverse lookup http://benramsey.com/code/source.php?file=md5.php | 17:16 |
| kanzure | Hi all. | 19:04 |
| bkero | Afternoon | 19:10 |
| kanzure | Anything new? | 19:10 |
| kanzure | Hm. Looks like there's a meeting with the local bioreactor professor at 430. | 19:11 |
| 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) | 19:12 |
| kanzure | ASM mirror complete. Downloaded 2.03 GB in 207553 files. | 19:56 |
| kanzure | http://heybryan.org/~bbishop/docs/matweb/wtf.html Search the source code for 'WTF' to see something interesting. | 20:05 |
| kanzure | Hey ybit. Anything new? | 20:16 |
| kanzure | Heh, somebody in #biology is trying to identify some cryoelectroscopy images. IIRC, it's kind of like freeze fracture but more awesome. | 20:20 |
| kanzure | http://img47.imageshack.us/my.php?image=imageqm0.jpg | 20:22 |
| kanzure | Hey elias`. | 20:26 |
| 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 | 20:27 |
| 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 | 20:28 |
| ybit | it's nothing interesting | 20:29 |
| ybit | i get to work with some bio professor next semester studying tardigrades | 20:29 |
| ybit | maybe we will shift into discovering just what the mysterious object in the sky is that every news outlet keeps blabbing about | 20:30 |
| 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 | 20:31 |
| 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. | 20:32 |
| 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... | 20:33 |
| kanzure | link? | 20:35 |
| ybit | http://www.youtube.com/user/pgdavison8 | 20:37 |
| kanzure | ybit: I have some videos on my server if you want to take a look. | 20:40 |
| 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. | 20:41 |
| 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 | 20:42 |
| 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. | 20:43 |
| kanzure | http://heybryan.org/school/Biology/ | 20:44 |
| kanzure | Once I remember that I can link over to the videos. | 20:44 |
| kanzure | Aha | 20:45 |
| kanzure | http://heybryan.org/school/Biology/3-25-06,%20Protozoa%20Expedition%20Plan%20-%20real.html | 20:45 |
| kanzure | Those aren't my images. Crap. | 20:46 |
| 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 | 20:48 |
| 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? | 20:49 |
| kanzure | Diagram? | 20:50 |
| ybit | yeah, i figured | 20:50 |
| kanzure | Seriously though, that's confusing :) | 20:50 |
| ybit | :P | 20:50 |
| kanzure | diy bio group just made boingboing - http://www.boingboing.net/2008/09/17/diy-biohacking-in-th.html | 20:54 |
| ybit | oi willPow3r | 20:59 |
| 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 | 21:00 |
| 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 | 21:04 |
| willPow3r | i saw them yesterday | 21:05 |
| kanzure | Yeah, but fenn usually idles. | 21:05 |
| kanzure | Oh well. | 21:05 |
| 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 | 21:07 | |
| willPow3r | which chem are you taking? | 21:08 |
| ybit | chem 111 :) | 21:08 |
| willPow3r | general? | 21:09 |
| ybit | indeed | 21:09 |
| ybit | not much catching up to do really | 21:09 |
| willPow3r | i would hope not | 21:10 |
| willPow3r | even though the concepts are easy, theres a lot of them | 21:10 |
| xp_prg | hi all | 21:19 |
| willPow3r | whast up | 21:20 |
| xp_prg | anyone know bioperl stuff here? | 21:20 |
| bkero | oh hey bioperl | 21:25 |
| bkero | I've done some research into biosql, which is part of bioperl/biopython | 21:25 |
| ybit | what do you need help with xp_prg? | 21:30 |
| ybit | if nobody in here can help you, there's always #bioperl | 21:32 |
| willPow3r | timmy | 21:32 |
| xp_prg | timmy? | 21:49 |
| xp_prg | hahah | 21:49 |
| xp_prg | who are you? | 21:49 |
| willPow3r | master of the known universe | 21:51 |
| 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 | 21:52 |
| bkero | yea that | 21:53 |
| xp_prg | bkero want to teach me some bioperl man? | 21:53 |
| -!- xp_prg is now known as xp_lunch | 21:54 | |
| bkero | xp_lunch: Sorry man, I don't really know that much | 21:55 |
| bkero | Plus I'm at work. O_o | 21:55 |
| xp_lunch | well who does man! :( | 21:56 |
| xp_lunch | ok bbl | 21:56 |
| -!- marcel_away is now known as marcel_sleep | 22:28 | |
| -!- xp_lunch is now known as xp_prg | 22:56 | |
| 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 | 22:57 |
| 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? | 22:58 |
| 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? | 22:59 |
| kanzure | UT Austin, Texas | 23:01 |
| 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 | 23:15 |
| 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? | 23:17 |
| 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 | 23:18 |
| 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 | 23:19 |
| 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 ;-) | 23:20 |
| 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 | 23:21 |
| 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? | 23:22 |
| 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 .. :) | 23:23 |
| 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 | 23:24 |
| kanzure | Oops, did I kill both of you? :( | 23:26 |
| 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? | 23:32 |
| 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? | 23:35 |
| 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 | 23:40 |
| ende | xp_prg, unfortunately I don't think you're going to get very far with this line of questioning. | 23:41 |
| 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. | 23:42 |
| 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 | 23:43 |
| 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 | 23:44 |
| 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 | 23:45 |
| 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 | 23:46 |
| ende | I believe there are a lot of oncologists and immunologists that would look at you weird if they heard you say that | 23:47 |
| 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 | 23:48 |
| 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 | 23:49 |
| 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 | 23:50 |
| 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 | 23:51 |
| 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? | 23:55 |
| 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! | 23:58 |
| kanzure | ybit: Yep, that's the article I was thinking. | 23:59 |
| kanzure | Hm. John left> | 23:59 |
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