00:32:05 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 00:48:07 *** svensko has quit (Remote closed the connection) 00:49:59 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 00:56:06 *** synthase has quit (Read error: 110 (Connection timed out)) 00:56:14 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 01:02:52 *** svensko has quit (Remote closed the connection) 01:04:23 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 01:06:46 *** svensko has quit (Remote closed the connection) 01:08:13 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 01:24:21 *** svensko`laptop has quit (Remote closed the connection) 01:26:42 *** svensko`laptop (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 01:36:21 *** synthase has quit (Connection timed out) 01:36:28 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 01:40:11 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 02:43:40 *** synthase has quit (Connection timed out) 02:43:56 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 03:31:39 *** svensko`laptop has quit (Remote closed the connection) 03:49:24 *** synthase has quit (Read error: 60 (Operation timed out)) 03:54:20 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 05:20:31 flu: how do I find the number of slots on a particular queue? 05:21:06 seems that qsub rarely allocates jobs to all 'nodes', but I was wondering how I could check 05:27:59 seems we have 80 'slots' (qhost | grep tla | wc -l ---> 40, where each of our 'tla' machines has 2 cpu). 05:55:52 *** synthase has quit (Read error: 110 (Connection timed out)) 05:55:55 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 06:21:24 *** kanzure has quit (Success) 06:33:00 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 06:38:16 however, jobs often are not running when we have less than 80 jobs running 07:10:38 *** vimes656 (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 07:22:00 *** toru (n=gioby@137.204.142.219) has joined #bioinformatics 07:35:08 *** bbalajirao1 (n=balaji@203.77.201.162) has joined #bioinformatics 07:35:34 anybody acquainted with Pathway Tools? 07:36:21 not me 07:36:43 My installation is behaving strange. 07:38:43 er... asl? or distro, version, details... 07:38:48 etc. 07:39:39 Pathway Tools v12.0 on Fedora 9 32 bit intel 07:40:00 has the 'strange' only recently started? 07:40:13 it was there from the beginning. 07:40:36 have u a working installation? 07:41:15 no 07:41:19 what does it do? 07:42:25 http://bioinformatics.ai.sri.com/ptools/ 07:50:53 <_dan> "The 64-bit Linux version with all three tiers requires more than 4GB of RAM memory and has a long startup time. We only recommend downloading this version if you are planning to do large-scale comparative analyses." 07:50:57 <_dan> fear 07:51:23 <_dan> it even bundles its own webserver! 07:56:34 more interesting are the pathway prediction and editing tools 07:56:59 databases for different organisms are available for download. 08:07:31 *** synthase has quit (Read error: 110 (Connection timed out)) 08:10:09 *** bbalajirao1 has parted #bioinformatics () 09:16:31 *** bbalajirao1 (n=balaji@203.77.201.162) has joined #bioinformatics 09:24:44 *** highvoltz has quit () 09:28:54 *** bbalajirao1 has parted #bioinformatics () 09:54:00 *** kanzure has quit ("Leaving.") 09:54:12 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 10:00:53 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 10:45:25 win 34 10:45:34 (gah, sorry) 11:12:31 *** toru has quit ("Ex-Chat") 11:15:14 *** vimes656 has quit () 11:16:39 faceface, qconf -sq | grep slots 11:29:30 flu: is that giving me slots currently available? 11:29:54 actually slots has many lines (that don't begin with slot) 11:30:32 40 * 2 nodes (as estimated) 11:30:38 but they are not all being used... 11:30:57 qstat -u me | wc -l = 100 11:31:12 qstat -u me | grep " r " | wc -l = 60 11:31:44 I am only ever subitting 100 jobs at a time, but < 80 are set running at any one point in time 11:31:58 strange 11:36:56 you might have another limit or rule enforcing a cpu or memory usage limit which affects your slot usage. 11:38:09 can you use qmon? It is a little easier to use when tracking down problems like this. It is an X gui app. 11:40:31 OK 11:41:09 sorry, the last one should have beeen... 11:41:19 qstat grep " r " | wc -l = 60 11:41:26 (I am not the only user) 11:41:32 qmon runsup 11:42:07 until I try to use it that is... sigh... nm 11:50:21 *** nbarr (n=nbarr@213.162.13.162) has joined #bioinformatics 12:00:42 *** Pthagg (n=pthag@i-194-106-48-136.freedom2surf.net) has joined #bioinformatics 12:09:27 *** kanzure (i=bryan@dhcp-146-6-213-198.icmb.utexas.edu) has joined #bioinformatics 12:09:44 *** Pthagg has quit (Read error: 104 (Connection reset by peer)) 12:09:54 *** Pthag (n=pthag@i-194-106-48-136.freedom2surf.net) has joined #bioinformatics 12:10:08 so how do I use plot to get somethign like biplot? 12:10:33 Hm? 12:10:41 Standardized response: gnuplot docs 12:21:24 sorry, I meant R 12:21:27 #R 12:30:53 *** Pthagg (n=pthag@i-194-106-48-136.freedom2surf.net) has joined #bioinformatics 12:33:11 *** Pthag has quit (Connection reset by peer) 12:48:39 *** toru_ (n=gioby@137.204.142.219) has joined #bioinformatics 12:48:43 *** Pthagg has quit (Connection timed out) 13:04:52 *** synthase has quit (Read error: 60 (Operation timed out)) 13:09:24 *** faceface has quit ("Bye, and thanks... probably.") 13:13:43 *** toru_ has quit (Remote closed the connection) 13:23:52 *** nbarr has quit ("So Long, and Thanks for All the Fish") 14:22:57 Man, sometimes I submit several thousand jobs at a time. 14:24:03 svensko: I'm in gradschool for computational biology, and I do a bunch of bioinformatics. 14:24:17 I applied to several bioinformatics/compbio programs. 14:34:04 *** Cawiss (n=uzumaki@85.103.138.14) has joined #bioinformatics 14:44:58 *** Cawiss has quit ("Leaving") 16:00:57 *** kanzure has quit ("Leaving.") 16:24:10 *** vimes656 (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 16:39:34 *** pingou has quit (Read error: 110 (Connection timed out)) 16:42:25 *** vimes656 has quit (Read error: 110 (Connection timed out)) 16:50:24 *** highvoltz has quit () 17:26:51 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 17:49:17 *** svensko`laptop (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 17:49:27 wonklab, is it mostly programming? are you taking statistical classes? can you give me a general idea of what it's like? 17:56:35 depends onthe program 17:56:56 and who your advisor is even 17:57:02 or even the department you're doing it in 18:00:05 good points 18:01:38 the field is so frickin huge 18:01:45 plus the related subfields 18:02:27 I mean the evo-devo bioinformatics people work on things that are pretty different from the microarray people, from the data management/library sciences stuff, and from the structural biology stuff 18:14:21 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 18:31:01 *** spaes (n=username@c-24-5-55-238.hsd1.ca.comcast.net) has joined #bioinformatics 18:31:12 *** vimes656 (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 18:47:43 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 19:08:12 svensko: I do a decent amount of programming. 19:08:30 Including myself, we've got 3 serious programmers in our group. 19:08:52 And we have 9 students. 19:09:04 mostly perl i'm assuming? 19:09:12 were you self-taught? what was your undergrad in? 19:09:12 The others write some code, but it's mostly small analysis scripts. 19:09:24 I did CS. 19:09:33 ah so you already had the background 19:09:37 We're not really a perl shop. 19:09:47 Mostly C/C++ and Tcl. 19:10:01 that's what i'm worried about, i'm going into my senior year earning a BS in genetics and i feel very behind in the CS portion 19:10:02 Tcl only because it's what VMD uses. 19:10:27 Once you learn a language or two, it's not so hard picking others up. 19:10:47 that's what i've heard... i'm reading beginning perl right now, and i'll probably attempt python after that 19:11:15 I'm in a program for biophysics and computational biology, and I do MD and structure/sequence bioinformatics. 19:11:25 Lots of analysis on the MD. 19:11:57 A ton of the tools we use are written in C/C++ so it's good to know how to debug, build, and make those projects. 19:12:12 MD? 19:12:18 molecular dynamics 19:12:29 sounds frightening 19:12:39 It's pretty cool. 19:12:42 *** vimes656 has quit () 19:12:43 i'm hoping to go into evolutionary biology myself 19:12:49 Just bunches of atoms bouncing around. 19:12:54 i've never been a fan of physics or math (except for stats) 19:13:20 We write the bioinformatics plugin to VMD. 19:13:36 i see 19:14:01 do you have to do any actual research yourself? any lab time/ 19:14:08 'serious programmers' :) 19:14:16 It handles structure/sequence alignments, runs and imports BLAST stuff, pares down large alignments, lots of coloring for structure and sequence simultaneously. 19:14:33 We're all computational. 19:14:42 * kanzure does computational + lab work 19:14:47 For what it's worth. 19:14:58 But I'm only sitting next door to a bioinformatics lab. I'm actually in an evolutionary engineering lab. 19:15:02 MD requires insane computing. 19:15:06 Yep. 19:15:14 But I think it's worth it when you need it. 19:15:20 kanzure: Who's the bioinformatics prof? 19:15:22 http://heybryan.org/mediawiki/index.php/Comp_chem_linkdump 19:15:26 wonklab: Marcotte. 19:15:33 I did a project with David Hillis and Robin Gutell. 19:15:41 Oh, I interviewed at the Marcotte lab. 19:15:43 I've seen those names thrown around a bit. 19:15:46 Yeah? 19:15:52 I'm working next door, in the Ellington lab. 19:15:53 Also, one of my friends worked there as a computational lab tech. 19:16:05 faceface coauthored with a guy in Marcotte lab 19:16:28 There was a guy, rule30, who used to hang out here, and he might have worked in the Ellington lab as an undergrad. 19:16:48 He also worked for Gutell. 19:16:55 Gutell, I hear, is more of a corporate lab. 19:16:59 wow i'm jealous of you guys :P 19:17:00 i.e., close the doors, turn off the phones, ... 19:17:12 svensko: Don't be. I just showed up and demanded work. I'm not even an undergrad. :( 19:17:32 Gutell's lab was crazy fun when I was there. 19:17:33 how old are you? 19:17:41 So in the greater scheme of things, I probably should be doing dishes or something, but instead I'm running gels, transcriptions, and PDEs of fancy kinetics. 19:17:43 I'll probably visit at the end of July. 19:17:46 svensko: 18. 19:17:51 30 19:17:53 svensko: http://heybryan.org/ is more on me 19:17:53 wow 19:18:01 wonklab is just old because he hasn't gotten a phd yet :) 19:18:03 * kanzure hides 19:18:05 haha 19:18:06 heh 19:18:14 wonklab: I'll be there. Look for the bearded guy walking around. 19:18:16 I worked between undergrad and grad, too. 19:18:16 i thought i was getting a late start at 21 :X 19:18:27 Got the ol' compound interest ball rolling. 19:18:34 Heh. 19:18:46 Bearded guy... 19:18:49 * kanzure has an automated stock program. 19:18:58 Isn't that about half of academia? 19:19:08 yeah :( 19:19:13 his picture is on his page :P 19:19:18 hah 19:56:37 *** clarezoe has quit ("暂离") 20:02:20 bloop 20:12:32 I like combining evolutionary analysis with structure/dynamics analysis. 20:12:54 It gives you some focus while allowing you to make useful generalizations. 20:13:00 it all utimately comes together 20:13:23 Yeah, if evolution has kept it around, it's probably good for something. 20:14:08 We work on protein synthesis in our lab so a lot of our biomolecules are insanely old but decently conserved. 20:14:09 like my project evolved as a porkbarrel to support a datamining and datamodeling project but it was primarily structural and covers evolutionary analysis 20:14:30 "easy but boring" :) 20:15:04 Were you working with scent receptors? 20:15:12 I did a bunch of work on olfactory receptors but a lot of times it was like "SHUT UP ABOUT RHODOPSIN ALREADY" 20:15:26 heh 20:16:13 and now everyone is jizzing over the beta 2 adrenergic receptor being crystallized 20:16:51 which was groundbreaking work, but the initial structure paper was meh 20:17:33 I think it was very political. They knew they had to get something out there (about the crystallization) but they knew nobody would care if they couldn't produce a structure 20:17:59 so they tacked it on by putting it through god knows how many rounds of molecular replacement 20:18:11 (against rhodopsin, of course) 21:06:45 *** synthase has quit (Read error: 110 (Connection timed out)) 21:07:14 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 21:46:11 *** synthase has quit (Read error: 110 (Connection timed out)) 21:46:16 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 22:16:11 *** synthasee (n=synthase@68.63.20.12) has joined #bioinformatics 22:19:12 *** synthase has quit (Connection timed out) 22:56:49 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 23:05:59 *** synthasee has quit (Read error: 110 (Connection timed out)) 23:09:27 ooh, this biopuppy looks interesting