00:08:20 *** ybit has quit (Read error: 110 (Connection timed out)) 00:10:13 *** jm|earth has quit (Read error: 110 (Connection timed out)) 00:31:12 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 00:42:41 *** ybit has quit (Read error: 104 (Connection reset by peer)) 01:06:10 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 01:41:35 *** kanzure (n=bryan@adsl-76-229-131-214.dsl.pltn13.sbcglobal.net) has joined #bioinformatics 01:54:11 *** spaes (n=username@pool-96-235-13-41.pitbpa.east.verizon.net) has joined #bioinformatics 02:25:44 *** spaes has quit ("Leaving.") 04:19:02 o/ 05:06:34 *** synthase has quit (Read error: 60 (Operation timed out)) 05:31:51 *** biopunk has quit () 05:35:31 *** nordlicht (n=nordlich@141.53.70.85) has joined #bioinformatics 06:28:08 *** Narrenschiff_ (n=ritchie@mo-rsmitha21.op.umist.ac.uk) has joined #bioinformatics 07:48:39 *** levitation_ has quit (Connection timed out) 07:55:03 *** Narrenschiff_ is now known as Narrenschiff 08:04:37 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 08:10:48 *** levitation[A] (n=levitati@noorus.aklubi.ee) has joined #bioinformatics 08:53:40 *** platyhelminth (n=platyhel@88-122-30-218.rev.libertysurf.net) has joined #bioinformatics 08:54:44 *** flu has quit (Read error: 110 (Connection timed out)) 08:54:48 hi 08:55:00 i have a problem when i run pymol 08:55:02 python: can't open file '/__init__.py': [Errno 2] No such file or directory 08:55:06 in linux 08:55:23 i am nex in this 08:55:26 new 09:01:27 which OS ? how did you install it ? which command do you try to run ? 09:02:27 as i said linux. what command ? python 09:02:41 i installed it in gentoo (portage) 09:03:07 pymol 09:03:09 sorry 09:04:02 platyhelminth@PLATYHELMINTH ~ $ pymol 09:04:02 python: can't open file '/__init__.py': [Errno 2] No such file or directory 09:05:17 cat /usr/bin/pymol ? 09:06:14 http://pastebin.ca/1094582 09:06:46 echo ${PYMOL_PATH} ? 09:07:43 http://pastebin.ca/1094584 09:08:00 have a look if this file exist /usr/share/doc/pymol/PACKAGING if so reads it ;) 09:08:01 *** flu (n=jogoodma@conger.bio.indiana.edu) has joined #bioinformatics 09:11:52 pingou i dont have it 09:12:20 platyhelminth: basically you are missing the environment variable PYMOL_PATH 09:12:42 locate pymol ? 09:14:03 i can't do locate :) ; but i have a /usr/share/doc/pymol-0.99_rc10 directory 09:14:32 Oo 09:14:46 su -lc 'updatedb' 09:14:49 then locate pymol 09:16:30 " su -lc 'updatedb' " doesn't work, if you realy want i install locate, then i will re-read the gentoo handbook to install it 09:18:45 run updatedb as root 09:29:57 http://rafb.net/p/Yjqa4N48.html 09:30:28 to try just run 09:30:31 python /usr/lib64/python2.5/site-packages/pymol/__init__.py 09:31:21 WHOOA 09:31:27 it launched pymol 09:31:47 thank 09:32:06 :) 09:33:46 in /usr/lib64/python2.5/site-packages/pymol/setup you should have a setup.sh to should help you to create the right pymol launcher 09:45:16 *** nordlicht has quit ("Verlassend") 09:55:56 i wieved it : http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1W76 09:57:04 so it works 09:57:08 bye 09:57:11 *** platyhelminth has parted #bioinformatics ("Leaving") 10:10:52 *** highvoltz has quit () 10:58:52 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 11:05:54 *** craigoz (n=craigo@202.63.56.72) has joined #bioinformatics 11:11:41 *** craigoz has parted #bioinformatics () 12:38:20 *** conley (n=ibcliffo@spode.cs.vt.edu) has joined #bioinformatics 12:39:11 Hey, I'm working on a project that has grahps with many, many nodes, and I want to have an interactive interface where you can click on a cluster of them and examine. 12:39:26 Does anyone have a suggestion of an interactive graph visualization library I could use? 12:43:26 *** clarezoe has quit (Read error: 104 (Connection reset by peer)) 13:00:11 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 13:12:24 conley, do you want a web or a gui app? 13:14:32 you could always use the google map API 13:27:16 <_dan> conley: how many is 'many many'? 13:28:14 <_dan> are we talking 'oustide the bounds of cytoscape?' 13:28:53 _dan: 'many, many' is a lot :D 13:29:11 <_dan> i know, but some people 13:29:29 <_dan> think 'a lot' is 100, some 1000, some 100,000, some 1x10^9 ;) 13:29:54 some even more :D 13:30:46 _dan: so you eat a lot of snails ? 13:31:31 escargot! 13:34:36 <_dan> pingou: no that was our first attempt 13:34:40 <_dan> we are catching some more 13:34:46 <_dan> but we only have 7 at the moment 13:34:47 <_dan> :p 13:34:57 <_dan> in a couple of weeks we will try again 13:35:32 _dan: wait after the rain and go where the grass is high (I know this is quite uncommon in UK)( 13:35:56 _dan: if you know a place where there is nettle have a close look ;) 13:36:17 <_dan> well there's a big grassy field out the back of his house 13:36:19 <_dan> and its wet now 13:36:31 hm ^^ sounds good 13:36:35 <_dan> but he's mainly been collecting from his vegetable patch :) 13:36:45 <_dan> I shall tell him to search further afield :) 13:37:03 depends how fast you want to process the next test ^^ 13:37:18 * pingou tries to note somewhere where he could remember to get the recipe 13:37:37 <_dan> :) 13:42:28 *** faceface has quit (Read error: 104 (Connection reset by peer)) 13:42:51 *** faceface (n=dbolser@75.126.74.92) has joined #bioinformatics 13:53:31 *** kanzure has quit (Remote closed the connection) 14:59:10 Oh, sorry, I'm thinking like 10,000, but I imagine when you pick these libraries, beyond 500 is big 14:59:40 flu: gui app would be good 15:16:22 any particular language? 15:16:55 I'm wondering if maybe you could use R and a custom extension to do what you need. 15:25:44 _dan's suggestion of cytoscape is also good depending on the exact nature of your nodes. I've seen it scale past 10,000 so that shouldn't be a problem. 15:27:02 I would prefer not java 15:27:16 and insist on not C# 15:29:36 I wouldn't discount cytoscape just because it is java. You may be able to use it without writing any java code at all. 15:29:38 http://www.cytoscape.org/ 15:30:19 well, I can write java, I just have religious dogma against anything javaish 15:31:49 ok, but you may end up making your life much harder by sticking to that. 15:32:49 yea, I know :( 15:33:00 you may want to check out graphviz but it is a very low level graph generator. You would have to write a lot of code on top of it to do what you want. 15:34:53 Yea, I have 15:35:04 My prof has a something on top called geewhiz 15:35:21 but I'm guessing it doesn't have a ton of functionality 15:36:05 I'd say R with extensions or cytoscape are probably your best bet. 15:36:28 ok, I'm checking them out 15:38:18 Have you ever heard of networkx? 17:08:49 *** bruno_ (n=bruno@190.191.166.114) has joined #bioinformatics 17:38:47 *** Narrenschiff has quit () 17:52:00 *** biopunk (n=p@h164n2c1o261.bredband.skanova.com) has joined #bioinformatics 17:55:00 *** highvoltz has quit () 18:16:14 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 18:20:41 *** clarezoe has quit (Read error: 113 (No route to host)) 18:30:38 *** Elatt (n=bleh@75-134-87-246.static.aldl.mi.charter.com) has joined #bioinformatics 18:46:24 *** Elatt has quit (Connection reset by peer) 18:50:43 *** Elatt (n=bleh@75-134-87-246.static.aldl.mi.charter.com) has joined #bioinformatics 18:56:04 *** Elatt has quit (Connection reset by peer) 19:42:52 *** ybit has quit (Connection timed out) 19:52:59 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 19:56:34 *** pingou_ (n=pingou@AMontsouris-158-1-9-119.w92-128.abo.wanadoo.fr) has joined #bioinformatics 20:07:04 *** pingou has quit (Read error: 110 (Connection timed out)) 20:09:33 *** ybit has quit (Connection timed out) 21:32:22 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 21:48:29 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 23:02:38 *** bruno_ has quit (Read error: 110 (Connection timed out)) 23:35:54 *** ybit has quit ("Konversation terminated!")