00:57:37 *** CowbertD1 (n=cowbert@c2.8d.5646.static.theplanet.com) has joined #bioinformatics 00:57:48 *** CowbertDH has quit (Read error: 54 (Connection reset by peer)) 01:22:51 *** Splicer has quit (Read error: 110 (Connection timed out)) 01:59:04 *** kanzure has quit ("Leaving.") 01:59:22 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 02:06:05 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 02:06:36 *** bbalajirao has parted #bioinformatics () 03:40:25 *** qsun (n=user@d58-106-235-8.bla3.nsw.optusnet.com.au) has joined #bioinformatics 03:55:02 *** svensko`laptop has quit (Remote closed the connection) 04:13:18 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 04:13:38 *** bbalajirao has parted #bioinformatics () 04:29:22 *** pingou (n=pingou@AMontsouris-152-1-72-43.w83-202.abo.wanadoo.fr) has joined #bioinformatics 04:35:46 *** qsun has quit (Read error: 113 (No route to host)) 04:36:18 *** qsun (n=user@d58-106-209-188.bla3.nsw.optusnet.com.au) has joined #bioinformatics 06:20:24 *** synthase has quit (Read error: 110 (Connection timed out)) 07:16:00 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 07:16:13 *** bbalajirao has parted #bioinformatics () 07:26:38 *** jm|earth (n=jm@p57B9CD8D.dip.t-dialin.net) has joined #bioinformatics 07:34:12 *** vimes656 (n=vimes656@181.Red-80-36-242.staticIP.rima-tde.net) has joined #bioinformatics 08:20:40 *** bbalajirao (n=balaji@203.77.201.162) has joined #bioinformatics 08:20:50 *** bbalajirao has parted #bioinformatics () 08:24:56 *** qsun has quit ("Leaving") 09:59:30 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 10:03:38 *** highvoltz has quit () 10:12:57 *** oss (n=hb@60.219.209.61) has joined #bioinformatics 10:15:05 Is there any good software for annotation? I want to so with soybean genes. 10:21:38 <_dan> annotation of what? 10:21:54 genes 10:22:04 <_dan> with what information? 10:22:06 I use Linux. 10:22:15 I mean soybean genes. 10:22:16 <_dan> GO terms? BLAST identities? 10:22:34 <_dan> I thought the soybean genome was pretty well annotated already :) 10:22:50 NCBI BLAST identities 10:23:06 webservices ? taverna ? 10:23:10 Well, I could learn it more if I could. 10:23:26 <_dan> oss: tell us a bit more detail abnout what you're trying todo 10:24:14 okay. I'm a system administrator only, my members need a annotation software for their work. 10:24:38 <_dan> yes, ok, but there are any number of things you can annotate a gene with 10:24:40 emboss does that ? 10:24:49 Seems not. 10:25:05 I know Apollo and Ariemis. 10:25:40 <_dan> artemis is good for visualisation and annotation 10:26:06 <_dan> gbrowse might fit the bill too 10:26:28 * pingou should have a closer look to gbrowse 10:26:37 <_dan> http://soybeangenome.siu.edu/cgi-bin/gbrowse/soybeanv4 10:26:45 <_dan> there's a gbrowse installation over soybean 10:27:04 Artemis is okay? 10:27:24 <_dan> its fine if you want a java desktop app yeah 10:27:36 <_dan> people use artemis quite productively here 10:30:38 okay, I got it. And I have a BLAST output results, the artemis can read it? 10:31:19 <_dan> yeah 10:31:42 <_dan> artemis is designed to overlay blast information iirc 10:32:13 Okay, any way, is there a parallel bio-software list on the web? 10:32:54 sort of on the biolinux project 10:33:54 I can find them in its site? 10:35:05 <_dan> parallel as in MPI/HPC/batch job stuff? 10:35:44 <_dan> i don't know of a list of software 10:35:55 <_dan> but this mailing list is pretty good: http://www.bioinformatics.org/lists/bioclusters 10:36:22 I mean MPI/PVM/HPC programs. 10:36:23 <_dan> <- does a lot of sysadmin btw 10:36:39 <_dan> oss: I don't think you will find a list 10:36:44 <_dan> BLAST comes in an MPI aware form 10:36:55 <_dan> as do other packages, but not consistently 10:37:05 <_dan> often things are 'embarassingly parallel' 10:37:13 <_dan> so just batching them up does the job 10:37:28 Okay, I understand your words. 10:37:40 Have you ever used CMap? 10:39:09 <_dan> no.. the knowledge representation software? 10:40:56 *** svensko has quit (Remote closed the connection) 10:44:08 Well, members need it. :) 10:44:31 Do you use bioperl? 10:44:42 <_dan> never seen it beofore, it looks like the child of a marriage of mindmapping and ontologies 10:44:46 <_dan> I have used bioperl yes 10:45:44 What do you think of it? 10:45:55 <_dan> its got a lot easier to install recently 10:46:01 <_dan> its fine - it mostly works 10:46:15 <_dan> you need to use the 'unstable' release for just about anything 10:46:31 <_dan> the actual release is not well maintained for bug fixes 10:46:56 <_dan> I don't follow the mailing list anymore, but that was the consensus when I stopped :) 10:47:17 I see. Do you work round by HPC? 10:51:01 <_dan> sort of, I run a 2000 CPU campus grid and have 3 clusters ranging from 32-96 CPUs 10:51:21 * pingou goes to work for _dan :D 10:51:25 <_dan> :) 10:51:55 So great. What resource management software do you use? 10:52:40 <_dan> for job scheduling? Condor mainly, SGE if I must 10:53:20 <_dan> I've previously used OpenPBD 10:53:23 <_dan> PBS 10:53:24 <_dan> even 10:53:29 <_dan> but didn't like it 10:53:33 SGE, I use SGE now. 10:53:47 I should learn more experience from you. 10:54:38 You set up parallel environment? 10:56:27 <_dan> MPI, yes and that integrates quite well with Condor 10:56:57 <_dan> although.. it's rare we have any use for it from the biologists 10:57:04 <_dan> its there if they need it :) 10:57:31 I have a problem when I use SGE. 10:57:40 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 10:57:47 Could SGE improve efficiency? 10:58:13 <_dan> I don't know.. I just find it difficult to maintain but I suspect it's just lack of familiarity 10:59:12 Yes, seems that. My cluster is small, in fact. 10:59:21 5 nodes with 20 CPU. 11:01:34 What skills should a bio-bluster sysadmin grasp? 11:02:06 <_dan> to be honest, some familiarisation with the tools would probably be more important than worrying too much about the infrastructure 11:02:23 <_dan> I'm a biologist by training, the sysadmin just landed in my lap because I knew Linux 11:03:00 <_dan> keeping things up to date is a challenge 11:03:17 <_dan> giving users realistic expectations of what the compute will do for them 11:03:31 Yep, I write a shell script to update database from website....... 11:03:42 <_dan> beacuse we're scaling up I'm having to deal with things I didn't used to (TB RAID, LVM etc etc) 11:03:52 Thank you very much. 11:04:17 <_dan> thats ok, we dont get too many sysadmins here :) 11:04:30 Anyway, could you tell me your email add? I hope when I have problem I can ask you for help. 11:04:39 If you don't mind. 11:04:40 :) 11:05:52 <_dan> sure d.c.swan@ncl.ac.uk 11:06:24 <_dan> I've been doing sysadmin for biosciences since my PhD in 1995, so I hope I will be able to help ;) 11:06:40 ^^ 11:06:55 You are so kind, in fact I'm only a bachelor in China. 11:07:11 So you could realize that my poor English. 11:07:34 <_dan> its ok, it's a very international channel here :) 11:08:45 Yes, I also maintain the cluster for the lab, anyway, I know a little perl. 11:08:59 So I think it would be bad for me, right? 11:09:38 what would be ? perl ? 11:09:53 <_dan> Perl is a good enough solution for most bio tasks 11:10:08 Yes, I can just write simple perl codes and I always use shell and sed. 11:10:27 perl is I think the most widely used language in bioinfo 11:10:28 <_dan> although the peopple who prefer Python will tell you that Python is the best choice these days, or even Ruby 11:10:36 <_dan> but there's so much legacy perl code in bioinformatics 11:11:26 and there starts the usual flame on the different programming language ^^ 11:11:35 I see, so I should learn perl well. 11:12:57 <_dan> learn it well enough to do what you need to do :) 11:13:20 I believe you. :) 11:13:31 the best programming languages is anyway the one with which you feel the more confortable 11:13:39 Thank you really. 11:13:41 and the one with which you can the best work 11:16:34 Yes, I'll try. Dan, can you help me to find some good guide to install CMap? 11:16:40 It's based on website. 11:18:17 <_dan> just to confirm we're talking about: http://cmap.ihmc.us/download/ 11:18:19 <_dan> ? 11:18:58 looks like a sort of webservices based api no ? 11:19:46 Hmm, http://gomd.org/ 11:20:03 you can find Cmap, that's what I say. 11:20:31 But I can't find a good guide, I suppose that you can help me. 11:20:31 This site is under construction. -> http://gomd.org/ 11:20:46 <_dan> ITYM http://gmod.org ? 11:21:18 <_dan> ahh 11:21:22 <_dan> ok different Cmap :) 11:21:41 yes, sorry for my error. 11:28:36 <_dan> the INSTALL.pod for Cmap doesn't look too bad once you have installed the prerequesites 11:29:21 Yes, but when I want to add my own data, it seems not good. 11:29:59 <_dan> is it working ok with the demo data? 11:30:37 Yes, work well. 11:31:58 <_dan> you have read the ADMINISTRATION.pod? 11:33:15 A little, you know my English level. :( 11:33:24 <_dan> yeah I appreciate it's long and complex 11:33:34 So I hope I can get a step by step guide. 11:35:31 <_dan> might be better off asking on the mailing list as I'm not familiar with Cmap - I've looked online and the only 'guide' I can see is a pay per view article on Wiley Interscience 11:48:15 Okay, thank you very much~ 11:48:30 I will try to join the mailing list. 11:49:47 I think that a bio sysasmin is really hard. 11:50:25 <_dan> its hard because you end up dealing with lots of really badly written software and documentation ;) 11:51:06 Hahaha, yes. 11:51:18 Do you have an icq? 11:51:33 <_dan> icq is not too popular here 11:51:53 <_dan> so no - sorry I don't 11:52:54 Not at all. Are you always in this channel? 11:53:11 yes even when he is not there ^^ 11:53:31 <_dan> if it's in working UK hours I might be here :) 11:54:10 Okay, it's 1:56 PM in UK? 11:54:41 <_dan> 2:56 PM 11:54:50 <_dan> summertime clock - not GMT 11:57:30 Ahh, okay. 12:05:41 Thank you very much today~ 12:05:53 <_dan> no problem :) 12:06:03 And I hope we can make a long time relationship~ :) 12:06:23 You can call me Amy. <- My english name. 12:06:43 12:06:46 My add. 12:07:37 <_dan> ah gmail, I do everything in gmail :) 12:08:12 yes, my favorite. 12:08:58 * pingou solved the pb in another way :) 12:23:48 *** craigoz has quit ("Leaving.") 12:28:15 Dan, it's time to go now. 12:28:20 Thank you today~ 12:28:22 Really. 12:30:52 Bye bye~ 12:30:56 *** oss has parted #bioinformatics ("Leaving") 13:20:38 *** synthase has quit (Connection timed out) 14:21:47 omg a girl! 14:21:50 on IRC! 14:22:02 aww she left 14:23:38 *** CowbertD1 is now known as CowbertDH 14:43:20 CowbertDH: Exactly my thoughts. 14:53:29 lol 15:03:01 *** vimes656 has quit () 17:06:43 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 17:12:05 *** Splicer (n=p@h133n2c1o261.bredband.skanova.com) has joined #bioinformatics 17:41:17 *** svensko has quit (Remote closed the connection) 17:46:47 *** highvoltz has quit () 18:07:58 *** highvoltz (i=rogers@66.225.200.177) has joined #bioinformatics 19:08:55 *** mercutio22 (n=htorres@c9515180.virtua.com.br) has joined #bioinformatics 20:17:16 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 21:47:24 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 21:59:13 *** jm|earth has quit (Read error: 110 (Connection timed out)) 22:11:01 *** svensko has quit (Read error: 104 (Connection reset by peer)) 22:12:20 *** svensko (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 22:12:40 *** svensko`laptop (n=svensko@cpe-071-068-240-183.sc.res.rr.com) has joined #bioinformatics 23:21:44 *** highvoltz has quit ()