00:25:43 *** ybit has quit (Remote closed the connection) 00:27:11 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 00:31:31 *** ybit has quit (Read error: 104 (Connection reset by peer)) 00:31:40 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 01:26:25 *** synthase has quit (Read error: 110 (Connection timed out)) 01:26:44 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 01:54:55 *** mercutio22 has quit () 02:06:08 *** synthase has quit (Connection timed out) 02:06:13 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 02:23:12 *** ybit has quit (Remote closed the connection) 02:23:22 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 03:17:34 *** ybit has quit (Remote closed the connection) 03:17:47 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 03:28:11 *** pingou__ (n=pierrey@AMontsouris-152-1-80-163.w83-202.abo.wanadoo.fr) has joined #bioinformatics 03:28:19 *** _dan_ (n=dan@shady.org) has joined #bioinformatics 03:28:19 *** _dan has quit (Read error: 104 (Connection reset by peer)) 03:28:29 *** _dan_ is now known as _dan 03:40:07 *** pingou_ has quit (Read error: 110 (Connection timed out)) 03:42:30 *** Splicer has quit () 04:03:19 *** kanzure has quit (Remote closed the connection) 04:25:39 *** pingou__ is now known as pingou_laptop 04:25:47 *** pingou_laptop is now known as pingou_fix 04:30:54 hi 04:52:30 *** pingou_fix has quit ("leaving") 04:55:54 *** pingou_ (n=pingou@AMontsouris-152-1-80-163.w83-202.abo.wanadoo.fr) has joined #bioinformatics 05:19:25 *** synthase has quit (Read error: 110 (Connection timed out)) 05:19:40 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 05:58:19 *** pingou_ has quit ("leaving") 05:58:31 *** pingou_ (n=pingou@AMontsouris-152-1-80-163.w83-202.abo.wanadoo.fr) has joined #bioinformatics 05:59:06 *** pingou_ has quit (Client Quit) 06:22:16 *** pingou (n=pingou@AMontsouris-152-1-80-163.w83-202.abo.wanadoo.fr) has joined #bioinformatics 06:57:10 *** synthase has quit (Read error: 110 (Connection timed out)) 07:26:31 *** toru (n=gioby@137.204.142.219) has joined #bioinformatics 08:36:40 the most beautiful thing in the world is: compiz 09:18:25 <_dan> it is quite pretty 09:45:11 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 09:50:26 *** highvoltz has quit () 10:55:02 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 10:58:34 I agree but I've found it not very practical in my day to day use. 10:59:03 I first thought that some of the features would make life easier but other things cropped up that made it more painful 10:59:18 e.g. the huge delay when resizing windows 11:16:48 flu: it depends on the hardware you are using 11:17:13 I don't use compiz on my laptop either, for example, because it is too slow 11:17:30 but now I have a new computer... and it is very cool! :) 11:32:58 *** synthase has quit (Read error: 110 (Connection timed out)) 11:33:25 *** clarezoe has quit (Read error: 104 (Connection reset by peer)) 11:34:33 this was on a dual quad core cpu with a fairly new nvidia card using the opensuse version of compiz 11:35:02 I also had problems with it locking up after extended use 11:35:28 maybe its gotten better since I last tried it (~Jan I think) 11:37:51 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 11:58:02 flu: yeah, try updating it 12:00:45 I'm waiting until I have time to upgrade to opensuse 11 as it built into the standard distribution now, so it should be a bit more stable "in theory". 12:13:48 *** Pthag (n=pthag@i-194-106-48-136.freedom2surf.net) has joined #bioinformatics 12:18:30 *** Pthagg (n=pthag@i-194-106-48-136.freedom2surf.net) has joined #bioinformatics 12:19:47 *** Pthag has quit (Remote closed the connection) 12:39:58 *** Pthagg has quit (Read error: 110 (Connection timed out)) 12:54:56 *** Pthag (n=pthag@i-194-106-48-136.freedom2surf.net) has joined #bioinformatics 13:13:01 *** Pthag has quit (Connection timed out) 13:51:20 *** toru has quit ("Ex-Chat") 13:56:11 faceface: You around? 13:56:23 I'm doing some neuroinformatics. 13:56:34 I want to do brainal geotagging, but there's no standardized reference model and expecting one to emerge is stupid. 13:56:38 What's my alternative ? 13:56:58 I'm considering the cases of whole gene expression studies like reactome.org perhaps? 14:06:51 *** oss (n=hb@125.211.159.88) has joined #bioinformatics 14:06:56 *** cow_2001 (i=nobody@bzq-79-176-157-220.red.bezeqint.net) has joined #bioinformatics 14:06:59 woah. 14:07:02 Hello, is there any program to parse the NCBI BLAST output result? 14:07:09 I mean program, not perl modules. 14:07:40 *** cow_2001 has parted #bioinformatics () 14:07:54 why don't you want perl modules? 14:08:30 I'm a newbie in perl. 14:08:56 So any suggestion? 14:09:09 the bioperl modules :-) 14:09:47 Okay, :) Laugh at me. :) 14:10:10 I really need help. I hopw I can get some package to do that. 14:10:15 seriously, any of the bio* folks have blast parser modules. bioperl, biopython, biojava 14:10:36 the bioperl module is the best in my opinion. 14:10:45 Yep, I know. Anyway, it's difficult for me. 14:11:40 which ncbi blast format are you trying to parse, xml, text, asn? 14:12:13 did you try a search for "ncbi blast parser" there seem to be some useful hits there. 14:12:39 just text. I also try to search but nothing, 14:15:58 http://bioinfo.iq.usp.br/zerg/ 14:17:02 <_dan> everyone should write their own blast results parser at least once 14:17:04 you won't find may blast parsing applications, mostly libraries. The reason being that everyone usually wants to do their own thing with blast results. That means tweaking the actions taken when a parser encounters various fields. 14:17:11 <_dan> you can't be a ioinformatician until you have ;) 14:17:11 s/may/many/ 14:17:21 * flu seconds _dan 14:17:36 I knew this, it's a library. 14:18:35 <_dan> http://www.nature.com/nature/journal/v417/n6885/full/417119a.html 14:18:55 <_dan> last line of "Bio* projects reduce the pain" 14:18:56 <_dan> ;) 14:19:55 Seems that. So I ahve to reqrite perl script to do that, 14:20:24 http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FASTA_reports_with_Search_and_SearchIO 14:22:55 personally, I prefer the XML formatted output because it is a little more sane than the standard text output. That and I use XSLT to generate HTML reports from them. 14:23:38 Yes, right to do that. 14:29:09 there are some things that aren't as sane as the text format though...like the way they implemented the subject/hit alignment 14:31:06 Okay. Thank you, I'll try to write a script. 14:31:21 *** oss has quit ("Leaving") 14:34:05 yeah if you have a choice between XML or regular plain text, go with the XML 14:34:21 MultiSeq has a frontend for BLAST. 14:34:28 Oh, he's gone. 14:35:21 Anyway, we can take BLAST results and import all the sequences into an alignment editor. 14:35:27 otherwise you'll find yourself rewriting your own parser 14:35:33 yeah 14:35:34 Even load structures if they exist. 14:36:09 And you can filter by all sorts of stuff like only get Bacteria, or only get sequences below some e-score. 14:36:57 I wonder if he had a homework assignment or if this was a legit request. 14:37:11 nothing wrong with a homework assignment 14:38:03 no but asking for a program to copy or borrow from for his homework assignment would be 14:38:42 his specific request for a program versus a library had me wondering about that. 14:38:55 his or her 14:41:56 well reading library code is a pain 14:42:14 I try to avoid them if possible 14:42:22 especially perl modules ugh 14:48:31 *** rogers (i=rogers@bling.bling.org) has joined #bioinformatics 14:49:03 *** highvoltz has quit (Remote closed the connection) 15:06:44 *** rogers has quit () 15:06:55 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 15:40:42 *** Cawiss (n=uzumaki@85.103.138.14) has joined #bioinformatics 17:39:25 *** highvoltz has quit () 17:49:11 *** Cawiss has quit ("Leaving") 18:06:25 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 18:31:13 *** Pthag (n=pthag@i-194-106-48-136.freedom2surf.net) has joined #bioinformatics 18:41:42 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 19:33:52 *** Pthag has quit (Connection timed out) 21:07:16 *** kanzure has quit (Remote closed the connection) 22:38:55 anyone here ever gone to grad school for bioinformatics? 22:44:02 *** CrimsonScythe has quit (Read error: 110 (Connection timed out)) 22:47:29 *** CrimsonScythe (n=CrimsonS@unaffiliated/crimsonscythe) has joined #bioinformatics