00:34:45 *** ybit (n=u1@unaffiliated/ybit) has joined #bioinformatics 00:36:54 *** synthase (n=synthase@69.254.170.145) has joined #bioinformatics 00:46:39 *** synthasee has quit (Connection timed out) 02:10:46 *** synthasee (n=synthase@69.254.170.145) has joined #bioinformatics 02:20:46 *** synthase has quit (Connection timed out) 03:51:24 *** h2i (n=u1@unaffiliated/ybit) has joined #bioinformatics 03:54:31 *** ybit has quit (Read error: 110 (Connection timed out)) 04:02:55 *** h2i has quit (Read error: 104 (Connection reset by peer)) 04:16:03 *** sparta has quit (Remote closed the connection) 04:18:41 *** kanzure has quit ("Leaving.") 04:43:26 *** Cawiss (n=uzumaki@85.100.84.94) has joined #bioinformatics 04:50:18 *** Cawiss has quit ("Leaving") 05:44:31 *** ajai (n=jason@maggie.csse.unimelb.edu.au) has joined #bioinformatics 05:48:14 *** spaes has quit ("Leaving.") 06:02:46 *** sparta (i=ca36b00b@gateway/web/ajax/mibbit.com/x-1dd94ae78000c30d) has joined #bioinformatics 06:21:41 *** faceface has parted #bioinformatics () 06:57:57 *** faceface (n=chatzill@bioinformatics.org) has joined #bioinformatics 07:26:18 *** toru (n=gioby@137.204.142.89) has joined #bioinformatics 07:32:11 *** toru has quit (Read error: 104 (Connection reset by peer)) 08:00:03 *** tvparys (n=tvparys@fvmsfw00.ugent.be) has joined #bioinformatics 08:02:47 Hi all. I've set up a local installation of GBrowse. Strange thing is: when I try to upload extra tracks using the web interface, the new files are plainly ignored. No new tracks appear, no new file appears on the server. Apache has rw-access on the correct dirs as far as I now. Anyone recognises this problem? 08:03:23 not recognized here 08:03:29 what lang is GBrowse 08:03:44 check the error log for that lang on Apache 08:06:32 GBrowse is written in Perl. And indeed, the apache log gives errors ( Use of uninitialized value in hash element at /var/www/cgi-bin/gbrowse line 2899) 08:07:01 but it would be hard to believe that such a basic feature would still contain bugs 08:09:20 is there a mailing list for GB? 08:10:40 <_dan> i just tried to get to their mailing list archives on sourceforge but it wouldnt let me! 08:11:35 <_dan> there's a gmod-gbrowse mailing list 08:11:54 _dan, where are you working ? 08:12:44 <_dan> its ok i got in i think sourceforge broked for a bit 08:12:53 <_dan> im at Newcastle Uni in the UK pingou_work 08:13:13 faceface: I'll search on for a while and then bother them on the mailing list. I'm starting to suspect something about problems with line endings, as some of the users on windows machines seem to be able to upload their files. Thanks anyway. 08:13:16 _dan, any link with the cardiff uni ? 08:14:44 <_dan> pingou_work: no, that ad just came through on a bioinformatics mailing list i am on which is why i posted it yesterday 08:14:50 <_dan> as people were asking :) 08:14:57 ah ok thanks :) 08:15:05 * pingou_work just realised he can not apply... 08:15:22 <_dan> :( 08:15:35 <_dan> i have installed gbrowse but it worked first time, so not much help on the diagnosis front ;) 08:15:54 _dan, "open to UK citizens and EU citizens that have been resident in the UK for at least 3 years" 08:16:17 <_dan> ah 08:16:24 <_dan> the residency requirements bite again 08:17:19 (also the date does not fit...) but thanks any way L:) 08:17:21 -L 08:25:36 *** synthasee has quit (Success) 08:26:19 tvparys: ahhh... you know dos2linux? 08:28:23 <_dan> and for those needing os x solutions flip is bloody amazing for that 08:45:53 faceface: yes I do. Tried converting my files, both ways. No difference. Very strange. 08:48:31 faceface: btw: apparently even hitting the 'delete file' button gives the same errors in the apache log. So it might be browser related instead of file related. 08:53:16 *** nsh (n=chatzill@wikipedia/nsh) has joined #bioinformatics 09:09:37 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 09:13:18 *** tvparys has parted #bioinformatics ("Kopete 0.12.7 : http://kopete.kde.org") 09:16:33 or the error is not the source of the bug 09:56:13 *** ajai has parted #bioinformatics () 09:58:22 *** kanzure has quit ("Leaving.") 10:03:59 *** synthase (n=synthase@69.254.170.145) has joined #bioinformatics 10:15:53 *** highvoltz has quit (Client Quit) 11:00:28 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 11:03:22 *** rogers (i=rogers@bling.bling.org) has joined #bioinformatics 11:05:12 *** rogers has quit (Client Quit) 11:08:47 *** rogers (i=rogers@bling.bling.org) has joined #bioinformatics 11:11:47 *** highvoltz has quit (Remote closed the connection) 11:13:25 *** rogers is now known as highvoltz 11:57:05 *** dozer (n=nmrp3@79-76-184-243.dynamic.dsl.as9105.com) has joined #bioinformatics 12:08:07 *** Cawiss (n=uzumaki@85.100.84.94) has joined #bioinformatics 12:58:54 *** nsh has quit ("ChatZilla 0.9.82.1 [Firefox 2.0.0.14/2008040413]") 13:16:00 *** synthase has quit (Connection timed out) 17:41:04 mm, been quiet today 17:52:19 *** highvoltz has quit () 17:56:21 *** spaes (n=username@adsl-75-36-146-76.dsl.pltn13.sbcglobal.net) has joined #bioinformatics 18:12:25 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 18:42:24 *** synthase (n=synthase@69.254.170.145) has joined #bioinformatics 19:44:01 *** kanzure (n=bryan@cpe-70-113-54-112.austin.res.rr.com) has joined #bioinformatics 19:45:21 <_dan> dozer: yes after the excitement of yesterday, everyones been very busy ;) 19:45:37 lol 19:45:48 've spent the day fighting with the REST support in CXF 19:49:44 <_dan> ahh 19:52:24 the #cxf room on irc.codehaus.org has not been very forthcomming in helping me get things working 19:52:48 <_dan> how broken is cxf? :p 19:53:13 not sure if it is them or me 19:53:23 * _dan reads about cxf 19:53:25 I'm getting run-time class not found exceptions 19:54:10 and I wanted this paper editing app all done and dusted today 19:55:00 <_dan> yeah i know 19:55:17 <_dan> fuck im tired 19:55:21 <_dan> i got up at 5.30am this morning 19:56:40 ouch 19:56:56 <_dan> needless to say im a bit fucking grumpy 19:57:06 <_dan> which might explain why i went out with h this evening 19:57:12 <_dan> and managed to come back without her 19:58:56 double ouch 19:59:00 she still out? 20:00:06 <_dan> s/still out/stomping angrily around town after leaving the bar and refusing to get in a taxi with me 20:00:47 <_dan> we were out for Steph's birthday, fortunately this all occured after we had parted company with them 20:01:18 k 20:05:27 * spaes looks up "cxf" 20:06:55 hmm frameworks... 20:07:01 ! 20:07:31 cxf is a dream to use for web services (SOAP) 20:07:50 so far, can't say the same about its REST support 20:09:35 sorry for disturbing :) 20:09:46 I am planning to go over to UK in 2 weeks 20:10:06 Is it common to mail someone from a lab to ask to visit when you are student ? 20:10:20 it seems that there are too many frameworks, standardization needed 20:10:28 pingou: no, what is weird about taht? 20:10:34 spaes: but that breaks the linux model! 20:10:34 I would like to meet someone from the Cardiff bioinfo groups or so... (phD related) 20:10:52 CowbertDH, was just wondering whether it is 'common' 20:11:03 spaes: also most of the frameworks suck in one way or another 20:12:25 CowbertDH: right, i guess by standardization i mean that i'd like to see less people touting frameworks that suck 20:13:21 the java frameworks seem to be producing shared java5 annotations 20:13:28 so you annotate your code according to the standard 20:13:43 and then fingers crossed, you can chose most frameworks at run-time 20:15:21 what if you hate java though? 20:16:00 you run away ?? :) 20:16:56 lol, grab ruby on rails or haskell? 20:17:24 does someone has some example of ruby code somewhere ? 20:17:30 * pingou never seen any ;/ 20:18:24 what does haskel have to do with RoR? 20:19:20 haskel and ruby 20:20:40 *** dozer has parted #bioinformatics ("Kopete 0.9.2 : http://kopete.kde.org") 20:20:44 also I never liked how in RoR the "model" part had to be coopted into the framework layer instead of staying at the db level 20:21:05 (since activerecord only saw the db as a storage engine, not a real db) 20:53:15 Where can I see the dopamine synthesis pathway? 20:53:24 what database ? 21:02:21 http://en.wikipedia.org/wiki/Dopamine#Biochemistry 21:02:28 Did you check kegg? 21:02:55 wonklab: yes 21:03:15 I did kegg pathway, reactome, chemipedia, wikipathway, pubchem, and entrez 21:03:36 it's a good bet I'm using these interfaces poorly 21:03:41 It's cool how dopamine's a couple of steps away from tyrosine and serotonin's a couple of steps away from tryptophan. 21:04:39 *** _dan has quit (leguin.freenode.net irc.freenode.net) 21:04:39 *** orbitz has quit (leguin.freenode.net irc.freenode.net) 21:04:39 wonklab: So since these reactions are all catalyzed by enzymatic pathways, uhh, I'm thinking about importing them into bacteria for easy triggering, or eukaryotes if I can find an easy way to manipulate them as well. 21:04:40 Pretty similar changes, too. 21:05:51 Sounds like fun. 21:05:55 You need some dopamine? 21:06:21 *** orbitz (n=orbitz@c-98-204-107-254.hsd1.md.comcast.net) has joined #bioinformatics 21:06:21 *** _dan (n=dan@shady.org) has joined #bioinformatics 21:30:45 wonklab: Just need a general neurochem kit. :) 21:30:54 and the costs are way too high. 21:31:04 *** _dan has quit (leguin.freenode.net irc.freenode.net) 21:31:04 *** orbitz has quit (leguin.freenode.net irc.freenode.net) 21:36:08 *** orbitz (n=orbitz@c-98-204-107-254.hsd1.md.comcast.net) has joined #bioinformatics 21:36:08 *** _dan (n=dan@shady.org) has joined #bioinformatics