Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-05-01

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All times shown according to UTC.

Time Nick Message
07:45 faceface perl_splut: I think this comes from GFF
07:45 faceface i.e. its confusing as_text with as_gff_string
07:45 * faceface guesses
12:09 faceface_ joined #bioperl
13:13 deafferret perl_splut: just saw your bioperl-l posts. My answer yesterday solved your problem, didn't it?
13:13 deafferret post. singular.
13:14 * deafferret doesn't use the mailing list since my posts tend to never arrive
13:30 faceface joined #bioperl
14:11 faceface how can I pounce on buel ?
14:55 faceface s
15:11 deafferret pounce on?
15:12 faceface deafferret: its a concept from im
15:12 faceface internet messenger
15:12 faceface like pidgeon thing
15:13 perl_splut yes, it worked, deafferret. Thanks
15:13 deafferret http://jays.net/images/noidea.jpg
15:13 deafferret perl_splut: cool!
15:13 deafferret I thought I didn't leave you hanging, but reading the post I wasn't sure  :)
15:13 * perl_splut pounces on buel *
15:14 perl_splut sorry... my job is a bit weird... I do coding, lab work, and am also mr. RandomTask
15:14 killface joined #bioperl
15:14 killface Actually pidgeon works
15:15 perl_splut can be annoying at times as it means my focus tends to bounce around a lot
15:19 philsf joined #bioperl
15:41 rbuels joined #bioperl
15:42 maceface rbuels: !
15:42 faceface how are you?
15:43 faceface I wanted to ask if you have a sequence set to represent the tomato mitochondrial genome?
15:43 maceface left #bioperl
15:44 faceface I found 166 contigs from http://www.mitochondrialgenome.org/, but nothing substantial
15:44 faceface do you just fall back on arabidopsis? or isn't this your thing?
15:45 rbuels um, there was a project to do the mito
15:45 rbuels in....argentina?
15:45 rbuels lemme see
15:45 faceface yeah, that is how I found http://www.mitochondrialgenome.org/
15:45 rbuels that's probably it then   :-\
15:46 faceface you get there by linking through argentinian flag
15:46 faceface OK.
15:46 rbuels yep
15:46 rbuels hehee.  "linking through the argentinian flag"
15:46 faceface I blasted the arabidopsis chloroplast and found (for example) "Brassica napus mitochondrial DNA, complete genome"
15:46 faceface is there one that is best for sol?
15:47 rbuels i think they've been mostly using the arabidopsis one if they really need a complete one
15:47 faceface rbuels: well... first I had to search the site for "mitochondria" ;-)
15:47 rbuels otherwise the draft tomato one
15:47 faceface right
15:47 faceface oh yeah, because I read that in the spec
15:47 faceface hmm... I'll grab some and see what the differences are
15:47 faceface nicotina!
15:48 faceface BA000042.1
15:48 rbuels oh yes they have that too
15:48 rbuels this might be a good question for lukas
15:48 faceface should be better than arabidopsis I think ... right
15:48 rbuels join #cxgn on irc.perl.org
15:48 rbuels he's in there now
15:48 faceface really? awesome
15:48 faceface how do I open a new server tab in irssi
15:48 faceface ?
15:48 rbuels i dunno
15:49 rbuels never used irssi
15:49 deafferret faceface: new server tab?
15:49 faceface actually its a pain, the university blocks irc
15:49 deafferret I'm connected to 3 servers, 10 channels
15:49 rbuels wow.
15:49 deafferret so ssh out to a screen/irssi  :)
15:49 faceface screen -S chat ssh -L 2222:irc.freenode.net:6667 dmb@bioinformatics.org -t "perl -e 'while(1){print qq(Chat port sleeping ... zzz\n); sleep 299}'" # ;-)
15:49 rbuels i can understand why they block it though.  most personnel don't use it, and it's the primary botnet control channel
15:50 faceface yup
15:50 deafferret faceface: wow  :)
15:51 faceface screen -S chat ssh -L 2223:irc.perl.org:6667 dmb@bioinformatics.org -t "perl -e 'while(1){print qq(Chat port sleeping ... zzz\n); sleep 299}'"
15:51 rbuels at the gmod meeting in toronto last year, the venue was blocking everything but port 80
15:51 faceface lol
15:51 rbuels that was fun
15:51 rbuels lukas and i called our sysadmin and he made a virtual machine with ssh on port 80
15:51 faceface deafferret: how to switch server?
15:51 rbuels and posted the login/pass on the wall of the conference room
15:51 faceface heheh
15:52 rbuels ssh port forwarding is nice
15:52 faceface dear IT secuity, please try harder. sincerly, bioinformatics types
15:52 deafferret faceface: /win 1 Control-X
15:52 faceface /win?
15:53 deafferret /win changes "windows"... I have 24 "windows"
15:53 perl_splut uni here blocks IRC, but only on port 6667
15:53 perl_splut so, servers like freenode that run on 6668 or other ports aren't blocked
15:53 deafferret uni here runs there own IRC server :)
15:53 faceface perl_splut: nice
15:53 perl_splut that only helps if it links into other networks, deafferret
15:54 perl_splut else you're just talking to yourselves, heheh
15:56 deafferret yup. talking to ourselves is exactly the point. if there is a point.  :)
15:58 deafferret faceface: you don't type /win all the time using irssi?
15:58 faceface perl_splut: but it 'shows willing'
15:58 faceface deafferret: its new to me
15:58 deafferret that's how you switch between channels
15:58 deafferret ahh
15:58 faceface minter
15:59 faceface I was using ctrl-n
15:59 deafferret so when you first get into irssi you have 1 window, the control window
15:59 faceface so never had more than 9!
15:59 deafferret faceface: ah. I got up to 24, so I can't hit Control-24  :)
15:59 deafferret I don't think
15:59 deafferret so /win 1 takes you to window 1,  then control-X to switch between servers
16:00 faceface deafferret: so I just issue another /server command?
16:00 faceface and then ctrl-x?
16:00 faceface I'll try ...
16:01 deafferret /connect irc.perl.org  /connect irc.freenode.net   Control-X Control-X Control-X
16:01 deafferret you connect once, and irssi stays connected
16:01 deafferret /server list is the only /server command I use
16:01 rbuels deafferret: you in #catalyst and those others right now?
16:01 deafferret yup
16:02 rbuels under jh?
16:02 rbuels or df?
16:02 deafferret yup
16:02 deafferret jhannah is taken on freenode
16:02 deafferret (by me, years ago)
16:03 deafferret #  jhannah on irc.perl.org #perl-help, #poe, #catalyst, #tt
16:03 deafferret # jhannah on irc.ist.unomaha.edu: #uno
16:03 deafferret # deafferret on irc.freenode.net #bioperl, #OmahaLUG
16:16 rbuels deafferret: where do channel logs typically end up?  i'd assume that most big channels have bots in them doing logging
16:16 rbuels on a web server somewhere right?
16:16 deafferret I don't think there is a "typical". it varies by channel
16:16 deafferret you can have irssi do your own logging with a single command
16:16 deafferret autolog on or something like that
16:17 rbuels yes but then i have to leave my computer on  :-\
16:17 deafferret the server running screen/irssi has to be on, yes.  :)
16:17 deafferret If you want to ssh to NE you can use irssi here.
16:17 rbuels heh no thanks
16:18 rbuels where does #catalyst keep logs, or does it
16:18 deafferret you'd have to ask in there
16:19 deafferret or just read mine  http://clab.ist.unomaha.edu/~jhannah/irclogs/Perl/
16:19 rbuels hmm that's a good idea
19:13 ChanServ joined #bioperl

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