Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-02-15

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All times shown according to UTC.

Time Nick Message
01:28 brunov joined #bioperl
06:49 bag joined #bioperl
07:52 faceface no, I forgot it was @_
07:52 faceface i.e. no trick ;-)
12:54 brunov joined #bioperl
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15:47 flu joined #bioperl
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17:36 deafferret faceface:   :)
17:38 faceface yo
17:38 faceface hclust(dist(my.m))
17:38 faceface Error: cannot allocate vector of size 1.3 Gb
17:39 faceface bleah
17:43 deafferret MOAR RAM
17:43 deafferret I have the same problems here in Nebraska, so if you fix yours fix mine too please  :)
17:47 faceface I just have a list of pairs, like x, y / y, z / p, q, etc.
17:47 faceface how do I find the 'connected components' of the graph formed by these pairs?
17:47 faceface I know its DFS...
17:48 rbuels DFS
17:48 faceface ahh
17:48 rbuels directed .... something?
17:48 faceface Depth first search
17:48 rbuels ooh
17:49 faceface or is it...
17:49 faceface wfs?
17:49 rbuels if you're just doing connected components, you could use a set-merging algorithm
17:49 * rbuels looks for it
17:49 faceface I could use graph::summut
17:49 faceface or summut::graph
17:50 faceface rbuels: since your here its time for me to leave :/
17:50 rbuels lol
17:50 faceface you could be a bit more considerate and work during the night!
17:50 rbuels usually i'm around a bit earlier than this
17:50 faceface what was I going to ask you...
17:50 rbuels oh oh
17:50 rbuels wait
17:50 rbuels http://www.omii.ac.uk/index.jhtml
17:50 rbuels do you know if the US has anything like it?
17:50 faceface how do you write GFF to describe alignments of sequence markers on a genome?
17:51 rbuels right now, i just blast the marker sequences against he genome
17:51 rbuels and just sort of say 'the marker is here'
17:51 faceface not that I know of
17:51 rbuels well, 'the marker sequence is here'
17:51 faceface and use 'match_part' in ur blast?
17:51 rbuels erm, yeah, match and match_part
17:51 faceface how do you filter out markers that hit multiple times
17:51 rbuels i haven't been
17:51 faceface I've requested a new ontology term 'anchored sequence marker' ... they will make it!!!
17:52 rbuels i mean, something like that could be pointing out an assembly error
17:52 faceface oh
17:52 faceface perhaps that is where I've been going wrong.
17:52 rbuels or it could be ... i dunno
17:52 faceface rbuels: but the match may be really poor
17:52 rbuels a marker that sucks
17:52 faceface what is your threshods
17:52 rbuels yeah, i use a very stringent blast
17:52 faceface hods damit!
17:52 * rbuels carries the hod
17:52 faceface what if the sequence is from pepper and you happen to work in potoato
17:52 * rbuels looks for the blast params
17:52 faceface yay!
17:52 * faceface really has to go
17:52 faceface (sorry dude
17:53 faceface don't know about the grids
17:53 rbuels oh well fine then
17:53 faceface prolly you got summut
17:53 faceface eeep!
17:53 faceface plz help me!
17:53 rbuels o_O?
17:53 faceface I'll be back.... tomorrow...
17:53 rbuels you could send me an email too
17:53 faceface if you couls paste up the params I'd be greatful
17:53 faceface okey
17:53 faceface tye
17:53 rbuels that's an asynchronous form of online communication.
17:53 faceface oh
17:53 faceface I'll give it a go some time
17:53 faceface have a nice day
17:54 rbuels lol night
17:54 faceface lets compromise... good afternoon
17:54 * rbuels nods cordially
17:54 rbuels and to you sir.
17:54 rbuels now go away.
17:55 rbuels ;-)
17:55 deafferret rbuels: night? where are you?
17:56 rbuels not night for me.  night for him.
17:56 rbuels morning for me.
17:56 deafferret very well. as you were
17:56 rbuels see, i'm a giver.
17:57 rbuels deafferret: what's the wiki backend running this, do you recognize it?
17:57 rbuels http://www.omii.ac.uk/wiki/AboutUs
18:00 deafferret dunno. looks like they're using YUI stuff.  http://developer.yahoo.com/yui/
18:00 deafferret http://developer.yahoo.com/yui/articles/skinning/
18:02 rbuels http://www.omii.ac.uk/wiki/Mai​n?do=Diff&r1=33&r2=32
18:02 rbuels does YUI have an integrated wiki or something?
18:02 deafferret It's JSPWiki http://www.jspwiki.org/
18:02 rbuels ah
18:03 deafferret I rule
18:03 deafferret super slueth
18:03 rbuels deafferret++ # teh wiki sloth
18:04 deafferret looks sharp. I'm a Mediawiki addict, myself
18:08 deafferret hmm... $thisproject is hard. I'm spending most of my time chasing the results I *didn't* get
18:09 deafferret which is harder than the results I did get. bummer.
18:16 deafferret oops. 8 hours of processing down the drain. Turns out U and T and different letters
18:16 rbuels wow, who would have thought.
18:16 * deafferret blames the school system
18:17 deafferret These 1.2M results strangely don't include any miRNA seed regions with U chars.  :)
18:17 * deafferret takes a victory lap
18:51 dnewkirk joined #bioperl
19:44 deafferret woof. RosettaDock.
20:04 rbuels what are you barking about
20:04 rbuels speak, deafferret!  speak!
20:40 deafferret protein docking looks harder than sleeping
20:41 bag_ joined #bioperl
20:44 deafferret ironically, i dock a gajillion proteins every night while I sleep. easy peasy.
21:30 deafferret oh, R. why do you torture me so.  Error: cannot allocate vector of size 2.1 Gb
22:27 driveby_bot joined #bioperl
22:27 driveby_bot /home/svn-repositories/bioperl: r16835 (cjfields) : use test_input_file() for file path consistency
22:27 driveby_bot Diff: http://tinyurl.com/yhlbsnx
22:30 driveby_bot joined #bioperl
22:30 driveby_bot /home/svn-repositories/bioperl: r16836 (cjfields) : bioperl -> BioPerl
22:30 driveby_bot Diff: http://tinyurl.com/ykm75ug
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