Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-12

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All times shown according to UTC.

Time Nick Message
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13:47 Jun joined #bioperl
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15:34 Jun It seems so many people went to the ISMB/BOSC ...
15:35 rbuels yeah...everybody but me
15:35 * rbuels sobs
15:39 * faceface too
15:57 * deafferret comforts the losers
16:34 pyrimidine joined #bioperl
16:35 * pyrimidine pats rbuels on the head for not going to ISMB
16:37 deafferret rewarding the slackery?
16:38 pyrimidine deafferret: no, just taking pity on a poor soul for missing a very good meeting
16:38 pyrimidine :)
16:40 * Jun waves goodbye~
16:41 pyrimidine o/
16:41 deafferret ah. 'pat on the head' to comfort, not to reward   :)
16:41 deafferret good rbuels. good boy for staying home.
16:41 Jun Hi, pyrimidine. Can you recommend some book or website explaining the web request using LWP?
16:42 deafferret http://search.cpan.org/perldoc?LWP   ?
16:42 Jun I am thinking of writing something smart to parse http://pfam.sanger.ac.uk/family/alignment/do​wnload/gzipped?acc=PF00452&alnType=ncbi
16:43 Jun Ok, if reading perldoc for LWP is the best way, I will try it...
16:43 deafferret you can just fetch that URL with wget or curl...
16:43 deafferret LWP is an amazing stack of powerful user agent software -- but overkill for "download this URL"
16:43 Jun yep, but I want to do things more general and consistent, e.g. writing a package like Bio::DB::GenBank
16:43 deafferret LWP simulates web browsers
16:44 pyrimidine deafferret++
16:44 Jun ok, that makes sense
16:45 deafferret if you're just fetching a URL or two you don't need LWP. If you're writing an intelligent web spider with lots of smart guts then LWP is great  :)
16:45 Jun I am thinking of writing a package of Bio::DB::Pfam, which retrieve general informations from Pfam, and alignments...
16:45 pyrimidine sounds good to me
16:45 pyrimidine There are a few basic tools in bioperl for this
16:46 Jun I will read perldoc of LWP tomorrow, and see whether I can work with it
16:46 pyrimidine Bio::Webagent, Bio::DB::GenericWebAgent, and others
16:47 pyrimidine Jun: talked about  the GSoC project at BOSC, got a good response
16:47 Jun ok, sounds interesting
16:47 Jun really? that is cool. Hope I was there...
16:48 pyrimidine Peter Rice (EMBOSS) and Jim Procter (Jalview) wanted to keep up to date with it
16:48 pyrimidine so went very well
16:48 Jun I talked about bioinformatics in a vision research conference, and got no response .... it seems it is not a good idea :P
16:48 Jun that is great ...
16:49 Jun Because the next thing I want to do is to know how JalView retrieve alignments from the online databases
16:50 Jun Ok, I have to go now. Email me the date when you want to have a meeting. See u~
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18:24 deafferret -blink-    http://github.com/organizations/bioperl ?
18:24 deafferret does "organization" status do cool things?
18:24 deafferret do I submit "upgrade to an organization" requests for my other organizations?
18:25 deafferret is there still a "bioperl" username password into github?
18:26 pyrimidine deafferret: re: organizations, yes, it does cool things
18:27 deafferret Your search - site:help.github.com organization - did not match any documents.
18:28 pyrimidine deafferret: http://github.com/blog/674​-introducing-organizations
18:29 pyrimidine so, no user name/pass any more.
18:29 pyrimidine we have a list of designated owners, team members, etc.
18:31 deafferret huh. cheapest "business" is $25/month
18:31 deafferret not sold  :)
18:32 pyrimidine still have the individual accounts
18:32 deafferret (need private repos, only 3 collabs)
18:32 deafferret ya
18:33 deafferret number of collabs in private repos is what drives the pricing now...
18:34 deafferret err... is someone paying $25/month to github now?  http://github.com/plans
18:34 deafferret for "unlimited teams" ?
18:35 deafferret oh... there's the "open source" plan
18:35 pyrimidine I could see a small 'organizations working for businesses who don't want to buy a $2K-3K server, pay a sysadmin salary, etc.
18:35 pyrimidine but yes, there's the OS one
18:35 deafferret very interesting
18:36 * deafferret rubs rbuels' chin
18:37 deafferret ha! jhannah++ 29 followers -- the most in the BioPerl Organization  :)
18:37 deafferret people love me
18:37 deafferret and my lack of code
18:39 deafferret github++
18:40 pyrimidine github got lots of love at BOSC, from all the Bio*
18:43 deafferret all perl?
18:45 pyrimidine perl, python, ruby
18:46 deafferret looks like biopython has current changes, but no org members yet  :)
18:46 deafferret and bioruby hasn't changed in 6 months
18:47 deafferret neat stuff  :)
18:48 pyrimidine I think the two of them haven't converted to org status yet in github
18:48 deafferret http://github.com/biopython
18:49 pyrimidine oh, I guess peter did switch them over
18:50 pyrimidine odd that there aren't any public members listed.  But that's off by default
18:50 pyrimidine so not terribly surprising, actually
18:50 deafferret "needed for Python 3"   wow    :)    http://wiki.python.org/moin/Python2orPython3
18:51 pyrimidine biopython is slowly moving that direction, acc to brad chapman
18:52 pyrimidine IMHO they're in a stickier mess with python2->3 than with perl5->6
18:52 pyrimidine b/c the changes from python2 to python3 were significant, but not significant enough for many users to jump to python3
18:52 pyrimidine perl6 is (pretty much) a new language
18:53 deafferret :)
18:53 pyrimidine p6 is very different from perl5, yet with enough similarities to make it still perl
18:54 pyrimidine not to mention, part of the p6 spec is a backwards-compat mode, to use p5 code in p6
18:55 deafferret changelog is full of "for Python 3"    :)   http://github.com/biopython​/biopython/commits/master/
18:56 deafferret "(and you can't do this in Python 3) "
18:56 pyrimidine right, but just for those bits
18:56 pyrimidine I wouldn't say that all tests pass for python3
18:56 pyrimidine at least not yet
18:56 pyrimidine but it'll get there
18:57 pyrimidine hah, met tiago at BOSC, nice guy: http://github.com/tiagoantao
18:58 pyrimidine the biopy group is pretty nice altogether, not interested in getting into lang war stuff (bioruby the same)
18:59 pyrimidine but there were a few at BOSC that wanted to push 'python >> perl' bit, which is not the place to do that
18:59 pyrimidine might get booed out of the room
19:03 deafferret huh? I would think an open marketplace of ideas would be welcomed
19:04 deafferret if someone in the room thinks perl is better than python, then they should present why
19:04 pyrimidine exactly
19:04 pyrimidine but that's not typically what happens
19:06 deafferret boo
19:23 pyrimidine I think it's okay to needle each other a bit, if it's good-spirited, but that intent sometimes doesn't translate well to everyone
19:24 pyrimidine the complaints about the Rails folks, for instance
19:24 deafferret competition is healthy for everyone.  :)   as are wedgies
19:24 pyrimidine agreed
19:24 deafferret who complains about Rails? If you don't like it, don't use it
19:24 deafferret if you don't want to hear someone whine about Rails, don't go in that room at that time
19:24 deafferret or is BOSC single-track?
19:25 * deafferret is spoiled on YAPC / OSCON
19:25 pyrimidine that's very likely one of the reasons for the enlightened perl movement
19:25 pyrimidine (competition, that it)
19:25 deafferret have you seen perl5i? that's another exciting "screw it, I'm heading this direction" prject
19:25 pyrimidine BOSC is single-track
19:25 deafferret ah
19:26 deafferret single-track explains a lot
19:26 deafferret (voting with your feet)++
19:26 pyrimidine but there were pretty good feelings cross-lang there
19:27 pyrimidine only one talk had a small jib: "Bioconductor with Python, What else?"
19:27 pyrimidine but even that is justified
19:27 pyrimidine where are the R-Perl bindings or projects?
19:28 pyrimidine whereas python and ruby both have ones
19:28 pyrimidine (don't get me started on RSPerl)
19:30 pyrimidine so, overall pretty nice
19:30 deafferret I just R CMD BATCH stuff   :)
19:32 deafferret my .pl files use Template Toolkit to generate .R files, then I BATCH them and then read in the result files
19:32 deafferret cheese__
19:32 deafferret ++
19:32 deafferret oops  :)
19:32 pyrimidine hey, it works
19:32 pyrimidine I think the toolkit that talk I mentioned essentially did the same thing
19:33 deafferret that lets the R experts hand me big gobs of R that I use verbatim
19:33 deafferret if I do something fancy with them then they can no longer stare at it with me
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20:37 deafferret ... um ... is Fungus the ONLY animal/plant with more than ONE assembly in existence?
20:37 deafferret (complete genome)
20:37 deafferret mouse seems to have tons of 'em, only one fully assembled
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20:42 rbuels Fungus?
20:43 rbuels that's awfully .... non-specific
20:58 pyrimidine deafferret: don't let Dr. Stajich catch you saying that
21:00 pyrimidine http://www.pnas.org/content/107/26/11889
21:09 pyrimidine ;-)
21:11 rbuels PNAS!
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