| Time |
S |
Nick |
Message |
| 07:49 |
|
|
melic joined #bioperl |
| 08:09 |
|
|
levi_ joined #bioperl |
| 09:22 |
|
|
vinnana joined #bioperl |
| 11:30 |
|
|
Levi_ joined #bioperl |
| 12:07 |
|
|
brandi joined #bioperl |
| 12:07 |
|
|
brandi left #bioperl |
| 12:18 |
|
|
brandi joined #bioperl |
| 12:18 |
|
|
brandi left #bioperl |
| 13:47 |
|
|
Jun joined #bioperl |
| 14:18 |
|
|
jhamilton joined #bioperl |
| 15:34 |
|
|
brandi joined #bioperl |
| 15:34 |
|
|
brandi left #bioperl |
| 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/famil[…]0452&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~ |
| 17:28 |
|
|
dnewkirk joined #bioperl |
| 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-int[…]ing-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/bi[…]n/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 |
| 19:44 |
|
|
buelsbot joined #bioperl |
| 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 |
| 20:42 |
|
|
bag joined #bioperl |
| 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! |
| 21:19 |
|
|
dnewkirk joined #bioperl |
| 21:28 |
|
|
pyrimidine left #bioperl |
