| Time |
S |
Nick |
Message |
| 04:49 |
|
|
rbuels_ joined #bioperl |
| 11:30 |
|
|
elTigre joined #bioperl |
| 15:42 |
|
|
rbuels joined #bioperl |
| 15:48 |
|
* deafferret |
waves |
| 16:57 |
|
|
ende joined #bioperl |
| 17:00 |
|
* ende |
waves |
| 17:01 |
|
* deafferret |
tips his hat |
| 17:11 |
|
ende |
so once a chan is registered to someone, I think it's impossible for it to expire |
| 17:11 |
|
ende |
that sucks, I really wanted #diyg |
| 17:11 |
|
ende |
for http://sourceforge.net/projects/diyg/ |
| 17:18 |
|
deafferret |
you can petition the ops channel, but they didn't help me get my Nick back from NickServ, even after 18 months -shrug- |
| 17:18 |
|
ende |
they told me basically the same thing |
| 17:18 |
|
ende |
btw anyone here frequent gmod useres? |
| 17:18 |
|
ende |
seems like gmod could really use an irc presence |
| 17:18 |
|
deafferret |
rbuels is I believe |
| 17:19 |
|
rbuels |
yeah i work at sgn.cornell.edu |
| 17:21 |
|
rbuels |
interesting, i didn't know about diyg |
| 17:22 |
|
ende |
yeah, I think some folks in the gmod community might be interested in it |
| 17:22 |
|
ende |
they just seem like they'd fit well together |
| 17:22 |
|
rbuels |
ever been to any of the gmod meetings? |
| 17:23 |
|
ende |
I haven't. I was just asking brian osborne if he thought that might be a useful way to make inroads |
| 17:24 |
|
rbuels |
oh you work with brian? |
| 17:24 |
|
rbuels |
(or you were asking electronically) |
| 17:24 |
|
rbuels |
? |
| 17:24 |
|
ende |
well, occasionally we're in the same office, but yeah electronically |
| 17:25 |
|
ende |
we're the primary developers for diya (a microbial genome annotation pipeline) |
| 17:25 |
|
rbuels |
what makes it microbial-specific? |
| 17:27 |
|
ende |
primarily the particular selection of annotation tools that it was originally designed to use |
| 17:27 |
|
rbuels |
hmmm |
| 17:27 |
|
ende |
(although it's incredibly modular at this point, and most of those tools could be theoretically swapped out for more eukaryotic-specific ones) |
| 17:28 |
|
rbuels |
where do you work, what was this developed as part of, etc, |
| 17:28 |
|
ende |
navy medical research center |
| 17:29 |
|
ende |
high throughput pathogen genomics sequencing lab |
| 17:32 |
|
rbuels |
hmmm |
| 17:33 |
|
rbuels |
what's the mission of the high throughput pathogen genomics sequencing lab |
| 17:33 |
|
rbuels |
quick characterization of pathogens in the event of biowarfare? |
| 17:36 |
|
ende |
Something like that. |
| 17:37 |
|
rbuels |
how does this relate to ergatis? |
| 17:38 |
|
rbuels |
http://gmod.org/wiki/TIGR-Workflow_/_Ergatis |
| 17:39 |
|
* deafferret |
has been to one GMOD meeting a couple years back at CSHL |
| 17:40 |
|
perl_splut |
http://www.cio.com/article/490[…]ce=nlt_cioinsider |
| 17:42 |
|
rbuels |
well sun is headed downward as well |
| 17:42 |
|
rbuels |
it's the inevitable commoditization of any maturing industry |
| 17:43 |
|
rbuels |
and Sun and SGI have never been very well positioned to ride that out |
| 17:43 |
|
rbuels |
IBM did it by changing mostly to be a consulting business |
| 17:43 |
|
rbuels |
Sun at least has Java |
| 17:43 |
|
rbuels |
SGI never did anything to dodge that inevitable bullet |
| 17:49 |
|
ende |
rbuels: whats your involvement with gmod? |
| 17:49 |
|
rbuels |
to this point, not much |
| 17:49 |
|
rbuels |
mouthing off mostly |
| 17:50 |
|
rbuels |
yeah, i guess that would characterize it |
| 17:51 |
|
rbuels |
i mostly mouth off about integration |
| 17:51 |
|
rbuels |
bioinformatics is so fragmented, because it's mostly academic |
| 17:51 |
|
rbuels |
and academics don't really work together |
| 17:52 |
|
rbuels |
these are of course gross generalizations |
| 17:52 |
|
rbuels |
but i think that they hold true in a broad sense |
| 17:53 |
|
ende |
I generally agree |
| 17:54 |
|
deafferret |
It seems to me the most widely published seem to be the least cooperation minded. |
| 17:54 |
|
ende |
I think part of the perceived necessity in 'pipelining' stems from the nature of bioinformatics software in general |
| 17:54 |
|
deafferret |
those that cooperate a lot tend to publish a lot less |
| 17:54 |
|
rbuels |
yes that is quite true jay |
| 17:55 |
|
rbuels |
mostly because cooperative projects usually make glacial progress |
| 17:55 |
|
rbuels |
because there is very little accountability in academia |
| 17:55 |
|
rbuels |
my other pet peeve |
| 17:55 |
|
rbuels |
ende: please elaborate |
| 17:56 |
|
ende |
um.. inconsistent/incompatible I/O formats? |
| 17:56 |
|
ende |
so the pipelining comes in.. glueing rigid bits together that do not fit naturally. |
| 17:56 |
|
ende |
that's all I mean |
| 17:57 |
|
perl_splut |
heheh |
| 17:57 |
|
perl_splut |
or in my labs case where they just store the data in random forms in excel |
| 17:57 |
|
rbuels |
yep, the i/o format thing is a specific consequence of the fragmented nature of bioinformatics |
| 17:58 |
|
rbuels |
and it stays fragmented because cooperation does not usually yield much progress |
| 17:58 |
|
rbuels |
biologists sure love excel. |
| 17:58 |
|
perl_splut |
not sure about that. We do a lot of collaborative work here that seems to be making progress |
| 17:59 |
|
perl_splut |
they might, but most don't seem to know anything about how to make it work for them |
| 17:59 |
|
perl_splut |
70 people in this lab, and only 3 of us know even a basic thing like click-drag the corner to get excel to autofill/increment in cells |
| 18:00 |
|
ende |
I think projects just require time to mature |
| 18:00 |
|
ende |
look at bioperl |
| 18:00 |
|
ende |
I'd generally consider that a success |
| 18:00 |
|
rbuels |
....generally, yes |
| 18:01 |
|
perl_splut |
yet bioC and biopython aren't nearly as big in terms of modules :) |
| 18:01 |
|
ende |
one of the ideas behind DIYG in general is simplifying deployment by making use of various technologies |
| 18:01 |
|
ende |
like virtualization |
| 18:01 |
|
ende |
creating a 'genomics analysis pipeline' Virtual Appliance |
| 18:01 |
|
rbuels |
biologist downloads vmware player, virtual appliance, runs analyses. |
| 18:02 |
|
rbuels |
is that the vision? |
| 18:02 |
|
ende |
yes |
| 18:02 |
|
ende |
greatly reduces the amount of installation, version matching, database building, etc |
| 18:03 |
|
perl_splut |
yep |
| 18:03 |
|
rbuels |
what lab are you in perl_splut |
| 18:04 |
|
perl_splut |
biodesign institute |
| 18:04 |
|
rbuels |
and what are examples of the collaborations you guys do that make good progress |
| 18:04 |
|
rbuels |
(got a url for biodesign institute?) |
| 18:05 |
|
ende |
by the way, if any of you are interested in diya (the annotation pipeline) or diyg in general as a project consortium, we're very welcoming ;) |
| 18:05 |
|
perl_splut |
biodesign.asu.edu |
| 18:05 |
|
deafferret |
perl_splut: add yourself! http://bioperl.org/wiki/IRC :) |
| 18:07 |
|
perl_splut |
two biggest is for microarray printing (techniques and technologies) and vaccine technologies with other labs here |
| 18:07 |
|
rbuels |
deafferret: did you set up the bioperl wiki? |
| 18:08 |
|
* deafferret |
blames ende |
| 18:09 |
|
ende |
whatd I do? |
| 18:09 |
|
rbuels |
set up the bioperl wiki i suppose |
| 18:10 |
|
perl_splut |
nah. I prefer some anonymity :) |
| 18:11 |
|
rbuels |
prefer to hang separately? |
| 18:25 |
|
perl_splut |
something like that |
| 18:43 |
|
perl_splut |
trying to recode genes so that they all contain unique sequences. Wonder if there is a faster way than regexp and perl code. The regexp is fast, but think the slowdown is in the actual recoding section |
| 18:43 |
|
deafferret |
what does recode a gene mean? |
| 18:44 |
|
perl_splut |
swap out codons for other codons that also code for that AA |
| 18:44 |
|
deafferret |
ah, k |
| 18:45 |
|
deafferret |
if you're dealing with many genomes at once I would think the "is this unique now?" part would be the slowest |
| 18:45 |
|
perl_splut |
not genomes, just genes |
| 18:45 |
|
deafferret |
"unique" across how many genes? |
| 18:46 |
|
perl_splut |
however many fit in 25kb |
| 18:46 |
|
perl_splut |
which results in about 8k regexp |
| 18:47 |
|
deafferret |
aren't many single genes > 25kb? |
| 18:47 |
|
perl_splut |
nope |
| 18:47 |
|
perl_splut |
most of ours are in the 1.6kb range |
| 18:48 |
|
perl_splut |
it takes about 8-10 hours to recode 7 genes using my current methodology |
| 18:48 |
|
deafferret |
don't know how to help w/o seeing your source. github.com it or something? |
| 18:48 |
|
perl_splut |
since I do a walking window to be sure of uniqueness |
| 18:52 |
|
perl_splut |
here's the two main functions that do the recoding |
| 18:52 |
|
perl_splut |
http://rafb.net/p/Z0R9z273.html |
| 18:55 |
|
rbuels |
might want to profile it on a test set |
| 18:55 |
|
rbuels |
to see where it's spending most of its time |
| 18:56 |
|
rbuels |
the olde-timey perl profiling tools should be fine |
| 18:56 |
|
rbuels |
http://www.perl.com/pub/a/2004[…]25/profiling.html |
| 18:56 |
|
rbuels |
i don't really see any recoding in the code here though |
| 18:57 |
|
rbuels |
this looks like finding and removing restriction sites |
| 18:58 |
|
perl_splut |
I use the same code for the various steps of recoding |
| 18:59 |
|
perl_splut |
http://rafb.net/p/dW0PKd93.html |
| 18:59 |
|
perl_splut |
what differs from a restriction site and any other kind of site is the pattern. There really isn't any other difference, heheh |
| 19:01 |
|
deafferret |
Devel::NYTProf for the win |
| 19:03 |
|
perl_splut |
thanks |
| 19:45 |
|
deafferret |
seriously. it's super-sexy if you're not familiar with it. :) |
| 20:11 |
|
perl_splut |
whee... 36 packages to update |
| 20:13 |
|
deafferret |
:) |
| 21:04 |
|
|
driley joined #bioperl |
| 21:40 |
|
perl_splut |
wow... that really slows down the code, heheh |
| 21:40 |
|
deafferret |
perl_splut: sure, but the ratios are valid :) |
| 21:40 |
|
perl_splut |
good thing I'm only trying this with one 4kb gene |
| 22:05 |
|
perl_splut |
seems that devel::nytprof has some idiotically hardcoded paths or something as it is trying to load lib/Posix.pm, but isn't finding it as it is doing ../../lib/Posix.pm... heheh |
| 22:10 |
|
deafferret |
perl_splut: I hit a bug last year that was fixed by using SVN version instead of CPAN http://code.google.com/p/perl-devel-nytprof/ |
| 22:11 |
|
deafferret |
no clue if that would help you or not in your circumstance |
| 22:11 |
|
perl_splut |
version I have is 2.09 from Mar 29 '09 |
| 22:54 |
|
perl_splut |
hmm.. not sure how to read the results. the code spent far more time doing stuff than nyt seems to be saying... |
| 22:55 |
|
perl_splut |
or is that time per call... |
| 22:55 |
|
deafferret |
perl_splut: I don't remember the details, but I remember that slapped me in the face with several of my inneficiencies last year |
| 22:57 |
|
perl_splut |
Profile of <code> for 484s, executing 34034430 statements and 4924431 subroutine calls in 155 source files and 52 string evals |
| 22:58 |
|
perl_splut |
14million statements were in the Bio::PrimarySeq module, heheh |
| 22:58 |
|
deafferret |
that's a lot. :) |
| 22:59 |
|
perl_splut |
yeah, but the numbers don't seem to make sense to me |
| 22:59 |
|
perl_splut |
so, not sure I'm seeing where my inefficiencies might be coming from |
| 22:59 |
|
deafferret |
I remember bouncing back and forth between "oh wow, that's cool!" to "what the fuck is that?" |
| 23:00 |
|
deafferret |
well, you could start at the top of your % time elapsed and see if you can speed up the heavy hitters somehow |
| 23:02 |
|
perl_splut |
don't see that in the html output... |
| 23:02 |
|
deafferret |
haven't used it in a while. if you want to tarball your results and upload them somewhere I could take a look |
| 23:03 |
|
* deafferret |
kicks $vendor_pos repeatedly |
| 23:05 |
|
perl_splut |
not sure I can as this reveals my whole code |
| 23:05 |
|
deafferret |
shucks. my evil plan failed :) |
| 23:09 |
|
perl_splut |
http://innovationsinmedicine.org/nytdevel/ |
| 23:09 |
|
perl_splut |
that's just the index page and css |
| 23:28 |
|
perl_splut |
hmm, looks like it spent 113s calling translate_as_string from the Bio::Perl module... |
| 23:30 |
|
ende |
sourceforge is sweet |
| 23:30 |
|
ende |
their hosted apps selection |
| 23:30 |
|
ende |
not only Trac, which I can't live without, they even host wordpress now |
| 23:30 |
|
ende |
development blogging, imagine that |
| 23:30 |
|
ende |
http://apps.sourceforge.net/wordpress/diyg/ |
