Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-06

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Time Nick Message
06:51 kyanardag joined #bioperl
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14:32 Meteorswarm joined #bioperl
14:33 Meteorswarm Hi; I'm new to bioperl and trying to parse a tigrxml file with the built-in parser, but I get an error saying it can't find the right package.  I just installed 1.6.0 with the instructions from the wiki.  What can I do?
14:37 Meteorswarm this is the error dump: git://gist.github.com/163345.git
14:38 Meteorswarm bah
14:38 Meteorswarm http://gist.github.com/163345
15:06 rbuels Meteorswarm: XML::SAX is required by some of the parts of bioperl
15:07 rbuels the error you see there is a standard one saying 'you need to install this module'
15:07 rbuels Meteorswarm:  the reason its installation wasn't part of the standard bioperl install is because only a few parts of bioperl use it
15:08 Meteorswarm rbuels: thanks.  I'm running cpan's update; I'll see if that fixes it.  It seems like it was installing it
15:13 rbuels you'll need to specifically install it, because XML::SAX is marked optional
15:13 rbuels because if we required installation of every single module that's used in all of bioperl, it would have like 3x the dependencies
15:13 rbuels that said, this behavior by bioperl is stupid and broken and this is something we're working on
15:13 Meteorswarm how do I install it specifically?
15:14 rbuels just run 'cpan'
15:14 rbuels and type 'install XML::SAX'
15:14 Meteorswarm ok, I'll do that as soon as it's done updating
15:14 Meteorswarm thanks for the help
15:14 rbuels no prob
15:15 Meteorswarm hmm, the cpan update seems to be hanging after failing a test.  Is this normal?
15:15 rbuels oh interesting, i see that you're at cornell
15:15 rbuels sometimes....
15:15 rbuels it depends on what module is being installed
15:15 rbuels if you paste in the error with gist i could be more specific
15:16 Meteorswarm oh, it just gave me a warning, looks like a server was being slow
15:17 Meteorswarm http://gist.github.com/163368
15:17 Meteorswarm rbuels: I see you're at cornell too, or at least on their internet connection
15:18 rbuels yeah, i work at sgn.cornell.edu
15:18 Meteorswarm I'm not familiar with that one
15:18 * rbuels looks at your error
15:19 Meteorswarm oh, solanaceae
15:19 rbuels yep
15:19 Meteorswarm nifty; I'm working on Glycine
15:19 Meteorswarm well, and medicago for this project
15:19 rbuels we're also kind of morphing into a development shop supporting bioperl and gmod projects too
15:19 Meteorswarm nice
15:19 Meteorswarm this is the first use of bioperl in my lab; we've been using home-grown stuff, but I don't want to write my own XML parser
15:20 rbuels lol
15:21 rbuels this is not good that the tests are depending on neb.com responding
15:21 rbuels whatever neb.com is
15:22 Meteorswarm this is just an update, it might not be bioperl
15:22 Meteorswarm well, nevermind, it looks like those are bioperl packages
15:22 rbuels yeah
15:24 Meteorswarm it's giving it five tries... this is going to take a while
15:25 rbuels this needs to go to the mailing list
15:25 rbuels well....
15:25 rbuels what was your exact command you used to start the installation
15:26 Meteorswarm cpan update
15:26 Meteorswarm I can give you more of the details
15:27 Meteorswarm although it's probably at 10,000 lines of output now
15:27 rbuels what were the actual commands you typed
15:28 Meteorswarm I'm afraid I don't understand
15:29 Meteorswarm I typed cpan, then help, then clean, then upgrade
15:31 Meteorswarm also, it's given up on that server and has moved on
15:32 rbuels you'll probably have to 'force install BioPerl' anyway
15:32 rbuels cause that test failure will cause it to not want to install it
15:33 Meteorswarm in cpan?
15:33 Meteorswarm (I'm sorry, I'm not really used to dealing with all these perl modules)
15:37 rbuels yes, i was referring to typing that command in the cpan shell
15:37 rbuels sorry about being slow, i was looking into why that test is using a remote server
15:37 Meteorswarm no problem, I'm patient
15:38 rbuels cause it was my understanding that those tests were supposed to be disabled when bioperl is being installed from cpan like now
15:38 Meteorswarm I'm just glad to get any help :D
15:39 Meteorswarm so once this finishes should I install XML::SAX first or force install BioPerl first?
15:40 rbuels either one.
15:40 rbuels just ctrl-c to break out of it in fact
15:40 rbuels and go back to the command line
15:40 rbuels the system command line.
15:41 rbuels 'rm -rf ~/.cpan/build' to remove anything that might be hanging around dirty
15:41 Meteorswarm that won't mess up the install?
15:41 Meteorswarm the update*
15:41 rbuels nah, not really
15:41 Meteorswarm k
15:41 rbuels and it's better than sitting around waiting for something that's not going right anyway
15:42 rbuels ctrl-c, exit the cpan shell, get back to the system command line
15:42 rbuels rm -rf ~/.cpan/build to remove anything that might be in a weird state from breaking out of this
15:42 Meteorswarm ah, logical
15:42 rbuels then run the 'cpan' or 'sudo cpan' or whatever command to get back to the cpan shell
15:43 Meteorswarm should I be running cpan with sudo priveliges?
15:43 rbuels and type 'install Bio::Perl'
15:43 Meteorswarm yeah, looks like I have to be
15:43 rbuels the precise answer to that is it depends on if you are installing the modules you're getting into the system dirs, or into your own dir
15:44 Meteorswarm ah
15:44 rbuels in this case, you are installing into your system perl
15:44 Meteorswarm yeah, I'm using sudo now
15:44 Meteorswarm so I tried to install XML::SAX but it's saying YAML isn't installed
15:45 Meteorswarm although it says this might be harmless?
15:45 rbuels well...what operating system are you using?
15:45 Meteorswarm linux
15:45 Meteorswarm ubuntu 9.04
15:45 rbuels because you can usually install a lot of these things with packages
15:46 rbuels which is easier
15:46 Meteorswarm well, I tried to use the bioperl package from the repositories, but I think it's broken since it didn't work at all
15:46 rbuels i'm sure it did work.
15:47 rbuels sudo apt-get install bioperl libyaml-perl libxml-sax-perl
15:47 rbuels and that should get you running with little effort
15:48 rbuels see, the reason it's so hard to install things with cpan is because cpan is non-platform-specific, and there are so many things that are different between mac, windows, vms, linux, solaris, etc
15:48 rbuels which is why there is all this testing
15:48 rbuels and all this output to allow people to diagnose failures
15:48 Meteorswarm ah
15:48 Meteorswarm it is pretty verbose
15:49 rbuels but packages that you install with apt have already been configured and built and tested on ubuntu specifically
15:49 rbuels so they are much quicker to install, because somebody else has already done the cpan work
15:49 rbuels perl modules go from developer version control -> cpan -> OS vendor packagers -> OS packages
15:50 Meteorswarm when I installed bioperl from apt I couldn't even compile something with Bio::SeqIO in it, but I could have screwed something up
15:50 rbuels type that sudo apt-get install command i gave you
15:50 Meteorswarm so what happens if I install from apt after doing all this mucking about with cpan?
15:50 Meteorswarm rbuels: should I kill the cpan installer, then?
15:50 rbuels sure.
15:51 rbuels there is a hierarchy of perl modules on any system
15:51 rbuels system meaning 'machine'
15:51 rbuels well you can see it actually
15:51 rbuels perl -E 'say for @INC'
15:52 rbuels shows you all the places perl lookes for modules
15:52 rbuels and that's the order that it looks for htem
15:52 rbuels when you install modules with 'sudo cpan', they go into /usr/local/*
15:52 Meteorswarm uhh... http://gist.github.com/163381
15:52 rbuels installed with apt, they go into /usr/lib/*
15:53 rbuels yeah, you have XML::SAX already installed in /usr/local/ i guess
15:53 Meteorswarm yeah, I installed it manually
15:53 Meteorswarm just now
15:54 Meteorswarm well, the code compiles now
15:54 rbuels well, we could either try to remove it in favor of the (older) one from ubuntu, or we could try using the ubuntu bioperl with it
15:54 rbuels it's probably fine to use the one you just installed into /usr/local/
15:54 rbuels so just take the libxml-sax-perl package off of that command
15:55 Meteorswarm could not find ParserDetails.ini in /usr/local/share/perl/5.10.0/XML/SAX
15:55 rbuels oh
15:55 rbuels these stupid xml parsers.
15:55 Meteorswarm sorry for all the hassle
15:55 rbuels sigh
15:56 rbuels XML is misused a lot.
15:56 Meteorswarm so I hear
15:56 rbuels most of the things people use it for, it is not well-suited for
15:56 rbuels anyway
15:56 rbuels umm.
15:56 Meteorswarm unfortunately, I'm stuck with it, since the medicago annotations are in XML
15:57 rbuels sudo rm -rf /usr/local/share/perl/5.10.0/XML/SAX*
15:57 rbuels just blow it away
15:57 rbuels sudo apt-get install bioperl libyaml-perl libxml-sax-perl
15:57 rbuels and then do that again
15:59 Meteorswarm Can't locate XML/SAX/Writer.pm in @INC
15:59 rbuels running what?
15:59 Meteorswarm sorry
15:59 rbuels (what program says that?)
15:59 Meteorswarm trying to load Bio::SeqIO::tigrxml
15:59 Meteorswarm with my script
16:00 rbuels sudo apt-get install libxml-sax-writer-perl
16:00 rbuels (are you noticing a pattern here?)
16:00 Meteorswarm are all these thing separate packages?
16:00 rbuels most of them
16:00 Meteorswarm ok, now it load (I just have to get it to do what I want now >.<)
16:00 rbuels lol.
16:01 rbuels keep in mind that the bioperl that's in ubuntu is 1.5.2
16:01 rbuels apt-cache show bioperl will show you that
16:01 Meteorswarm that's fine, i'm pretty sure this stuff is trivial
16:01 Meteorswarm I just want to get the gene locations out of this tigrxml file
16:01 rbuels i don't know much about you, your lab, or your workflow, but probably sticking to debian packages would be the best way for you to go
16:02 rbuels based on our conversation thus far
16:02 Meteorswarm that would be much easier.  I just didn't know they exist
16:02 rbuels there are packages for a lot of perl modules
16:02 rbuels if you want modules Foo::Bar, you would do apt-cache search libfoo-bar-perl
16:02 rbuels if you want modules Foo::Bar, you would do apt-cache search foo | grep perl
16:03 rbuels or something like that
16:03 rbuels the usual package name for Foo::Bar would be libfoo-bar-perl
16:03 Meteorswarm I should have thought of that, thanks
16:04 rbuels does your lab use a version control system for your scripts?
16:04 rbuels if not, i'd highly recommend it
16:04 Meteorswarm no, it's just me and one other person writing
16:05 rbuels even for single-person projects, version control is indispensable when writing any kind of code, in my opinion
16:05 rbuels but, your mileage may vary
16:05 * rbuels shrugs
16:05 Meteorswarm I don't really know how to use it.  I'll look into it when I start working again after the semester starts (I'm an undergrad)
16:05 rbuels what are you majoring it
16:05 rbuels in
16:06 Meteorswarm double - biology and CS
16:06 Meteorswarm gah
16:06 rbuels heh.
16:06 Meteorswarm I'm trying to use the example from the wiki to parse this file
16:06 Meteorswarm and it's not parsing
16:06 rbuels what's the error
16:06 Meteorswarm nothing; it just looks at me
16:07 rbuels runs for a really long time?
16:07 Meteorswarm it seems to be running indefinitely
16:07 rbuels or just prints nothing?
16:07 Meteorswarm and prints nothing
16:07 rbuels if it's parsing a big file it could take a while...
16:08 Meteorswarm ah, didn't realize
16:08 rbuels you could run your script with perl -d to snoop on what it's doing if you want
16:08 Meteorswarm 2g megs?
16:08 Meteorswarm 26*
16:08 rbuels 26 mb is the size of the medicago annotation file?
16:09 rbuels also, could you put your script into gist?
16:09 rbuels as an aside, if you are a CS major, you need to learn a version control system.  right now.
16:09 Meteorswarm http://gist.github.com/163390
16:09 Meteorswarm rbuels: I suppose you're right
16:09 rbuels i was CS/EE
16:10 rbuels i went to cornell too
16:10 Meteorswarm nice
16:10 rbuels graduated in 03, meng 04
16:10 Meteorswarm you on the ACSU posters?
16:10 rbuels no, i wasn't in acsu
16:10 Meteorswarm the loop in that file is straight from the wiki
16:10 rbuels i was only minoring in cs
16:10 Meteorswarm ah
16:11 rbuels but yes, version control is at the absolute foundation of software development
16:11 rbuels i would recommend that the first version control system you learn be git
16:12 rbuels since if you learn git, any other vc system will be trivial
16:12 Meteorswarm I'll look into it
16:12 Meteorswarm I only have today and tomorrow before I go home, so now isn't the time to start
16:12 rbuels do you have a link to the file you're parsing?
16:12 rbuels i could download it and take a look
16:13 * deafferret lools
16:13 rbuels haha
16:13 Meteorswarm http://www.medicago.org/genome/downloads/Mt2/MT​2.0_medicago_chrX_20080103_NoOverlap.xml.tar.gz
16:13 Meteorswarm I'm parsing the first one as a test
16:14 * rbuels downloads it
16:15 Meteorswarm it's a biggie
16:15 rbuels when the semester starts up again, start using git for all your class projects
16:16 rbuels as the projects get bigger, you will be *very* glad you are using version control
16:16 rbuels especially if you are working with one or more partners
16:16 Meteorswarm I'm taking functional programming, so I think I'll need all the help I can get
16:17 rbuels cs 312x?
16:17 rbuels (don't remember what the extra numbers are they have been adding on)
16:17 rbuels that's a good course
16:17 Meteorswarm I keep hearing horror stories...
16:17 rbuels functional programming is very important for learning to be a better programmer
16:18 rbuels it is true that SML is not usually used in the real world, but that's not the point
16:18 Meteorswarm yeah, I already have a good grasp of basic recursion, but a deeper understanding is always useful
16:20 Meteorswarm I don't think it's parsing.  It's not using much CPU or RAM and it's not blocking for IO
16:20 rbuels it's not blocking for i/o?
16:20 rbuels are you sure?
16:21 Meteorswarm vmstat indicates no blocked processes
16:21 rbuels test2.pl tigrxml < medicago_chr0_20080103.xml
16:21 rbuels is how you should be running it
16:21 rbuels cause it is taking the xml on stdin
16:21 Meteorswarm without the <; it should be picking it up from STDIN anyway
16:22 Meteorswarm I'll try it again though
16:22 Meteorswarm well, that was different
16:22 rbuels no, for it to get things on stdin, you have to do either < or cat file | test2.pl
16:22 rbuels it was blocking on io
16:23 rbuels and now let me guess, the bioperl parser is not happy with it
16:23 rbuels cause that's what i am getting
16:23 Meteorswarm well, I think I got confused because while(<>) does read @ARGV
16:23 Meteorswarm yeah
16:23 Meteorswarm it's not parsing it happily
16:24 rbuels welcome to bioinformatics.
16:24 Meteorswarm yeah...
16:24 Meteorswarm am I stuck, then?
16:25 rbuels well the next thing to do is figure out why the parser doesn't like it
16:25 rbuels is this a crappy file, or is the parser buggy
16:25 rbuels it's one of the two
16:25 deafferret rbuels++  # welcome lol
16:25 rbuels yes deafferret knows exactly what i'm talking about
16:25 rbuels deafferret: should Meteorswarm learn to use version control, as a CS undergrad?
16:26 rbuels hehe
16:26 Meteorswarm well, for my purposes, should I just try to write my own parser?
16:26 rbuels depends on what your purposes are...
16:26 deafferret only if he ever wants to code anything anywhere  :)
16:26 rbuels exactly my sentiments.
16:26 deafferret if you're never going to read or alter source code, then version control is a total waste of time.  :)
16:27 rbuels hehe
16:27 rbuels hmmm let's see what's wrong with this file
16:27 nErVe joined #bioperl
16:27 rbuels deafferret, would you like to play along at home?
16:27 deafferret what are we talking about parsing? medicago_chr0_20080103.xml?
16:27 rbuels it's so fun....
16:27 rbuels http://www.medicago.org/genome/downloads/Mt2/MT​2.0_medicago_chrX_20080103_NoOverlap.xml.tar.gz
16:27 rbuels is the dataset
16:28 rbuels and http://gist.github.com/163390 is his script
16:28 deafferret Universitry of Nebraska Medical Center - Durham Research Center JOINS THE FRAY!! :)
16:28 rbuels and Bio::SeqIO::tigrxml does not like this
16:28 rbuels lol
16:28 Meteorswarm it doesn't seem to like half the tags it sees
16:28 rbuels Meteorswarm: are you sure this is tigrxml?
16:29 Meteorswarm it should be, but I can check again
16:29 * rbuels would not be surprised if the tigrxml format is not actually defined by anybody
16:29 Meteorswarm http://biolinx.bios.niu.ed​u/bios546/tigrxml_dtd.htm
16:29 deafferret Perl? ewww...
16:29 Meteorswarm is the specs my "boss" sent me
16:29 Meteorswarm for tigrxml
16:29 rbuels heh.
16:30 Meteorswarm on closer inspection, it's entirely possible this isn't tigrxml
16:30 Meteorswarm but that's not what I've been told
16:31 rbuels well it does have a <TIGR> top-level element
16:31 rbuels maybe that's enough for the medicago people to say it's tigr xml
16:31 rbuels lol
16:31 Meteorswarm medicago.org claims it's tigrxml
16:32 Meteorswarm "    MT2.0_medicago_chrX_20080103_NoOverlap.xml.tar.gz — Detailed Psuedomolecules annotation in TIGR XML format. "
16:32 deafferret Tommy Boy:   The reason why they have a guarrantee on the box is because they know all they sold you is a guarranteed piece of shit. Hell, I can take a crap in a box and slap a guarrantee on it for you, if that's what you want. But then all you have is a guaranteed piece of shit!
16:33 deafferret s/guarantee/tigrxml/
16:33 deafferret /g
16:33 Meteorswarm deafferret: nice
16:33 rbuels well it could also be that tigrxml.pm sucks
16:34 Meteorswarm either way, I'm stuck for now, so I'll start making a workaround
16:34 rbuels probably want to use xml::twig
16:34 rbuels sudo apt-get install libxml-twig-perl
16:34 rbuels perldoc XML::Twig
16:34 rbuels that's one of the least-unpleasant xml parsers
16:34 deafferret installing deps over here
16:35 Meteorswarm rbuels: thanks, that looks handy
16:35 deafferret heh. PERIGRIN XML parser... I just can't get away from #catalyst...
16:36 rbuels perigrin did twig/
16:36 rbuels oh, what's his new one
16:36 Meteorswarm thanks for all the help, I'm going to go take lunch and then set to work on twig
16:36 rbuels the one he talked about at yapc
16:36 rbuels Meteorswarm: ok, good luck
16:36 deafferret Meteorswarm: wait 30s
16:37 deafferret http://pastebin.com/m1731f197
16:37 deafferret is that where you guys are stuck too?
16:37 rbuels yeah that's what i get too
16:37 deafferret k. yay! stuck w/ rbuels!  :)
16:37 deafferret is that where Meteorswarm is stuck?
16:37 rbuels yeah i think so
16:37 deafferret roger
16:41 deafferret voicemail wars for a few minutes
16:41 rbuels probably send this stuff to the bioperl list?
16:41 rbuels i am quickly running up on enotime
16:42 deafferret http://github.com/jhannah/san​dbox/tree/master/Meteorswarm
16:42 deafferret we should have a common #bioperl repo
16:47 rbuels heh.  this could be it
16:47 deafferret assuming you + whoever doesn't care about my other sandbox junk  -shrug-
16:51 rbuels this seems to be a misunderstanding of how coords are supposed to be in tigrxml?
16:51 rbuels the parser is looking for <COORDS>?
16:51 rbuels and the file has <COORDSET>...
16:51 rbuels ?
16:52 rbuels see line 187 of tigrxml.pm?
16:52 deafferret medicago_chr0_20080103.xml is VERY different from bioperl-live/t/data/test.tigrxml
16:54 rbuels god it sure is
16:54 deafferret how deep does he need? I could XML::Twig up a simple parser if he only cares about a few fields
16:54 deafferret I'm not really interested in a 2 months "TIGR XML" history project
16:55 rbuels sigh
16:55 rbuels we should ask about this on the mailing list though at least
16:55 rbuels i'll write a quick thing
16:56 deafferret k. I pushed up a the_errors.txt file too.
17:34 Meteorswarm deafferret: I just need to extract the gene locations.  We have some sequences we built ourselves and I have a program to build a consensus, but I need to know where the genes are to do so in a meaningful way.
17:37 deafferret so you only need to extract 2-4 fields?
17:38 Meteorswarm I think just gene name and both ends would suffice
17:38 Meteorswarm let me pull up a gff3 file to check
17:38 Meteorswarm yeah, and the chromosome it's on
17:38 deafferret k. well, I'm impatient, so if I were you I'd punt Bio::SeqIO::tigrxml and use XML::Twig to parse the XML
17:39 Meteorswarm I don't really understand how twig works; is there more documentation than perldoc?
17:39 Meteorswarm yeah, this needs to be done asap, so I think I have to drop tigrxml
17:39 deafferret we're talking about parsing medicago_chr0_20080103.xml and similar, right?
17:39 deafferret xmltwig.com
17:39 deafferret lemme do you up a 5m demo
17:40 deafferret while you    perl -MCPAN -e 'install XML::Twig'   :)
17:40 Meteorswarm I have it installed
17:40 deafferret you need expat too ---  oh good
17:41 Meteorswarm libxml-twig-perl in the ubuntu repos
17:41 deafferret k. so if we look at the top of medicago_chr0_20080103.xml then the first set of data you want out is...?
17:42 deafferret chr00_pseudomolecule_IMGAG_V2 1 16948850    ?
17:42 Meteorswarm I don't think so, let me look
17:42 Meteorswarm I don't quite understand why they have a chromosome zero; maybe it's stuff they couldn't assign
17:44 Meteorswarm but what I want is the data in the gene list - AC144644_1, 59252 to 59461
17:44 Meteorswarm at least, that's how I'm interpreting the file
17:49 rbuels chr0 is usually stuff you can't physically map
17:49 rbuels meaning they don't know where in the genome it is
17:49 Meteorswarm perhaps I should be looking at chromosome one then, although it doesn't really matter for getting the program designed
17:51 deafferret Meteorswarm: here you go   http://github.com/jhannah/san​dbox/tree/master/Meteorswarm
17:51 deafferret xmltwig.pl
17:52 Meteorswarm thanks
17:52 deafferret rbuels: oh? is that the convention. look at you, teaching me stuff today  :)
17:53 * deafferret mails the tuition check
17:53 rbuels what, are going to lool now too?
17:54 deafferret we all have lool, deep within us. you just have to learn how to let it out
17:55 Meteorswarm deafferret: is there a way to get that to take STDIN rather than a specified file?
17:59 deafferret hmm... you probably have to slurp it all into mem and then parse($allofthat)
17:59 deafferret local $/ = undef; $xml = <>; $twig->parse($xml);
18:00 Meteorswarm sensible
18:00 deafferret until your file gets too big  :(
18:00 deafferret but you should be OK with these... RAM is cheap  :)
18:00 Meteorswarm this machine has 2G, these files are only 20-50 megs, I'll be fine :)
18:01 Meteorswarm but yeah, I've gotten familiar with memory constraints
18:02 Meteorswarm deafferret: wonderful, that program looks like it's doing just what I wished for; thanks a bundle!
18:02 deafferret woot!  :D    next comes the "oh, wait" moment  :)
18:03 Meteorswarm fiddlesticks
18:04 deafferret biology is really flipping good at dashing dreams  :)
18:04 Meteorswarm ah, but I'm paid by the hour :P
18:04 deafferret lol   yay!
18:05 Meteorswarm I'm not *totally* sure those are the gene names, the file kind of sucks, let me go see if a coworker knows
18:06 deafferret sure. from that demo you should be able to XML::Twig anything you want out of there  :)
18:06 Meteorswarm I'm sure I'll have more questions :D
18:06 deafferret XML::Twig has a billion billion fancy methods in it if you don't like the ones I tend to use
18:07 deafferret there's lots of ways to do it in there
18:07 deafferret I'm leaving for dirtbiking in a couple minutes. back this evening... I'm in here many hours a day 5-6 days a week
18:07 Meteorswarm thanks for all the help; have fun
18:08 deafferret :)   aim for the trees!
18:12 rbuels lord
18:12 deafferret &   stunt action!!
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