Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-07-25

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All times shown according to UTC.

Time Nick Message
01:16 kyanardag joined #bioperl
01:28 robotman joined #bioperl
01:28 robotman hello
01:29 robotman I am considering adding functionailty to bioperl and wondering if it is appropriate
01:30 robotman I am writing perl to control a tecan bio robot.  Currently there is zero souce for such control, except for some visual basic stuff.
01:30 robotman any comment?
01:32 robotman i.e. Bio::Robot::Tecan
01:33 robotman with socket support for client/server
01:38 deafferret I know nothing about tecan. You might try emailing the bioperl-l mailing list
01:40 robotman the tecan part I can figure out.  The robot uses strings.  My question is more about, is this interesting to add to bioperl?
01:41 rbuels robotman: possibly.
01:42 rbuels robotman: are these robots common?
01:42 robotman an example robot command is, fyi : Dispense(1,">> Water <<43","BUFFER_UL",0,0,0,0,0,0,0,0,0,​0,0,11,1,1,"0C0840000000000000",0);
01:42 robotman these robots are very common in bio labs
01:42 robotman tecan is one major vendor.   beckman is another
01:43 rbuels if you'd like to put your code up on github i could take a look
01:43 rbuels pyrimidine would probably take a look too
01:43 rbuels (cjfields)
01:43 robotman the PC app that controls the robot allows for commands to be passed thru a pipe.   So I have set up perl client/server which allows network machines to send robot commands thru the PC.
01:44 robotman I only have hacked the client-server currently.  It is at  http://jcline.svn.sourceforge.net/viewv​c/jcline/laboratory-robots-tecan/tests/
01:45 * rbuels looks
01:46 robotman the tecan has a couple hundred APIs.  So perl methods needed as wrappers for these.   mostly string manipulation.
01:47 robotman maybe, depending, the module would keep state.  so the user perl app could reference trays or tubes at a higher level than the tecan low level "move arm to X.  grip arm.  Move arm to Y." ..etc
01:49 rbuels what is the gemini applicaiton
01:49 robotman I have not yet scoped biojava yet, that might be the other choice.   other labs use java to preprocess/autogenerate the robot commands.   or C if they are nuts
01:49 rbuels not that much difference between java and c
01:49 robotman windows gui
01:49 rbuels ah
01:50 robotman it is a gui script thing
01:50 rbuels i could see this becoming quite a useful set of modules
01:50 robotman it would be masochism to do it in C, no easy string stuff
01:51 rbuels perhaps some sort of common API could be designed to control tecan, beckman, etc bots
01:51 robotman maybe if they are similar, I am not sure.  beckman uses "bioscript"
01:52 robotman I have not looked at that
01:52 robotman tecan is suprisingly open system.  all api's given.   others, I dont know, if they are string command or binary or closed system
01:53 rbuels hmmm.  well, the first steps here would be to put this code in modules, document them with POD, then put them in a standard CPAN distribution directory structure, and write some automated tests
01:54 rbuels probably would want to make some kind of module that is a mock robot to use as a test harness
01:56 robotman at least gemini gui app has a "simulate" mode
01:57 robotman the worst problem is the possibility to get the robot into deadlock.   i.e.  one arm can't move because the other arm is in the way.  apparently no s/w detection for that error so it just sits there.
01:57 rbuels heh.
01:57 robotman what is "standard CPAN distribution directory structure"
01:57 rbuels yeah, i was getting to that
01:58 deafferret http://search.cpan.org/~petdance/Modu​le-Starter-1.50/lib/Module/Starter.pm
01:59 rbuels mv tests Bio-Robot-Tecan; mkdir Bio-Robot-Tecan/lib; mkdir Bio-Robot-Tecan/t;
01:59 rbuels and then convert your .pl files to .pm files
01:59 rbuels and write POD
01:59 rbuels and commit that to your sf.nt
01:59 rbuels sf.net
01:59 rbuels i mean
02:00 rbuels that gets us started on the road to Well Packaged Perl Code
02:01 robotman Starter.pm is a template or something to run?
02:01 deafferret run module-starter. move your code into that.
02:01 rbuels that would work too
02:01 rbuels deafferret's idea is an alternate method using the Module::Starter thingy from cpan
02:02 rbuels once it is in modules, and a standard dir structure, and has POD, then we can look at it again
02:03 rbuels and then we can help you get it up on CPAN
02:03 deafferret module-starter blows out all the boilerplate of a well formed module distribution
02:03 deafferret I loves it.
02:03 rbuels roighto.
02:04 robotman I see
02:05 rbuels and once it's on CPAN, then we can start thinking about it being part of the bioperl project
02:05 robotman does any similar perl module already exist on cpan?
02:05 rbuels and then you're hitting the big time ;-)
02:05 rbuels i dunno....
02:05 * rbuels looks
02:06 rbuels no matches for 'tecan'...
02:06 deafferret search.cpan.org is your friend
02:06 rbuels yep, go to search.cpan.org and type things in the search box to see what's out there
02:06 robotman I didnt find anything in any journals either, it is like no one has even thought of doing this
02:07 rbuels oh i'm sure they have, they just haven't moved beyond the level you're at now, with a few little scripts that work most of the time for them
02:08 deafferret rbuels: you have no proof of that. big my rooster back its yellow book
02:09 rbuels wtf are you talking about
02:09 rbuels do i need to convert you back to a sulfide metabolism?
02:09 rbuels http://www.google.com/search?q=rooster+yellow+book
02:09 deafferret it's free association night here in #bioperl. cheese doodles fan grant stanley when overclocked
02:09 rbuels are you talking about rooster's auto care in Boise?
02:10 deafferret hell no. them's punk ass bitches
02:10 deafferret (channeling The Wire)
02:10 rbuels lol
02:10 deafferret hellz no
02:10 robotman any reason I should do this in bioperl instead of biopython?
02:11 deafferret python said nasty things about my grandma
02:11 robotman I havent written much in python anyway
02:11 * deafferret suspects he's no longer being helpful
02:11 deafferret is there a #biopython ? lets invade
02:12 rbuels heh, there is one but nobody's in there.  they have a chanserv though.  just not cool enough to use irc
02:12 rbuels robotman: all software needs a maintainer.  you're it, unless somebody else wants to take it up.
02:13 deafferret robotman: usually you write code in whatever language you find most useful to you. in my case, BioPerl is everywhere and does everything I need, so I stick to Perl. -shrug-
02:16 robotman right, adding it to bioperl distribution would make it more easily found as well.  rather than more mothballed code
02:17 robotman what do you think of the Tisdall Perl for Bioinformatics books?
02:18 deafferret ya. there's been lots of talk lately about the monolithic BioPerl distro being a bad idea. So we're working on spitting up into lots of little CPAN dists instead of one huge monster. So your new Bio::Robot::Whatever would be a welcome addition to the Bio::* family!  :)
02:18 robotman I thought they were interesting but didnt get me doing much useful stuff
02:18 deafferret so bioperl-l would probably have thoughts about what namespace you should use
02:18 deafferret but, as rbuels said: step 1 is getting it ready to go. POD, tests, etc
02:18 robotman yes, cpan has lots of 'robots' for web, not for physical robots
02:18 rbuels Module::Build::Authoring is a good doc to read on search.cpan.org
02:19 deafferret I went through some O'Reilly Perl/BioInf books. I'm been doing Perl for approximately forever though, so they didn't help me much
02:19 deafferret s/m/ve/
02:20 rbuels i have to jet gents
02:21 robotman thanks for the comments
02:21 rbuels email bioperl-l see if anybody else is interested in this
02:21 deafferret when you're a jet you're a jet for life
02:21 robotman any further pls send to jcline@ieee.org
02:21 deafferret or send me one of the robots and I'll test out your code for you
02:21 robotman especially regarding namespace..
02:22 rbuels robotman:  email a link to your code and what you told us to bioperl-l@lists.open-bio.org
02:22 deafferret $robot->dominate('globe')
02:22 biorobot YES MASTER|||
02:22 * deafferret laughs maniacally
02:22 robotman ok I am off as well
02:22 rbuels oh, um, i was going wasn't i
02:22 robotman bye
02:23 rbuels enough tomfoolery.
02:23 deafferret nope
02:23 rbuels robotman: email the list!
02:23 deafferret you were staying
02:23 deafferret STAY, rbuels! SIT!
02:23 * rbuels growls and lifts his leg....
02:23 rbuels to go!  &
02:23 * deafferret takes the treats away
20:47 biomoose joined #bioperl
20:47 biomoose biomoose: Siddhartha Basu master SHA1-b11cc61
20:47 biomoose Added Location role
20:47 biomoose http://bit.ly/HBVH7
20:47 biomoose left #bioperl

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