[Bioperl-l] Bio::Robotics namespace discussion

[Smithies, Russell]

I "acquired" an old Biomek 1000 that I'm thinking of modernising. It was originally controlled by a monstrously large but slow pc (IBM Value Point Model 466DX2 computer with Microsoft Windows* Version 3.1)
My plan is to fit a 3-axis CAD/CAM stepper controller (about $60) and use software like mach3 www.machsupport.com along with G-code to control it.
I come from an engineering background so it seemed like the easy way to me :-)

Now I just need a bit of free time to get it working...

--Russell


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Jonathan Cline
> Sent: Thursday, 30 July 2009 2:07 p.m.
> To: bioperl-l at lists.open-bio.org
> Cc: Jonathan Cline
> Subject: [Bioperl-l] Bio::Robotics namespace discussion
> 
> I am writing a module for communication with biology robotics, as
> discussed recently on #bioperl, and I invite your comments.
> 
> Currently this mode talks to a Tecan genesis workstation robot (
> http://images.google.com/images?q=tecan genesis ).  Other vendors are
> Beckman Biomek, Agilent, etc.  No such modules exist anywhere on the
> 'net with the exception of some visual basic and labview scripts which I
> have found.  There are some computational biologists who program for
> robots via high level s/w, but these scripts are not distributed as OSS.
> 
> With Tecan, there is a datapipe interface for hardware communication, as
> an added $$ option from the vendor.  I haven't checked other vendors to
> see if they likewise have an open communication path for third party
> software.  By allowing third-party communication, then naturally the
> next step is to create a socket client-server; especially as the robot
> vendor only support MS Win and using the local machine has typical
> Microsoft issues (like losing real time communication with the hardware
> due to GUI animation, bad operating system stability, no unix except
> cygwin, etc).
> 
> 
> On Namespace:
> 
> I have chosen Bio::Robotics and Bio::Robotics::Tecan.  There are many
> s/w modules already called 'robots' (web spider robots, chat bots, www
> automate, etc) so I chose the longer name "robotics" to differentiate
> this module as manipulating real hardware.  Bio::Robotics is the
> abstraction for generic robotics and Bio::Robotics::(vendor) is the
> manufacturer-specific implementation.  Robot control is made more
> complex due to the very configurable nature of the work table (placement
> of equipment, type of equipment, type of attached arm, etc).   The
> abstraction has to be careful not to generalize or assume too much.  In
> some cases, the Bio::Robotics modules may expand to arbitrary equipment
> such as thermocyclers, tray holders, imagers, etc - that could be a
> future roadmap plan.
> 
> Here is some theoretical example usage below, subject to change.  At
> this time I am deciding how much state to keep within the Perl module.
> By keeping state, some robot programming might be simplified (avoiding
> deadlock or tracking tip state).  In general I am aiming for a more
> "protocol friendly" method implementation.
> 
> 
> To use this software with locally-connected robotics hardware:
> 
>     use Bio::Robotics;
> 
>     my $tecan = Bio::Robotics->new("Tecan") || die;
>     $tecan->attach() || die;
>     $tecan->home();
>     $tecan->pipette(tips => "1", from => "rack1");
>     $tecan->pipette(aspirate => "1", dispense => "1", from => "sampleTray", to
> => "DNATray");
>     ...
> 
> To use this software with remote robotics hardware over the network:
> 
>   # On the local machine, run:
>     use Bio::Robotics;
> 
> 	my @connected_hardware = Bio::Robotics->query();
>     my $tecan = Bio::Robotics->new("Tecan") || die "no tecan found in
> @connected_hardware\n";
>     $tecan->attach() || die;
>     $tecan->configure("my work table configuration file") || die;
>     # Run the server and process commands
>     while (1) {
>       $error = $tecan->server(passwordplaintext => "0xd290");
>       if ($tecan->lastClientCommand() =~ /^shutdown/) {
>         last;
>       }
>     }
>     $tecan->detach();
>     exit(0);
> 
>   # On the remote machine (the client), run:
>     use Bio::Robotics;
> 
>     my $server = "heavybio.dyndns.org:8080";
>     my $password = "0xd290";
>     my $tecan = Bio::Robotics->new("Tecan");
>     $tecan->connect($server, $mypassword) || die;
>     $tecan->home();
>     $tecan->pipette(tips => "1", from => "rack200");
>     $tecan->pipette(aspirate => "1", dispense => "1",
>     	from => "sampleTray A1", to => "DNATray A2",
>     	volume => "45", liquid => "Buffer");
>     $tecan->pipette(drop => "1");
>     ...
>     $tecan->disconnect();
>     exit(0);
> 
> 
> 
> --
> 
> ## Jonathan Cline
> ## jcline at ieee.org
> ## Mobile: +1-805-617-0223
> ########################
> 
> 
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