[Pipet Devel] The Loci Project

J.W. Bizzaro bizzaro at bc.edu
Sat Apr 3 19:18:38 EST 1999

Hello Grail developers!

The Loci Project developers have been seriously discussing the use of Grail in
our project.  Let me tell you a bit about the project.

Loci is a framework for connecting various "computational biology" programs
together via Python and XML.  We are using a Python workflow and object server
called "PAOS", by Carlos Maltzahn, who has joined us.  And Loci will provide a
highly graphical front end to command-line programs by using James Henstridge's
PyGTK and PyGNOME bindings.

A "locus" is any tool in Loci, either graphical or analytical.  Each "GUI locus"
will essentially be an XML browser, but not a generic browser requiring XSL's. 
We are working on our own DTD's for the description of biomolecular data, and
the GUI "loci" will be made to display those.

But this is where it gets real fun.  The XML (called LocusML) will not only
describe the biological data but embed a Python script to make the GUI.  So each
GUI locus is a skeleton (written in C-GTK or PyGTK) that can read a Python
script that calls on C-GTK "biowidgets" and PyGTK widgets.  The result is a
browser that can run applets in its window.

Sound familiar?

PAOS really becomes important because we plan to have command-line programs and
databases reside on servers distributed throughout the Internet.  What happens
is a Loci user requests an analysis of some data, PAOS sends the request to the
appropriate server, the command-line program performs the analysis, the server
sends the analysis back BUT also attaches the appropriate GUI for
display/visualization, and finally the GUI locus is brought up to display the
GUI (applet) and the analysis.

I can't stress enough how VERY unique and complex this project is.  So rather
than starting from scratch, we know we should make use of other programs that
match certain parts of Loci.  Of course Grail is something like the GUI locus,
with the exception that the locus uses XML and PyGTK.  But I did just see a
message on this list about someone wanting to switch Tkinter for PyGTK ;-)

The project has obviously just begun.  We have more than one dozen "biohackers"
that have been helping hammer out the design and are ready to begin coding.  If
some Grail developers would like to take Grail in this new direction, we would
be ecstatic!

The Loci Project is the first project of an upstart scientific organization
called "The Open Lab".  The Lab is Internet-based and developing open-source
software, in addition to carrying out computational biology research.  It is
unfunded at the time, but that may change since we have routes to fund
scientific projects.

For more information on Loci, please visit our (incomplete) Web site:

and the mailing list archive:


If you would like to help implement Loci, PLEASE contact me (Jeff):

    bizzaro at bc.edu

Thank you!
J.W. Bizzaro                  mailto:bizzaro at bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/

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