Object-oriented (OO) concepts are built into most modern programming languages and databases. BioLegato brings OO concepts to the laboratory biologist. BioLegato is best thought of as a GUI that launches other programs. As in most GUIs, each BioLegato window consists of a canvas for displaying and manipulating data, and a set of pull-down menus. In the OO paradigm, the canvas corresponds to the data, and the menus correspond to the methods associated with that data. Rather than being hard-coded, menus and canvas are read at runtime. To specify the contents of menus, we have created a small language, PCD. Canvases are implemented as Java plugins. Thus, a new GUI can be created by choosing a canvas appropriate to the data and writing menus in PCD. By analogy, BioLegato can be thought of as a generic Object class, which can be reused and extended.
    Programs in the BIRCH bioinformatics system can be run through a growing number of BioLegato interfaces: bldna, for DNA sequences; blprotein for proteins; blmarker for molecular markers; bltree for phylogenetic trees, and birch, a launcher for programs in BIRCH. A BioLegato database client is in the prototype stage. Virtually all methods in BioLegato call external programs, meaning that BioLegato can run either locally installed programs or remote web services. Wherever possible, the output appears in a new BioLegato window, allowing ad hoc pipelining. For example, when bldna translates a DNA sequence, the protein output pops up in a blprotein window. The programmability of BioLegato speeds development of new GUIs for almost any sort of data, giving biologists objects that behave like the real-world entities they represent.

BIRCH Web site: http://home.cc.umanitoba.ca/~psgendb