The Bio-jETI Framework - User-Level Workflow Design: A Bioinformatics Perspective - page 35

technology or input/output behavior. They can be seen as very simple
forms of ontologies, namely with a built-in is-a relation (subset concepts).

•

An important characteristic of the jABC is the formally defined structure
of its models, which facilitates the application of different flavors of formal
methods. For instance, in addition to the component-level validation that
is performed by the LocalChecker, it is also possible to verify global prop-
erties of a workflow model. Section 2.2 details how this constraint-guarded
workflow design is facilitated by the GEAR model checking plugin [35, 36].

• The SIBCreator plugin assists in the development of new SIBs. It can

be used in a top-down as well as in a bottom-up mode: In the top-down
mode, the SIB is specified via the SIBCreator, including information such
as name, parameters, branches, and implemented interfaces. From this
specification a skeletal SIB class is generated that then has to be equipped
with execution code to be readily usable. If a library containing the ex-
ecution code is already available, the SIBCreator can also be applied in
a bottom-up mode: methods from the libraries can be selected and the
SIBCreator generates SIBs that are tailored to their invocation.

Fig. 2.4 Schematic overview of the jABC framework as used for Bio-jETI

Summarizing the above, Figure 2.4 gives a schematic overview of the basic
parts of the jABC, the plugins and the associated technologies that have been
used in the scope of the Bio-jETI incarnation of the framework. The jABC
readily provides the menus that are common also to other programs (such
as file loading, saving, project management, etc.) and the canvas and func-
tionality for working with directed graphs, as well as menus and inspectors
for different purposes. The “*” characters around the latter are to denote
that these are the principal components to be extended and customized by
the plugins in order to add specific functionality. Some of the plugins (Tracer,
LocalChecker and TaxonomyEditor) work completely within the jABC frame-
work, while the others integrate external functionality provided by associated
technologies. For more detailed information about the architecture and plugin
concept of the jABC framework, see [306, 229, 235].