The Bio-jETI Framework - User-Level Workflow Design: A Bioinformatics Perspective - page 34

successful or not (typically used labels therefore are default and error ,
respectively).

•

The Genesys plugin, a jABC plugin for using the Genesys code generator
framework [144, 142], can be used to automatically compile any executable
workflow model into a single deployable application that can be run inde-
pendently of the jABC. The generated application can be, in the easiest
case, a standard Java application or Servlet, which can be deployed to any
platform for which a Java virtual machine is available (nowadays ranging
from mobile phones to supercomputers). The code generators that are
used within Bio-jETI also interpret jABC models as control flow graphs,
using principally the same mechanisms as the Tracer does.
Genesys supports two major classes of code generators: Extruders ,
which directly use the execution facilities of the jABC framework (pro-
viding features like thread and event handling, and special types of SIBs
and SIB parameters), and Pure Generators , which compile for the run-
time engine provided by a platform of choice (like, e.g., the Java Runtime
Environment (JRE)), and where the resulting code is totally independent
of the jABC framework.

• jETI (Java Electronic Tool Integration) [202] is a platform for easy de-

ployment of file-based command line tools as remote services. A more
detailed description of the platform is given in the next section. The jETI
plugin is used to accomplish the communication with jETI services.

• With the LocalChecker , SIB configurations can be validated during work-

flow development. The LocalChecker provides means to specify properties,
preconditions, and environment conditions at the component level. Exam-
ples of local check properties are the correct setting of parameters and the
correct and complete connection of a SIB in the surrounding model (e.g.,
no dangling mandatory exits for a SIB) - cases where erroneous configu-
rations would hamper the correct execution of the control flow.

• The PROPHETS plugin [232, 234] enables constraint-driven workflow de-

sign according to the loose programming paradigm of [178]: rather than
requiring workflow designers to model everything explicitly, the workflow
model does only have to be specified roughly in terms of ontologically
defined “semantic” entities. These loose specifications are then automat-
ically concretized to fully executable concrete workflows by means of a
combination of different formal methods. The PROPHETS plugin is intro-
duced and discussed in detail in Section 2.3, where the topic of constraint-
driven workflow composition in the jABC is addressed.

Additionally, Bio-jETI makes use of the following feature plugins:

• The TaxonomyEditor plugin can be used to define special-purpose clas-

sifications of the SIB libraries, called taxonomies. By default, the jABC
presents the available SIBs according to their location (as Java classes)
in the Java package hierarchy. Taxonomies group services according
to specific classification criteria or viewpoints, such as function, origin,