Related Work - User-Level Workflow Design: A Bioinformatics Perspective - page 158

systems that have been made for a particular field of biological research (Sec-
tion 8.1.3). Finally, Section 8.1.4 gives a survey of the presented systems and
compares them to Bio-jETI with respect to the requirements for workflow
management systems identified in Section 1.1.3.
Note that this selection of workflow systems raises no claim to complete-
ness 1 , but rather aims at giving a representative overview of the variety of
systems that is available. Further reviews of workflow systems from different
perspectives can be found, for instance, in [242, 106, 355].
8.1.1 Domain-Independent Workflow Systems in
Bioinformatics
As a general review of domain-independent workflow systems would be beyond
the scope of this work, this survey is restricted to domain-independent systems
thathave known applications in the bioinformatics domain. In contrastto many
of the frameworks that are the subject of the following sections, these systems
are usually based on sound softwareengineering techniques and thus they main-
tain the power of, for instance, model-driven design paradigms when they are
used in the bioinformatics domain. These systems become domain-specific es-
sentially by the definition of an appropriate domain model, that is, the inte-
gration of domain-specific services and the formal definition of semantic meta-
information. Clearly, Bio-jETI also falls in this category of systems.
BPEL
BPEL (lately also termed BPEL4WS, Business Processes Execution Lan-
guage for Web Services) [30, 140] is a framework for the composition of
Web Services into processes, explicitly following the SOA (Serive-Oriented
Architecture) paradigms. BPEL is the de-facto standard for business pro-
cess modeling and has been implemented by a number of frameworks, for
instance by ActiveVOS (formerly ActiveBPEL), Sun's OpenESB and IBM's
WebSphere Process Server. Although being conceived for business process
modeling, BPEL has also been used for the realization of scientific workflows
(cf., e.g., [79, 117]).
BPEL workflows are composed from Web Services. The relationship be-
tween the services is defined by means of control-flow constructs (such as
if-conditions, for-each- and while-loops) and activity containers (such as se-
quence and flow). The data is represented by XML documents, on which
XPath and XQuery operations can be performed. An important notion of
BPEL is to expose the entire workflow model as Web Service again, so that
hierarchical composition is directly supported.
1 A complete review is probably out of scope of any work. As of June 2012,
Wikipedia's “bioinformatics workflow management systems” entry [340] alone
lists 28 examples and includes references to further systems, and still covers only
a small number of the actually available systems.