Introduction - User-Level Workflow Design: A Bioinformatics Perspective - page 29

1. Introduction to the addressed biological questions and the associated
analysis methods and software.
2. Presentation of exemplary service libraries and workflows for the ap-
plication scenario. Note that although this is not shown explicitly,
executable workflows are developed in all examples.
3. Application of the constraint-driven workflow design methodology to
the workflow scenario. Therefore, it is shown how the respective do-
main models are equipped with adequate semantic annotations and
how they are used for (semi-) automatic composition of already known
and of new workflows. The developed domain models are (deliberately)
not “perfect” (if this is actually possible), but thus they are suitable
to illustrate crucial aspects of the domain modeling.
Note that the process of domain modeling and workflow design with
Bio-jETI is described most elaborately for the first example application
(Chapter 3). In particular, Sections 3.3.3 and 3.3.4 discuss and illustrate
in detail an exemplary workflow composition problem and solution refine-
ment strategy, showing the considerable impact that constraints can have
on the obtained solutions. This demonstrates how the framework enables
the user to “play” with synthesis configurations and constraints in order
to explore the solution space interactively and finally arrive at an ade-
quate set of constraints. In order to avoid unnecessary redundancies, the
presentation of the other examples is shorter in this regard and restricted
to the summarizing description of the finally applied constraints.

• Chapter 7 gives an analysis and evaluation of the loose programming ap-

plications, drawing first conclusions and highlighting distinctive features.
The “lessons learned” from the work on the applications are furthermore
used to assess the capabilities and limitations of the developed methodol-
ogy and to formulate pragmatics that provide guidance for its successful
application.

• Chapter 8 discusses the relation of Bio-jETI to other approaches to bioin-

formatics workflow management. Therefore, it reviews a selection of dif-
ferent workflow systems that have been applied to or designed for the
bioinformatics domain and compares them to Bio-jETI. Additionally, it
investigates the substantial differences between control-flow-oriented and
data-flow-oriented workflow modeling.

• Chapter 9 concludes this topic with a summary and a discussion of re-

maining challenges and their implications for future work.