GeneFisher-P - User-Level Workflow Design: A Bioinformatics Perspective - page 97

Fig. 4.10 Loose programming of a GeneFisher-P workflow
4.3.2 Exemplary Workflow Composition Problem
Figure 4.10 (top) shows an example of a loosely specified GeneFisher work-
flow: Instead of modeling one of the (four) variants of the primer design
workflow explicitly, only the starting point (selection of an input file) and the
end point (storing of the result) are given. The connecting loose branch can
then be concretized dynamically into the currently intended, concrete primer
design workflow.
The lower part of the figure shows three possible workflow concretizations,
corresponding to variants of the GeneFisher-P workflows as described in Sec-
tion 4.2. The first variant simply performs the backtranslation and primer
design that is suitable for an input file that contains a single amino acid
sequence, while the third and fourth variant additionally perform the align-
ment computation, backtranslation and consensus calculation steps that have
to be performed prior to primer design in case of an input file that contains
multiple amino acid sequences. The inclusion of the respective services in the
solution can simply be achieved by constraints that enforce their existence.
Likewise, the other variants of the primer design workflow can be created by
varying the constraints.