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Chapter 2 Modeling Genome Data Processing Pipelines

In order to conduct analyses on genome data, different calculation steps have to be done in a specific order, which constitutes a genome data processing pipeline. Still a lot of research is in process, in order to find faster and more reliable ways to do various analyses, so single steps or the whole sequence of the pipelines might be subject to change. Amodular and flexibleway to configure pipelines could simplify their use and the sharing of pipelines between researchers. With a possibility to configure pipelines without altering source code, bioinformaticians and technicians would be relieved of the task to rewrite a pipeline every time a single algorithm changes. This contribution proposes to use common process modeling tools for the abstract representation of genome data processing pipelines. The benefits and drawbacks of different process model notations are examined with special focus on the possibilities to specify execution semantics. As a prototype, a system for the parsing and execution of genome data processing pipelines specified in business process model and notation, is introduced.