MoBiFlow: Principles and Design of a Workflow System for Molecular Biology

Web-based problem solving environments provide sharing, execution and monitoring of scientific workflows. Where they depend on general purpose workflow development systems, the workflow notations are likely far too powerful and complex, especially in the area of biology, where programming skills are rare. On the other hand, application specific workflow systems may use special purpose languages and execution engines, suffering from a lack of standards, portability, documentation, stability of investment etc. In both cases, the need to support yet another application on the desk-top places a burden on the system administration of a research lab. In previous research the authors have developed the web based workflow systems Calvin and Hobbes, which enable biologists and computer scientists to approach these problems in collaboration. Both systems use a server-centric Web 2.0 based approach. Calvin is tailored to molecular biology applications, with a simple graphical workflow-language and easy access to existing BioMoby web services. Calvin workflows are compiled to industry standard BPEL workflows, which can be edited and refined in collaboration between researchers and computer scientists using the Hobbes tool. Together, Calvin and Hobbes form our workflow platform MoBiFlow, whose principles, design, and use cases are described in this paper.