PEPAʼd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, Illustrated by a Pacific Oyster Case Study

We present a Bio-PEPA (Biochemical-Performance Evaluation Process Algebra) computational model for the Pacific oyster, derived from a DEB (Dynamic Energy Budget) mathematical model. Experience with this specific model allows us to propose a generic scheme for translation between the widely-used DEB theory and Bio-PEPA. The benefits of translation are that a range of novel analysis tools become available, therefore improving the potential to understand complex biological phenomena at a systems level. This work also provides a link between biology, mathematics and computer science: such interlinking of disciplines is the core of the systems approach to biology.