A Case Study of ObjectOriented BioChemistry A Unified Specification of the Coagulation Ca.pdfVIP

14 Genome Informatics 14: 14–22 (2003) A Case Study of Object-Oriented Bio-Chemistry: A Unified Specification of the Coagulation Cascade Jacqueline Signorini Patrick Greussay sign@ai.univ-paris8.fr pg@ai.univ-paris8.fr Artificial Intelligence Laboratory, Universit´e Paris-8, 93526 Saint-Denis, France Abstract We propose a case study where a familiar but very complex and intrinsically woven bio- computing system - the blood clotting cascade - is specified using methods from software design known as object-oriented design (OOD). The specifications involve definition and inheritance of classes and methods and use design techniques from the most widely used OOD-language: the Unified Modeling Language (UML), as well as its Real-Time-UML extension. First, we emphasize the needs for a unified methodology to specify complex enough biological and biochemical processes. Then, using the blood clotting cascade as a example, we define the class diagrams which exhibit the static structure of procoagulant factors of proenzyme-enzyme conversions, and finally we give a dynamic model involving events, collaboration, synchronization and sequencing. We thus show that OOD can be used in fields very much beyond software design, gives the benefit of unified and sharable descriptions and, as a side effect, automatic generation of simulation software. Keywords: object-oriented design, UML specifications, blood clotting cascade, proteolytic enzyme networks. 1 Introduction OOD for non-software complex systems: Object-oriented progr