This thesis studies the feasibility and methodology of applying state-of-the-art computer technology in scientific workflow modelling, within a collaborative environment. The collaborative environment also indicates that the people involved include non-computer scientists or engineers from other disciplines. The objective of this research is to provide a systematic methodology based on a web environment for the purpose of lowering the barriers brought by the heterogeneous features of multi-institutions, multi-platforms and geographically distributed resources which are implied in the collaborative environment of scientific workflow.