The work described in this paper is a contribution to the problems of managing in data-intensive scientific applications. First, we discuss scientific workflows and motivate there use in scientific applications. Then, we introduce the concept of cooperative processes and describe their interactions and uses in a flexible cooperative workflow system called \textit{Bonita}. Finally, we propose an approach to integrate and synthesize the data exchanged by the mapping of data-intensive science into Bonita, using a binary approach, and illustrate the endeavors done to enhance the performance computations within a dynamic environment.