Scientific workflows (SWFs) aim to automate cooperative design through compilation of known sequences of actions for routine procedures. However, current SWF systems lack the ability, in the one hand, to capture the context in which a SWF is designed and developed, and, in the other hand, to deliver a real-time assistance to help designers to make effective decisions in the selection of relevant SWFs for their problem. We propose a context-oriented framework for improving cooperative SWF design. This framework allows making context explicit and realizing the contextualization of SWFs in a SWF repository (and thus sharable with other scientists). Context is made explicit thanks to Contextual Graphs (CxGs), a formalism for representing uniformly all the ingredients of a cooperative SWF design process. Thus, scientists can customize information and formalize their research and strategies in a shared context. We use the context-oriented framework in an application in virtual screening. Finally, context-based formalisms, such as CxGs, appear as the key element to enhance users' cooperation during the SWF design phase.