This paper is a contribution to concepts and methodologies of context definition in Engineering Model System (EMS). Change for contextual modeling was important paradigm shift in engineering at beginning of this new century. By now, EMS is a very complex model because it is required to serve all engineering activities during lifecycle of an engineering achievement (EA). In an EMS, the structure of contexts serves integration as glue. An EA is the objective of an engineering program and generally is an industrial or commercial product. Four new concepts and methods were introduced during the work for this paper with the requirement of their integration in EMS namely the Integrated Lifecycle Engineering (ILE), the Integrated Autonomous Model System (IAMS), the Reactive Context Structure (RCS), and the Integrated Research Project (IRP). ILE organizes research intensive engineering activities to support connection between essential engineering and relevant modeling software platform (MPS) activities. ILE includes fundamental and problem solving research in new context. IAMS is based on formerly published EMS concepts and includes new specifics. In the center of IAMS, enhanced structure of context definitions and their organization constitute glue in the demanded complex model. IAMS is characterized as an enhanced media for engineering communication. RCS serves as integrated unit of IAMS to enhance context driven reactive communication. In this way, IAMS includes two ways reactive context driven connection between IAMS and the physically operated Cyber Physical Biological System (CPBS) it represents. IAMS serves as digital twin of CPBS. The above new concepts and methods are suitable to develop as user defined components in EMS using MPS resources. IRP is introduced as a specific integrated application of ILE, IAMS, and RCS, concentrating on PhD student research specifics.