Conceptualization and design of intellectualized, socialized, and personalized cyber-physical systems (CPSs) needs exploration and synthesis of novel knowledge. In turn, it raises the need for a combined use of interdisciplinary, multidisciplinary, and transdisciplinary research. Supradisciplinary research emerged as a new doctrine of combining these research approaches from epistemological, methodological, and procedural perspective. However, no methodology can be found in the literature that could facilitate the practical execution of supradisciplinary research programs and projects. This position paper proposes a conceptual framework that can be used as a blueprint of operationalization of such undertakings. The framework rests on six generic pillars: (i) problematics, (ii) infrastructure, (iii) methodics, (iv) stakeholders, (v) operations, and (vi) knowledge.The framework arranges the concerns in a procedural logic - as they should be considered by the research managers and cyber-physical system developers. In its current form, the framework does not cover the specific societal and personal issues of a successful organization of the inquiry at individual researchers, research teams, and research community levels. Notwithstanding, the framework can facilitate management of research organization tasks, joint formation of shared research infrastructure, setting up concrete research programs, projects, and processes, academic partnering and public stakeholder involvement, process flow management and capacity/competence allocation, and knowledge synthesis, assessment, and consolidation in a holistic manner. Follow up community-based research may focus on the practical application and testing of the framework in concrete cases – a task that an individual researcher cannot address.