This paper presents HyperGraphOS, a significant innovation in the domain of operating systems, specifically designed to address the needs of scientific and engineering domains. This platform aims to combine model-based engineering, graph modeling, data containers, and documents, along with tools for handling computational elements. HyperGraphOS functions as an Operating System offering to users an infinite workspace for creating and managing complex models represented as graphs with customizable semantics. By leveraging a web-based architecture, it requires only a modern web browser for access, allowing organization of knowledge, documents, and content into models represented in a network of workspaces. Elements of the workspace are defined in terms of domain-specific languages (DSLs). These DSLs are pivotal for navigating workspaces, generating code, triggering AI components, and organizing information and processes. The models' dual nature as both visual drawings and data structures allows dynamic modifications and inspections both interactively as well as programaticaly. We evaluated HyperGraphOS's efficiency and applicability across a large set of diverse domains, including the design and development of a virtual Avatar dialog system, a robotic task planner based on large language models (LLMs), a new meta-model for feature-based code development and many others. Our findings show that HyperGraphOS offers substantial benefits in the interaction with a computer as information system, as platoform for experiments and data analysis, as streamlined engineering processes, demonstrating enhanced flexibility in managing data, computation and documents, showing an innovative approaches to persistent desktop environments.