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This paper describes a design process to support the development of a learning collaboratory, a distributed, computer-based, virtual space for learning and work. A learning collaboratory, as a distributed distance learning environment, offers great opportunities to expand the way people teach and learn and to broaden educational opportunities to an ever increasing range of learners. The challenge is to design distance learning technologies that engender meaningful learning experiences that take full advantage of the power of computer-mediated communication to support innovative learner-centered and collaborative interactions between students, teachers, subject experts, and resources. First, the paper describes the learning collaboratory design framework (LUCIDIFY), a design process that integrates methods and concepts from cognitive systems engineering, theories of learning and instruction, distributed computing, and computer-supported collaborative learning to guide the principled design of learning collaboratories. Next, the paper describes how LUCIDIFY was used in the design and implementation of the collaborative learning environment for operational systems (CLEOS), a learning collaboratory for teachers, students, and practitioners in the physical sciences. CLEOS features two virtual instrument tutorials, an asynchronous messaging system, a project-based design and management application, and a collaborative multi-user domain infrastructure.