The modern education system strives for an individualised approach, allowing each student to unlock his or her potential. Hybrid intelligent systems play a key role in this process. These systems offer level adaptation. Complex knowledge is presented according to the individual needs of each student. They aim at developing creativity. Students are given the opportunity to realise their potential in solving a variety of problems. Hybrid systems encourage multiple goals. Students become participants in a multifaceted learning process and have the opportunity to choose the direction of their activity. There is a synthesis of two disciplines, which allows solving complex problems with the help of computer modelling. As a result, students self-organise. They become active participants of the educational process, form their own way of development. They master not only knowledge, but also methods of scientific cognition, which allows them to apply modern achievements in science. The aim of this work is to create a system that will allow students to develop their scientific potential in the conditions of digital transformation. The basis of this work is a hybrid intellectual environment. Such an environment provides the development of hierarchical databases and fundamental problem sets for students’ research activities. Intellectual management within such an environment provides directed development of project-research activity.