Cell-based immunotherapies are a modern treatment approach holding promise to utilize nature’s own power to treat diseases that develop on the ground of immune system aberrations. Such diseases include cancer that develops and progresses via immune escape and on the other hand rejection of transplanted organs that need to be accepted by the immune system. Because the functions of distinct immune cell populations are highly plastic and interdependent, a better understanding of the complex regulation of immune system responses is indispensable for the optimization of cell therapies. The central goal of MODICELL therefore is to learn how to effectively instruct immune cells prior to being transferred to excite immune system responses tailored to patients’ needs. MODICELL will particularly seek to understand how to support immune activity in cancer patients by enhancing anti-cancer immunity and in transplantation immunology by inducing controlled tolerance to prevent organ rejection. MODICELL will accomplish this goal by testing agent-based models in a multidisciplinary platform combining academic expertise and industrial know-how. One academic institution will provide computer modelling to generate predictions on the interaction of immune cells under various conditions, providing hits for the other partners to test. The SMEs will use different but complementary strategies for enhancing anti-cancer immune therapies. On the other side of the immune spectrum, another academic partner will focus at enhancing tolerance in transplantation. MODICELL’s approach will enable all partners to optimise and synergize efforts to reach their goals at covering a large range of immune system responses. Thus, MODICELL will provide a highly dynamic platform for expertise and knowledge transfer between distinct sectors that can only succeed by bridging human resources, technology and creativity from the academic and industrial backgrounds.