An appropriate arranging of science, technology, and innovation systems (STIS) becomes essential for emerging countries. A good management of the system allows a more efficient use of the natural and human resources and a better answer to global challenges. Data about the Cuban Science, Technology, and Innovation System (CSTIS) and its characteristics are rare in the literature. This Perspective introduces a general landscape about the growth of the CSTIS focused on the development of computational sciences and its relation to the biotechnological and pharma technologies. General features, main results, and challenges of the CSTIS system are presented here. On the other hand, growth of computational sciences is crucial because they allow to save material and human resources, energy and time, and their progress become critical as a support of the applied research, mostly in the field of the biotechnology and pharma industry. In this paper, the most relevant Cuban groups that perform research in computational chemistry, computational physics and bioinformatics are reported. According to my opinion, the training of new professionals in transdisciplinary fields (like bioinformatics), new technological infrastructure available and the accumulated experience of the computational research groups is a good platform to think about a promising future of these sciences and their contribution to the Cuban economy and society. Cuba's experiences in the management of the STIS may be very useful for emerging countries, especially those with low financial resources.