The research is structured following the scale of the examined levels of analysis, from macro to micro. The first level shows the dynamic analysis of the studied system as a whole (worldwide biofuel research and innovation), and serves as an introduction to the complex system model. The second level of analysis focuses on a meso level focusing on the country level. After the meso level, the study narrows with the analysis of the system at the micro level, this corresponds to organizations such as universities and businesses. Finally, two complementary analyses will be made. The first focuses on the intricacies of the system itself and the elements that compose it - patents and publication in this case - . The second is a validation exercise where, as a baseline, a more basic approach will be used and compared the general approach taken throughout the thesis.