Improvement of bioengineering courses through systems biology and bioprocess modeling

This joint project applied MATLAB and Simulink to improve courses for Metabolic Engineering, Parameter Estimation for Engineering, Process Dynamics and Control, and a Process Control Laboratory in the Department of Energy, Environmental, and Chemical Engineering (EECE) at Washington University in St. Louis (WUSTL) in 2011-2013. The project also improved the existing bioengineering courses in the Department of Biosystems & Agricultural Engineering (BAE) at Michigan State University (MSU),specifically Microbial Systems Engineering and Analysis of Biological Systems in 2012~2014. Both MATLAB and Simulink were used in these courses. More than 100 undergraduate and graduate students per year from both universities have been enrolled in the classes in the past two years. The teaching approach was to introduce MATLAB and Simulink to bioengineering courses. Using computational modeling tools, students developed the equations for various applications in systems biology and bioengineering, solved the forward and the inverse problems, used Simulink to perform process control/design of engineering projects, and finally optimized bioprocesses (both static and dynamic modes) using MATLAB tool boxes. Moreover, students were exposed to real experiments in the bio-reaction lab where data were collected. For all courses, each student had a MathWorks-supplied license to use all necessary toolboxes. The class material is designed to teach bioengineering students multiple-scale modeling skills in both bioprocess engineering and systems biology so that they can have a holistic understanding of both scale-up fermentation engineering design and the microbial metabolism in response to bioreactor heterogeneity. Such skills are especially valuable for students looking to work in bioprocessing companies. Assessment was made through homeworks, projects, exams on MATLAB/Simulink, comments from students and other instructors, and feedback from alumni. Several of the students have now implemented MATLAB/Simulink in their research, introducing new methods to their advisors. Outcomes included a webpage with slides and notes posted for public access; two journal articles published, one book chapter published and two submitted, and one graduate course on MATLAB/Simulink that became a required course for graduate students in the Department of BAE at MSU.