This video shows preliminary testing results of our Beaglebone Black-based hardware setup of a continuous-culture bioreactor used to grow microorganisms under precisely-controlled conditions. Such systems are used a variety of systems biology experiments by our collaborators at UTSW, with broad applications such as understanding antibacterial resistance acquisition, and more generally, evolution. The model-based design and analysis of the reconfigurable continuous-culture bioreactor led to insights and issues in existing systems and designs, and our redesign increases confidence of the validity of data recorded during experiments, in addition to being about two orders of magnitude less expensive than comparable systems. This is done by performing detailed systems modeling and analysis, as well as relying on high-confidence embedded system components, such as the Xenomai Linux real-time operating system (RTOS).
A preliminary description of the model-based design and analysis appeared in the paper “Model-based design and analysis of a reconfigurable continuous-culture bioreactor,” Luan Viet Nguyen, Eric Nelson, Amol Vengurlekar, Ruoshi Zhang, Kristopher I White, Victor Salinas, and Taylor T. Johnson, in Proceedings of the 4th ACM SIGBED Workshop on Design, Modeling, and Evaluation of Cyber Physical Systems (CyPhy 2014), Berlin, Germany, April 2014 (available online), a workshop affiliated with the Cyber-Physical Systems Week (CPSWeek) 2014. The system was designed almost entirely by the UTA CSE and EE graduate and undergraduate coauthors, in conjunction with assistance and feedback from the biology coauthors at UTSW and supervision by Dr. Taylor Johnson of the Computer Science and Engineering Department at The University of Texas at Arlington.
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