Teaching Systematic, Reproducible Model Development Using Synthetic Biology

Authors

DOI:

https://doi.org/10.18260/2-1-370.660-132665

Abstract

We present an educational unit to teach computational modeling, a vital part of chemical engineering curricula, through the lens of synthetic biology. Lectures, code, and homework questions provide conceptual and practical introductions to each computational method involved in the model development process, along with perspectives on how methods can be iterated upon to arrive at a final model. Ultimately, this content can be applied broadly to address questions in synthetic biology and classical chemical engineering.

Author Biographies

Kate E. Dray, Northwestern University

Kate E. Dray was a PhD candidate in the department of Chemical and Biological Engineering at Northwestern University at the time of this study, and she has since graduated. Her research focuses on systematizing the model development process in synthetic biology to improve rigor and reproducibility of the process. She has also developed and analyzed numerous dynamic models of synthetic biological systems designed to improve mechanistic understanding and drive future experimentation. 

Kathleen S. Dreyer, Northwestern University

Kathleen S. Dreyer is a PhD candidate in the department of Chemical and Biological Engineering at Northwestern University. Her research involves developing dynamic models of synthetic biological systems to predict outcomes of novel design choices. Her work focuses on automating the design process to expand predictive capability of models beyond that of intuition-guided manual design. She served as the Teaching Assistant in the computational biology course where the described educational unit was first implemented. 

Julius B. Lucks, Northwestern University

Julius B. Lucks, PhD, is a Professor of Chemical and Biological Engineering at Northwestern University. He earned his PhD in Chemical Physics at Harvard University. His research focuses on elucidating the principles of RNA folding and function, and using these principles to create biotechnologies that benefit humanity. He is the PI on the first National Science Foundation Research Training Program in Synthetic Biology, aimed at developing new approaches to teach synthetic biology across disciplines. 

Joshua N. Leonard, Northwestern University

Joshua N. Leonard, PhD, is an Associate Professor of Chemical and Biological Engineering at Northwestern University. He earned his PhD in Chemical Engineering at the University of California-Berkeley. Leonard leads a research team focused on employing synthetic biology and computational systems biology to address unmet needs in biotechnology, including engineered cell and gene therapies. As a Charles Deering McCormick Professor of Teaching Excellence, his educational interests include enhancing training in critical thinking and making computational methods accessible to engineering students and researchers across disciplines.

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Published

2023-06-28

Issue

Vol. 57 No. 3 (2023): Summer 2023

Section

Manuscripts