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Industrial and Operations Engineering pres.

Departmental Seminar (899): Allen Holder, Rose-Hulman Institute of Technology — Robust Analysis of Metabolic Pathways

Robust Analysis of Metabolic Pathways

Departmental Seminar (899): Allen Holder, Rose-Hulman Institute of Technology Departmental Seminar (899): Allen Holder, Rose-Hulman Institute of Technology
Departmental Seminar (899): Allen Holder, Rose-Hulman Institute of Technology
The Departmental Seminar Series is open to all. U-M Industrial and Operations Engineering graduate students and faculty are especially encouraged to attend.

The seminar will be followed by a reception in the IOE Commons (Room 1709) from 4 p.m. to 5 p.m.

Title:
Robust Analysis of Metabolic Pathways

Abstract:
Flux balance analysis (FBA) is a widely adopted computational model in the study of whole cell metabolisms, often being used to identify drug targets, to study cancer, and to engineer cells for targeted purposes. The most widely used model is a linear program that maximizes cellular growth rate subject to achieving steady metabolic state and to satisfying environmental bounds. Quadratic and integer modifications are also common. Standard stoichiometry decides the preponderance of data in all instances, and hence, the majority of information defining an optimization model is certain. However, several key parts of a model rely on inferred science and are less certain; indeed, the method of deciding several of these values is opaque in the literature. This prompts the question of how the resulting science might depend on our lack of knowledge. We suggest a robust extension of FBA called Robust Analysis of Metabolic Pathways (RAMP) that accounts for uncertain information. We show that RAMP has several mathematical properties concomitant with our biological understanding, that RAMP performs like a relaxation of FBA in practice, and that RAMP requires special numerical awareness to solve.

Bio:
Allen Holder earned his PhD in applied mathematics from the University of Colorado at Denver in 1998. He has since studied applications of optimization in medicine, economics, production planning, analytics, and computational biology. He is currently a Professor of mathematics at the Rose-Hulman Institute of Technology, where he regularly directs some of the nation's best undergraduates through their first research experiences. He won the 2000 Pierskalla award for his work on the optimal design of radiotherapy treatments, and he won Rose-Hulman's Outstanding Scholar Award in 2015. He has held several editorial positions and has regularly served the INFORMS Health Applications Society and the INFORMS Computing Society, chairing the former in 2005 when it was a section. He recently co-authored a book titled "An Introduction to Computational Science" with his friend and colleague Dr. Joseph Eichholz. He is the proud father of two teenagers, and he fiddles with an old guitar in his spare time.
Departmental Seminar (899): Allen Holder, Rose-Hulman Institute of Technology Departmental Seminar (899): Allen Holder, Rose-Hulman Institute of Technology
Departmental Seminar (899): Allen Holder, Rose-Hulman Institute of Technology
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