Project Spotlight. Modeling


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Predictive tools, like models, can be used to predict the changes required in a cell to produce a given bioproduct. The modeling technologies are still in their infancy but are becoming more accurate thanks to the research that has been done in the last decade.

New developments in modeling technology allow members of the USTAR-funded Synthetic Bioproducts Center at USU to accurately predict improved synthetic biological processes that can be used to manufacture products—including biliverdin, bioplastics and spider silk proteins.

Using these mathematical models of cells, SBC team members can determine which metabolic pathways need to be changed or modified to optimize the cell to maximize the production of a given bioproduct—a necessary step in scaling up the biomanufacturing process.

Associated Faculty

Students Involved

Name Designation
Sarah Allred Masters Student
Michaela Hugie PhD Student
Harsh Dosi Graduate Student
Sumit Singh Graduate Student
Vipul Oswal Graduate Student


Title Presenters Venue Year
Efficient Systems for Monitoring and Recovering Polyhydroxyalkanoates (Poster) Elisabeth Linton, Trent Mortensen, Ronald C. Sims, H. Scott Hinton, and Charles D. Miller Institute of Biological Engineering 2009 Annual Conference 2009
Design of a gene expressions system for Rhodobacter sphaeroides J. Huo, R. C. Sims, and H. S. Hinton Institute of Biological Engineering 2010 Annual Conference 2010
CyanoBricks: Genomic Engineering Tools for the Photosynthetic Cyanobacterium Synechocystis Charles D. Miller, Cody Tramp, Alex Hatch, Cole Peterson, Brad Henrie, Shujie Shen, Abiezer Tejeda, Eduardo Monzon, H. Scott Hinton, and Ronald Sims Institute of Biological Engineering 2011 Annual Conference 2011
Designing predictive mathematical models for the metabolic pathways associated with polyhydroxybutyrate synthesis in Escherichia coli Angela Dixon, Ronald C. Sims, Charles D. Miller, and H. Scott Hinton Institute of Biological Engineering 17th Annual Conference 2012
Pathway Pioneer: A Network Visualization and Flux Analysis Tool Nicholas S. Flann, Jonathan Valiente, Misty Wallace, Richard Brown, Scott Hinton Annual Conference of the Institute for Biological Engineering 2013
Pathway Pioneer: A web-based metabolic network layout tool for comprehensive visualization of complex networks Harsh Dosi, Sumit Kumar Singh, Nicholas S. Flann, H. Scott. Hinton 2014 IBE Annual Meeting 2014
Pathway Pioneer: a tool for metabolic network visualization and flux analysis (Poster) Sumit Kumar Singh, Harsh Dosi, Vipul Oswal, Nicholas S. Flann; H. Scott. Hinton 2014 IBE Annual Meeting 2014