About CE 395 A

Advanced topics in recently developed technical areas. Hours and credits as arranged.


Prereq: Biology, Chemistry; Graduate standing or instructor permission; Open to degree and CDE students

Section Description

This course explores conventional and novel methods for modeling biological processes, including kinetic and stoichiometric modeling and constraint-based metabolic modeling. The course includes theory (mass balance, Monod kinetics, biochemistry, microbial energetics, and thermodynamics) and practice (constructing and running models with Python and analyzing results). No previous coding experience is required, but it is expected that students will teach themselves basic Python commands and data structures using freely available online resources. The free, open source CobraPy package will be used. No textbook is required, but peer-reviewed publications will be assigned for reading.

Section Expectation

This course will be taught using an in-person or mixed modality. Lectures will be recorded and posted online. Attendance at lectures is expected. Working in a group with 1 or 2 other students is required. Students will submit their own projects for grading but are encouraged to work with their peers.


Evaluation is based on two (2) course projects that will involve coding. You will be assessed based on the overall performance of your modeling code and answers to specific questions. For one project, you will model biological processes involved in wastewater treatment. For a second project, you will construct a metabolic model of a single organism.

Course Dates



Hills Agri Sci 017 (View Campus Map)


to on Monday, Wednesday and Friday

Important Dates

Note: These dates may not be accurate for select courses during the Summer Session.

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