BIOCB 6620 - Dynamic Models and Data in Biology

Spring. 4 credits. Student option grading.

Recommended prerequisite: Completion of mathematics requirements for biological sciences major or equivalent. Co-meets with BIOCB 3620.

A. Hein.

Life is dynamic and ever-changing. Because of this, a central tool used to study living systems are dynamic models. This course provides an introductory survey of the development, computer implementation, and applications of dynamic models in biology, as well as statistical and machine learning methods for building such models from biological data. Case-study format covering broad range of biological applications including gene regulation, neurobiology, physiology, behavior, epidemiology and ecology. Students learn mathematical methods for interpreting and building biological systems models, as well as computational methods for simulating models on the computer using a scripting and graphics environment.

Outcome 1: Students will be able to read a dynamic model, interpreting its equations as statements about underlying biological processes and the assumptions made about the rates and consequences of those processes.

Outcome 2: Students will be able to adapt existing models for applications to related systems or alternative scenarios.

Outcome 3: Students will be able to write computer programs (using R) to numerically solve low-dimensional matrix equations (deterministic and stochastic), difference equation, differential equation, and agent-based models for biological systems.

Outcome 4: Students will be able to write computer programs (using R) to estimate the parameters and structure of dynamic models from real data.

Outcome 5: Students will be able to locate equilibria, compute Jacobians, evaluate local stability through eigenvalue calculations and other methods, and interpret these results in terms of asymptotic system dynamics and bifurcations.

Outcome 6: Students will be able to read and understand biological research papers that use modeling as a primary methodology.

Outcome 7: Students will be able to formulate meaningful research questions about biological systems that can be addressed using dynamic models and data, and apply the skills learned in the course to answer those questions.