Problem Solving with Computational Models
Instructors: Melissa Kemp, Eberhard Voit, Wendy Newstetter
The format for this class departs from convention in computational modeling courses and is designed to be accessible to BME and non-BME majors who wish to gain a fundamental understanding of how to assess biological questions with computational tools. Our approach is to introduce the material in a top-down manner, first through the use of an available model of a disease and then by developing modeling expertise that ultimately permits the design of new models. The syllabus is summarized in the diagram below.
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Click here for a paper about this course.
Biochemical Systems Analysis
Instructor: Eberhard O. Voit
The course introduces students interested in bioinformatics and systems biology to the computational analysis of biochemical systems. It briefly reviews traditional concepts of enzyme catalyzed reactions, but places its main emphasis on modern methods of biochemical systems analysis with algebraic and computational means. The course discusses alternative modeling approaches, the design of pathway models, parameter estimation, steady states and stability, sensitivity and gain analysis, numerical evaluations of transients, phase-plane analysis, and the simulation of biomedically relevant scenarios. The theoretical concepts are applied in comprehensive case studies. Upon successful completion of the course, the student will be familiar with traditional and modern methods of enzyme kinetics and metabolic pathways. S/he will be able to design biochemical systems models from scratch and execute standard procedures of parameter estimation, steady-state analysis, and assessments of model robustness. S/he will be in a position to simulate the dynamics of metabolic pathways in response to transient and permanent perturbations. Students are expected to study the book, read additional scientific articles, and execute homework assignments and computer laboratory projects.
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Models in Biology and Medicine
Instructor: Eberhard O. Voit
The course introduces the student to a representative set of models that elucidate the nature of biological and medical phenomena. Upon completion of the course, the student will understand the rationale behind the models, explore their potential and limits, and execute standard analyses and simulations. Examples that are discussed include classical models, such as biochemical system models and parasite-host models, as well as modern models taken from the current literature.
Text: Leah Edelstein-Keshet: Mathematical Models in Biology, Birkhäuser Series (McGraw Hill), NY 1987
Additional Reading: E. O. Voit: Computational Analysis of Biochemical Systems, Cambridge University Press, 2000
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