Laboratory for Biological Systems Analysis
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Course Materials

Problem Solving with Computational Models

Instructors: Melissa Kemp, Eberhard Voit, Manu Platt

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.

Click here for a detailed syllabus.

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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Biomedical Systems and Modeling

Instructor: Eberhard O. Voit, Melissa Kemp, Peng Qiu, Denis Tsygankov, Chris Kieslich

This required undergraduate course introduces students to the new world of systems biology. It discusses deterministic and stochastic models, static networks and dynamic systems, and illustrates modeling methods with applications to genetics, metabolism, signaling, populations, medicine and drug developments and other areas.

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"Where Life becomes Numbers and Numbers Come to Life"