Biochemical Systems Analysis
Instructor: Eberhard O. Voit, Ph.D.
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.
Text:
Voit, E.O.: Computational Analysis of Biochemical Systems (with
software PLAS), Cambridge University Press, 2000
Grading:
Two exams, one project @ 25% each
Homework @ 25% (Emphasis on effort rather than correctness)
Weekly Syllabus
Week 1:
Introduction: Issues of Reductionism and Integration;
Need for Mathematical and Computational Analysis
Week 2:
Graphical Representation of Biochemical Systems; “Maps”
Week 3:
Traditional Models of Enzyme Catalyzed Reactions
Week 4:
Modern Models of Biochemical Systems
Week 5:
From Maps to Equations
Week 6-7:
Computer Simulation
Week 8-9:
Parameter Estimation
Week 10:
Analytical Steady-State Evaluation
Week 11:
Sensitivity Analysis
Week 12:
Case Study 1—Anaerobic Fermentation Pathway in Saccharomyces cerevisiae
Week 13:
Case Study 2—A Sequence of Models Describing Purine Metabolism
Week 14:
Case Study 3—Integration of Biochemical and Genomic Data
Week 15:
Related Scientific Developments