Modeling of Biological Systems

(Department)  Biomedical Engineering         (Division)      Bioelectric
 (Level and Major)  Master and PhD

Course Title                   Modeling of Biological Systems
Number of Credits       3             Prerequisite -
Lecturer Farzad Towhidkhah

Course Description
Biological systems are so complicated and too hard to understanding. Numerous ethical issues are usually requested to perform any experiment on biological systems. These experiments involve a lot of energy and cost. One of the tools to understanding biological systems is modeling. In this course, different classical and basic methods and approaches are introduced to identify and model biological systems computationally.
Course Goals and Objectives
 The main goal of this course is to give the student the capability of describing biological system from a systematic viewpoint and to learn different classical and basic methods of system identification and modeling.
Course Topics        
  • Chapter 1 - Introduction
    • Basic definitions and terms
    • Types of models
    • Modelling approaches (Analytical and Experimental)
  • Chapter 2 - Analytical Modeling
    • Analytical modeling steps
    • Analog systems (Electrical, Mechanical, Chemical)
  • Chapter 3 - A Review of the Possibilities and Statistics
    • Random variables
    • Random processes
    • Statistical models and testing of hypotheses
  • Chapter 4 - Experimental Modeling (System Identification)
    • Classical temporal and frequency methods (impulse response, step response, frequency response)
    • Correlation Analysis
    • Frequency spectrum estimation
    • Parametric methods
  • Chapter 5 - Parameter Estimation Methods
    • Least Square method
    • Instrumental Variable method
    • Maximum likelihood method
    • Prediction error method
  • Chapter 6 – State space modeling
  • Chapter 7 - Transfer of substances in the body and its models
    • Material transfer by fluid flow
    • Material transfer by infusion
    • Compartmental Models
  • Chapter 8 - Practical Examples of Modeling Biological and Physiological Systems
  • Circulation system modeling
  • Respiratory system modeling
  • Modeling of body movement control system
  • modeling of body heat transfer system
  • Chapter 9 - New topics in modeling nonlinear and biological systems
The course aims to:
  •  Understanding the main characteristics of biological systems from computational viewpoints
  • Being familiar with system identification basic methods and modelling approaches

Reading Resources
  1. Haefner, J. W. (2005). Modeling Biological Systems:: Principles and Applications. Springer Science & Business Media.
  2. Dokholyan, N. V. (Ed.). (2012). Computational modeling of biological systems: from molecules to pathways. Springer Science & Business Media.
  3. Rao, V. S. H., & Rao, P. R. S. (2009). Dynamic models and control of biological systems. Springer Science & Business Media.
  4. Rideout, V. C. (1991). Mathematical and computer modeling of physiological systems (p. 71). Englewood Cliffs, NJ:: Prentice Hall.
  5. Spain, J. D. (1982). BASIC microcomputer models in biology. Adison.
  6. Adams, L. (1967). Applications of Control Theory to Physiological Systems Howard T. Milhorns.
  7. Ljung, L. (1999). System identification. Wiley encyclopedia of electrical and electronics engineering, 1-19.
  8. Ljung, L., & Glad, T. (1994). Modeling of dynamic systems. PTR Prentice Hall.
  9. Norton, J. P. (2009). An introduction to identification. Courier Corporation.
  10. Ljung, L., & Söderström, T. (1983). Theory and practice of recursive identification. MIT press.
  11. Söderström, T., & Stoica, P. (1989). System identification. Prentice-Hall International.
Midterm Exam, Final Exam, Seminar, Final Project, Exercises

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