Course detail

Biological System Modelling

FEKT-MMOBAcad. year: 2018/2019

The course is dedicated to the modeling of biological systems. Students gain theoretical knowledge in the field of modeling terminology, classification of biological systems, modeling objectives, identification of model parameters and methods of its description. Students will gain practical skills in the design of a mathematical model, its analysis, practical implementation in MATLAB and Simulink and model simulation.

Learning outcomes of the course unit

The graduate of the course:
• Is able to identify the basic elements, links and state variables of biological systems
• Can describe the activity of biological systém using set of equations
• Can solve the system of differential equations using Euler's method and Runge-Kutta methods
• Is able to analyze the stability of equilibrium states of the model using the Jacobi matrix
• Can construct an implementation scheme of a model from the system of equations
• Can construct a system of equations from the model implementation scheme
• Is able to implement a computer model in MATLAB and Simulink
• Is able to simulate a computer model in MATLAB and Simulink
• Is able to discuss the results of a computer model simulation

Prerequisites

The student who enters the course should be able to: • Analyze simple electrical circuits using Ohm's law and Kirchhoff's laws • Find the analytical solutions of simple differential equations • Solve the system of equations using matrices • Create a simple program in MATLAB that contains loops, conditions, and mathematical equations

Co-requisites

Not applicable.

Recommended optional programme components

Not applicable.

Recommended or required reading

Holčík, J., Fojt, O.: Modelování biologických systémů (Vybrané kapitoly), skripta VUT v Brně, 2001. (CS)
JIŘÍK,R.: Modely v biologii a epidemiologii. El. skripta VUT v Brně, 2006. (CS)
Pazourek, J.: Simulace biologických systémů. GRADA, Praha 1992. (CS)
V. Eck, M. Razím, Biokybernetika, skripta ČVUT v Praze, 1998. (CS)
Murray, J.D.:Mathematical Biology,Springer Verlag, Berlin 1989. (EN)
ALLMAN, E.S., RHODES, J.A.: Mathematical Models in Biology: An Introduction. Cambridge University Press, 2004. (EN)

Planned learning activities and teaching methods

Teaching methods depend on the type of course unit as specified in the article 7 of BUT Rules for Studies and Examinations. Teaching methods include lectures and computer laboratories (modeling in Matlab and Simulink). Course is taking advantage of e-learning (Moodle) systém.

Assesment methods and criteria linked to learning outcomes

Computer exercises: 25 points - solving tasks during the exercise, the minimum for the credit and admission to the final examination is to obtain at least 10 points
Final exam: 75 points - exam is written and consists of three parts with 25 points each. The first part verifies the general theoretical knowledge of biological systems modeling, the second part verifies the theoretical knowledge and practical skills in the field of population models and the third part verifies the theoretical knowledge and practical skills in modeling of the human body systems.
For successful completion of the course, it is necessary to obtain from the written exam at least 35 points and in a total at least 50 points.

Language of instruction

Czech

Work placements

Not applicable.

Course curriculum

1. Modeling and Simulation - basic concepts, classification of models
2. Modeling and Simulation - identification of model parameters, ways of describing the model
3. Mathematical and computer models - mathematical model analysis, computer modeling and simulation
4. Models of single populations - continuous: Malthus, Pearl-Verhulst and Hutchinson
5. Models of single populations - discrete: Malthus, Pearl-Verhulst, Leslie and Hutchinson
6. Models of interacting populations - predator-prey models: Lotka-Volterra and Kolmogorov
7. Models of interacting populations - models of competition and symbiosis
8. Models of cardiovascular system - hemodynamic parameters, Windkessel models
9. Models of action potential pulse - Hodgkin-Huxley model
10. Models of respiratory system - mechanical ventilation
11. Pharmacokinetic models - compartment model of diffusion, the pharmacokinetic parameters, single-compartment models
12. Pharmacokinetic models - two-compartment and three-compartment models
13. Epidemiological models - the SIR model, SEIR, SI and SIS.

Aims

The aim of the course is to provide students the basic knowledge and skills in design of mathematical models of biological systems, their analysis, computer implementation and subsequent simulation.

Specification of controlled education, way of implementation and compensation for absences

Computer exercises are compulsory, properly excused exercises absences can be substitute at another time after consultation with the teacher.

Classification of course in study plans

  • Programme IT-MGR-2 Master's

    branch MBI , any year of study, winter semester, 4 credits, optional
    branch MPV , any year of study, winter semester, 4 credits, optional
    branch MGM , any year of study, winter semester, 4 credits, optional
    branch MSK , any year of study, winter semester, 4 credits, optional
    branch MIS , any year of study, winter semester, 4 credits, optional
    branch MBS , any year of study, winter semester, 4 credits, optional
    branch MIN , any year of study, winter semester, 4 credits, optional
    branch MMM , any year of study, winter semester, 4 credits, optional

  • Programme EEKR-M1 Master's

    branch M1-BEI , 1. year of study, winter semester, 4 credits, optional specialized
    branch M1-KAM , 2. year of study, winter semester, 4 credits, optional interdisciplinary

  • Programme EEKR-CZV lifelong learning

    branch ET-CZV , 1. year of study, winter semester, 4 credits, optional specialized

Type of course unit

 

Lecture

26 hours, optionally

Teacher / Lecturer

Computer exercise

13 hours, optionally

Teacher / Lecturer