450-4046/01 – Simulation and Modelling of Biological Systems (SMBS)

Gurantor departmentDepartment of Cybernetics and Biomedical EngineeringCredits4
Subject guarantordoc. Ing. Štěpán Ožana, Ph.D.Subject version guarantordoc. Ing. Štěpán Ožana, Ph.D.
Study levelundergraduate or graduateRequirementChoice-compulsory
Year2Semestersummer
Study languageCzech
Year of introduction2010/2011Year of cancellation2016/2017
Intended for the facultiesFEIIntended for study typesFollow-up Master
Instruction secured by
LoginNameTuitorTeacher giving lectures
OZA77 doc. Ing. Štěpán Ožana, Ph.D.
Extent of instruction for forms of study
Form of studyWay of compl.Extent
Full-time Credit and Examination 2+2
Combined Credit and Examination 2+12

Subject aims expressed by acquired skills and competences

The student will be able to use Matlab&Simulink to perform simulation or modelling of basic Physiological processes. Students are gradually introduced to the storyline and physiological modeling of the cardiovascular, endocrine, gastrointestinal and respiratory tract of cardiovascular, endocrinous, gastrointestinal and respiratory system.

Teaching methods

Lectures
Tutorials

Summary

Students will expand knowledge of modeling and simulation applied to biomedicine. The derivation of mathematical models and the simulation of selected physiological processes will be shown. Mathematical models will be compiled on a personal computer using Matlab & Simulink and practical examination of some of them will be done as the laboratory task.

Compulsory literature:

Murray,J.D.:Mathematical Biology,Springer Verlag, Berlin 1989

Recommended literature:

Ljung, L.: System Identification, Theory for the User, Prentice Hall, 1987 Murray,J.D.:Mathematical Biology,Springer Verlag, Berlin 1989 Rowe,G.W.:Theoretical Models in Biology,Oxford Univ.Press, Oxford 1994 Mathematical Biology. Berlin, Springer Verlag 1993., Carson,E., Cobelli,C.: Modelling Methodology for Physiology and Medicine. S. Diego, AP 2001 van Wijk van Brievingh R.P., Moeller D.P.F. (ed.) Biomedical Modeling and Simulation on a PC (A Workbench for Physiology and Biomedical Engineering), New York Springer Verlag, 1993, Keener J., Sneyd J.: Mathematical Physiology. New York Springer Verlag, 1998

Way of continuous check of knowledge in the course of semester

Credit part: It consists of the final credit test, 9-25 points, and individual project 1-10 points (both parts are obligatory for completion of the subject). Project is handed over by the email, deadline is the end of the credit week. Obtaining credit is possible from the 14th week of the semester. Necessary minimum for the credit part is 10 points, maximum 35 points. It is necessary to achieve 80% of course attendance. Exam part: It consists of written part and oral part. Written part includes theoretical part 5-20 points and practical part 10-35 points, together 15-55 pts. The oral part is evaluated between 1-10 pts. All three part of the exam are obligatory, minimum for oral part is 1point. Overall evaluation is between 51-100 points according faculty study code.

E-learning

Další požadavky na studenta

A student must be able to demonstrate that his project was carried out on his own. Credit test, theoretical and practical exam must be processed on student’s own, any violation may be a reason for unsuccessful result of a given part. Unless otherwise noted, only desktop laboratory PCs are allowed to use during education process, and only programs related to the subject. Detailed rules for a specific classroom are determined by a special document posted at the entrance to the classroom.

Prerequisities

Subject has no prerequisities.

Co-requisities

Subject has no co-requisities.

Subject syllabus:

Lectures: 1. Introduction to the problematic of modeling and simulation. Basic dynamic systems and their characteristics. Derivation of mathematical models, forms of descriptions of continuous and discrete systems. Methods of system identifications, experimental identification by deterministic signals, statistic identification of the systems, correlation methods, parameter estimation of the models. 2. Features of biological models. Compartment and multicompartment models. Mathematical description, case studies in biomedicine. 3. Continuous models of single-species population. Sampling and quantization requirement. Malthusian growth model, analysis, solution features. Continuous logistic model with constant and varying parameters. Analysis, solution features. 4. Continuous logistic catch model. Continuous models of single-species population with delay. Analysis, solution features. 5. Discrete models of single-species populations. Discrete variants of Malthusian and logistic model. Analysis of its behavior. Graphical solution of difference equation. Deterministic chaos, butterfly effect, attractors. Lorenz attractor, examples of basic fractals. 6. Discrete models of single-species populations with delay. Models with age structure-Leslie model. Two-species population models. Predator-Prey model. Analysis of Lotka-Volterra model. 7. The Kolmogorov model. Predator-Prey model with delay. Models of two-species. Competitive and cooperative models. 8. Epidemiologic models. Model SIR. The Kermack-McKendrick model - derivation, analysis of solution features. Conditions of epidemic spread, maximal infected toll estimation, death toll estimation. 9. Models SI, SIS. Analysis of solution features. Model SIR with disease vector and vaccination. Models SEIR. Analysis of solution features. Models of venereal diseases – determination of coupling model. Analysis of solution features. Model of AIDS spreading. 10. Modeling of cardiovascular system and its regulation. Aorta pressure, systole, diastole. Model of circulatory system, electromechanical equivalents. Nonlinear model of left ventricle. The Windkessel model. Global model of cardiovascular system, vascular bed, heart. 11. Modeling of respiratory system. Breathing, exchange and transport of gas in lungs. Average alveolar pressure and arterial partial pressures. 12. Modeling of endocrine system. Regulation of glucose in blood by kidneys, insulin and glucagon. Description and solution of the model. 13. Models of gastrointestinal system. Regulation of acidity of gastric juice. Description and solution of the model. 14. Behavior models, catastrophic theory. Model of aggressive behavior, Zeeman catastrophic machine. Model of phase transport. Basic types of catastrophes. Model of war activities. Syllabus of Exercises 1. MATLAB - Simulink. Introduction to Simulink environment. Demonstration of graphical programming of simple case studies. Methodology of design and analysis of mathematical models. Examples of 2nd order systems in Simulink Model of blood glucose regulation. 2. Compartment models – principle, setup of the mathematical model. Simulation in Simulink environment (model of food-intake control) 3. Compartment models - models with varying parameters (continuous and discrete), analysis of stability. 4. Continuous models of single-species population-continuous Malthusian growth model, analysis, experiments with model parameters in MATLAB-Simulink 5. Continuous models of single-species population-continuous logistic model, analysis, experiments with model parameters in MATLAB-Simulink 6. Implementation of time delays into the single-species models, Simulation experiments with modified models in MATLAB-Simulink. 7. Discrete models of single-species populations (discrete variants of Malthusian and logistic model), simulation and analysis in Simulink environment. 8. Discrete model of single-species population with age structure-Leslie model, simulation and analysis in Simulink environment. 9. Two-species population models. Predator-Prey model. Design, simulation and analysis in Simulink. 10. Two-species population models. Predator-Prey model with delay. Design, simulation and analysis in Simulink. Equilibrium determination and stability, experiments in Simulink. 11. Epidemiologic models. Model SIR, structure design, simulation in Simulink, model analysis. Model SIR with disease vector and vaccination. 12. Models of venereal diseases (coupling model) -model of AIDS spreading. Structure design, simulation in Simulink, model analysis. 13. Identification of the parameters of SIR model by Newton method. 14. The "Saccade" analysis, Westheimer model. Muscle model.

Conditions for subject completion

Full-time form (validity from: 2010/2011 Winter semester, validity until: 2016/2017 Summer semester)
Task nameType of taskMax. number of points
(act. for subtasks)
Min. number of points
Exercises evaluation and Examination Credit and Examination 100 (100) 51
        Exercises evaluation Credit 35 (35) 10
                Test Other task type 25  9
                Projekt Project 10  1
        Examination Examination 65 (65) 16
                Teoretická část Other task type 20  5
                Praktická část Other task type 35  10
                Ústní zkouška Oral examination 10  1
Mandatory attendence parzicipation: 80% attendance at the exercises

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Occurrence in study plans

Academic yearProgrammeField of studySpec.FormStudy language Tut. centreYearWSType of duty
2016/2017 (N2649) Electrical Engineering (3901T009) Biomedical Engineering K Czech Ostrava 2 Choice-compulsory study plan
2016/2017 (N2649) Electrical Engineering (3901T009) Biomedical Engineering P Czech Ostrava 2 Choice-compulsory study plan
2015/2016 (N2649) Electrical Engineering (3901T009) Biomedical Engineering K Czech Ostrava 2 Choice-compulsory study plan
2015/2016 (N2649) Electrical Engineering (3901T009) Biomedical Engineering P Czech Ostrava 2 Choice-compulsory study plan
2014/2015 (N2649) Electrical Engineering (3901T009) Biomedical Engineering K Czech Ostrava 2 Choice-compulsory study plan
2014/2015 (N2649) Electrical Engineering (3901T009) Biomedical Engineering P Czech Ostrava 2 Choice-compulsory study plan
2013/2014 (N2649) Electrical Engineering (3901T009) Biomedical Engineering P Czech Ostrava 2 Choice-compulsory study plan
2013/2014 (N2649) Electrical Engineering (3901T009) Biomedical Engineering K Czech Ostrava 2 Choice-compulsory study plan
2012/2013 (N2649) Electrical Engineering (3901T009) Biomedical Engineering P Czech Ostrava Optional study plan
2012/2013 (N2649) Electrical Engineering (3901T009) Biomedical Engineering K Czech Ostrava Optional study plan
2011/2012 (N2649) Electrical Engineering (3901T009) Biomedical Engineering P Czech Ostrava Optional study plan
2011/2012 (N2649) Electrical Engineering (3901T009) Biomedical Engineering K Czech Ostrava Optional study plan
2010/2011 (N2649) Electrical Engineering (3901T009) Biomedical Engineering P Czech Ostrava 1 Optional study plan
2010/2011 (N2649) Electrical Engineering (3901T009) Biomedical Engineering P Czech Ostrava 2 Optional study plan
2010/2011 (N2649) Electrical Engineering (3901T009) Biomedical Engineering K Czech Ostrava 1 Optional study plan
2010/2011 (N2649) Electrical Engineering (3901T009) Biomedical Engineering K Czech Ostrava 2 Optional study plan

Occurrence in special blocks

Block nameAcademic yearForm of studyStudy language YearWSType of blockBlock owner