Modelling of Biosystems (B-KUL-I0V02A)

6 ECTSEnglish52 First termCannot be taken as part of an examination contract
Norton Tomas (coordinator) |  Aerts Jean-Marie |  Norton Tomas
POC Bio-ingenieurswetenschappen

New technology offers great potential to develop tools that allow online monitoring of biological systems (human, animal, plant, cell, etc.) in numerous application domains, such as monitoring of animal and plant production processes, animal welfare monitoring, plant stress monitoring, driver drowsiness monitoring, athletic performance monitoring, pain monitoring, physical and mental state monitoring, etc. Essential in these applications is the ability to model such complex biosystems based on compact dynamic data-based modelling approaches.

Lectures

The student
- knows techniques that allow to integrate real-time measurements, modelling and process management for individual biological systems (human, animal, plant) at different scales (cell, organism, ecosystem);

- learns systems thinking by dividing the process into its various components based on measurement data of the system under consideration and available knowledge as a basis for the elaboration of process management technology;

- recognises that living organisms are complex, individually different, time-varying, dynamic systems and that today it is possible to measure in real-time various bioresponses related to the state of the living organism;

- gains an understanding of approaches of dynamic data-based modelling that allow accurate modelling and prediction of physiological responses in individual living organisms;

- is able to independently develop strategies for real-time monitoring and control for individual and time-varying biological systems;

- can reflect in a critical and solution-oriented manner on how the combination of measurements and real-time modelling, as a basis for monitoring for biological systems, can be an important tool for engineers in the field of biosystems engineering.

- maintains/acquires awareness of the plagiarism and GenAI use policy of KU Leuven and the faculty.


Practical exercises

The student
- applies the theory of the lectures and can identify dynamic data-based models of the biosystems under consideration based on available data from biological systems;

- learns to independently divide the problem into its main components, formulate objectives, set a time schedule, critically evaluate the literature and critically evaluate the results obtained with attention to the social and economic context;

- learns to make agreements, to communicate in writing and orally, and to present

Knowledge of these topics is required in order to start this course:

  • Mathematics (Bachelor’s level):
    • Calculus
    • Differential equations
    • Linear algebra

 A student should have these skills in order to start this course:

  • Basic programming (preferably Matlab)

Furthermore, the student possesses analytical problem solving skills and demonstrates a sense of accuracy.


This course unit is a prerequisite for taking the following course units:
I0J68A : Controle van biosystemen
I0J72A : Control of Biosystems

This course is identical to the following courses:
I0P13B : Integratie van biologische responsies in procesmanagement (No longer offered this academic year)
I0J67A : Modelleren van biosystemen

Activities

3 ects. Modelling of Biosystems: Lectures (B-KUL-I0V02a)

3 ECTSEnglishFormat: Lecture26 First term
POC Bio-ingenieurswetenschappen

Part 1 – Introduction

- Chapter 1. Introduction and examples

Part 2 - Real-time measurement of bioresponses

- Chapter 2. Advanced sensors & measurement systems.

- Chapter 3. Image processing & sound analysis

Part 3 - Digital signal processing

- Chapter 4. Introduction to linear time invariant systems

- Chapter 5. Impulse and frequency response of linear time invariant systems

- Chapter 6. The z-transform and poles/zeros of discrete time linear time invariant systems

- Chapter 7. Discrete Fourier transforms

 Part 4 - Data-based modeling of bioresponses

- Chapter 8. Introductory concepts

- Chapter 9. Generation of measurement data for data-based modeling

- Chapter 10. Time-invariant parameter estimation in the time and frequency domain

- Chapter 11. Determining model complexity

- Chapter 12. Biological interpretation of data-based models

- Chapter 13. Time-variant parameter estimation

- Chapter 14. Introduction to artificial intelligence

- Chapter 15. Machine learning and deep learning

 Part 5 - Management of biological processes

- Chapter 16. Model-based monitoring of bioresponses

- Chapter 17. Integration of bioresponses into practice

Slides, articles, copies of chapters from books and recording are available via Toledo.

Blended learning - Class recording - Traditional lecture

3 ects. Modelling of Biosystems: Practical Exercises (B-KUL-I0V03a)

3 ECTSEnglishFormat: Practical26 First term
POC Bio-ingenieurswetenschappen

Practical sessions on:

- Digital Signal Processing;

- Least Squares parameter estimates of simple linear models;

- System identification based on Matlab toolboxes (SID & CAPTAIN) to estimate and evaluate ARX models;

- Methods to perform time-variant parameter estimates;

- Model-based monitoring of a biosystem.

 

The students will maintain/acquire awareness of plagiarism and GenAI by using the Toledo tutorial "Information literacy KU Leuven libraries (Science and Technology)" (NL/EN) and testing it. The test is not compulsory.

Slides, recordings

Blended learning - Class recording - Computer session - Paper - Practice session

Discussion

Evaluation

Evaluation: Modelling of Biosystems (B-KUL-I2V02a)

Type : Partial or continuous assessment with (final) exam during the examination period
Description of evaluation : Written, Participation during contact hours, Oral, Paper/Project
Type of questions : Open questions
Learning material : None


For the lectures you will be evaluated by means of a written exam. Knowledge in the subject matter is examined on the basis of theoretical questions. This educational activity counts for 50% of the total score.

 

For the practical exercises you are evaluated based on

1) the work you did during the practical exercises,

2) a report of a computer modelling exercise and

3) the discussion of the results based on the report.

The evaluation of the practical exercises counts for 50% of the total score and is performed outside the normal exam period.

Retake for the practical exercises is not possible. The marks of the practical exercises of the first examination period will be carried over to the second examination period.