Modelling of Biosystems (B-KUL-I0V02A)
Aims
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
Previous knowledge
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.
Order of Enrolment
This course unit is a prerequisite for taking the following course units:
I0J68A : Controle van biosystemen
I0J72A : Control of Biosystems
Identical courses
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
Is included in these courses of study
- Master in de bio-ingenieurswetenschappen: biosysteemtechniek (Leuven) (Gerichte minor Applications for Human Health Engineering) 120 ects.
- Master in de bio-ingenieurswetenschappen: landbouwkunde (Leuven) (Gerichte minor Applications for Human Health Engineering) 120 ects.
- Master in de bio-ingenieurswetenschappen: milieutechnologie (Leuven) (Gerichte minor Applications for Human Health Engineering) 120 ects.
- Courses for Exchange Students Faculty of Bioscience Engineering (Leuven)
- Master of Biomedical Engineering (Programme for students started before 2021-2022) (Leuven) 120 ects.
- Master in de bio-ingenieurswetenschappen: landbeheer (Leuven) (Gerichte minor Applications for Human Health Engineering) 120 ects.
- Master of Bioscience Engineering: Human Health Engineering (Leuven) 120 ects.
- Master of Bioscience Engineering: Human Health Engineering (Leuven) (Thematic Minor: Applications for Human Health Engineering) 120 ects.
- Master in de bio-ingenieurswetenschappen: levensmiddelenwetenschappen en voeding (Leuven) (Gerichte minor Applications for Human Health Engineering) 120 ects.
- Master in de bio-ingenieurswetenschappen: katalytische technologie (Leuven) (Gerichte minor Applications for Human Health Engineering) 120 ects.
- Master of Bioscience Engineering: Agro- and Ecosystems Engineering (Leuven) (Gerichte minor Applications for Human Health Engineering) 120 ects.
- Master of Bioscience Engineering: Cellular and Genetic Engineering (Leuven) (Thematic minor: Applications for Human Health Engineering) 120 ects.
- Master of Biomedical Engineering (Programme for students started in 2021-2022 or later) (Leuven) 120 ects.
Activities
3 ects. Modelling of Biosystems: Lectures (B-KUL-I0V02a)
Content
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
Course material
Slides, articles, copies of chapters from books and recording are available via Toledo.
Format: more information
Blended learning - Class recording - Traditional lecture
Is also included in other courses
3 ects. Modelling of Biosystems: Practical Exercises (B-KUL-I0V03a)
Content
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.
Course material
Slides, recordings
Format: more information
Blended learning - Class recording - Computer session - Paper - Practice session
Discussion
Evaluation
Evaluation: Modelling of Biosystems (B-KUL-I2V02a)
Explanation
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.
Information about retaking exams
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.