Masters' Program

See also the PhD program.

Computation Biology (FALW 471013)

Study guide > Faculteit der Aard- en Levenswetenschappen > Biology (MSc) > Elective options > Computational Biology

Course leader: B. W. Kooi
Participants: graduate students in Biology, Medical Biology, Health Sciences, Ecology
Preliminary knowledge: Batchelor courses Computer Science or equivalent courses
Material Selection of Scientific papers Total workload: 6 cp
Frequency: yearly

Aim: Nonlinear dynamics system theory is applied to models of biological systems. Both, discrete time and continuous time systems as well as their relationship is dealt with. The course emphasizes the application of bifurcation theory to study the long-term dynamic behavior of systems. This behavior can be a point, a limit cycle or a chaotic attractor. Also time-separation techniques will be discussed in the context of perturbation theory. The theory will be elucidated food chains and food webs, as examples of small-scale ecosystems. Also examples for Neuro Sciences and Molecular Biology are discussed. Computer packages will be demonstrated and the applied numerical techniques are described.

Contents: The focus will be on the following subjects

• Mathematical modelling of biological systems in ecology, neural sciences and microbiology
• Ordinary, delay and partial differential equations and their basic mathematical properties
• Difference equations and maps
• Transient or short term dynamics versus asymptotic behavour or long-term dynamics
• Stability of equilibria or limit cycles
• Boundedness of solution and structural stability
• Numerical techniques for solving nonlinear set of equations and approximation of solutions of ordinary, delay and partial differential equations
• Examples: Leslie matrix models, simple food webs, cable theory for passive dendrites, yeast glycolysis

Working method:

• Lectures (20 hours) to discuss the theory
• Practical methods (80 hours) were the students will work with different computer programs, Auto, Content, (for bifurcation analysis) Maple or Mathematica, (for symbolic calculations) Octave or Matlab (for matrix calculation). The exercises aim to support the theory as well as show how the theory can be applied. Material from the course on Basic Methods in Theoretical Biology wil be used.
• Self study (38 hours)
• Examination (2 hours)

Research methods (FALW )

Aim: Within the course WTC Research methods, a module Theoretical methods in natural sciences is given (0.75 cp). The aim is to discuss the interrelationships between theoretical and experimental aspects of research in the natural sciencies, and the roles of modelling and statistics.

Contents: The focus will be on the following subjects

• Empirical cycle
• Criteria for useful models
• Dimension analysis
• Testing models to data
• Experimental desing

Working method:

• Lectures (10 hours)
• Self study (4 hours)
• Discussion (4 hours)
• Exercises (2 hours) on dimension analysis, consistency, model properties.

Basic methods in Theoretical Biology

Aim: This course is a do-it-yourself course for students who do not take the courses Modelling & Statistics and Computational Biology for one reason or another, but still want to know the basic material, e.g. to qualify for a traineeship in Theoretical Biology. The course is further specified in a web site and is completed with an examination.

Traineeships for graduates

• have completed successfully the graduate courses Modelling & Statistics and Computational biology
• or have completed the self-study program Methods in Theoretical biology (including an examination)

Total workload: 30-36 cp

Procedure & subject: The topic of the traineeship relates to one of departments' current research projects, within the framework of departments' research program. It is identified in collaboration with S. A. L. M. Kooijman, who will contact the daily supervisor. Before the actual start of the traineeship, the supervisor will, in collaboration with the student, complete the definition form for the traineeship, which specifies the supervising responsibilities, the scientific problem, the work program, the time schedule, and the endpoints.

Contents: All traineeships have the modules:

• Identification and motivation of scientific problem
• Review of the literature on this problem
• Formulation of assumptions about the biological system that is involved
• Derivation of model(s) for the system
• Analysis of model properties
• Search for relevant data from the literature
• Test model predictions to data
• Formulation of conclusions in relation to problem
• Report results in written and oral form
• Summary of results, which is included in the traineeship definition form

Writing reviews for graduates

• have completed successfully the graduate courses Modelling & Statistics and Computational biology
• or have completed the self-study program Methods in Theoretical biology (including an examination)

Total workload: 8.6 cp

Procedure & subject: See traineeship.

Contents of the review:

• Significance of the subject
• Selection strategy of material (papers/books)
• Selection of results with consensus
• Significance of these results
• Main controversies
• Motivated choice between alternative hypotheses
• Priorities for future reseach
• Conclusions/evaluation
• Summary