Computationele biologie (2026/2027: Periode 3)

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Cursusdoel

Learning goals
Computational Biology uses computer modeling to investigate biological problems. The course teaches a variety of modeling techniques and techniques to analyse the model behaviour. Moreover, biological theory obtained by computational modeling is examined.

Skills
Computational biology is a discipline by itself. Nevertheless interfaces with many different parts within biology, as well as computer science.
Skills Part of the course? Explicitely examined?
Writing x x
Presenting x x
Data handling x
Practical research skills x
General research skills
Co-operation x X
Critical thinking x x
Career orientation
Interdisciplinarity

Vakinhoudelijk

Admission requirements
Mandatory prerequisite knowledge of Biological models and Statistics (former Quantitative Biology) and Genomics. It is strongly recommended to do course Biological Modeling (year 2) beforehand, but students with similar knowledge can be accepted too. For students outside of the UU Biology programme, please contact the coordinator to discuss your pre-knowledge level.

Study path
The Computational Biology course is a core course of the study path Theoretical Biology and Bioinformatics. Moreover, the course offers you strong theoretical support in the Molecular and Ecological directions.

Language
This course is given entirely in English

Content
During the course, the emphasis will be on composing exact models, based on specific hypotheses. The models are analysed, the results yielding insights in the original biological system. The models that are studied address fundamental questions from a variety of biological fields, among which:

Evolutionary dynamics
  • Eco-evolutionary dynamics and spatial pattern formation,
  • Host-pathogen co-evolution,
  • Genome evolution, e.g. Interaction between gene regulation and evolution,
  • Evolution of complexity, robustness and evolvability.

Developmental dynamics (from genes to organisms) (plant and animal models will be used)
  • Pattern formation,
  • Cell differentiation,
  • Morphogenesis and mechanical interactions between cells,
  • Evo-Devo (evolution of development).

Network dynamics
  • Gene regulation and metabolic networks,
  • RNA interference.

Behavior
  • Behavioral self-structuring through local interactions,
  • Interface between learning and evolution.

(Spatial) pattern formation and emergent properties are common themes emphasized in all these areas and the related general theory is introduced as a separate module.
Several different model formalisms are used, namely:
  • Non-linear differential/difference equations (ODE and maps),
  • Reaction Diffusion Systems (PDE),
  • Cellular automata machines,
  • Event based models,
  • Individually oriented models,
  • Evolutionary computation,
  • Hybrid models using several combinations of the above formalisms.

Analysis tools include bifurcation analysis, sensitivity analysis, and various pattern analysis techniques.

Teaching formats
A typical day starts with lectures, followed by computational modelling exercises, including a mini project, about which a report is to be written. Literature will be handed out related to the computer exercises, and at the end of the course, literature seminars are given by the students.

Grading
To pass this course, a minimum of 5,5 is mandatory. The student's final mark is based on primarily the written exam; and rounded off based on the literature seminar and the mini project report.

Materials
  • Practicum handleidingen, sheets en literatuur,
  • A (decent) laptop is required for the tutorials

Werkvormen

Computerpracticum

Hoorcollege

Werkcollege

Toetsing

Eindresultaat

Verplicht | Weging 100% | ECTS 7,5

Ingangseisen en voorkennis

Ingangseisen

Je moet inschreven staan voor een van de volgende opleidingen:

  • Scheikunde
  • Biologie
  • Molecular and Biophysical Life Sciences

Voorkennis

Mandatory prerequisite knowledge of Biological models and Statistics (former Quantitative Biology) and Genomics. It is strongly recommended to do course Biological Modeling (year 2) beforehand, but students with similar knowledge can be accepted too. For students outside of the UU Biology programme, please contact the coordinator to discuss your pre-knowledge level.

Voertalen

  • Engels

Cursusmomenten

Gerelateerde studies

Tentamens

Er is geen tentamenrooster beschikbaar voor deze cursus

Verplicht materiaal

  • HANDLEIDING
    Practicum manuals, sheets en literature
  • SOFTWARE
    A (decent) laptop is required for the tutorials

Aanbevolen materiaal

Er is geen informatie over de aanbevolen literatuur bekend

Coördinator

prof. dr. P. Hogeweg P.Hogeweg@uu.nl

Docenten

prof. dr. P. Hogeweg P.Hogeweg@uu.nl

Inschrijving

Deze cursus is open voor bijvakkers. Controleer wel of er aanvullende ingangseisen gelden.

Inschrijving
Van maandag 2 november 2026 tot en met vrijdag 20 november 2026

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