Computational Biology

Course manual 2025/2026

Course content

Computational modelling focuses on modelling and analysis of biological systems. Emphasis will be on the modelling of regulatory networks and metabolic pathways.and cell-based modelling techniques. Examples will be discussed from systems biology and biomedical applications. A brief introduction to the biological background needed will be provided in this course.

Study materials

Literature

• To be announced.

Objectives

• Explain the fundamental principles governing computational models of biochemical reactions, metabolic pathways, gene regulatory networks, spatiotemporal dynamics and reaction-diffusion processes.
• Implement computational models based on ordinary differential equations and partial differential equations to investigate biological systems.
• Differentiate between various spatiotemporal modeling techniques and their applications in computational biology and biomedicine.
• Validate the results obtained from computational models by comparing them against experimental data or other models.
• Develop a (simple example) spatio-temporal computational model involving biochemical reactions and cellular dynamics..

Teaching methods

• Lecture
• Computer lab session/practical training

Lectures and practical assignments.

Learning activities

Attendance

This programme does not have requirements concerning attendance (Ter part B).

Assessment

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Contact information

Coordinator

• dr. Vivek Sheraton Muniraj