Computational Biology

Course manual 2024/2025

Course content

This course delivers an in-depth exploration of modeling and analyzing complex biological systems, drawing on principles from systems biology and biomedical applications. It integrates various mathematical and computational techniques to investigate biological processes across multiple scales, from molecular interactions to cellular dynamics and population-level phenomena. You will learn to develop mathematical models and carryout numerical simulations of chemical, gene regulation, and spatio-temporal cellular interactions. The course will also provide introductions to relevant biological concepts.

Study materials

Literature

• Will be available through canvas

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
• Self-study

Lectures and self-study focus on the understanding, analysis, and creation levels of learning objectives, while lab sessions are designed to address the application and evaluation levels.

Learning activities

Attendance

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

Assessment

Lab assignments 50% Exam 50%

Assignments

Students will work on assignments in groups, but their evaluations will be conducted individually

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