Modeling Life

Course goals

The course aims to provide students with an introductory understanding of computational modeling to study living systems, and their large range of applications.

Content

Have you ever wondered how cells “know” which genes to express at a given time and place, or how a plant seed “decides” when is the best time to germinate? Or would you like to know what the stripes of a zebra, the fingers on your hand, and the patterning of vegetation in dry ecosystems have in common? The aim of this course is to learn how computational models can be used to help address these questions, and how to use models for questions where experimentation is not possible.  

Living systems like those mentioned above are made up of many different interacting elements, from genes, to cells, tissues, organs, organisms, and ecosystems. In this course on Modeling Life you will learn to use computational models to understand how these interactions together produce self-organizing mechanisms, from the gene regulatory networks processing information and making cell fate decisions, to how cell-to-cell communication enables the regular distribution of tissues (i.e., fingers) and organs (e.g. lateral roots in plants), how mechanical processes shape tissues in morphogenesis, and finally, how evolution shapes these and many other processes. Additionally, you will learn how to create models, which model type to pick and how to judge the quality of the model. 

This course will consist of lectures (HC) covering various modelling approaches to study life at different levels accompanied by computer practicals (WC) where students will get hands-on experience on running computational models of the development or the evolution of animals, plants, and microbial systems. The students will learn how to formulate a computational model to address specific questions (algorithmic thinking), how to analyze the output of the model, and how to question a model based on the underlying assumptions. The students will learn to use modern tools like AI assisted programming to develop their models. 

Modeling Life is a course offered at two levels: Level 3 for the Biology bachelors program, and Master level. The assessment methods are of a higher level of difficulty for MSc level students, as specified below.

Details of the assessment difference between BSc (level 3) and MSc level:
- Test: 30% of the exam questions will be different between tests for the BsC and the MSc level students. For BsC students we will evaluate their capacity to select the correct equation/code from predefined options (multiple choice questions), while for MSc students we will evaluate their capacity to write equations and/or code on their own (open questions). 
- Research proposal (mini project): The students will work on a mini project to develop a computational model to answer specific questions defined in discussion with the supervisor. BsC students will need to answer at least two questions predefined by the supervisor. MSc level students must answer four questions, including predefined and original questions formulated by the students.