Biological Networks (BioNet)

Skills

• Understand the central dogma, DNA-->RNA-->Proteins and will be able to write equations and algorithms associated to each of the steps. Such models involves stochastic molecular events and knowledge of time-scales associated to basic processes inside a living cell.
• Understand how the same genome can give rise to widely different genetic activity. Such epigenetics is an important part of life-death decisions in the microbial world, as well as for the development of multicellularity.
• Understand principles for gene regulation, meaning that the central dogma is supplemented with numerous back-arrows. An important part of being alive is feedback, and the student should know about feedback associated to both metabolism, and feedback associated to stress.
• Understand and model oscillations of gene expression inside living cells. This include feedback from stress to the regulation of proteins that counteracts the stress.
• Ability to construct quantitative models for living systems, and thereby increase the students intuition about modeling as a scientific method.

Knowledge

The student will obtain knowledge about networks and information processing in living systems, including physics of gene regulation, dynamics on biological networks. The gained understanding will center around the following fundamental equations and algorithms:

• Models of biological transcription and translation.
• Monods Growth law.
• Gene activity as function of protein regulatory input.
• Event driven simulation for gene expression.
• Dynamical models of gene regulatory circuis.
• Equations for bi-stability using positive feedback.
• Epigenetics and read-write enzymes.
• Equations for metabolic fluxes and their regulation.
• Equations for push-pull reactions in signalling cascades.
• Equations for adaptive responses.
• Gene expression and spatio-temporal patterns.
• Predator-prey modeling and its application to microbial ecology.

Competences

This course give the student a quantitative understanding of cellular and microbial biology.
The course gives the student competences to make and evaluate dynamical models.