Advanced Systems Biology

Are you curious to understand how a biological system operates? Are you interested in knowing which elements of the system are responsible for certain characteristics that are experimentally observed? Do you want to be able to use this knowledge as a steppingstone to build model that can reproduce the behavior of a complex living system? If your answer is yes!, you should immerse yourself in the world of Systems Biology! Systems Biology aims to understand the properties and characteristics of living systems by considering the relationships and interactions among their constituents. It does so by employing theoretical and experimental tools borrowed from different disciplines. The unifying theme in System Biology is mathematical modelling which is the use of mathematical tools to create models that are able to (possibly) reproduce (predict) the behavior of a biological system as observed in nature or in the laboratory. By confronting the model predictions with experimental data you will be able to refine your model to bring it closer to reality and to generate new hypothesis that could be experimental tested.
This course will cover several (advanced) topics in Systems and Synthetic Biology and every week brings in a different application or biological problem. The topics covered are: Modelling of chemical reaction networks, Biochemical kinetics, Analysis of dynamic mathematical models (using Ordinary Differential Equations), Metabolic and Gene regulatory networks, Spatio-temporal models and pattern formation (using Partial Differential Equations), Stochastics modelling and Model and Data fitting.
The course alternates lectures on theoretical aspects of Systems Biology with exercises and computer/computational practicals where you will develop programming and analysis skills by modelling and investigating exemplary biological systems.
During each week theory and very diverse applications are presented and discussed: for instance you will learn how to model the biochemical process that gives birth to the stripes on the fur of your cat, how to describe the fact that cells are similar but not identical and how this can affect biological phenomena or how to determine the unknown parameters of your mathematical model starting from experimental data.
At the end of the course you will have the opportunity to build and analyse your own mathematical model describing exemplar biological systems information about the biological system.

After successful completion of this course students are expected to be able to:

• Describe and analyze a biological system in terms of ordinary or partial differential equations
• Describe the properties of a dynamic biological system given its mathematical formulation
• Recognize the different properties of the tools used to simulated and analyze biological systems
• Recognize the advantages and limitations of different tools and apply them critically given a problem
• Organize, present and discuss (both written and oral) the properties of a mathematical model and the results of computer simulations

Assumed Knowledge:
General Biological knowledge, Introduction to Systems & Synthetic Biology (SSB50806), Molecular Systems Biology (30306), Modelling in Systems Biology (SSB30806), Modelling Biological Systems (EZO23306).