The aim of the course is to give the students a fundamental understanding of: 1) how high-throughput biological data can be analyzed and 2) how mathematical modeling of biological systems can be used to gain novel biological insight. The students will be presented with a number of examples from analysis of transcriptome data from different studies of yeast, mouse and human tissues. They will further get hands-on experience with analysis of raw data from transcriptome experiments, and will be introduced to how proteome and metabolome data can be analyzed using similar statistical techniques. The students will be presented with methods for reconstruction of metabolic network models, analysis and use of these for simulation of biological functions in living cells. The students will further learn how to perform simulation of kinetic models and analyze reaction networks in terms of flux control. Finally the students will learn about integrated data analysis through a number of different examples. The overall objective is that by passing this course the students should be able to work independently in the field of systems biology.

**Course content**
The course gives an in-depth description of how genomics have impacted systems biology and paved the way for high-throughput biological studies. There is special focus on transcriptome analysis and how these data are analyzed using different statistical methods such as t-test, ANNOVA, SVD and clustering. Concepts of proteomics will be presented and how interaction networks can be used for integrated analysis of high-throughput experimental data. The course will further give insight into how metabolic networks can be reconstructed from biochemical and genomic information. Topological analysis of large genome-scale metabolic models (GSMM) will be performed. Simulation of simple metabolic network models will be performed. The course will also introduce kinetic models and demonstrate the use of these for analysis of different types of biological systems, e.g. protein aggregation and cell death and analysis of flux control in reaction series in metabolic networks. Throughout the course there will be given examples from studies of yeast, nutritional studies using mouse models, and from analysis of clinical data.

Examination
Four hour written, open book exam, which will take place on December 15, 2011. Reports from exercises have to be approved for passing the course.

General information
The course will be given in English. The course is mandatory for Chalmers students following the Biotechnology MSc program.

Teaching Materials/Literature
The following textbook will be used in the course:

- A. Malcolm Campbell & L. J. Heyer (2007) Discovering Genomics, Proteomics, & Bioinformatics, 2. Edition, Pearson Benjamin Cummings, San Fransisco

This can be ordered via the bookstore Cremona. Besides this textbook there will be used chapters from other textbooks and different research papers will together with slides and exercises be provided to the students during the course. **It is expected that the students read the specified material for passing the exam and the uploaded slides are primarily meant as supportive information.**

**Responsible**
Professor Jens Nielsen

Systems Biology, Department of Chemical and Biological Engineering, Chalmers

Tel: +46 31 772 3804

E-mail: nielsenj@chalmers.se