Scientific Program

The course will be open for students with experimental and/or theoretical background. It is expected that students with different backgrounds will stimulate and support each other. To achieve this the students will be assigned to groups of varying size, and in these groups the students will jointly work on different tasks. In the lab (both wet and computer) the students will work in small groups (two students in each group), whereas for presentation exercises the students will work in groups of four. Social events in the beginning and towards the end of the course will help to form a coherent group of students participating at the course, and this will form a very important network well beyond the course. The aim is to generate a group of thirty motivated and highly interacting students.
In order to prime the students for the course they will prepare themselves depending on their level in experimental and computational biology. As a basis for mathematical modeling the books “Systems Biology in Practice” (Klipp, Herwig, Kowald, Wierling, Lehrach) and “Metabolic Engineering: Principles and Methodologies” (Stephanopoulos, Aristidou, Nielsen) should be studied in advance of the course. Background in genomics and omics technologies will be acquired through studying “Discovering Genomics, Proteomics & Bioinformatics” (Campbell, Heyer), also in advance of the course (this textbook will also be used during the course). To introduce principles of cellular metabolism, physiology and cell biology different book chapters and review articles will be distributed to the students. To introduce specific pathways studied in the course review and research articles will be distributed. From the beginning of April 2010 a website will be opened that allows communication between students and teachers. Here the students will also be able to ask questions to the teachers, who will answer posed questions weekly.

The course program focus on modeling of metabolism, omics analysis and bioinformatics, and it will consist of the following elements:

• Introduction. Definition of biological systems. Introduction to Systems Biology. Overview of metabolism and cell biology. Fundamentals of mathematical modeling.
• Metabolic modeling. Reconstruction of metabolic network models. Analysis of simple metabolic models. Assumptions underlying flux balance analysis. Metabolic flux analysis. Going to genome-scale. Elementary flux modes. Analysis of network structures. Flux constraining using 13C-labelled substrates. Metabolic control analysis. Thermodynamic analysis of metabolic networks.
• Genomics and omics analysis. Genome sequencing and analysis. Comparative genomics. Transcriptome analysis. Proteome analysis. Metabolome analysis. Data normalization, statistical analysis, clustering analysis and principal component analysis. Integrated data analysis. Different datasets will be analyzed from raw data to biological conclusions. Data from yeast, mouse and human studies will be analyzed.
• Applications. Metabolic engineering for the production of fuels and chemicals. Production of heterologous proteins (enzymes and protein drugs). Production of antibiotics. Nutritional studies using mouse models. Integrated analysis of mouse tissues from nutritional studies. Analysis of metabolism in different human tissues using biopsies and tracer studies from the clinic.

The days will have fix points with a lunch break from 12:00-13:00, a supper break from 18:00-19:00, as well as presentations from students 19:00-21:00. All students will have to present and discuss their project. In addition scientific presentations from some of the teachers will be integrated into the program. In some of the evenings social events will be organized.

15 ECTS points are suggested for this course.

Confirmed teachers
Jens Nielsen, Chalmers University of Technology
Dina Petranovic, Chalmers University of Technology
Goutham Vemuri, Chalmers University of Technology
Sergio Bordel Velasco, Chalmers University of Technology
Wanwipa Vongsangnak, Chalmers University of Technology
Intawat Nookaew, Chalmers University of Technology

Confirmed guest lectures
Jörg Stelling, ETH Zürich
Vassily Hatzimanikatis, EPFL

Teaching materials/literature
The following textbooks and reading material will be used at the course:

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


• B. O. Palsson (2006) Systems Biology. Properties of Reconstructed Networks, Cambridge University Press, New York

It is expected that all students have acquired these textbook before the course and studied them according to the detailed course program that will be send to students admitted to the course. Besides these two text books there will be used different research papers and exercises that will be provided to the students during the course. This additional material will be made available at www.sysbio.se/ICSBM2010/program (password will be given to students admitted to the course).