Course syllabus
Course-PM
KMG060 KMG060 Systems biology lp1 HT24 (7.5 hp)
Course is offered by the department of Life Sciences
Contact details
Yun Chen, examiner. E-mail: yunc@chalmers.se
Course purpose
The aim of the course is to give the students a fundamental understanding of: 1) how mathematical modeling of biological systems can be used to gain novel biological insight and 2) how high-throughput biological data can be analyzed. The students will be presented with a number of examples from analysis of transcriptome data from different organisms. They will further get hands-on experience with analysis of 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. Finally, the students will learn about integrated data analysis through different examples. The overall objective is that by passing this course the students should have a solid overview of how systems biology impacts modern medical, biotechnological and nutritional research.
Schedule
Course literature
The textbook “Systems Biology: Constraint-Based Reconstruction and Analysis”, by Bernhard Ø Palsson, will be used for portions of the course. You can find a digital version of this book at the Chalmers library (https://doi-org.proxy.lib.chalmers.se/10.1017/CBO9781139854610). Additionally, research papers and other relevant material will be provided to the students in digital form, together with slides and exercises. This material will be made available in the student portal Canvas http://canvas.chalmers.se. It is expected that the students read the uploaded slides and specified material for passing the exam.
Course design
The course gives a description of how systems biology is impacting medicine, biotechnology and nutrition. The core of systems biology is quantitative analysis of cellular functions and in the course all key cellular processes will be discussed in a quantitative fashion. The course is organised with lectures, computational exercises, quizzes, and assignments. The course will give insight into how metabolic networks can be reconstructed from biochemical and genomic information. Topological analysis of large genome-scale metabolic models (GEM) will be performed and the basic principles for operation of large metabolic networks will be discussed and analyzed. The course will also give a brief introduction to different methods for generating so-called omics data, e.g. transcriptome, proteome and metabolome data, and how these can be analyzed. Finally, the course will present, using quantitative data, what are key drivers for cellular growth and what are constraining cellular growth. Throughout the course there will be given examples from studies of yeast, nutritional studies, and from analysis of clinical data.
Changes made since the last occasion
A summary of changes made since the last occasion.
Learning objectives and syllabus
- Knowledge and understanding
After completion of the course the student shall be able to:
- State and define the principles of systems biology
- Formulate key cellular processes like transcription, translation, signaling and protein secretion in a quantitative fashion
- Describe metabolic network reconstruction based on biochemical and genomic information
- Describe and explain how constraints and objective functions are underlying principles of flux balance analysis
- Describe the use of genome-scale metabolic models in research on human disease
- Present 5 examples of how GEMs can be used in modern biology
- Competence and skills
The student that has passed the course is expected to be able to:
- Use matrix notation to describe the stoichiometry of metabolic networks
- Explain how genome-scale metabolic models (GEMs) can be used for analysis of cellular physiology
- Explain and apply the principles of RNAseq
- Explain and apply the principles of proteomics
- Explain and apply the principles of metabolomics
Examination form
Exam dates: 1 November 2024, 09 January and 26 August 2025
Examination in this course will be in the form of a four-hour written exam. Reports from exercise 1 and 3 have to be approved for passing the course.
For the final exam, the grades are U (fail), 3, 4, and 5. You need
50% to pass (3),
70% for 4
and 85% for 5.
Rules for the written exam:
- Four-hour written exam.
- Questions are in English.
- There are no negative points and it is possible to get partial points for written answers.
- The maximum total points from the written exam is 100%