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Syllabus for

Academic year
KMG060 - Systems biology  
Systembiologi
 
Syllabus adopted 2020-02-19 by Head of Programme (or corresponding)
Owner: MPBIO
7,5 Credits
Grading: TH - Pass with distinction (5), Pass with credit (4), Pass (3), Fail
Education cycle: Second-cycle
Major subject: Bioengineering
Department: 28 - BIOLOGY AND BIOLOGICAL ENGINEERING


Teaching language: English
Application code: 08112
Open for exchange students: Yes
Block schedule: C
Maximum participants: 60

Module   Credit distribution   Examination dates
Sp1 Sp2 Sp3 Sp4 Summer course No Sp
0107 Examination 7,5c Grading: TH   7,5c   24 Oct 2020 pm J,  07 Jan 2021 am J,  24 Aug 2021 pm J

In programs

MPBIO BIOTECHNOLOGY, MSC PROGR, Year 1 (compulsory)
MPCAS COMPLEX ADAPTIVE SYSTEMS, MSC PROGR, Year 2 (elective)
MPCAS COMPLEX ADAPTIVE SYSTEMS, MSC PROGR, Year 1 (compulsory elective)
MPENM ENGINEERING MATHEMATICS AND COMPUTATIONAL SCIENCE, MSC PROGR, Year 2 (elective)
MPENM ENGINEERING MATHEMATICS AND COMPUTATIONAL SCIENCE, MSC PROGR, Year 1 (compulsory elective)

Examiner:

Martin Engqvist

  Go to Course Homepage


Eligibility

General entry requirements for Master's level (second cycle)
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling the requirements above.

Specific entry requirements

English 6 (or by other approved means with the equivalent proficiency level)
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling the requirements above.

Course specific prerequisites

Chemistry, biochemistry, mathematics (linear algebra, multivariable analysis, differential equations), cell and molecular biology.

Aim

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 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.

Learning outcomes (after completion of the course the student should be able to)

A student that has passed the course is expected to be able to:

  • Describe the principles of systems biology

  • Describe key cellular processes like transcription, translation, signaling and protein secretion in a quantitative fashion

  • Use matrix notation to describe the stoichiometry of metabolic networks

  • Describe metabolic network reconstruction based on biochemical and genomic information

  • Describe how genome-scale metabolic models (GEMs) can be used for analysis of cellular physiology

  • Describe 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

  • Describe how meta-omics data can be analyzed

  • Describe the principles of RNAseq

  • Describe the principles of proteomics

  • Describe the principles of metabolomics

  • Give 5 examples of how GEMs can be used in modern biology


Content

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 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.

Organisation

The course involves lectures and computer exercises.

Literature

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 ping pong http://pingpong.chalmers.se.

Examination including compulsory elements

Examination in this course will be in the form of a four hour written exam. Reports from all exercises have to be approved for passing the course.


Published: Mon 28 Nov 2016.