Systems Biology in Practice

6 EC

Semester 2, period 5

5304SBIP6Y

Owner Master Bioinformatics and Systems Biology (joint degree)
Coordinator Filipe Branco dos Santos
Part of Master Biological Sciences, Master Life Sciences, track Systems Biology, Master Biological Sciences, track Green Life Sciences, Master Life Sciences, track Bioinformatics, Master Bioinformatics and Systems Biology (joint degree), Master Bioinformatics and Systems Biology (joint degree), track Systems Biology, year 1Master Forensic Science, year 2
Links Visible Learning Trajectories

Course manual 2024/2025

Course content

Throughout the course, the same experimental material will be used. Microorganisms will be cultured under a set of different conditions in the group Molec Microbial Phys and their physiology will be quantified in terms of metabolic fluxes. Transcriptome analysis of the cells will show how and to what extent the environment affects the metabolic network at the genetic level. Finally the same cells will be analyzed at the level of their protein composition by a proteomic analysis and by enzyme activity assays in vitro. Lectures on more general subjects of Microbiol Systems Biology will be organized to give the students a flavor of practice and application.
The content of the course can be summarized:

  • Theory and practice growth of bacterial growth, flux analysis, biochemical assays;
  • Theory and practice of genetic tools, gene expression, transcriptomics;
  • Theory and practice of mass spec and proteomics;
  • Data analysis, protein identification, systems biology of micro organisms

Study materials

Literature

  • Lecture contents.

Objectives

  • learn how information obtained by experiments at the level of cellular behaviour, genetic profile and enzymatic make-up can be combined in order to get insight in the mechanisms underlying regulation and adaptation of microbial organisms [knowledge and understanding]
  • be familiar with the basic techniques and principles of microbial physiology, transcriptome analysis, [applying knowledge and understanding].
  • be familiar with the basic techniques and principles and data handling and analysis of   massspectrometry data [applying knowledge and understanding].

Teaching methods

    Lectures and practicals.

    Learning activities

    Activity

    Number of hours

    Computerpracticum

    24

    Hoorcollege

    36

    Practicum

    56

    Presentatie

    4

    Werkcollege

    4

    Zelfstudie

    8

    Zelfstudie

    36

    Assessment

    Item and weight Details

    Final grade

    Fraud and plagiarism

    The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

    Course structure

    Weeknummer Onderwerpen Studiestof
    1
    2
    3
    4
    5
    6
    7
    8

    Additional information

    Location: Science Park



    Contact information

    Coordinator

    • Filipe Branco dos Santos