Course detail

Systems Biology

FEKT-MPA-SYSAcad. year: 2021/2022

The course is oriented to gain knowledge of methods used in systems biology, creating models of cellular organisms and possibilities of their usage. It aims on computational methods used to describe behavior of living organisms on molecular level that are utilizable in cellular biology, biochemistry, and biotechnology.
Studied models are represented by extensive network graphs. Special attention is paid to both methodologies of model analysis, static as well as dynamic, especially using quantitative ODE models. The concept of hierarchy is followed and all functional layers, from gene regulatory network to signaling pathways and metabolic networks, are presented. Examples of models are given on systems of particular, especially unicellular, organisms.

Learning outcomes of the course unit

Students will be able to:
- mathematically describe the main components of gene expression
- mathematically describe the main components of signal transduction pathways
- analyze network graphs using network motifs
- name the main network motifs of transcriptional networks and signal-transduction pathways
- explain function of the main motifs of transcriptional networks and signal-transduction pathways
- describe experimental mathods in systems biology

Prerequisites

Students enrolled in this subject should be able to describe cellular systems, its main components regarding structure and function; analyze systems of ordinary differential equations and apply basic knowledge of probability distribution and combinatorics. In general, knowledge on the Bachelor's degree level is requested.

Co-requisites

Not applicable.

Recommended optional programme components

Not applicable.

Recommended or required reading

Konopka, A.K. Systems Biology: Principles, Methods, and Concepts. CRC, 2006, ISBN: 978-0824725204 (EN)
Klipp, E., Liebermeister, W., Wierling, C., Kowald, A., Lehrach, H., Herwig, R. Systems Biology: A Textbook. Wiley, 2009. ISBN: 978-3-527-31874-2 (EN)
Alon, U: An Introduction to Systems Biology, Design Principles of Biological Circuits. CRC, 2007, ISBN: 1-58488-642-0 (EN)
Maly, Ivan V. Systems biology. Humana Press, New York 2009. ISBN 978-1-934115-64-0. (EN)
Rosypal, S. Nový přehled biologie. Scientia, Praha 2003. ISBN 80-7183-268-5 (CS)
Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Encyclopedia of systems biology. Springer, New York 2013. ISBN 978-144-1998-644. (EN)

Planned learning activities and teaching methods

Techning methods include lectures and computer laboratories. Course is taking advantage of e-learning (Moodle) system.

Assesment methods and criteria linked to learning outcomes

up to 16 points for reports from computer exercises
up to 14 points for completion and presentation of the semestral project
up to 70 points for exam.
Examination has an oral form.

Language of instruction

English

Work placements

Not applicable.

Course curriculum

1. Introduction to systems biology
2. Laboratory techniques for systems biology
3. Model organisms, biological networks and pathways
4. Basics of dynamic analysis of continuous models
5. Enzyme kinetics
6. Regulation of transcription
7. Prediction of network motifs, autoregulation motif
8. FFL motif
9. Additional network motifs
10. Gene ontology
11. Qualitative Boolean models
12. Gene regulatory network inference and parameter estimation
13. Project presentations

Aims

The aim of the subject is to provide students with basic knowledge of computational models in cellular biology and way of their use, knowledge of analysis methods applied to models in systems biology.

Specification of controlled education, way of implementation and compensation for absences

Laboratory tutorials are compulsory, properly justified absence can be compensated based on agreement of the tutor (usually in the last semester week).

Classification of course in study plans

  • Programme IT-MGR-2 Master's

    branch MBI , any year of study, summer semester, 5 credits, elective

  • Programme MITAI Master's

    specialization NADE , any year of study, summer semester, 5 credits, elective
    specialization NBIO , any year of study, summer semester, 5 credits, elective
    specialization NGRI , any year of study, summer semester, 5 credits, elective
    specialization NNET , any year of study, summer semester, 5 credits, elective
    specialization NVIZ , any year of study, summer semester, 5 credits, elective
    specialization NCPS , any year of study, summer semester, 5 credits, elective
    specialization NSEC , any year of study, summer semester, 5 credits, elective
    specialization NEMB , any year of study, summer semester, 5 credits, elective
    specialization NHPC , any year of study, summer semester, 5 credits, elective
    specialization NISD , any year of study, summer semester, 5 credits, elective
    specialization NIDE , any year of study, summer semester, 5 credits, elective
    specialization NISY , any year of study, summer semester, 5 credits, elective
    specialization NMAL , any year of study, summer semester, 5 credits, elective
    specialization NMAT , any year of study, summer semester, 5 credits, elective
    specialization NSEN , any year of study, summer semester, 5 credits, elective
    specialization NVER , any year of study, summer semester, 5 credits, elective
    specialization NSPE , any year of study, summer semester, 5 credits, elective

  • Programme MPC-BTB Master's, 1. year of study, summer semester, 5 credits, compulsory

Type of course unit

 

Lecture

26 hours, optionally

Teacher / Lecturer

Exercise in computer lab

26 hours, compulsory

Teacher / Lecturer