PA052 Introduction to Systems Biology

Faculty of Informatics
Autumn 2010
Extent and Intensity
2/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
prof. RNDr. Luboš Brim, CSc. (lecturer)
doc. RNDr. David Šafránek, Ph.D. (lecturer)
Guaranteed by
prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing - Faculty of Informatics
Thu 16:00–17:50 B411
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 22 fields of study the course is directly associated with, display
Course objectives
At the end of the course, students will be capable of employing abstract computer-scientific thinking in the field of biological systems modeling.
  • 1.History and scope of Systems Biology 2.Basic notions - Living organism as a system with precisely given structure and functionality - In silico modeling - Abstraction - Model as a formal system - Simulation and prediction 3.Sources of biological data - Databases of biological knowledge 4.A typical research scenario in Systems Biology - Use of informatics and mathematical methods 5.Specification of a biological system - Biological networks and pathways - SBML language 6.Static analysis of biological systems - Analysis of biological networks and pathways 7.Modeling and simulation of dynamic mechanisms of living organisms 8.Modeling of Escherichia coli bacteria - Genetic regulatory network of E. coli - Models of loccomotion organ synthesis and chemotaxis - Nutritional stress response models – Models of starvation 9.Case studies of other in silico models 10.Model validation - In silico analysis vs. experimental analysis 11.Design and reconstruction of biological networks - Syntetic Biology - Example of reconstruction of E. coli
    recommended literature
  • ALON, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. : Chapman & Hall/Crc, 2006. info
Teaching methods
lectures, readings
Assessment methods
Final exam is written. In the case homeworks are assigned, these are counted by maximum of 30% to the final mark. No study materials are allowed during the final examination.
Language of instruction
Further Comments
Study Materials
The course is taught annually.
Teacher's information
The course is also listed under the following terms Autumn 2011, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, Spring 2018, Spring 2019, Spring 2020, Spring 2021.
  • Enrolment Statistics (Autumn 2010, recent)
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