IV117 Introduction to Systems Biology

Faculty of Informatics
Autumn 2008
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
doc. RNDr. David Šafránek, Ph.D. (lecturer)
Guaranteed by
prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Timetable
Wed 16:00–17:50 B410
Prerequisites
This is an interdisciplinary course suitable for both bachelor and master students.
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 37 fields of study the course is directly associated with, display
Course objectives
This is a bachelor-level course devoted to application of computer-scientific methods and tools in the emerging field of Systems Biology. The course is focused on functional aspects of mechanisms that drive living organisms. The main goal of this course is to show students that abstract computer-scientific and mathematical methods can be effectively employed for in silico modeling and analysis of living organisms. Moreover, to enhance practicle skills, students have to apply some of the techniques and software tools to analysis of a small in silico model of some primitive organism in the range of a semestral project.
Syllabus
  • 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 - Network motifs and biological circuits
  • 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
Literature
  • ALON, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/Crc, 2006. info
  • Computational modeling of genetic and biochemical networks. Edited by James M. Bower - Hamid Bolouri. Cambridge: Bradford Book, 2001, xx, 336. ISBN 0262524236. info
Assessment methods
The course classification consists of a written final examination and work on a student project. The student project makes one half of the classification.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
Teacher's information
http://www.fi.muni.cz/~xsafran1/IV117/
  • Enrolment Statistics (recent)
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