PB050 Modelling and Prediction in Systems Biology

Faculty of Informatics
Autumn 2009
Extent and Intensity
1/1. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
RNDr. David Šafránek, Ph.D. (lecturer)
Guaranteed by
prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing - Faculty of Informatics
Timetable
Wed 16:00–17:50 B410
Prerequisites
This is an interdisciplinary course that extends the knowledge of bachelor students. The course is especially recommended for students of Bioinformatics.
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 able to apply abstract computer-scientific thinking to in silico modeling and analysis of living organisms. Students will become familiar with a variety of tools devoted to modeling and simulation in systems biology. Relevant practical skills will be obtained by working on a semestral project.
Syllabus
  • History and scope of systems biology.
  • Basic notions: living organism as a system with precisely given structure and functionality, in silico model, abstraction, simulation and prediction, model validation.
  • Sources of biological data: databases of biological knowledge.
  • Specification of a biological model: biological networks and pathways, SBML language.
  • Static analysis of biological systems: analysis of biological networks and pathways, network motifs and biological circuits.
  • Modeling and simulation of biological systems dynamics: hypotheses prediction.
  • Modeling of Escherichia coli bacteria: genetic regulatory network, models of loccomotion organ synthesis and chemotaxis, nutritional stress response models.
  • Robustness and parameter sensitivity.
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
Teaching methods
Lectures and optional homeworks. Group projects.
Assessment methods
Written final examination (50%), semester project (50%).
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2010, Autumn 2011, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, Autumn 2017, Autumn 2018, Autumn 2019.
  • Enrolment Statistics (Autumn 2009, recent)
  • Permalink: https://is.muni.cz/course/fi/autumn2009/PB050