System Biology

Completion:accreditation+exam (written)
Type of
Hour/semLecturesSem. ExercisesLab. exercisesComp. exercisesOther
Guarantee:Provazník Ivo, prof. Ing., Ph.D., DBME
Lecturer:Jiřík Radovan, Ing., Ph.D., DBME
Faculty:Faculty of Electrical Engineering and Communication BUT
Department:Department of Biomedical Engineering FEEC BUT
Learning objectives:
  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.
  The course is oriented to knowledge of methods of systems biology, design of models of cellular organisms and possibilites of their use. It is aimed at computational methods for description of living organisms on the molecular level applicable in cellular biology and biochemistry. The considered models are represented by networks. Methodology of analysis of these models by means of network motifs is emphasised. The theory of network analysis is applied to models of sensory and developmental transcription networks, models of signal transduction networks and neural networks. These models are illustrated on specific organisms, especially unicellular organisms.
Knowledge and skills required for the course:
  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.
Learning outcomes and competences:
  Students will be able to mathematically describe the main components of gene expression, mathematically describe the main components of signal transduction pathways, mathematically describe the main components of neuronal pathways, analyze network graphs using network motifs, name the main network motifs of transcription, signal-transduction and neuronal-system networks, explain principles of the main network motifs of transcription, signal-transduction and neuronal-system networks, describe experimental mathods in systems biology.
Syllabus of lectures:
  1. Definition of Systems biology, related fields
  2. Biological introduction, model organisms
  3. Kinetics of chemical reactions
  4. Transkription networks
  5. Network motifs of negative autoregulation
  6. Network motifs FFL
  7. Network motifs SIM, generalized motifs FFL, DOR
  8. Developmental transcription networks, signal-transduction network motifs
  9. Model of chemotaxis of escherichia coli
  10. Multi-layer network motifs, network motifs of neural networks
  11. Principles of proofreading of gene expression
  12. Experimental methods in systems biology - optical methods
  13. Experimental methods in systems biology - NMR and ultrasonography methods
Fundamental literature:
  • 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)
  • Konopka, A.K. Systems Biology: Principles, Methods, and Concepts. CRC, 2006, ISBN: 978-0824725204 (EN)
  • Alon, U: An Introduction to Systems Biology, Design Principles of Biological Circuits. CRC, 2007, ISBN: 1-58488-642-0 (EN)
  • Rosypal, S. Nový přehled biologie. Scientia, Praha 2003. ISBN 80-7183-268-5 (CS)
Controlled instruction:
  Laboratory tutorials are compulsory, properly justified absence can be compensated based on agreement of the tutor (usually in the last semester week).