PB172 Systems Biology Seminar

Faculty of Informatics
Spring 2020
Extent and Intensity
0/2/0. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
RNDr. David Šafránek, Ph.D. (lecturer)
Guaranteed by
RNDr. David Šafránek, Ph.D.
Department of Machine Learning and Data Processing - Faculty of Informatics
Contact Person: Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing - Faculty of Informatics
The seminar is focused on studying and presentation of selected scientific articles/book chapters in the field of computational systems biology. Students are assumed to understand elementary notions from biology and chemistry (grammar school level), to know basic principles of the systems biology paradigm, and to be interested in deeper understanding of the field. Previous successful studying of PB050 is welcome.
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 the course is directly associated with
there are 80 fields of study the course is directly associated with, display
Course objectives
At the end of the course students should be able to: understand key results of computational systems biology; work with a scientific paper; extract the information from literature; prepare and give an oral presentation.
Learning outcomes
At the end of the course students should be able to:
- analyse a scientific paper;
- combine and infer the information from scientific literature;
- discuss pros and cons of computational methods in systems biology;
- contrast conceptual errors in analysed publications by employing suitable arguments.
  • Overview of elementary notions and paradigms.
  • Selection of seminar topics (papers) and explanation of their significance.
  • Studying of the selected topics.
  • Presentation and discussion.
  • Formal methods for computational systems biology : 8th International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2008 : Bertinoro, Italy, June 2-7, 2008 : advanced lectures. Edited by Marco Bernardo - Pierpaolo Degano - Gianluigi Zavattaro. Berlin: Springer, 2008. x, 523. ISBN 9783540688921. info
  • ALON, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. : Chapman & Hall/Crc, 2006. info
  • NOBLE, Denis. Music of life : biology beyond the genome. Oxford: Oxford University Press, 2006. xiii, 153. ISBN 9780199295739. info
  • Systems biology : definitions and perspectives. Edited by Lilia Alberghina - Hans V. Westerhoff. Berlin: Springer, 2005. xvii, 408. ISBN 354022968X. info
  • Computational modeling of genetic and biochemical networks. Edited by James M. Bower - Hamid Bolouri. Cambridge: Bradford Book, 2001. xx, 336. ISBN 0262524236. info
  • Foundations of systems biology. Edited by Hiroaki Kitano. London: MIT Press, 2001. xv, 297. ISBN 0262112663. info
Teaching methods
Student presentations, discussions.
Assessment methods
oral presentation of the selected topic
Language of instruction
Further Comments
The course is taught each semester.
The course is taught: every week.
The course is also listed under the following terms Spring 2010, Autumn 2010, Spring 2011, Autumn 2011, Spring 2012, Autumn 2012, Spring 2013, Autumn 2013, Spring 2014, Autumn 2014, Spring 2015, Autumn 2015, Spring 2016, Autumn 2016, Spring 2017, Autumn 2017, Spring 2018, Autumn 2018, Spring 2019, Autumn 2019.
  • Enrolment Statistics (recent)
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