PA183 Project in Systems Biology

Faculty of Informatics
Autumn 2021
Extent and Intensity
0/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
doc. RNDr. David Šafránek, Ph.D. (lecturer)
RNDr. Matej Troják, Ph.D. (assistant)
Guaranteed by
doc. RNDr. David Šafránek, Ph.D.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics
Timetable
Thu 16. 9. to Thu 9. 12. Thu 10:00–11:50 A418
Prerequisites
The subject requires knowledge of elementary modeling and simulation methods for biological systems dynamics. Previous undertaking of the related subjects PB050 and PA054 is welcome, but not necessary. Students who finished laboratory exercises of PV225 can use the obtained data for development of a related in silico model.
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
Course objectives
At the end of the course students should be able to:
search in public databases of biological knowledge;
create an in silico model of a biological system;
apply methods of computational systems biology to model analysis;
predict hypotheses regarding emergent properties of the modeled biological system.
Learning outcomes
At the end of the course students should be able to:
use public databases of biological knowledge;
construct an in silico model of a biological system;
apply methods of computational systems biology to model analysis;
infer hypotheses regarding emergent properties of the modeled biological system.
Syllabus
  • Overview of key notions
  • Setting of project topics
  • Project realization
  • Final student presentation
Literature
    recommended literature
  • KLIPP, Edda. Systems biology in practice : concepts, implementation and application. Weinheim: Wiley-Vch, 2005, xix, 465. ISBN 3527310789. info
  • Computational modeling of genetic and biochemical networks. Edited by James M. Bower - Hamid Bolouri. Cambridge: Bradford Book, 2001, xx, 336. ISBN 0262524236. info
    not specified
  • KLIPP, Edda. Systems biology : a textbook. Weinheim: Wiley-VCH Verlag, 2009, xxi, 569. ISBN 9783527318742. info
  • VRIES, Gerda de. A course in mathematical biology : quantitative modeling with mathematical and computational methods. Philadelphia, Pa.: Society for Industrial and Applied Mathematics, 2006, xii, 309. ISBN 0898716128. URL info
  • ALON, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/Crc, 2006. info
Teaching methods
Group projects, student presentations. Discussions.
Assessment methods
final report of the group project (2 pages A4), oral presentation of the results
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2010, Spring 2011, Spring 2012, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, Autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2021, recent)
  • Permalink: https://is.muni.cz/course/fi/autumn2021/PA183