PV225 Laboratory of Systems Biology

Faculty of Informatics
Autumn 2020
Extent and Intensity
1/2/0. 3 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: z (credit).
prof. Ing. Miloš Barták, CSc. (lecturer)
doc. RNDr. David Šafránek, Ph.D. (lecturer)
Ing. Jan Červený, Ph.D. (seminar tutor)
Guaranteed by
doc. RNDr. David Šafránek, Ph.D.
Department of Machine Learning and Data Processing - Faculty of Informatics
Contact Person: doc. RNDr. David Šafránek, Ph.D.
Supplier department: Department of Machine Learning and Data Processing - Faculty of Informatics
There are no preconditions. Students are expected to be interested in overlapping disciplines combining Biology and Informatics.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 3/10, only registered with preference (fields directly associated with the programme): 3/10
fields of study / plans the course is directly associated with
there are 75 fields of study the course is directly associated with, display
Course objectives
At the end of the course students should be able to: understand physiology of plants and bacteria at very elementary level; understand most important methods of experimental measuring; measure data using particular techniques; summarize and interpret the measured data.
Learning outcomes
At the end of the course students should be able to:
- interpret basic aspects of physiology of plants and bacteria at elementary level;
- solve problem of parameter identification of a model with respect to experimental data;
- select and use a suitable tool for parameter identification;
- process a set of experimentally measured data for use in a suitable tool.
  • I Metabolomics
  • I.1 Metabolomics (Introduction; Metabolites; Metabolite Fingerprinting and Footprinting; Metabolite Profiling; Target-based analysis of metabolites)
  • I.2 Role of metabolomics in Systems Biology (Microbial metabolomics; Plant metabolomics; Human metabolomics)
  • I.3 Assey preparation (Obtaining media; Stopping of metabolism)
  • I.4 Methods used in metabolomics
  • I.5 Metabolomic data analysis

  • II Photobiology
  • II.1 Photochemical processes in photosynthesis
  • II.2 Role of photosynthesis in Systems Biology
  • II.3 Theoretical foundations of Fluorometrics
  • II.4 Methods of induced fluorescence
  • II.5 Obtaining and analysis of fluorometrics data
  • Metabolomics : a powerful tool in systems biology. Edited by Jens Høiriis Nielsen - Michael C. Jewett. Berlin: Springer, 2007. xv, 284. ISBN 9783540747185. info
  • Metabolome analyses : strategies for systems biology. Edited by Seetharaman Vaidyanathan - George G. Harrigan - Royston Goodacre. New York: Springer, 2005. xix, 390. ISBN 0387252398. info
  • Metabolomics : the frontier of systems biology. Edited by Masaru Tomita - Takaaki Nishioka. Tokyo: Springer, 2005. viii, 256. ISBN 4431251219. info
Teaching methods
Photobiology of Photosynthesis: Lecture and practical training exploiting recent fluorometric techniques Metabolomics : Lecture and practical training oriented on the application of capillary electrophoresis for the study of metaboleme of bacterium Paracoccus denitrificans
Assessment methods
2 student projects, final reports
Language of instruction
Follow-Up Courses
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught: in blocks.
Teacher's information
The course is also listed under the following terms Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, Autumn 2017, Autumn 2018, Autumn 2019.
  • Enrolment Statistics (recent)
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