Application of bioinformatic methods

General data

Course ID:	6.1-AoBM
Erasmus code / ISCED:	(unknown) / (unknown)
Course title:	Application of bioinformatic methods
Name in Polish:	Application of bioinformatic methods
Organizational unit:	Faculty of Natural Sciences and Technology
Course groups:
ECTS credit allocation (and other scores):	(not available) Basic information on ECTS credits allocation principles: the annual hourly workload of the student’s work required to achieve the expected learning outcomes for a given stage is 1500-1800h, corresponding to 60 ECTS; the student’s weekly hourly workload is 45 h; 1 ECTS point corresponds to 25-30 hours of student work needed to achieve the assumed learning outcomes; weekly student workload necessary to achieve the assumed learning outcomes allows to obtain 1.5 ECTS; work required to pass the course, which has been assigned 3 ECTS, constitutes 10% of the semester student load. view allocation of credits
Language:	(unknown)
Type of course:	obligatory courses
Short description:	Knowing and understanding the basic concepts and definition relevant to bioinformatics. Knowing and understanding the bioinformatics methods of DNA analyses, and acquiring the skill of their application in various fields of life sciences. Acquiring the skill of the use of computer techniques in bioinformatics. Knowing the bioinformatic databases and their functioning.
Full description:	A. Lecture: Essential bioinformatics. Molecular databases as sources of DNA sequences used in various fields of life sciences. Analyses of mitochondrial and nuclear DNA. DNA polimorphism. Molecular markers in phylogenomics, phylogeography, ecology, conservation biology, forensic biology, medicine and biodiversity studies. Computer programms enabling the use of bioinformatic data in various fields of life sciences. B. Laboratory: Computer programms and bioinformatic databases in phylogenomic and phylogeographic analyses. Haplotype analyses. Procedures of downloading the DNA sequences from GenBank. Sequence alignments and analyses. Substitution model selection. Tree construction using different algorithms. Oral presentation of results of computer analyses and simulations (accompanied by the electronic presentation). C. Conversatory: Mitochondrial, chloroplast and nuclear genomes, their structure, function and evolution. DNA sequences alignment. Molecular clock and its calibration. Usefulness of the molecular clock in phylogenomics and phylogeography. Molecular markers in phylogenomics, phylogeography, conservation biology and biodiversity studies – examples. Computer programms used in phylogenomics and phylogeography. Application of bioinformatic methods in studies on fossils. Basics of the structural bioinformatics.
Bibliography:	A. obligatory literature: A.1. used during lectures and laboratory sessions - Xiong J. Essential bioinformatics. Cambridge University Press, 2006. - Freeland J.R. Molecular ecology. John Wiley & Sons Ltd., 2005 - Hall B.G. Phylogenetic trees made easy: A how-to manual. Third edition. Sinauer Associates Inc., 2008. - specialised literature. A.2. lectures for self-study – as above B. additional literature - Avise J.C. Phylogeography: the history and formation of species. Harvard University Press, 2001. - Higgs P.G., Attwood T.K. Bioinformatics and Molcular Evolution. Blackwell Science Ltd., 2005. - specialised literature.
Learning outcomes:	Knowledge K_W01_/ P7S_WG recognizes research problems from the borderline of biological sciences K_W02_ /_ P7S_WG interprets the complexity of processes and phenomena in nature, the solution of which requires an interdisciplinary approach K_W04_/_ P7S_WG performs multi-aspect comparative analysis of the molecular, cellular and physiological mechanisms of the functioning of organisms K_W05_/_ P7S_WG describes the rules and mechanisms of molecular and cellular development of organisms, including embryogenesis K_W12_/_ P7S_WG recognizes the dynamic development of biological sciences K_W15_/_ P7S_WG searches and uses specialized bioinformatics tools, useful in solving problems studiowanej specjalności nauk biologicznych Skills K_U02_/ _ P7S_UK fluent in the scientific literature of the biological specialty he is studying in his mother tongue, and speaks English at a level B2+ K_U03_ /_ P7S_UW demonstrates the ability to critically analyze and select biological information, especially from electronic sources K_U05_ /_ P7S_UW uses statistical methods and IT techniques and tools to describe biological phenomena and analyze specialized statistical data K_U07_/_ P7S_UW critically confronts biological information from various sources and draws justified conclusions on this basis K_U08_ /_ P7S_ presents critically the research work in the field of selected specialty in biological sciences with the use of verbal communication and multimedia Social competencies K_K01_/_ P7S_KK aware of the complexity of biological phenomena and processes K_K04_ / _ P7S_KK recognized sources of scientific information and using the principles of critical reasoning in resolving practical problems K_K06_ /_ P7S_KK systematycznie aktualizuje wiedzę biologiczną i informacje o jej praktycznych zastosowaniach zastosowaniach
Assessment methods and assessment criteria:	Conditions to get credits for: A. Way of final evaluation: • lectures: a grade • laboratory: a grade • conversatory: a grade B. Form of testing: • lecture: final written test (including open and closed questions) • laboratory: oral presentation of results of computer analyses and simulations (accompanied by the electronic presentation) • conversatory: oral presentations based on literature studies accompanied by the electronic presentation C. Basic criteria • L: positive rating over 50% of points scored (in the examination test) • Lab: evaluation of results obtained during computer analyses Conv: evaluation of the oral presentations accompanied by the electronic presentation

This course is not currently offered.

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