R for biologists with Metagenomics
Informacje ogólne
Kod przedmiotu: | 2600-OG-EN-RBM |
Kod Erasmus / ISCED: |
13.1
|
Nazwa przedmiotu: | R for biologists with Metagenomics |
Jednostka: | Wydział Nauk Biologicznych i Weterynaryjnych |
Grupy: |
Przedmioty ogólnouniwersyteckie |
Punkty ECTS i inne: |
5.00
|
Język prowadzenia: | angielski |
Wymagania wstępne: | (tylko po angielsku) Background knowledge of biology and mathematics |
Rodzaj przedmiotu: | przedmiot fakultatywny |
Całkowity nakład pracy studenta: | (tylko po angielsku) Contact hours with teacher: np. - participation in laboratory 45 hrs - consultations- 20 hrs Self-study hours: np. - preparation for laboratory - 10 hrs - preparation for test- 20 hrs Altogether: 1000 hrs (4 ECTS) |
Efekty uczenia się - wiedza: | (tylko po angielsku) W1: Student has basic knowledge of biology and/or environmental sciences W2: Student possesses knowledge how to organize information for environmental data bases W3: Student is familiar with mathematics and statistics at a basic level that allows describing natural phenomena W4: Student is acquainted with using computer and windows-based programme |
Efekty uczenia się - umiejętności: | (tylko po angielsku) U1: Student is able to search information with most popular web browsers U2: Student is capable of preparing final report and draw certain conclusions which may be useful in future. U3: Student has basic skills in data collection U4: Student can analyze information from the support forums |
Efekty uczenia się - kompetencje społeczne: | (tylko po angielsku) K1: Student understands the significance of continuous improvement of knowledge through scientific and popular scientific journals - K2: Student understands the need for using mathematical, statistical and IT methods for developing and presenting results and analyzes K3: Student is sensitive to reliability of conducted analyzes and expert opinions K4: Student is aware of importance of team work K5: Student identifies strengths and weaknesses of the results K6: Student participates in critical analysis of the results K7: Student can cooperate with others |
Metody dydaktyczne: | (tylko po angielsku) Teaching methods : -problem lecture - classes -case studies |
Metody dydaktyczne podające: | - wykład problemowy |
Metody dydaktyczne poszukujące: | - ćwiczeniowa |
Skrócony opis: |
(tylko po angielsku) The aim of the course is to familiarize students with backgrounds of R and additionally with the methods of obtaining genetic material from the environment as well as the processing and analysis of information obtained as a result of next generation sequencing (NGS) enabling inference about the structure, biodiversity and functions of microorganisms. |
Pełny opis: |
(tylko po angielsku) Exercise 1 Installation of R and R Studio, Creating your first R script. Exercise 2 Structure of functions with different number of arguments. Different data types Exercise 3 Different objects in R: vector, matrix, array, list, data frame Exercise 4 Creating project in R. Working with data frame Exercise 5 Report Writing in R Markdown Exercise 6 Creating function with R Exercise 7 Case studies. Exercise 8 Introduction to metagenomics. Matagenomics as a tool in the ecology of microorganisms. The importance of metagenomics and development perspectives. Isolation of biological material for metagenomic analyzes. Methods and tools for DNA / RNA isolation. Requirements and quality of genetic material. Exercise 9 Bioinformatics analysis used in NGS data processing. Taxonomy analysis of microorganism communities. Numerous and rare OTUs, Venn diagrams. Ways to visualize data from taxonomy. Exercise 10 Alpha diversity. Analysis of biodiversity of microorganism communities. Dilution curves, indicators of species richness (Sobs, Chao1, ACE). Alpha diversity. Biodiversity indicators of microorganism communities (Shannon-Wiener index, Simpson index). Equivalence indicators. Exercise 11 Beta diversity. Distance, similarity / similarity of communities. Cluster analysis. Beta diversity. Consulting methods (PCA, PCoA). Exercise 12 Beta diversity. Hypothesis testing (ANOSIM, SIMPER, PERMANOVA). Other methods for visualizing data from NGS sequencing. Correlations and heatmaps. Exercise 13 Genome sequencing Use of genome information to identify microorganisms (ANI, in silico DDH). Genomic annotation in Rast Server. The role of microorganisms in the environment. Exercise 14, 15 Students' own work. Development of analysis results, report preparation and presentation of conclusions. |
Literatura: |
(tylko po angielsku) 1. Donovan, T., Brown, M., & Katz, J. (2015). Vermont Cooperative Fish and Wildlife Research Unit R Projects: R for Fledglings. Retrieved from https://www.uvm.edu/rsenr/vtcfwru/R/?Page=fledglings/fledglings.htm 2. Biecek P. 2014. Przewodnik po pakiecie R 3. Murrel P. 2006 R Graphics 4. Verzani J.2005. Using R for Introductory Statistics 5. Benedetti C (Ed) Metagenomics, Methods, Application and Perspectives (2014) Nova Publishers, New York 6. Izard J, Rivers M.C (Eds) Metagenomics for Microbiology, Academic Press, Elsevier 7. Li R.W (Ed) Metagenomics and its applications in agriculture, biomedicine, and environmental studies (2011) Nova Science Publishers. 8. Magurran AE, McGill BJ (Eds) Biological diversity: frontiers in measurement and assessment (2011) Oxford University Press |
Metody i kryteria oceniania: |
(tylko po angielsku) Assessment methods: Tests in moodle or Microsoft Teams. Class attendance, preparation for classes, active participation, preparation of report on conducted analyzes.- written examination Assessment criteria: fail- less than 60% satisfactory- 60-70% satisfactory plus- 71-80% good – 81-87% good plus- 88-94% very good- more than 94% |
Praktyki zawodowe: |
(tylko po angielsku) not applicable |
Zajęcia w cyklu "Semestr zimowy 2022/23" (zakończony)
Okres: | 2022-10-01 - 2023-02-19 |
Przejdź do planu
PN LAB
WT ŚR CZ PT |
Typ zajęć: |
Laboratorium, 45 godzin
|
|
Koordynatorzy: | Marcin Koprowski | |
Prowadzący grup: | (brak danych) | |
Lista studentów: | (nie masz dostępu) | |
Zaliczenie: | Zaliczenie na ocenę |
Zajęcia w cyklu "Semestr zimowy 2023/24" (zakończony)
Okres: | 2023-10-01 - 2024-02-19 |
Przejdź do planu
PN LAB
WT ŚR CZ PT |
Typ zajęć: |
Laboratorium, 45 godzin
|
|
Koordynatorzy: | Marcin Koprowski | |
Prowadzący grup: | Agnieszka Kalwasińska, Marcin Koprowski | |
Lista studentów: | (nie masz dostępu) | |
Zaliczenie: | Zaliczenie na ocenę |
Właścicielem praw autorskich jest Uniwersytet Mikołaja Kopernika w Toruniu.