Universität Wien
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301026 SE Computational methods in microbial ecology (2025S)

3.00 ECTS (2.00 SWS), SPL 30 - Biologie
Continuous assessment of course work

We 05.03. 13:15-16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1

Details

max. 18 participants
Language: English

Lecturers

    Classes (iCal) - next class is marked with N

    • Wednesday 19.03. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 26.03. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 02.04. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 09.04. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 30.04. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 07.05. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 14.05. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 21.05. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 28.05. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 04.06. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 11.06. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 18.06. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
    • Wednesday 25.06. 13:15 - 16:00 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1

    Information

    Aims, contents and method of the course

    • Mathematical concepts in microbial ecology
    • Statistics of high-dimensional data
    • Estimating diversity and composition of microbial communities
    • Databases and resources in microbial ecology
    • DNA sequencing in microbial ecology (amplicon sequencing, shotgun metagenomics)
    • Computational pipelines for amplicon sequencing: overview, features, evaluation
    • Phylogenetic analysis
    • Fundamentals of machine-learning for microbial ecology
    • Intro to high performance computing

    Assessment and permitted materials

    Regular quizzes and homework assignments. Homeworks contribute 50% to the final grade and quizzes contribute 50%. Participants should bring a laptop for in-class exercises. A passing grade is >50% of combined assessments.

    Minimum requirements and assessment criteria

    Minimum requirements: No computer programming knowledge required.

    Assessment criteria:
    Understanding relevant mathematical and computational methods in microbial ecology. Applying these methods to typical problems in microbial ecology and designing experiments. Performing mathematical and computational experiments using typical software programs. Presenting and interpreting the results of mathematical and computational experiments. Understanding and discussing recent scientific literature.

    Examination topics

    This course will consist of theoretical lectures, discussion of selected scientific papers and practical exercises (mainly using the computers of the participants).

    Reading list

    Will be provided throughout the course on the e-learning platform.

    Association in the course directory

    MMEI II-2.2, MMEI III

    Last modified: Fr 10.01.2025 00:02