mar622 - Profile Module R programming for (meta)-genomic sequence analysis (Vollständige Modulbeschreibung)

mar622 - Profile Module R programming for (meta)-genomic sequence analysis (Vollständige Modulbeschreibung)

Originalfassung Englisch PDF Download
Modulbezeichnung Profile Module R programming for (meta)-genomic sequence analysis
Modulkürzel mar622
Kreditpunkte 6.0 KP
Workload 180 h
Einrichtungsverzeichnis Institut für Chemie und Biologie des Meeres (ICBM)
Verwendbarkeit des Moduls
  • Master Microbiology (Master) > Mastermodule
Zuständige Personen
  • Garcia, Sarahi Lorena (Modulverantwortung)
  • Eren, Ahmet Murat (Modulberatung)
Teilnahmevoraussetzungen
Kompetenzziele

The course will provide students with a general understanding of the utility of the UNIX terminal environment and shell scripting, Python programming language and its scripting abilities, and basics of R programming. The course is designed for life scientists with mock or real-world datasets that convey typical characteristics of what researchers often encounter in data-enabled microbiology, and help them develop dry-lab skills the way they developed wet-lab skills.

Specialist skills:

The students:
- Develop an appreciation of different scripting and programming tools and recognize task-specific best practices
- Learn the basics of how to solve bioinformatics challenges in reproducible manner

Methodological competence

The students:
- Can use BASH scripting to organize datasets and implement batch work solutions
- Can use Python for quick and effective data mining and reporting
- Can use R for statistical inference and exploratory visualization needs
- Able to generate reproducible .sh, .py, and .R files, and use Jupyter notebooks
- Develop an appreciation of the basics of programming, data structures, and algorithms

Modulinhalte

- Basics of BASH, Python, and R, and how they integrate with one another.

- Description of a science question, dataset to address it, and a step-wise computational strategy.

- Goal-oriented community scripting to explore alternative solutions.

- Individual scripting to establish a student-specific solution.

Literaturempfehlungen

will be announced

Links
Unterrichtssprache Englisch
Dauer in Semestern 1 Semester
Angebotsrhythmus Modul
Aufnahmekapazität Modul 16
Modulart Wahlpflicht / Elective
Modullevel AC (Aufbaucurriculum / Composition)
Lehr-/Lernform Block course:
SE/Ü: Programming for microbiologists
Vorkenntnisse Familiarity and competence in basic terminal usage
Lehrveranstaltungsform Kommentar SWS Angebotsrhythmus Workload Präsenz
Seminar 2 WiSe 28
Übung 4 WiSe 56
Präsenzzeit Modul insgesamt 84 h
Prüfung Prüfungszeiten Prüfungsform
Gesamtmodul

Will be announced

1 Examination performance:

Portfolio (max. 3 pieces of work) or minutes (approx. 15-20 pages)

Active participation in seminars and exercises.