C3780 Bioinformatics Workflow Managers

Přírodovědecká fakulta
jaro 2026
Rozsah
2/2/0. 5 kr. Ukončení: zk.
Vyučováno kontaktně
Vyučující
Nicolas Blavet, Ph. D (přednášející)
Mgr. Vojtěch Bystrý, Ph.D. (přednášející)
doc. RNDr. Radka Svobodová, Ph.D. (přednášející)
Garance
doc. RNDr. Radka Svobodová, Ph.D.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Kontaktní osoba: RNDr. Tomáš Raček, Ph.D.
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Omezení zápisu do předmětu
Předmět je nabízen i studentům mimo mateřské obory.
Mateřské obory/plány
Cíle předmětu
This course aims to provide students with practical skills in bioinformatics workflow management using management systems such as Galaxy, Nextflow, and Snakemake. The course focuses on: develop skills in workflow writing, automation, and management; enhance workflow design and its implementation using different managers; improve workflow efficiency and reproducibility.
Výstupy z učení
Upon completing the course, students will understand the structure and syntax of different workflow managers, including Galaxy, Nextflow, and Snakemake. They will be able to write, design, and implement bioinformatics workflows using these tools, automate and manage bioinformatics pipelines efficiently, and optimize workflows for better performance, scalability, and reproducibility.
Osnova
Throughout this course, we will provide an overview of different workflow managers, specifically Galaxy, Nextflow, and Snakemake, to examine their advantages, disadvantages, and requirements. The specific features of each workflow manager will be assessed. For Galaxy, we will explore its interface and its use in creating and managing complex bioinformatics pipelines. In the case of the Snakemake workflow management system, we will show the basic syntax for defining rules for the execution of specific processes and its use in developing modular and reproducible workflows. For the Nextflow workflow management system, we will cover its basic syntax and domain-specific language (DSL), with the goal of constructing complex and dynamic workflows. Ultimately, the learning of each selected workflow management system will be coupled with the creation of real complex workflows using real data.
Literatura
  • Finotello, F., Calura, E., Risso, D., Hautaniemi, S., & Romualdi, C. (2020). Multi-omic data integration in oncology. Frontiers in oncology, 10.
  • Demirbaga, Ü., Aujla, G. S., Jindal, A., & Kalyon, O. (2024). Big Data Analytics: Theory, Techniques, Platforms, and Applications. Springer Nature
  • Bioinformatics with Python cookbook: use modern Python libraries and applications to solve real-world computational biology problems. Packt Publishing Ltd.
Výukové metody
Student projects, their presentations and discussions.
Metody hodnocení
The student will be assessed based on a written project proposal (1-2 A4 pages) and a final presentation according to rules that will be specified at the beginning of the semester.
Vyučovací jazyk
Angličtina
Další komentáře
Předmět je vyučován každoročně.
Výuka probíhá každý týden.
  • Permalink: https://is.muni.cz/predmet/sci/jaro2026/C3780