Reproducible data analysis
Reproducible data analysis
A micro-credential that spans a total of 9 days
General context
Reproducible Data Analysis: an Essential Capability in Modern Science - a micro-credential
What are Micro-credentials?
Micro-credentials consist of one or several courses. The scope is expressed in ECTS credits (study credits), guaranteeing high-quality standards and certification. These short learning packages are designed to be easily combined with a job.
Micro-credentials equip you with the skills to remain competitive and are accredited by Flemish universities and promoted by the Flemish government, and the European Commission.
The scientific method is historically linked to the possibility that other researchers can replicate and verify its results. As scientific analysis becomes more complex and interdisciplinary, ensuring reproducibility becomes more challenging, especially in fields that combine different expertise. To promote transparency, consistency, and robustness in science, journals, funders, and institutions encourage using tools and practices that enhance reproducibility.
Learn about version control, containers, pipelines, and data reproducibility. This will steer you towards the reproducibility of your research and the impact and reliability of research findings and methods. Moreover, using the techniques introduced here, you can collaborate and experiment in ways that allow reproducibility and creativity to coexist and thrive.
This course = 3 ECTS issued by UGent university
Individual courses are also open for registration:
Version control with Git/GitHub
Introduction to High Performance Computing
Containerisation with Docker and Apptainer
Automated pipelines with Nextflow
- Use Git and GitHub for version control, reproducible, and easy-to-share code, text documents, and other appropriate data for this context.
- Differentiate between Docker and Apptainer images to select the appropriate tool for various computing environments.
- Develop and adapt container recipes for use both locally and on supercomputers, considering system-specific requirements.
- Run and modify Nextflow pipelines using best practices such as configuration files and modular components.
- Explain how containerization and version control contribute to reproducibility and shareability in computational research.
Project evaluation and an oral assessment.
It is ideal for researchers, students, and professionals from any background who are interested in improving their data analysis skills, enhancing research reproducibility, and connecting with a diverse community of peers and experts.
- Use simple shell commands (Linux, for example). You can use this e-learning material to prepare for the course.
- Experience with scripting is preferred (point to resource for catch-up before the course).
- Create a VSC account.
Trainers
Bruna Piereck
Bruna Piereck is a bioinformatics trainer at VIB and ELIXIR-BE training coordinator deputy. She obtained a Master and PhD degree in Molecular Genetics, with a focus on Bioinformatics from the Federal University of Pernambuco, Brazil, in 2019. During her PhD, she had the chance to collaborate with the university of Luxembourg and the McGill university in Quebec Canada for a short time. Ever since she has been involved with teaching and research and Since March 2022, she joined VIB with the mission of teaching and assist other trainers in a variety of topics.
Alexander Botzki
Alexander Botzki at the Flemish Institute of Biotechnology, Belgium has with his group the mission of providing technology training in domains of VIB Technologies, Bioinformatics & AI, Software Development, and Research Data Management. Between 2014 and 2022, he was head of the VIB Bioinformatics Core. From September 2009 to July 2014, he was responsible for the roll-out of E-Notebook (electronic lab notebook) to VIB's researchers within 75 research groups.
Before joining VIB, Alexander worked on various computational biology projects for Algonomics (bought by Lonza, 2008-2009) and DevGen (now Syngenta, from 2006-2008). During Alexander's PostDoc at Sanofi Aventis in Strasbourg, he executed various virtual screening campaigns on the compound selection of the merged enterprise. He received his doctoral degree with the group of Prof. Dr. Armin Buschauer (University of Regensburg, Germany) on 'Structure-based design of hyaluronidase inhibitors'.
Kobe Lavaerts
Bioinformatician at VIB Nucleomics Core in Leuven. Currently mainly focusing on operating and developing routine pipelines for processing raw sequencing data.
Nicolas Vannieuwkerke
Nicolas Vannieuwkerke is a bioinformatician at CMGG (UZ Ghent) who mainly focuses on developing and maintaining Nextflow pipelines for the diagnostic NGS analyses. He is a very active member of the Nextflow community as a Nextflow ambassador and is part of the nf-core core team. Nf-core is the largest Nextflow community that creates and maintains a number of best-practice pipelines and developer resources.
Bart Mesuere
Professor of Big Data Science.
Specialties: algorithms, data structures, web development, data visualization, computational biology, bioinformatics, computational metaproteomics
Program
- Intro Day - 29 September 2025
- Git & GitHub - 9 & 10 October 2025
- HPC intro - 17 October 2025
- Docker and Apptainer - 23 & 24 October 2025
- Nextflow - 27 & 28 November 2025
- Project day - 12 December 2025
Intro with real cases and challenges in making data analysis more reproducible
9 October 2025 - Concepts, basic usage & collaboration
10 October 2025 - Branching, Forking and Solving conflicts
Find out more here.
23 October 2025 - Docker concepts, running and building containers
24 October 2025 - Apptainer concepts, running, and building containers
Find out more here.
27 November 2025 - Building blocks, Process, and Best practices
28 November 2025 - Config files, Containers, and Guided challenge
Find out more here.
Oral presentation and evaluation
Practical info
29 September 2025 - 12 December 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
29 September 2025 - 12 December 2025
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
29 September 2025 - 12 December 2025
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
29 September 2025 - 12 December 2025
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.
29 September 2025 - 12 December 2025
Ghent - VIB/UGent FSVM II
This Micro-credential = 3 ECTS