Reproducible data analysis
Reproducible data analysis
A micro-credential which spans a total of 9 days.
General context
Reproducible Data Analysis: an Essential Capability in Modern Science - a micro-credential
What is 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 meant to easily combine 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.
Course Context:
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 specially in fields that combine different expertise. To promote transparency, consistency and robustness in science, journals, funders, and institutions are encouraging the use of 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, as well as the impact and reliability of research findings and methods. Moreover, using the methods introduced here you can collaborate and experiment in ways that allow reproducibility and creativity to coexist and thrive.
This course = 3 ECTS emmited by UGent university
- To use Git and GitHub for version control, reproducible and easy to share code, text documents, and other appropriate data for this context;
- To use Git and GitHub for individual projects and for collaboration;
- To use, adapt and write containers locally and in a super computer, understanding the different systems and its particularities;
- To use and to differentiate Docker containers and Apptainer images and their particular usage.
- To run, adapt and write NextFlow pipelines locally and in a super computer,
- To understand and to make use of best practices for NetFlow pipelines, such as config-files and modules;
Project evaluation and a Oral evaluation.
* Being able to use simple shell commands (Linux for example), you can use this e-learning material to prepare.
* Experience with scripting is preferred (point to resource of catch-up before the course)
* Creating 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
28 February | 9h30-17h00 |
Intro with real cases and challanges in making data analysis more reproducible
10 March | 9h30 - 17h00 | Concepts, basic usage & collaboration
11 March | 9h30-17h00 | Branching, Forking and Solving conflicts
28 March | 9h30 - 13h30 | Concepts, organization and how to use
31 March | 9h30 - 17h00 | Docker concepts, runing and building containers
01 April | 9h30 - 17h00 | Apptainer concepts, runing and building containers
28 April | 9h30 - 17h00 | Building blocks, Process and Best practices
29 April | 9h30 - 17h00 | Config files, Containers and Guided challange
12 May | 10h00 - 17h00 | Oral presentation and evaluation
Practical info
28 February 2025 - 12 May 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
28 February 2025 - 12 May 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.
28 February 2025 - 12 May 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.
28 February 2025 - 12 May 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.
28 February 2025 - 12 May 2025
Ghent - VIB/UGent FSVM II
Day 1: L5 room, 5th floor
All the other sessions: L4 room, 4th floor
This Micro-credential = 3 ECTS