Tutorials and further material for the "Learning Data Management and Workflow Analyses: a hackathon from the EMBRC’s EMO BON (marine metagenomics) project" hackathon

The European Marine Omics Biodiversity Observation Network (EMO BON) is the flagship marine metagenomics project of the European Marine Biological Resource Centre (EMBRC). Sampling bimonthly at 16 sites throughout Europe, EMO BON aims to provide standardised marine metagenomics data, and data products, for marine scientists to use freely.

In this hackathon, EMBRC scientists will describe how EMO BON is driven by Open Science principles and the use of FAIR data standards, and demonstrate how data is managed and analysed within the project.

The use of standardised descriptions of data provenance and other metadata (data describing the data) will be emphasised through the use of vocabularies and ontologies and their importance for interoperability with other data sources and databases.

The analytical workflows used by EMO BON will be introduced and the basic concepts of how to write workflows (analysis pipelines) and how to execute them in a containerised environment will be described.

Participants will run and edit a simple workflow written in the Common Workflow Language for genomics data analysis and execute it on a High-Performance Computing cluster. An additional exercise will describe how to package one of the tools into a Docker container image.

This hackathon is intended to emphasise the broad concepts of data management and bioinformatic analyses of genomic data. Some basic UNIX commands you will need can be found here.

• Introduction by Cymon Cox (5')
• What is the EMBRC/EMO BON? by Ioulia Santi (10')
• Open Science principles and data provenance by Katrina Exter (30')
• Workflows and containerisation, and how to use them effectively by Haris Zafeiropoulos (~15')
• Hands-on by Haris remotely, and Cymon, Bruno, Joao on site (~3h)
• (Optional extra exercise If you have time and would like to learn more about Docker)
• Wrap-up by Cymon Cox (15')

• Cymon Cox - CCMAR, Faro, PT
• Joao Brazao - CCMAR, Faro, PT
• Bruno Louro - CCMAR, Faro, PT
• Gianluca de Moro - CCMAR, Faro, PT
• Katrina Exter - VLIZ, Ostend, BE
• Haris Zafeiropoulos, HCMR, Heraklion, GR
• Ioulia Santi - EMBRC-HQ & HCMR, Heraklion, GR