This BoF is to bring together FOSDEMers involved in or interacting with others doing computational biology and bioinformatics, and anyone interested in learning more about how open source powers computational biology research around the world.

Open source and free software has long history in the computational biology community, forming the backbone of many high-quality tools. However, their adoption in research, industry, and healthcare settings is not yet universal. FOSDEM provides the ideal platform to bridge this gap by drawing upon best practices in computer science and applying them to the biological context.

Currently, bioinformatics is underrepresented at FOSDEM. This BoF seeks to change that by creating a space to share insights, demonstrate projects, and discuss the future of open-source bioinformatics.

Goals

1. Establish the foundation of a bioinformatics community at FOSDEM.
2. Explore effective and emerging practices for open-source software, systems, and infrastructure in computational biology across public, private, and academic sectors.
3. Showcase projects and spread the word about upcoming events.

Proposed Outline of the session

• Intros
• Open HPC infrastructure stack
  • Demo: Snakemake on the Dutch Tier 1 (SLURM powered) supercomputer Snellius (10min)
  • Discussion: Processing sensitive information on HPC clusters, Schedulers (i.e., Slurm [on K8s?]), HPC file systems (FOSS: Lustre Gluster, CephFS SaunaFS vs closed: i.e. WekaFS).
• Workflow systems and reproductibilty
  • Demo: Nextflow and the nf-core initiatve (10min)
  • Discussion: choosing a workflow language (snakemake, nextflow, common Workflow Language), ensuring reproducibility
• Open Web facing infrastructure and APIs
  • Demo: Slivka-Bio (https://compbio.dundee.ac.uk/slivka) and friends (10min)
  • Discussion: Galaxy, Jupyter, and local, national, and international platforms for computational biology
• Closing Discussion
  • Keep in contact at https://matrix.to/#/#fosdembioinformatics:matrix.org