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cff-version: 1.2.0
title: omnibenchmark
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: 'Izaskun '
    family-names: Mallona
    orcid: 'https://orcid.org/0000-0002-2853-7526'
  - given-names: Almut
    family-names: Lütge
    orcid: 'https://orcid.org/0000-0003-1104-727X'
  - given-names: Ben
    family-names: Carrillo
    orcid: 'https://orcid.org/0009-0003-5704-4151'
  - given-names: 'Daniel '
    family-names: Incicau
    orcid: 'https://orcid.org/0009-0001-1748-6145'
  - given-names: Reto
    family-names: Gerber
    orcid: 'https://orcid.org/0000-0001-5414-8906'
  - given-names: 'Anthony '
    family-names: Sonrel
    orcid: 'https://orcid.org/0000-0002-2414-715X'
  - given-names: Charlotte
    family-names: Soneson
    orcid: 'https://orcid.org/0000-0003-3833-2169'
  - orcid: 'https://orcid.org/0000-0002-3048-5518'
    given-names: Mark
    name-particle: D
    family-names: Robinson
identifiers:
  - type: url
    value: 'https://arxiv.org/abs/2409.17038'
  - type: doi
    value: 10.48550/arXiv.2409.17038
repository-code: 'https://github.com/omnibenchmark/omnibenchmark/'
url: 'https://docs.omnibenchmark.org'
abstract: >-
  Benchmarking in bioinformatics is a process of designing,
  running and disseminating rigorous performance evaluations
  of methods (software). Benchmarking systems facilitate the
  benchmarking process by providing an entrypoint to store,
  coordinate and execute concrete benchmarks.

  We describe an alpha version of a new benchmarking system,
  Omnibenchmark, to facilitate benchmark formalization and
  execution in solo and community efforts. Omnibenchmark
  provides a benchmark definition syntax (in a configuration
  YAML file), a dynamic workflow generation based on
  Snakemake, S3-compatible storage handling, and
  reproducible software environments using EasyBuild, lmod,
  Apptainer or conda. Tutorials and installation
  instructions are available from this https URL. 
keywords:
  - benchmarking
  - reproducible
  - software
  - bioinformatics
  - continuous
  - community-driven
  - methods
  - metrics
  - Snakemake
  - conda
  - envmodules
  - Apptainer
  - workflow
license: Apache
commit: 9a71537
version: 0.2.1
