Benchmarks for Bioinformatics Workflow Bake Offs

Abstract

This BioHackathon Project focused on establishing a "Great Bake Off of Bioinformatics Workflows" by developing workflow-level benchmarks for evaluating tools in computational tasks. Initially tested in proteomics, the project expanded to genomics and metabolomics. Collaborating with ELIXIR Implementation Studies, the team created rudimentary benchmarks, aiming for formalization before production use. The project consolidated efforts to produce a minimum set of workflow-specific benchmarks, aligning tools and workflow definitions. Short-term goals include drafting benchmarks with examples, while long-term plans involve implementing them in the Workflomics project and Proteomics Community ELIXIR Implementation Studies for community sharing.

Authors 4

1. Vedran Kasalica

   Netherlands eScience Center

   Affiliation as printed

   BioHackathon Europe 2023 Barcelona , Spain, 2023

   Netherlands eScience Center , Science Park 402 , 1098 XH , Amsterdam , The Netherlands

   Netherlands eScience Center, Science Park 402, 1098 XH, Amsterdam, The Netherlands

2. Felipe Morato

   CSC - IT Center for Science (Finland)

   Affiliation as printed

   CSC - IT Center for Science , Keilaranta 14 , Espoo , Finland

   CSC -IT Center for Science, Keilaranta 14, Espoo, Finland

3. Anna-Lena Lamprecht

   University of Potsdam

   Affiliation as printed

   University of Potsdam , Institute of Computer Science , An der Bahn 2 , 14476 Potsdam , Germany

   University of Potsdam, Institute of Computer Science, An der Bahn 2, 14476 Potsdam, Germany

4. Magnus Palmblad Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center , Albinusdreef 2 , 2333 ZA , Leiden , The Netherlands

   Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands