Building a continuous benchmarking ecosystem in bioinformatics

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by Izaskun Mallona, Charlotte Soneson, Ben Carrillo, Almut Lütge, Daniel Incicau, Reto Gerber, Anthony Sonrel, Mark D. RobinsonBenchmarking, which involves collecting reference datasets and demonstrating method performance, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of methods. Although a lot has been written about how to design and conduct benchmark studies, this Perspective sheds light on a wish list for a computational platform to orchestrate benchmark studies. We discuss various ideas for organizing reproducible software environments, formally defining benchmarks, orchestrating standardized workflows, and how they interface with computing infrastructure.