Building a continuous benchmarking ecosystem in bioinformatics
Fuente:
arXiv
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| Auteurs principaux: | , , , , , , , |
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| Format: | Preprint |
| Publié: |
2024
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| Sujets: | |
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| _version_ | 1866916857414418432 |
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| author | Mallona, Izaskun Soneson, Charlotte Carrillo, Ben Luetge, Almut Incicau, Daniel Gerber, Reto Sonrel, Anthony Robinson, Mark D. |
| author_facet | Mallona, Izaskun Soneson, Charlotte Carrillo, Ben Luetge, Almut Incicau, Daniel Gerber, Reto Sonrel, Anthony Robinson, Mark D. |
| contents | Benchmarking, which involves collecting reference datasets and demonstrating method performances, 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_15472 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Building a continuous benchmarking ecosystem in bioinformatics Mallona, Izaskun Soneson, Charlotte Carrillo, Ben Luetge, Almut Incicau, Daniel Gerber, Reto Sonrel, Anthony Robinson, Mark D. Other Quantitative Biology Benchmarking, which involves collecting reference datasets and demonstrating method performances, 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. |
| title | Building a continuous benchmarking ecosystem in bioinformatics |
| topic | Other Quantitative Biology |
| url | https://arxiv.org/abs/2409.15472 |