How do we benchmark? A meta-analysis | BioInfoGRX (RSG Spain Granada)
Lenguaje: English Resumen: Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and ultimately guide users on what tools to use. Benchmarking can also be important for community building and advancing methods in a principled way. We conducted a meta-analysis of recent single-cell benchmarks to summarize the scope, extensibility, neutrality, as well as technical features and whether best practices in open data and reproducible research were followed. We will discuss these meta-analysis results and explore some of the available frameworks to streamline scientific benchmarking. Ponente: Dr. Izaskun Mallona MiniBiografia: Izaskun Mallona completed her PhD in plant developmental biology in 2012 (Marcos Egea lab, Spain), with an emphasis in methods development for gene expression quantification. After that, she switched to epigenomics (Miguel A. Peinado lab, Spain; Tuncay Baubec lab, Switzerland; Mark Robinson lab, Switzerland) and released several methods and tools to analyze, browse and visualize epigenetic data. As a biologist and computer engineer by training, she is interested in the interface between life and computer sciences, and advocates for open source and open science. Her current research interests include methods development, gene expression regulation, and single-cell technologies. Redes sociales de la ponente: izaskun.mallona@mls.uzh.ch https://twitter.com/IzaskunMallona Satisfaction Survey: https://bioinformaticsgrx.es/encuesta ¡Siguenos en tu red social favorita, para estar al día de todas nuestras futuras actividades! https://bioinformaticsgrx.es/redes-sociales-siguenos/
Lenguaje: English Resumen: Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and ultimately guide users on what tools to use. Benchmarking can also be important for community building and advancing methods in a principled way. We conducted a meta-analysis of recent single-cell benchmarks to summarize the scope, extensibility, neutrality, as well as technical features and whether best practices in open data and reproducible research were followed. We will discuss these meta-analysis results and explore some of the available frameworks to streamline scientific benchmarking. Ponente: Dr. Izaskun Mallona MiniBiografia: Izaskun Mallona completed her PhD in plant developmental biology in 2012 (Marcos Egea lab, Spain), with an emphasis in methods development for gene expression quantification. After that, she switched to epigenomics (Miguel A. Peinado lab, Spain; Tuncay Baubec lab, Switzerland; Mark Robinson lab, Switzerland) and released several methods and tools to analyze, browse and visualize epigenetic data. As a biologist and computer engineer by training, she is interested in the interface between life and computer sciences, and advocates for open source and open science. Her current research interests include methods development, gene expression regulation, and single-cell technologies. Redes sociales de la ponente: izaskun.mallona@mls.uzh.ch https://twitter.com/IzaskunMallona Satisfaction Survey: https://bioinformaticsgrx.es/encuesta ¡Siguenos en tu red social favorita, para estar al día de todas nuestras futuras actividades! https://bioinformaticsgrx.es/redes-sociales-siguenos/