Reusedata: An Open-Source, Open-Development Tool For Reusable & Reproducible Genomic Data Management
Channel: R Consortium
Date: 2022-09-09

Qian Liu Ph.D., Assistant Professor at Roswell Park Comprehensive Cancer Center, gave a short talk at the BioConductor Conference 2022. Lui gave her presentation on Reusedata: An Open-Source, Open-Development Tool For Reusable And Reproducible Genomic Data Management.

The fast-growing volume and complexity of genomic data resources bring exceptional opportunities to the research community, yet pose significant challenges to properly managing the data around access, curation, annotation, and storage. Individual data management can lead to substantial inefficiencies for repeated work and wasted computing resources, especially for those highly reused data curation steps such as the indexed reference genome. 

In the presentation, Lui introduced ReUseData, a workflow-based R package, to address these limitations by providing a systematic and simplified approach to standardize genomic data management and promote data sharing and reuse. ReUseData uses an innovative recipe strategy for standardized data curation, annotation, and automatic data generation by leveraging a workflow framework (Common Workflow Language) to provide stable runtime for command-line tools that are involved in data processing steps and creates data annotation/manifest files in standard formats (i.e., YAML and JSON) for easy interoperability with data analysis workflows. ReUseData creates and collects data recipes and generates cloud-ready curated data sets to promote the reusability, portability, scalability, and robustness of the genomic data ecosystem. The presentation concludes with a short Q&A session. 

Main Sections

0:00 Introduction
0:35 Genomix data resources access and pre-process
1:26 Traditional
3:11 ReUseData: An open-source, open-development tool for Reusable and reproducible genomic data management
3:46 Approach
4:28 ReUseData
6:12 ReUseData: take-home message
7:05 Thank you and Q&A 

More Resources 
Bioconductor Conference Site: https://bioc2022.bioconductor.org/ 
BioC2022 Github: https://github.com/Bioconductor/BioC2022 

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