Investing in Research Software Engineering for Expert Development and Dissemination of Bioconductor

This grant aims to support the career development of Lori Kern, a central developer of several facets of the NIH/NHGRI/NCI funded Bioconductor project: an open-source, open-development software project that develops, supports, and distributes software for genetic and genomic research, analysis, discovery and visualization. It will invest in the Research Software Engineer’s identified project goals to enhance and improve development and dissemination of Bioconductor. These goals include: Goal 1: Upgraded support for global computational genomic data science. This involves enhancing Bioconductor’s process for curating, documenting, and distributing Findable, Accessible, Interoperable and Reusable for Research Software (FAIR4RS) data and annotation for use in computational genomic data science. Experiment data, genomic reference information, and analytic algorithms are combined to produce statistical interpretations of novel experimental findings. Bioconductor strives to provide high quality data and up-to-date genomic annotations either through Bioconductor Hubs that reference remotely available data for download or traditional Bioconductor R packages. There are currently 71787 annotation resources from 2994 species available for download from the current AnnotationHub, 8332 Experiment data resources available in ExperimentHub, 926 standard Annotation Packages, and 430 standard Experiment Packages available in Bioconductor. Refinement and evaluation of currently available resources to ensure accuracy and relevance, and providing easier direct access in Bioconductor/R to other existing relevant genomic reference information, is essential for researchers to achieve novel experimental findings. Goal 2: Personal skill development that will enhance the sustainability of Bioconductor, with particular attention to concepts of cloud-scale research software, data, and genomic annotation production, management, and distribution as well as integration and collaboration with other relevant biological and bioinformatic communities. Goal 3: Project and Community leadership strengthening. Bioconductor leverages its extensive community to contribute and propel the project forward. With over 1192 active community developers, wrangling a highly technical and evolving ecosystem becomes vital. A balance of integrating cutting-edge, new technology and methodology with reliability and efficiency becomes essential to Bioconductor sustainability and relevance. Enhancements to the contribution process and learning opportunities for the community will help reach and connect the thousands of developers and millions of users. The outcomes will strengthen the well-established impact of Bioconductor in genome research in academia and industry.