Integration, optimization, and expansion of computational tools and resources for the Caenorhabditis Natural Diversity Resource

The goal of this application is to support Michael Sauria, PhD, as a Research Software Engineer (RSE) in the Andersen lab in the Department of Biology at Johns Hopkins University. He currently helps administer the Caenorhabditis Natural Diversity Resource (CaeNDR) under the direction of Erik Andersen, PhD. This project uses natural variation across three species of nematodes and thousands of strains to provide insights and resources for discovery not otherwise possible in genetically homogenous model organisms, such as natural differences in toxicant response and drug resistance in closely related parasitic nematodes. This RSE role will support several funded NIH projects by Andersen and many others by additional investigators across the evolutionary genetics and Caenorhabditis communities. In order to thrive and expand, CaeNDR requires a dedicated RSE, something it has been lacking since the Andersen lab moved from Northwestern University a year ago. This grant would provide Dr. Sauria the dedicated time necessary to oversee this project. In particular, he will overhaul the underlying infrastructure, including rebuilding the analysis pipelines to add robustness, flexibility, and quality assurance as well as migrating the project from Google Cloud Platform to Amazon Web Services. Dr. Sauria will develop additional tools and resources available to CaeNDR users to make better use of the hosted variation data, including strain-specific CRISPR-Cas9 guide RNA design, genome-wide association mapping tools in C. briggsae and C. tropicalis, sister species to C. elegans, and evolutionary statistics. Finally, Dr. Sauria will improve the user experience and user interface of CaeNDR by developing interactive tools for real-time data exploration, guided site and tool walkthroughs, and extensive documentation to support the analysis workflows as their own resource. Ultimately, this grant will support the harmonization of CaeNDR as a benchmark for other model systems, such as yeast, fly, and mouse, so that similar tools can be added to the Alliance of Genome Resources, leveraging natural variation as a powerful discovery platform. Project Number: 1R50ES037948-01 | Fiscal Year: 2025 | NIH Institute/Center: National Institute of Environmental Health Sciences (NIEHS) | Principal Investigator: Michael Sauria | Institution: JOHNS HOPKINS UNIVERSITY, BALTIMORE, MD | Award Amount: $155,000 | Activity Code: R50 | Study Section: Special Emphasis Panel[ZRG1 MCST-M (53)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11239451