Project Summary Improvements in the accuracy, length, throughput, and cost-effectiveness of sequencing technologies has resulted in a proliferation of multiple high-quality genome assemblies within many species. These pangenomes have garnered great interest from the research community because they provide an unbiased representation of sequence preservation and variation within a species that can not be matched by a single reference genome. The benefits of this representation are many. For instance, in biomedicine pangenomes can better reveal the genetic origins of certain diseases, help identify stable vaccine/drug targets, and can better characterize the evolution of cancers and tissue-specific mutations. However, the software used to analyze pangenomic data is still relatively new and changing rapidly, resulting in a knowledge gap between what tools are available and what tools are actually being used for biomedical research. To address this gap, we have developed a workshop for the New Mexico IDeA Networks for Biomedical Research Excellence (NM-INBRE) that teaches graduate students and researchers how to use graphical pangenomics tools for biomedical research. By instructing students in state-of-the-art pangenomics techniques we are expanding research opportunities for the students and increasing the number of competitive investigators in the scientific workforce. Unfortunately, the workshop is not free and it is only taught once annually to a limited number of students. Furthermore, the workshop uses a private server, requiring students to install the software in a different computing environment after the workshop to perform their own analyses. For these reasons, this project will adapt our NM-INBRE pangenomics workshop into an open-source Cloud Lab Module. Through the module students will learn how to operate in a preconfigured cloud environment in a cost-effective manner while becoming proficient in graphical pangenome analysis. The module will be made freely available online via the NIGMS Sandbox so anyone can work through the module themselves at their own pace. We will use the module materials to enhance our existing workshop and the materials will be free to use by anyone in their own curricula. Overall, the goal of the project is to adapt our existing NM-INBRE pangenomics workshop into a broadly available Cloud Lab Module to further reduce the pangenomics software knowledge gap while making access to this knowledge more equitable.

Project Narrative The New Mexico IDeA Networks of Biomedical Research Excellence (NM-INBRE) is strongly committed to (under)graduate research and education and strives to engage demographics underrepresented in STEM fields while expanding research/career opportunities for the students and increasing the number of competitive investigators in the scientific workforce. By adapting our existing NM-INBRE pangenomics workshop into an open-source Cloud Lab Module that can be taken independently or integrated into other curricula, we are greatly increasing the number of students and researchers that can utilize these modern pangenomics techniques in biomedical research. The short and long term benefits of this are many, including allowing current researchers to utilize these skills immediately in their biomedical research and arming students with these advanced skills prior to entering the (bio)medical workforce.