G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

Abstract

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. This requires access to good genome browsers to enable annotators to visualize and evaluate multiple lines of evidence (e.g., sequence similarity, RNA sequencing [RNA-Seq] results, gene predictions, repeats) and necessitates many volunteers to participate in the work. To address the technical barriers to creating genome browsers, the Genomics Education Partnership (GEP; https://gep.wustl.edu/) has partnered with the Galaxy Project (https://galaxyproject.org) to develop G-OnRamp (http://g-onramp.org), a web-based platform for creating UCSC Genome Browser Assembly Hubs and JBrowse genome browsers. G-OnRamp also converts a JBrowse instance into an Apollo instance for collaborative genome annotations in research and educational settings. The genome browsers produced can be transferred to the CyVerse Data Store for long-term access. G-OnRamp enables researchers to easily visualize their experimental results, educators to create Course-based Undergraduate Research Experiences (CUREs) centered on genome annotation, and students to participate in genomics research. In the process, students learn about genes/ genomes and about how to utilize large datasets. Development of G-OnRamp was guided by extensive user feedback. Sixty-five researchers/educators from >40 institutions participated through in-person workshops, which produced >20 genome browsers now available for research and education. Genome browsers generated for four parasitoid wasp species have been used in a CURE engaging students at 15 colleges and universities. Our assessment results in the classroom demonstrate that the genome browsers produced by G-OnRamp are effective tools for engaging undergraduates in research and in enabling their contributions to the scientific literature in genomics. Expansion of such genomics research/education partnerships will be beneficial to researchers, faculty, and students alike.

Development of a data science CURE in microbiology using publicly available microbiome datasets

“…Here we describe the development and implementation of a new data science CURE that leverages existing, published 16S rRNA gene amplicon sequencing datasets to study microbial community structure. Many new data science-driven CUREs have emerged in the last 2 years, especially in microbiome research ( Jung et al, 2020 ; Sargent et al, 2020 ; Sewall et al, 2020 ; Zelaya et al, 2020 ; Baker et al, 2021 ). Emerging CURE models in this area have focused on student-generated datasets coupling a dry-lab experience with a wet-lab component.…”

Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium

“…For the Alliance to take on this responsibility of WormBase, we need to support such satellite model organisms. Our plan is to support community gene structure annotation (e.g., for Drosophila , Sargent et al, 2020; for C. elegans , Moya et al 2023) using the Apollo curaton system designed specifically for such activity (Dunn et al, 2019).…”

Improving helminth genome resources in the post-genomic era

“…C. elegans, B. malayi, Dracunculus medinensis, Onchocerca volvulus, S. mansoni, Strongyloides stercoralis, T. trichiura, and Wuchereria bancrofti • Tools: gVAL [48], G-OnRamp [49].…”