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

• Published in: PLoS computational biology Vol. 16; no. 6; p. e1007863
• Main Authors: Sargent, Luke, Liu, Yating, Leung, Wilson, Mortimer, Nathan T, Lopatto, David, Goecks, Jeremy, Elgin, Sarah C R
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.06.2020; Public Library of Science (PLoS)
• Subjects: Algorithms; Animals; Annotations; Base Sequence; Bioinformatics; Biology; Biology and Life Sciences; Biomedical engineering; Collaboration; College students; Colleges & universities; Computational Biology - education; Computational Biology - methods; Computer applications; Computer Graphics; Cures; Data storage; Databases, Genetic; DNA sequencing; Drosophila melanogaster; Education; Galaxies; Gene expression; Gene sequencing; Genetic research; Genome; Genomes; Genomics; Genomics - education; Genomics - methods; Historically Black Colleges & Universities; Humans; Learning; Methods; Molecular Sequence Annotation; Nucleotide sequence; Partnerships; People and Places; Quality; Reconciliation; Research and analysis methods; Researchers; Ribonucleic acid; RNA; Schools; Science education; Sequence Analysis, RNA; Social Sciences; Software; Students; User-Computer Interface; United States; Oregon; United States > US; Illinois; Missouri
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1007863

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.