Fig 1.
A. Membership characteristics: participating faculty primarily teach genetics (although other disciplines are represented) and most often teach at primarily undergraduate institutions (PUIs) across the United States; faculty at community colleges and R1 research universities also participate. The geographical distribution of member schools and year of joining GEP are shown on the map. The member schools serve a diverse undergraduate student body, with 33% Minority-Serving Institutions (MSIs), including six Historically Black Colleges and Universities (HBCUs); 44% of the schools have 30% or more first-generation students, 11% have 30% or more nontraditional students (over 25 years of age), and 20% are commuter schools, with over 80% of the students commuting. See the Current GEP Members page (http://gep.wustl.edu/community/current_members) for a complete list of participating faculty with their schools. Map services and data available from the US Geological Survey, National Geospatial Program. B. Students in the GEP work together to produce high-quality annotation of a genome region or a collection of genes of interest identified by a Science Partner. “Student projects” are provided as genome browser pages (see lower portion of the figure), with one to seven potential genes (and other features of interest) for annotation. Browser tracks show available evidence for a gene, including gene conservation (sequence similarity track and additional BLAST searches), the presence of large open reading frames and other appropriate signals (ab initio gene predictions), and evidence of gene expression (RNA-Seq data, TopHat analysis results, etc.). Students work from these multiple lines of evidence, some of which may initially appear contradictory, to generate a gene model that they can defend. In the case shown, the sequence similarity search (BLAST) failed to identify putative upstream exons, whose presence is supported by RNA-Seq data and TopHat analysis. Students take responsibility for the workflow steps shown in light blue, while the Science Partner’s research group is responsible for the steps shown in gray. Pre-/post-course assessment has shown the effectiveness of such a collaborative annotation project both for supporting student learning about genes and genomes and in providing a research experience [17,21,22]. Biochem, Biochemistry; Evol. Bio., Evolutionary Biology; GEP, Genomics Education Partnership; RNA-Seq, RNA sequencing.
Fig 2.
After uploading data to Apollo via G-OnRamp’s "Create or Update Organism" tool, a user can choose which tracks to display with computational and experimental evidence, including submitted annotations from students, and begin to create her own gene model in a user-created annotations panel. Pictured is the Apollo interface showing provided sample data and computed lines of evidence, in addition to student annotation data and the final reconciled gene models (shown in the user-created annotations panel). The genome browser image illustrates a typical error by one student annotator at an intron/exon boundary. The standard protocol requires a minimum of two independent student submissions, followed by reconciliation by an experienced student annotator. Based on RNA-Seq data and the use of the noncanonical GC donor site in the informant species (Drosophila melanogaster), the reconciled gene model for the D. takahashii ortholog of eIF4G1 uses a noncanonical GC splice donor site instead of the GT donor site proposed by the student annotator. CDS, codon sequence; RNA-Seq, RNA sequencing.
Fig 3.
G-OnRamp is a Galaxy-based platform with analysis workflows that process a target genome assembly, transcripts and proteins from an informant genome, and RNA-Seq data from the target genome to create a genome browser for individual or collaborative annotation. Four sub-workflows (sequence similarity, ab initio gene predictions, RNA-Seq analysis, and repeats identification) run concurrently and generate the data for manual gene annotation. Data produced by the sub-workflows are used by the Hub Archive Creator (HAC) tool to create UCSC Assembly Hubs and by the JBrowse Archive Creator (JAC) to create JBrowse genome browsers. The Apollo interaction tools convert JBrowse genome browsers into an Apollo instance to facilitate collaborative annotations. Genome browsers produced by G-OnRamp can be transferred to the CyVerse Data Store via the CyVerse export tool for long-term storage and visualization. The “Tool Suites” panel (below) lists the primary tools in each sub-workflow and the tools provided by G-OnRamp to create and manage Apollo instances. See [20] and http://g-onramp.org for further details. RNA-Seq, RNA sequencing.
Fig 4.
Demographics of G-OnRamp workshop participants.
Of the 53 workshop participants eligible, 35 responded to the demographics questions (response rate = 66.0%). Many G-OnRamp workshop participants are tenure-line faculty members who work at PUIs, where they are involved in both teaching and research. Other participants focus mainly on research, either carrying out research or providing research support. PUI, primarily undergraduate institution.
Table 1.
Publicly available genome browsers.
Table 2.
Features: G-OnRamp provides….
Fig 5.
Survey responses on the utility of G-OnRamp.
An anonymous survey asked respondents (N = 35 of 53 eligible) to check “strongly agree,” “agree,” “neutral,” “disagree,” or “strongly disagree.” Participants ranged from those whose primary occupation is teaching to those managing a research support service (see Fig 4). Consequently from 20% to 38% of the participants checked “not applicable” for any given statement; these responses were removed before percentages were calculated. Overall, participants reported that G-OnRamp facilitates both research and teaching.
Fig 6.
Case study: Annotation using parasitoid wasp G-OnRamp browsers.
A. The workflow for identifying genes of interest and creating student annotation projects based on G-OnRamp browsers. B. The student annotation workflow. Students are assigned a project and will then work through either of the two sub-workflows depending on homology of the gene of interest to the reference genome. Boxes in yellow define the sub-workflow for genes with homology to the reference genome; cyan boxes define the sub-workflow for genes lacking homology to the reference genome. C. An example student annotation of a gene with no homology to the reference genomes (D. melanogaster or Nasonia vitripennis). Survey respondents identified lack of homology to an informant genome as one of the main challenges in annotating new species. RNA-Seq, RNA sequencing.
Fig 7.
Classroom implementation with G-OnRamp genome browsers. A. Implementations of the parasitoid wasp project during 2017–2018 and 2018–2019 characterized by institution type (n = 15), course level (n = 16), and course format (n = 16). B. Results from a survey of faculty who have used a G-OnRamp–generated genome browser in a course. Participants were asked to respond on a 5-point Likert Scale with NA as an option; of the 14 faculty responding to this portion of the survey, the four checking “NA” for these questions were removed before calculating percentage responses, giving n = 10. Responses are shown by percentage of respondents. C. Mean annotation post-course test scores: The mean for the wasp group is 9.1 (N = 173; SD = 3.6) and the mean for the other GEP students is 9.5 (N = 1,185; SD = 3.5). The difference is not significant (bars represent the means; error bars represent one standard deviation). D. Responses to the SURE survey questions: The means for the wasp project students are in red (N ranges from 181 to 195, as some students did not answer all questions) and the means for the other GEP students (working in Drosophila) are in green (N ranges from 1,200 to 1,270). For some items, the wasp group scores significantly higher than the comparison group; however, these results should be interpreted with caution, given the small sample size. CURE, Course-based Undergraduate Research Experience; GEP, Genomics Education Partnership; NA, Not Applicable; PUI, primarily undergraduate institution; MSI, Minority-Serving Institution; SURE, Survey of Undergraduate Research Experiences; UG, undergraduate.
Table 3.
Deployment options.