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