The Genomics Education Partnership: An Introduction to Bioinformatics in a Course-based Undergraduate Research Experience (CURE)

The Genomics Education Partnership (GEP; http://gep.wustl.edu) is a consortium of faculty members from over 100 colleges and universities who are involving students in Course-based Undergraduate Research Experiences (CUREs) in bioinformatics. Our project uses comparative genomics to study the unusual properties of the Drosophila Muller F element (dot chromosome) across recently sequenced Drosophila species. Students participate in both sequence improvement and gene annotation, and their results are reconciled and pooled for final analysis; our recent paper in G3 had 940 undergraduate co-authors (Leung et al. 2015 G3 5(5): 719-40). Students who participate show attitude and knowledge gains on assessment, irrespective of the type of institution or the implementation strategy used by the faculty member (ranging from short lab modules to stand-alone research courses and independent research projects). However, student gains are correlated with the amount of time spent on the project. GEP faculty members report that implementation of this research-based curriculum is strongly facilitated by core computational and pedagogical support from the Washington University team, and that a shared curriculum and organizational structure can mitigate issues caused by varying campus-level support. We are developing new curriculum designed to make the GEP project more accessible to beginning students, including those at community colleges; and working with Galaxy to develop G-OnRamp, software that will make it easier to get a new genome assembly up on a genome browser, enabling faculty to use this bioinformatics CURE strategy with other species. Supported by HHMI grant #52007051, NSF grant #1431407, and Washington University in St. Louis.