→ Poster doi:10.7490/f1000research.1112719.1
Rémi Marenco, George Washington University
Wilson Leung, Washington University in St. LouisSarah C.R. Elgin
, Washington University in St. LouisJeremy Goecks
, George Washington UniversityAbstract
We are developing a customized version of Galaxy called G-OnRamp that will enable biologists to annotate the functional elements of eukaryotic genomes using large genomic datasets, a task that can also serve as an introduction to other “big data” biomedical analyses. Genome annotation—identifying functionally active regions within a genome—requires the use of diverse datasets and tools, including sequence similarity to known genes, gene prediction models, and high-throughput genomic data. To construct this interactive Web-based environment for genome annotation, we are building on two successful efforts, the Genomics Education Partnership (GEP) and Galaxy.
GEP (http://gep.wustl.edu) is a consortium of over 100 colleges/universities that provides classroom undergraduate research experiences in genomics for students at all levels. Students perform primary research on selected regions of Drosophila genomes using genomic databases (e.g., FlyBase) and bioinformatics tools (e.g., BLAST) while learning about gene structure, evolution, programming, and other topics. GEP faculty are now interested in annotating other eukaryotic genomes, reflecting their diverse research interests.
G-OnRamp will extend Galaxy by providing (a) analysis pipelines for functional genomic data (e.g., ChIP-Seq, RNA-Seq); (b) interactive visual analytics to annotate a genome (e.g., create UCSC Assembly Hubs); and (c) capacity for collaborative genome annotation. The GEP will serve as a key use case to validate and refine G-OnRamp, ensuring that it satisfies real educational needs. In this poster and demonstration, we will describe G-OnRamp’s vision and showcase its current features. G-OnRamp is available under the Academic Free License, and the software will be available via https://github.com/goeckslab