Speaker Deck

PAG 2018 Galaxy Workshop - G-OnRamp

by Jeremy Goecks

Published January 17, 2018 in Science

G-OnRamp (http://gonramp.org) is a collaboration between two successful and long-running projects — the Genomics Education Partnership (GEP; http://gep.wustl.edu) and the Galaxy Project (https://galaxyproject.org). G-OnRamp provides biologists with an integrated, web-based, scalable environment for interactive annotation of eukaryotic genomes using large genomic datasets. It also provides educators with a platform to help undergraduates develop “big data” science skills through eukaryotic genome annotation.

GEP is a consortium of over 100 colleges and universities that provides Classroom Undergraduate Research Experiences (CURE) in bioinformatics/genomics for students at all levels. GEP faculty currently use the annotation of multiple Drosophilaspecies to introduce genomics and research thinking to undergraduates. Galaxy is a popular open-source, web-based scientific gateway for accessible, reproducible, and transparent analyses of large biomedical datasets. G-OnRamp extends Galaxy with tools and workflows that creates UCSC Assembly Hubs and Apollo/JBrowse genome browsers with evidence tracks for sequence similarity, ab initio gene predictions, RNA-Seq, and repeats. Educators can use this system to design CUREs based on their favorite eukaryotic species (e.g., parasitoid wasps).

G-OnRamp provides a VirtualBox virtual appliance and an AMI image for local and cloud (Amazon EC2) deployments. Future versions of G-OnRamp will (i) enable data storage with CyVerse; (ii) support additional configuration options for UCSC Assembly Hubs; and (iii) adapt GEP annotation tools for other informant species. We will host G-OnRamp training workshops in June and July 2018 at Washington University in St. Louis. If you are interested in attending, please sign up for the G-OnRamp mailing list at http://gonramp.org/signup. Supported by NIH 1R25GM119157.