Integrated Genome Browser (IGB) is a popular desktop genome browser used by thousands of scientists worldwide to visualize, explore, and analyze large-scale data sets from genomics. Implemented in Java, IGB can run on any computer platform and provides state-of-the-art, fast zooming and visual analytics functions. Since its inception, IGB has supported a data sharing and publication system called IGB Quickload, in which users deploy metadata and data files on Web sites and then share their data by publicizing the Quickload URL. However, many users lack access to hosting services or lack technical knowledge required to set and configure a Web site. To solve this problem and give users access to advanced computational power, we propose to integrate IGB and Quickload with CyVerse, a National Science Foundation-funded cyberinfrastructure project formerly called iPlant that launched in 2008. CyVerse contains a suite of user- friendly, Web-based data analysis and data storage tools accessible via a computational interface called the Agave API Web services. We will use the Agave Web services to connect IGB with CyVerse, enabling users to share data and collaborate using CyVerse infrastructure. We propose to perform this CyVerse-to-IGB integration in four phases, with each phase building on the next. First, we will add the ability for IGB users to log into their CyVerse accounts, browse data sets within IGB, and load data directly as new IGB tracks. In Phase 2, we will use the Agave metadata API to link data curation with visualization, thus facilitating data sharing, collaborating, and publication. In Phase 3, we will create tools for users to share and publicize their results with the larger scientific community, re-using metadata they created while viewing and interacting with their data. In Phase 4, we will empower users to perform more sophisticated visual analytics functions than are currently possible within IGB (or any desktop browser) by harnessing CyVerse computational resources. This will pave the way for our team and others to develop all-new visualizations that leverage advanced computing resources available from CyVerse. More generally, this project will build new understanding of how rich client, desktop applications like IGB can interact with and leverage cloud-based resources to benefit users and advance science.
Methods for generating genome-scale data sets are becoming cheaper and more accessible. We are rapidly approaching a time when public health professionals will be able to survey many people's genomes and relate genotype to disease susceptibility, overall health, and outcomes from specific treatments. However, to take advantage of these data, scientists need visualization and data sharing systems that make exploring and analyzing the data easier to accomplish. This project will develop a user-friendly yet innovative visualization and data sharing system that unites a popular genome browser (IGB) with publicly funded cloud-based resources. This work will accelerate the pace of discovery in the biosciences and ultimately lead to critical discoveries about the human genome and the role it plays in human health.
