Project Summary
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.