Visualization software for genomics

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To gain maximum benefit from big data in genomics, biologists need software tools that enhance our in- born cognitive and visual faculties. Our visual and cognitive systems possess extraordinary power to recognize patterns, and visual analytics software applications aim to enhance this ability by providing visual, interactive interfaces to data. My research focuses on developing visual analytics tools and associated resources for life scientists, using Integrated Genome Browser as a platform for delivery and experimentation. Integrated Genome Browser is a fast, highly customizable, freely available open source desktop genome browser application developed since the early 2000s that now serves thousands of users worldwide. By developing and supporting IGB for its thousands of users, my research contributes innovative new approaches for genome browsing that other visualization research programs can and do build upon. During the next five years, I will continue using state-of-the-art open source software development methods adapted to an academic setting to build and release advanced tools at low cost, while training students in computer science and bioinformatics. First, I will continue to develop new ways to exploit emerging public and private cloud infrastructure to meet biologists’ increasingly complex needs for advanced visual analytics. Using commercial and free-of-charge, public sector cloud platforms, my students and I will experiment with connecting Integrated Genome Browser to storage and visual analytics computing capability exceeding what is possible to achieve on a single, desktop computer. These advanced features within IGB will help move the entire field forward by demonstrating how application developers can harness the power of the cloud for visualizing data. Second, I will continue to build IGB and related tools into a platform that other developers can exploit and learn from. The field of genomics changes rapidly. As new methods and tools come on-line, developers need ways to create new visualization tools suited to these new methods. My research aims to provide a platform for experimentation that will enable developers in bioinformatics to build and release new visual analytics algorithms more rapidly to larger numbers of potential users. My group will continue to develop and support an App Store for IGB, an on-line clearinghouse for developers to distribute Apps and for users to find and install Apps relevant to their research. To support developers, we will continue to improve IGB’s internal application programmer’s interface (API), a collection of methods and classes crafted to enable developers of varying skill and knowledge to add new functions and features to the IGB interface. Third, my students and I will continue to explore larger concepts of community, open source software development, and humane software design by connecting tool builders with tool users to promote collaboration and innovation for the benefit of all.