The Plant Science Cyberinfrastructure Collaborative (PSCIC) program is intended by NSF to create a new type of organization – a cyberinfrastructure collaborative for the plant sciences - that would enable new conceptual advances through integrative, computational thinking. To achieve this, we have developed the “iPlant Collaborative” (iPC). The iPC will be fluid and dynamic, utilizing new computer, computational science and cyberinfrastructure solutions to address an evolving array of grand challenges in the plant sciences. It will be community-driven, involving plant biologists, computer and information scientists and engineers, as well as experts from other disciplines, all working in integrated teams. The iPC brings together strengths in plant biology, bioinformatics, computer science and high throughput computing as well as innovative approaches to education, outreach, and the study of social networks.
Several key principles guided our development of the iPC. Specifically, the iPC:
- is a cyberinfrastructure collaborative rather than purely a cyberinfrastructure,
- will enable multi-disciplinary teams to address grand challenges in plant science,
- will be an entity that is by, for and of the community,
- will train the next generation in computational thinking, and
- is designed to be able to reinvent itself as needs and technologies change.
The driving force behind the iPC is the nature of the grand challenges of the plant sciences, and all facets of the Collaborative are organized around those selected questions. The act of selecting these questions will be community-driven, and to facilitate that, we will host a series of workshops, each focused on a specific area of plant biology, but with participants cutting across the spectrum of the computational and biological sciences. The goal of each workshop will be to identify the “grand challenge” questions in that field, as well as the necessary strategies and approaches that will be needed to solve the question(s). Self-forming Grand Challenge Teams from the community (chosen by a community-representative Board of Directors) will then work with iPC personnel to develop ‘Discovery Environments’ (DEs), each of which will be a cyberinfrastructure within which the GC team (and the community) will address and solve the grand challenge (and related problems of interest). It is anticipated that DEs designed for different grand challenges will overlap and coalesce into a comprehensive cyberinfrastructure for the whole of the plant sciences. To achieve this coalescence, it will be necessary to simultaneously address 2-4 grand challenges covering a broad range of plant biology, from the molecular, cellular and developmental to the organismic, ecological, and evolutionary.
The cyberinfrastructure created by the iPC will provide the community with two main capabilities: it will provide access to world-class physical infrastructure – for example, persistent storage and compute power via local and national resources, and it will provide services that promote interactions, communications and collaborations and that advance the understanding and use of computational thinking in plant biology. Through these capabilities, the iPC will catalyze progress in targeted areas of plant biology, and more broadly advance the whole of plant science through new, creative, synthesis activities, and training the next generation of scientists in computational and collaborative thinking.
The cyberinfrastructure framework consists of a comprehensive combination of hardware (campus cluster and TeraGrid-based resources, primary and secondary data repositories, and advanced visualization facilities), software (open source, developed by a distributed team of developers and programmers), network fabric (including upgraded access to National Lambda Rail, Internet2, and TeraGrid), and a multi-disciplinary team of experts leading a large group that includes expertise in a broad range of plant science, computer networks, workflows, high-performance computing, algorithms, visualization, statistics, data mining, modeling and simulation, and bioinformatics. Distinct Discovery Environments will consist of community collaboration spaces, novel mathematical and computational approaches, semantic data analysis/discovery tools, an underlying cyberinfrastructure for access, analysis and collaboration, and both feedback processes and social network analyses for studying, evolving, and refining the Discovery Environments. The project is centered at the University of Arizona (Tucson, AZ) with Cold Spring Harbor Laboratory, Arizona State University, Purdue University, and the University of North Carolina, Wilmington, as partners.
The broader impacts of the iPC project will not be limited merely to the solution of currently intractable grand challenge questions, because at its core the iPC is actually a community building and educational enterprise designed to facilitate education and outreach. Grand Challenge teams and iPC staff will work together to educate students (K-12, undergraduate, and graduate, including underrepresented) through use and development of Discovery Environments. Thus, education and outreach efforts will permeate the iPlant Collaborative and will be coordinated and facilitated by dedicated senior personnel at the partner institutions.
For information, please contact the Collaborative Director, Richard Jorgensen (raj at ag.arizona.edu)
