PSCIC Full Proposal: The iPlant Collaborative: A Cyberinfrastructure-Centered Community for a New Plant Biology

亚利桑那大学：Richard Jorgensen(PI)、Gregory Andrews、Kobus Barnard、Susan Brown、Vicki Chandler、Nirav Merchant、Carolyn Napoli、suha Ram、Steven Rounsley亚利桑那州立大学：Daniel Stanzione冷泉港实验室：林肯·斯坦、多琳·韦尔普渡大学：Rebecca Doerge，北卡罗来纳大学威尔明顿分校：Ann Stapleton iFactory Collaborative(IPC)是一种新型的组织形式？为植物科学协作的网络基础设施-通过综合的计算思维(即使用系统级方法解决问题的多个抽象层次的思考)实现新的概念进步。IPC是流动的和动态的，利用新的计算机、计算科学和网络基础设施解决方案来应对植物科学中不断演变的一系列重大挑战。它是社区驱动的，涉及植物生物学家、计算机和信息科学家和工程师，以及来自其他学科的专家，他们都在综合团队中工作。IPC汇集了植物生物学、生物信息学、统计学、计算机科学和高通量计算的优势，以及教育、推广和社会网络研究的创新方法。几个关键原则指导了IPC的发展。具体地说，IPC：？网络基础设施是协作性的，而不是纯粹的网络基础设施？将使多学科团队能够应对植物科学中的重大挑战，？将成为一个由社区、为社区和为社区服务的实体？将培训下一代的计算思维，以及？IPC背后的驱动力是植物科学中重大挑战问题的性质，而合作的所有方面都是围绕这些选定的问题来组织的。选择这些问题的行动将是由社区驱动的，为了促进这一点，合作组织将主办一系列研讨会，每个研讨会侧重于植物生物学的一个特定领域，但参与者跨越计算和生物科学的范围。每个讲习班的目标将是确定该领域的重大挑战问题，以及解决问题所需的必要战略和方法(S)。然后，来自社区的自我组建的大挑战团队将与IPC人员合作开发一个？发现环境？(De)，这将是一个开放获取研究和教育的网络基础设施，专注于一个重大的挑战问题。随着时间的推移，针对不同重大挑战而设计的DES将重叠并合并为一个全面的网络基础设施，用于发现和学习。IPC创建的网络基础设施将为社区提供两个主要能力：它将提供对世界级物理基础设施的访问？例如，持久存储，以及通过地方和国家资源提供的计算能力，它将提供促进互动、通信和合作的服务，并促进对植物生物学中计算思维的理解和使用。通过这些能力，IPC将促进植物生物学目标领域的进展，并通过新的、创造性的、综合的活动，以及在计算(和协作)思维方面培训下一代科学家，更广泛地推动整个植物科学的发展。IPC项目的更广泛影响将不仅仅限于为解决目前棘手的重大挑战问题创造工具，因为IPC的核心实际上是一个社区建设和教育企业，旨在促进教育和推广。大挑战团队和IPC工作人员将共同努力，通过使用和开发发现环境来教育学生(K-12、本科生和研究生，包括代表不足的群体的成员)。因此，教育和外展工作将渗透到iPlant Collaborative中。

University of Arizona: Richard Jorgensen (PI), Gregory Andrews, Kobus Barnard, Susan Brown, Vicki Chandler, Nirav Merchant, Carolyn Napoli, Sudha Ram, Steven RounsleyArizona State University: Daniel StanzioneCold Spring Harbor Laboratory: Lincoln Stein, Doreen WarePurdue University: Rebecca Doerge, University of North Carolina at Wilmington: Ann StapletonThe iPlant Collaborative (iPC) is a new type of organization ? a cyberinfrastructure collaborative for the plant sciences - that enables new conceptual advances through integrative, computational thinking (i.e. thinking at multiple levels of abstraction using a systems-level approach to problem-solving). The iPC is fluid and dynamic, utilizing new computer, computational science and cyberinfrastructure solutions to address an evolving array of grand challenges in the plant sciences. It is 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, statistics, computer science and high throughput computing, as well as innovative approaches to education, outreach, and the study of social networks.Several key principles guided the 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 challenge questions in 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, the Collaborative 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 will then work with iPC personnel to develop a ?Discovery Environment? (DE), which will be a cyberinfrastructure for open-access research and education focused on a grand challenge question. Over time, the DEs designed for different grand challenges will overlap and coalesce into a comprehensive cyberinfrastructure for discovery and learning.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 broader impacts of the iPC project will not be limited merely to creating the tools for 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 members of underrepresented groups) through the use and development of Discovery Environments. Thus, education and outreach efforts will permeate the iPlant Collaborative.