SI2-SSE: GenApp - A Transformative Generalized Application Cyberinfrastructure

SI2-SSE：GenApp - 变革性通用应用程序网络基础设施

• 批准号: 1739549
• 负责人: David Fushman
• 金额: $ 13.04万
• 依托单位: University of Maryland, College Park
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-10-01 至 2020-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1739549&HistoricalAwards=false
• 关键词: SI2; SSE; GenApp; Transformative; Generalized

Scientific computing and computational analysis are becoming integral aspects of virtually any field of science, be it exact sciences like Physics, Chemistry and Biology, or social sciences. Efforts of many research laboratories are focused on creation of scientific codes for data generation, analysis and interpretation. However, publicly funded and often hard won scientific codes developed in a typical research laboratory too frequently become unsustainable beyond the lifetime of funding or shortly after staff rotation. Projects that are funded to afford expensive computer science expertise simply to maintain and update existing software divert scarce resources from the lab's primary goals and often translates the problem without resolving it. Only a select number of researchers receive sufficient funding to maintain and update software, limiting the dissemination of new ideas and techniques. The diversity and continually changing nature of software environments compounds the issues. Enabling user utilization presents hurdles in deployment, access and training. These issues also create barriers to the implementation of new ideas embodied in new codes. The GenApp project's goals are to address these issues. To begin with, GenApp enables the rapid dissemination of scientific codes to researchers with minimal software expertise. As more researchers use these codes, more of them become vested in the codes, which helps their sustainability. The fundamental goal of this project is to advance the GenApp framework into a transformative tool to broadly benefit the scientific software developer community. GenApp is a generalized application generation framework intended for rapid deployment of scientific codes, which can generate both science gateways and stand-alone applications. Among the main unique features of GenApp are the minimal technical expertise requirement for the end user and an open-end design ensuring sustainability of generated applications. To produce fully functional applications, GenApp weaves libraries of fragments and user defined modules as directed by simple definition files, created from a uniform, logical, and simple-to-encode general interface definition file provided by GenApp. This general definition file and the underlying software can be reused indefinitely to produce applications in a variety of existing and yet-to-be defined software environments. Preserving such simplicity with GenApp's maturation is one of the main developmental strategies. To achieve the goal of GenApp four focus Aims have been proposed. The first is infrastructure development, which includes general enhancements to the capabilities of GenApp. The second is documentation, training, dissemination, outreach and sustainability - all important aspects to produce a software product that is useful to the community. The third is simply feedback, since user and developer feedback will help drive the first two Aims. The final Aim includes two structural biology domain science applications that will adopt and drive GenApp development. GenApp will see its primary practical utilization in making highly demanding novel computational and analysis tools accessible to experimentalists and theoreticians working in the nuclear magnetic resonance (NMR) and small-angle scattering (SAS) domains of structural biology. The GenApp framework will serve as a platform for applications utilizing advanced tools requiring efficient use of HPC resources, tools for modeling SAS data with molecular simulations, and a large software suite for a combined analysis of NMR and SAS measurements coupled to computational modeling. Easy access to these powerful tools will enable hitherto impossible studies of a number of fundamental biological problems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

科学计算和计算分析几乎已成为任何科学领域的组成部分，无论是物理学，化学和生物学还是社会科学等精确的科学领域。许多研究实验室的努力集中在创建科学代码，以进行数据生成，分析和解释。但是，在典型的研究实验室中开发的公共资助且经常赢得的科学法规过于经常在资金的一生之后或工作人员轮换后不久变得不可持续。资助的项目仅仅是为了获得昂贵的计算机科学专业知识，只是为了维护和更新现有的软件从实验室的主要目标中转移稀缺资源，并且经常在不解决问题的情况下转化该问题。 只有许多研究人员获得足够的资金来维护和更新软件，从而限制了新想法和技术的传播。软件环境的多样性和不断变化的性质加剧了问题。 使用户利用能够在部署，访问和培训中提出障碍。 这些问题还为实施新代码所体现的新想法的实施造成了障碍。 Genapp项目的目标是解决这些问题。首先，GenApp可以将科学代码快速传播给具有最少软件专业知识的研究人员。随着越来越多的研究人员使用这些代码，越来越多的代码归属于代码，这有助于其可持续性。该项目的基本目标是将GenApp框架推向一种变革性的工具，以广泛地使科学软件开发人员社区受益。 Genapp是一个通用的应用程序生成框架，旨在快速部署科学代码，可以同时生成科学网关和独立应用。 GenApp的主要独特功能之一是最终用户的最低技术专业知识要求和开放式设计，以确保生成的应用程序的可持续性。为了产生功能齐全的应用程序，Genapp按照简单定义文件的指示编织片段和用户定义的模块，该文件是由GenApp提供的统一，逻辑和简单的常规接口定义文件创建的。 可以无限期地重复使用此一般定义文件和基础软件，以在各种现有和尚未定义的软件环境中生成应用程序。通过Genapp的成熟来保留如此简单是主要的发展策略之一。为了实现Genapp的目标，已经提出了四个重点目标。首先是基础设施发展，其中包括对GenApp能力的一般增强。第二个是文档，培训，传播，外展和可持续性 - 生产对社区有用的软件产品的所有重要方面。第三只是反馈，因为用户和开发人员反馈将有助于推动前两个目标。 最终目标包括两个将采用和推动GenApp开发的结构生物学领域科学应用。 Genapp将看到其主要的实用利用来使实验者和理论家在核磁共振（NMR）（NMR）和小角度散射（SAS）结构生物学的领域都可以使用高度苛刻的新型计算和分析工具。 GenApp框架将用作使用高级工具的应用程序，需要有效利用HPC资源，用于使用分子模拟的SAS数据建模工具以及用于NMR和SAS测量与计算建模的合并分析的大型软件套件。轻松访问这些强大的工具将使迄今无法对许多基本生物学问题进行研究。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛影响的评估标准来通过评估来支持的。

项目成果

ROTDIF-web and ALTENS: GenApp-based Science Gateways for Biomolecular Nuclear Magnetic Resonance (NMR) Data Analysis and Structure Modeling

ROTDIF-web 和 ALTENS：基于 GenApp 的生物分子核磁共振 (NMR) 数据分析和结构建模科学网关

• DOI: 10.17605/osf.io/t4gkh
• 发表时间: 2019
• 期刊: Gateways 2019
• 作者: Chen, Yuexi;Jeong, Cheol;Savelyev, Alexey;Krueger, Susan;Curtis, Joseph E;Brookes, Emre H;Fushman, David
• 通讯作者: Fushman, David