Continued Development and Maintenance of Appion Software

Appion 软件的持续开发和维护

• 批准号: 8536870
• 负责人: BRIDGET Olivia CARRAGHER
• 金额: $ 34.74万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8536870
• 关键词: Adoption; Algorithms; Application procedure; Area; Authorization documentation; Automation; Benchmarking; Cell physiology; Cellular Structures; Code; Communication; Communities; Community Developments; Computer software; Data; Data Collection; Data Set; Databases; Development; Documentation; Electron Microscopy; Ensure; Environment; Error Sources; Evolution; Flavoring; Funding; Goals; High Performance Computing; Internet; Link; Linux; Maintenance; Methods; Online Systems; Operating System; Output; Procedures; Process; Public Domains; Reporting; Research; Research Infrastructure; Resources; Seasons; Security; Site; Structural Biologist; System; Techniques; Testing; Update; Vision; Vocabulary; base; computerized data processing; computerized tools; data integration; graphical user interface; improved; interoperability; portability; programs; reconstruction; repaired; software development; structural biology; tool; usability; user-friendly; web based interface

DESCRIPTION (provided by applicant): Summary Electron microscopy (EM) has become firmly established in the armamentarium of tools available to structural biologists, providing three-dimensional reconstructions of components of the cell across a wide range of size scales. Our vision for this technique is to provide a straightforward manner in which users can proceed from raw data to reliable 3D reconstructions through a pipeline that both facilitates management of the processing steps and makes the results at each step more transparent. To this end we have developed Appion, a modular and transparent pipeline that integrates and provides interoperability between disparate software applications and procedures. The user manages and controls the software modules via a web-based interface, and all results are similarly available using web-based viewers directly linked to an underlying database that tracks all processes and data and provides communication between the software modules. Initial dissemination to the EM structural biology community was enabled by support provided by ARRA funding and here we request funds to provide continued support for the development and maintenance of Appion and to make it accessible to a much larger community of users. An essential aspect of this project is to ensure that Appion can be readily and continuously extended by the community to accommodate new software packages and algorithms as they become available. We have strong support from the EM community for the development of Appion and, very importantly, most of the major EM software developers support having their packages integrated into Appion, and distributed with the Appion installation. This community support and cooperation provides a unique opportunity to establish long needed software standards and interoperability for our community. Appion ensures that the most commonly used EM tools are readily accessible and also provides a way for developers of new tools to integrate them into an existing pipeline. This will bring much needed transparency to what is currently available and how to build on existing tools using a standardized vocabulary and data flow. Our specific aims are centered on (i) improving Appion portability across operating systems, and high-end computing environments; (ii) improving extensibility by simplifying methods for adding new modules to the software; (iii) ensuring the continued evolution of Appion by improving methods for updating and optimizing the underlying databases; (iv) improving the usability by extending and simplifying the installation process and improving the graphical user interface; (v) providing more extensive and comprehensive testing essential to ensuring the accuracy of the scientific results produced by the pipeline. All these efforts will of course be accompanied by the development of comprehensive documentation and tutorials.

描述(申请人提供)：总结电子显微镜(EM)已经成为结构生物学家可用的工具之一，提供各种大小范围的细胞成分的三维重建。我们对这项技术的愿景是提供一种直接的方式，在这种方式下，用户可以通过一条既便于处理步骤管理又使每个步骤的结果更加透明的管道，从原始数据进行到可靠的3D重建。为此，我们开发了Appion，这是一种模块化和透明的管道，集成了不同的软件应用程序和过程，并提供了互操作性。用户通过基于网络的界面管理和控制软件模块，使用直接链接到跟踪所有过程和数据并提供软件模块之间通信的底层数据库的基于网络的查看器，可以类似地获得所有结果。最初传播到EM结构生物学社区是由于ARRA Funding提供的支持，在这里，我们请求资金为Appion的开发和维护提供持续支持，并使更大的用户社区能够访问它。这个项目的一个基本方面是确保Appion可以随时地被社区不断地扩展，以适应新的软件包和算法。我们得到了EM社区对Appion开发的大力支持，而且非常重要的是，大多数主要的EM软件开发商都支持将他们的包集成到Appion中，并随Appion安装一起分发。这种社区的支持和合作为我们的社区提供了一个独特的机会，可以为我们的社区建立长期需要的软件标准和互操作性。Appion确保最常用的EM工具易于访问，并为新工具的开发人员提供了一种将其集成到现有管道中的方法。这将为当前可用的工具以及如何使用标准化的词汇和数据流在现有工具上构建提供亟需的透明度。我们的具体目标集中在(I)提高Appion在操作系统和高端计算环境中的可移植性；(Ii)通过简化向软件添加新模块的方法来提高可扩展性；(Iii)通过改进更新和优化底层数据库的方法来确保Appion的持续发展；(Iv)通过扩展和简化安装过程以及改进图形用户界面来提高可用性；(V)提供对确保管道产生的科学结果的准确性至关重要的更广泛和全面的测试。当然，所有这些努力都将伴随着编写全面的文件和教程。