Continued Development and Maintenance of Appion Software

电子显微镜（EM）已经牢固地建立在结构生物学家可用的工具宝库中，提供了各种尺寸尺度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简单的方式，用户可以通过管道从原始数据进行可靠的3D重建，这既有利于处理步骤的管理，又使每一步的结果更加透明。为此，我们开发了Appion，这是一个模块化和透明的管道，集成并提供了不同软件应用程序和过程之间的互操作性。用户通过基于web的界面来管理和控制软件模块，所有的结果都可以使用基于web的查看器直接链接到一个底层数据库，该数据库跟踪所有的过程和数据，并提供软件模块之间的通信。最初向EM结构生物学社区的传播是由ARRA基金提供的支持实现的，在这里，我们请求资金为Appion的开发和维护提供持续的支持，并使其能够被更大的用户社区使用。这个项目的一个重要方面是确保Appion可以随时和持续地被社区扩展，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，非常重要的是，大多数主要的EM软件开发人员都支持将他们的软件包集成到Appion中，并随Appion安装一起分发。这种社区支持和合作为我们的社区建立长期需要的软件标准和互操作性提供了一个独特的机会。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。这将为当前可用的内容以及如何使用标准化词汇表和数据流构建现有工具带来急需的透明度。我们的具体目标集中在(i)提高应用程序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，确保Appion的持续发展；（iv）通过扩展和简化安装程序和改善图形用户界面，提高可用性；(v)提供更广泛和全面的测试，以确保管道产生的科学结果的准确性。当然，所有这些努力都将伴随着全面文档和教程的开发。

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. PUBLIC HEALTH RELEVANCE: Electron microscopy (EM) is now established as an essential tool for studying macromolecular machines that are central to cellular function, and thus has a basic and fundamental relevance for both the healthy and diseased states. EM methods require access to an array of sophisticated computational tools and procedures, which presents a barrier to entry for newcomers and a potential source of errors. This project will provide unified access to an integrated set of interoperable tools that are easy to use, easy to adapt and extend, and fully documented.