Support and Development of EMAN for Electron Microscopy Image Processing

说明(申请人提供)：EMAN是一个用于二维和三维图像处理的透射式电子显微镜数据的软件套件。它最初的设计是专门执行一种称为单粒子重建的技术所需的计算。这项技术使10到1,000纳米范围内的分子和分子组件的结构可以在三维中完全确定。所研究的分子和组件涵盖了细胞过程的所有范围。使用这项技术研究的系统太过多样，无法充分描述，但一些例子包括：GroEL，一种分子伴侣，核糖体，所有活细胞中发现的最基本的组装之一，以及钙离子释放通道，肌肉功能的关键组成部分。这项技术在确定病毒结构方面也是至关重要的，这有助于了解它们的功能，从而设计出新的病毒疾病治疗和诊断方法。执行这些重建所需的计算量相当大，通常需要在现代PC集群上花费数万到数十万个CPU小时才能完成。EMAN旨在最大限度地使重建过程自动化，以获得更高分辨率的结构，并使处理比以前更快和更准确地进行。自最初发布以来，核心库还被用于与X射线结晶学、电子断层扫描、结构分析工具和分子可视化相关的项目。它还开始在其他高分辨率显微镜中找到一些用途，如原子力显微镜和非生物电子显微镜图像的图像处理。在这项提案中，我们请求支持继续开发和支持这一套餐，以造福世界各地的数百名用户。这将包括重新设计核心库，通过使用改进的Python界面、改进文档和用户支持以及更好的跨平台支持，使其更容易被基础科学家使用。该软件支持的工作通常被认为是基础科学，公众健康的好处来自于更好地了解细胞内的基本过程。这项技术也有更直接的应用。例如，对于生物恐怖防御，这项技术已被提出用于快速确定未知病原体的结构，从而能够快速识别和分发正确的对策。

DESCRIPTION (provided by applicant): EMAN is a software suite for two and three dimensional image processing of transmission electron microscopy data. Its original design was specifically to perform the compuations required for a technique known as single particle reconstruction. This technique allows the structure of molecules and molecular assemblies in the 10 to 1,000 nanometer range to be fully determined in three dimensions. The molecules and assemblies studied cover the full range of cellular processes. Systems studied using this technique are far too diverse to adequately describe, but some examples include: GroEL, a molecular chaperone, the ribosome, one of the most fundamental assemblies found in all living cells and Ca++ release channel, a critical component in muscle function. This technique has also been crucial in the determination of virus structures, which aid in understanding their function and hence design of new treatments and diagnoses for viral diseases. The computation required to perform these reconstructions is considerable, generally requiring tens to hundreds of thousands of CPU-hours on modern PC clusters to complete. EMAN was designed to automate the reconstruction process to the greatest extent possible to allow higher resolution structures to be obtained, and for the processing to occur more quickly and accurately than previously possible. Since its initial release, the core library has also been used in projects relating to x-ray crystallograpy, electron tomography, structure analysis tools, and molecular visualization. It has also begun to find some use in other high resolution microscopies, such as AFM and image processing of non-biological TEM images. In this proposal we request support to continue to develop and support this package for the benefit of its many hundreds of users worldwide. This will include redeisgn of the core library to make it easier to use by basic scientists through use of an improved Python interface, improvements to documentation and user support, and better cross-platform support. The work this software supports is generally considered basic science, with public health benefits coming from a better understanding of the fundamental processes within the cell. More direct applications of this technique also exist. As one example, for bioterror defence, this technique has been proposed for rapid determination of the structure of an unknown pathogen, allowing rapid identification and distribution of the correct countermeasures.