Compressive Structural BioInformatics: High Efficiency 3D Structure Compression

压缩结构生物信息学：高效 3D 结构压缩

• 批准号: 8870891
• 负责人: Peter W Rose
• 金额: $ 45.95万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-06-01 至 2018-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8870891
• 关键词: 3-Dimensional; Adopted; Adoption; Algorithms; Archives; Benchmarking; Big Data; Binding; Bioinformatics; Capsid; Chimera organism; Client; Collaborations; Complex; Computer software; Computers; Cryoelectron Microscopy; Data; Data Compression; Data Files; Databases; Development; Discipline; Disease; Drug effect disorder; Genomics; HIV; Imagery; Internet; Java; Knowledge; Libraries; Life; Medicine; Memory; Methods; Molecular Machines; Nucleic Acids; Performance; Process; Programming Languages; Property; Protein Analysis; Proteins; Pythons; Research; Resolution; Roentgen Rays; Running; Satellite Communications; Scientist; Shapes; Side; Speed; Stream; Structure; Students; Support System; System; Tablets; Techniques; Telephone; Television; Time; computerized data processing; dalton; distributed data; genome sequencing; handheld mobile device; laptop; memory process; molecular assembly/self assembly; open source; operation; public health relevance; structural biology; three dimensional structure; tool; transmission process; trend

 DESCRIPTION (provided by applicant): The Protein Data Bank (PDB) archive has doubled in size since 2008 and exceeded 100,000 entries in 2014. At the same time, the size and complexity of structures are increasing dramatically, for example the recently determined structure of the HIV-capsid contains about 2.5 million atoms. The emerging techniques of integrative Structural Biology are starting to determine structures of molecular machines in the mega-Dalton range by combining cryo-Electron Microscopy, Small-Angle X-ray Scattering, X-ray, and NMR at increasingly higher resolution. Interactive visualization of large complexes exceeds available network bandwidth and memory of typical scientists' desktops, laptops, or mobile devices. Large-scale structural analyses and queries of the archive have become a Big Data challenge. To make these structures accessible to all scientists, educators, and students, new ways of representing these data are required. In domains such as high-definition television, satellite communication, video or audio streaming, high-efficiency compression has been key to deliver interactive media to phones, tablets, laptops, and desktops. A similar trend has emerged in the handling of whole genome sequence data. An entire discipline "Compressive Genomics" has been developed to deal with data compression and development of algorithms to process these data. This proposal introduces the concept of "Compressive Structural Bioinformatics", a set of compression algorithms, applications, and workflows that analyze and visualize large structures and large sets of structures at an unprecedented speed (100-1000 fold speedup) and with minimal client side overhead. The aims of this project are: 1. Develop a compact and extensible representation of 3-D biomolecular structures, 2. Enable interactive visualization of large complexes by reducing network bandwidth and enabling data streaming, 3. Enable large-scale analyses of the PDB archive for I/O bound workflows, and 4. Develop open source software libraries. Through collaboration with developers of widely used visualization applications and distributed data-parallel workflow systems, the new techniques will be implemented, benchmarked, and reference implementations will be provided in several programming languages for easy adoption. It is expect that these new "Compressive Structural Bioinformatics" tools will enable transformative research as intended by the NIH's Big Data to Knowledge initiative.

 描述（由适用提供）：自2008年以来，蛋白质数据库（PDB）档案的大小增加了一倍，2014年超过100,000个条目。与此同时，结构的大小和复杂性急剧增加，例如，最近确定的HIV-CAPSID结构包含约250万个原子。综合结构生物学的新兴技术开始通过在越来越高的分辨率下结合冷冻电子显微镜，小角度X射线散射，X射线和NMR来确定巨型 - 达尔顿范围内的分子机器的结构。大型复合物的交互式可视化超出了典型科学家台式机，笔记本电脑或移动设备的可用网络带宽和内存。档案的大规模结构分析和查询已成为一个大数据挑战。为了使所有科学家，教育者和学生都可以访问这些结构，需要新的代表这些数据的方法。在高清电视，卫星通信，视频或音频流等领域中，高效压缩是将交互式媒体传递到电话，平板电脑，笔记本电脑和台式机的关键。整个基因组序列数据的处理中也出现了类似的趋势。已经开发了整个学科的“压缩基因组学”来处理数据的数据压缩和开发以处理这些数据。该建议介绍了“压缩结构生物信息学”的概念，这是一系列压缩算法，应用和工作流程，这些算法，应用程序和工作流程以前所未有的速度（100-1000折叠速度）分析和可视化大型结构和大型结构，并以最小的客户端侧面的头顶来分析和可视化。该项目的目的是：1。建立3-D生物分子结构的紧凑而可扩展的表示，2。通过减少网络带宽和启用数据流的启用大型复合物的交互式可视化，3。启用对I/O Bound Workfort的PDB档案的大规模档案分析，以及I/O Bound Workfort和4。开源软件图书馆。通过与广泛使用的可视化应用程序和分布式数据并行工作流程系统的开发人员的合作，将以几种编程语言提供新技术，并以几种编程语言提供新技术，以方便采用。可以预期，这些新的“压缩结构生物信息学”工具将使NIH的大数据旨在实现知识计划的变革性研究。