Continued Development and Maintenance of NMRView

NMRView 的持续开发和维护

• 批准号: 7280283
• 负责人: Bruce A Johnson
• 金额: $ 19.47万
• 依托单位: ONE MOON SCIENTIFIC, INC.
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7280283
• 关键词: Address; Algorithms; Arts; Benchmarking; Code; Communities; Complex; Computational Technique; Computer Hardware; Computer software; Count; Data Set; Development; Disease; Disease regression; Ensure; Funding; Goals; Grant; Imagery; Individual; Java; Learning; Ligand Binding; Maintenance; Methods; NMR Spectroscopy; Nucleic Acids; Process; Programming Languages; Property; Proteins; Research; Research Personnel; Resources; Scientist; Software Tools; Solutions; Source; Specificity; Structure; Techniques; Testing; Update; Validation; Work; base; computerized data processing; design; experience; human disease; improved; interest; microbial alkaline proteinase inhibitor; multicore processor; open source; programs; scripting interface; structural biology; tool

DESCRIPTION (provided by applicant): The structure, dynamics and ligand binding specificity of proteins and nucleic acids are properties that are key to an understanding of the mechanisms of human disease. Furthermore, the optimal design of molecules that can intervene therapeutically in disease processes relies on these same properties. NMR spectroscopy is one of the most versatile techniques to get this information. The very versatility of NMR, however, leads to a multitude of data sets, each of which potentially contributes to the solution of a complex computational problem. Extracting the information generated by modern NMR techniques is largely facilitated with computer software that can manipulate, analyze and visually present the data sets in a correlated manner. For the past 10 years, one of the primary software tools used by macromolecular-NMR scientists has been NMRView. The developer of NMRView is now an independent research scientist and this grant will provide the funding to maintain and further develop NMRView. One of the primary goals during this granting period will be to refactor the code to make it more maintainable, understandable and stable and to release the code as open source. As each section of code is refactored, a comprehensive testing and benchmarking framework will be developed to test that section of code. Similarly the core API and scripting interface for each module will be documented allowing end-users to more easily develop their own extensions of NMRView. Tutorials, based on real-world data sets, will be developed to aid in the learning of both NMRView and modern NMR techniques. Existing modules will be optimized and new modules developed for addressing state-of-the-art techniques in NMR. An example of this will be the optimization of automated assignment routines to facilitate their use in both conventional NMR research and high throughput structural biology initiatives. During this process, state-of-the-art computational techniques will be used to provide both a more advanced visualization interface and to improve the scalability of NMRView.

描述（由申请人提供）：蛋白质和核酸的结构，动力学和配体结合特异性是了解人类疾病机制的关键特性。此外，可以在疾病过程中干预的分子的最佳设计取决于这些相同的特性。 NMR光谱是获取此信息的最通用技术之一。但是，NMR的多功能性导致了多种数据集，每个数据集可能有助于解决复杂的计算问题的解决方案。提取现代NMR技术产生的信息主要是通过计算机软件来促进的，这些软件可以以相关的方式操纵，分析和视觉上显示数据集。在过去的10年中，大分子-NMR科学家使用的主要软件工具之一是NMRVIEW。 NMRVIEW的开发商现在是一名独立的研究科学家，该赠款将提供维护和进一步发展NMRVIEW的资金。在此授予期内的主要目标之一是重构代码，以使其更可维护，可理解和稳定，并将代码作为开源。由于对代码的每个部分进行了重构，将开发全面的测试和基准测试框架来测试该代码部分。同样，将记录每个模块的核心API和脚本接口，以使最终用户更容易地开发自己的NMRView扩展。基于现实世界数据集的教程将有助于学习NMRVIEW和现代NMR技术。现有的模块将得到优化，并开发出用于解决NMR最新技术的新模块。一个例子是优化自动分配程序，以促进其在常规NMR研究和高通量结构生物学计划中的使用。在此过程中，最先进的计算技术将用于提供更高级的可视化接口并提高NMRVIEW的可扩展性。