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Database-driven software for biological NMR analysis

用于生物 NMR 分析的数据库驱动软件

基本信息

批准号：
7015617
负责人：
MICHAEL R GRYK
金额：
$ 15.6万
依托单位：
UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
依托单位国家：
美国
项目类别：
财政年份：
2005
资助国家：
美国
起止时间：
2005-02-10 至 2009-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7015617
关键词：
Internet bioengineering /biomedical engineering bioinformatics chemical structure computational biology computer data analysis computer human interaction computer program /software computer system design /evaluation information systems macromolecule mathematical model model design /development nuclear magnetic resonance spectroscopy

项目摘要

DESCRIPTION (provided by applicant): NMR spectroscopy on biological macromolecules generates vast amounts of data and requires intricate knowledge of the molecular system under study for successful analysis of the acquired data. The size and complexity of the molecular systems have grown to the point where database integration is essential to improve the productivity of NMR studies, maximize the efficiency of NMR data analyses, and guarantee the validity of such analyses. In addition, there exist a large number of valuable NMR analysis tools, intricately interdependent in the information they provide and require. Due to this interdependence, a conceptual data model for both raw and analyzed NMR data is required to provide a database system capable of format conversion among the codependent software. In the absence of such a model, much NMR data is considered too complicated to be thoroughly treated and is effectively discarded. Until such a data model is developed and distributed, along with software to support it, the bulk of the information provided by biological NMR spectroscopy will continue to be lost. The long term goal of this research project is to develop and distribute such a conceptual data model. The implementation of the model will be supported by a multi-platform software application. The proposed application including data model and associated database will integrate the NMR data model and existing NMR data processing and analysis software (free and commercial products) to improve productivity at the data collection, data assignment, data analysis and structure determination phases. The R21 phase will focus on the data model/database design (in progress) and development of a prototype application including a Linux-based graphical user interface which will be capable of interacting with the database backend and other NMR software available for the Linux platform. During the R33 phase, a visual representation of the NMR data model will be developed for use by researchers, both to aid in learning the proposed application as well as in understanding NMR data. This representation will allow researchers to view NMR data at a range of levels of abstraction from the experiment level to the pulse-sequence level. In addition, in years 3 and 4, the software will be ported to the Mac OS X platform, with the database linked as a web-accessible backend available to both Linux and Mac clients. Documentation of the application will be completed in the R33 phase.

描述（由申请人提供）：生物大分子的NMR光谱产生大量的数据，需要对所研究的分子系统有复杂的了解，才能成功分析所获得的数据。分子系统的规模和复杂性已经增长到这样的程度，其中数据库集成对于提高NMR研究的生产率、最大化NMR数据分析的效率以及保证此类分析的有效性是必不可少的。此外，存在大量有价值的NMR分析工具，它们提供和需要的信息错综复杂地相互依赖。由于这种相互依赖性，一个概念性的数据模型，为原始和分析的NMR数据需要提供一个数据库系统，能够相互依赖的软件之间的格式转换。在没有这样一个模型的情况下，许多NMR数据被认为太复杂而无法彻底处理，并被有效地丢弃。在这样一个数据模型被开发和分发之前，沿着支持它的软件，生物核磁共振光谱学提供的大部分信息将继续丢失。本研究项目的长期目标是开发和分发这样一个概念数据模型。该模型的实施将得到一个多平台软件应用程序的支持。包括数据模型和相关数据库的拟议应用程序将整合NMR数据模型和现有NMR数据处理和分析软件（免费和商业产品），以提高数据收集，数据分配，数据分析和结构确定阶段的生产力。R21阶段将侧重于数据模型/数据库设计（正在进行中）和原型应用程序的开发，包括一个基于Linux的图形用户界面，该界面将能够与数据库后端和Linux平台可用的其他NMR软件进行交互。在R33阶段，将开发NMR数据模型的可视化表示供研究人员使用，以帮助学习拟议的应用程序以及理解NMR数据。这种表示将使研究人员能够在从实验水平到脉冲序列水平的一系列抽象水平上查看NMR数据。此外，在第3年和第4年，该软件将移植到Mac OS X平台，数据库作为一个可供Linux和Mac客户端访问的网络后端连接。申请文件将在R33阶段完成。