The CCPN data model for NMR spectroscopy: Development of a software pipeline
The CCPN data model for NMR spectroscopy: Development of a software pipeline
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DOI：
10.1002/prot.20449
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发表时间：
2005-06-01
影响因子：
2.9
通讯作者：
Laue, ED
中科院分区：
文献类型：
--
作者：
Vranken, WF;Boucher, W;Laue, ED
为了解决核磁共振（NMR）社区中的数据管理和数据交换问题，NMR社区协作计算项目（CCPN）创建了一个“数据模型”，该模型描述了NMR结构研究中所需的所有不同类型的信息，从分子结构和NMR参数到坐标。本文描述了一组软件应用程序的开发，使用的数据模型及其相关的库，从而验证了这种方法。这些应用程序是免费提供的，并为NMR数据的高通量分析提供了一个管道。三个程序直接与数据模型一起工作：CcpNmr分析，一个全新的分析和交互式显示程序，CcpNmr转换器，它允许将数据从NMR中常用的程序转移到数据模型，以及用于自动结构计算和分配的CLOUDS软件（卡内基梅隆大学），它被重写以直接与数据模型交互。扩展了用于结构计算的ARIA 2.0软件（巴斯德研究所）和用于约束验证的QUEEN程序（奈梅亨大学），以将其数据转换为数据模型。在这些开发过程中，数据模型已经过彻底的测试和使用，证明应用程序可以通过数据模型成功地交换数据。CCPN开发的软件架构现已准备好进行新的开发，例如与其他软件应用程序集成，以及将数据模型扩展到其他研究领域。(c)2005 Wiley-Liss，Inc.
To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR, community (CCPN) created a "Data Model" that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high-throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research. (c) 2005 Wiley-Liss, Inc.