SPL ENGINEERING CORE (FORMERLY THE BIRN SUBPROJECT)

SPL 工程核心（以前的 BIRN 子项目）

• 批准号: 7358984
• 负责人: STEVEN PIEPER
• 金额: $ 63.03万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-01 至 2007-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7358984
• 关键词: SPL; ENGINEERING; CORE; FORMERLY; BIRN

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Organizational Note- The major event of this reporting period is the successful reorganization of BIRN (Biomedical Informatics Research Network) involving the separation of its principal cores into autonomous and independent research efforts. At the time of the last competitive renewal, Morphometry BIRN (mBIRN), Functional BIRN (fBIRN), and the NAC Engineering Core functioned as a single entity. Although the BIRN Core was well reviewed by the study section (score 130) and funded for the 5-year cycle, as part of an overall restructuring, NCRR requested a multi-year reorganization. Completed in 2005, the reorganization of mBIRN and fBIRN into distinct organizational entities resulted in the successful submission, review, and funding of new U24 consortium grants for mBIRN and fBIRN, respectively. The mBIRN consortium, led by Dr. Bruce Rosen at MGH, commenced independent operation on October 1, 2004 and the fBIRN consortium, led by Dr. Steven Potkin of UC Irvine, assumed operation on December 1, 2005. The partial-year efforts of the fBIRN are presented in the NAC Research Progress report and are also covered in the fBIRN progress report. The mBIRN project has an independent progress report and is not directly addressed here. This Core of the NAC effort, formerly known as the BIRN Core, will henceforth be known as the NAC Engineering Core. NAC Engineering Efforts- The NAC Engineering efforts center around the creation and maintenance of the software environment needed to support the research activities of NAC researchers, collaborators, and users. Much of this activity is embodied in the 3D Slicer application software. The Slicer software provides a fully open source, cross platform, "point and click" end user application software environment for neuroimage analysis and related imaging applications. Within the NAC effort, Slicer is a critical medium for collaboration; a common usage pattern is required for novel algorithms to be implemented as Slicer Modules and delivered to clinical and applied science collaborators for use ''with their existing data and for the same application.'' This transitional pattern is possible as a consequence of ongoing efforts to ensure that algorithm developers are educated and supported in their use of the Center's common software practices. Another important aspect of this transitional pattern is the shared computational infrastructure which includes high performance graphics workstations, multi-CPU compute servers, tera-scale disk storage, and gigabit networking. This shared infrastructure permits algorithm developers to have controlled access to clinical and research data for developing and testing new approaches. The new software thus developed is easily tested by end-users who are running inside the same software environment. This rapid exchange between developers and users is crucial to effective development. During this reporting period, the NAC was grateful to accept an equipment supplement that permitted the purchase and installation of 70 new high-end workstations. This much-needed upgrade allowed the Center to migrate from the Sun Solaris operating system to a 64-bit Linux environment. As with all major upgrades, significant effort was dedicated to ensuring a graceful transition, particularly with respect to Slicer and its supporting software packages. We are pleased to report that this transition has been effected with minimal disruption, in large part owing to the excellent engineering represented in the software packages on which Slicer relies (VTK, ITK, Tcl/Tk). The further addition of a set of 16-CPU compute servers and a 200 node compute cluster are expected to result in additional demands for software maintenance and porting to enable further advanced research. An enduring feature of the NAC Engineering effort is an ongoing and rich collaboration with national-level consortia. In particular, the mBIRN and fBIRN efforts serve to define and develop best practices for image acquisition, calibration, data-sharing, and database/informatics; the NAC Engineering Core remains active in these research efforts with technology and benefits flowing in both directions. The National Alliance for Medical Image Computing, NA-MIC, has a similar synergistic relationship in the areas of algorithm development and software engineering methodologies. NA-MIC provides an important mechanism for direct interaction with the architects, developers, and maintainors of the Insight Software Toolkit (ITK), which in recent years has become the platform for much of the algorithm development work in NAC.

这个子项目是利用由NIH/NCRR资助的中心拨款提供的资源的许多研究子项目之一。子项目和调查员(PI)可能从另一个NIH来源获得了主要资金，因此可能会出现在其他CRISE条目中。列出的机构是针对中心的，而不一定是针对调查员的机构。组织说明--本报告所述期间的重大事件是生物医学信息学研究网络的成功重组，涉及将其主要核心分离为自主和独立的研究工作。在上一次竞争更新时，形态BIRN(MBIRN)、功能BIRN(FBIRN)和NAC工程核心作为一个实体运行。尽管BIRN核心得到了研究科的良好审查(得分130)，并为5年周期提供了资金，但作为整体重组的一部分，NCRR要求进行多年期重组。2005年完成后，mBIRN和fBIRN重组为不同的组织实体，成功地提交、审查和资助了分别用于mBIRN和fBIRN的新的U24财团赠款。MGH的布鲁斯·罗森博士领导的mBIRN财团于2004年10月1日开始独立运营，加州大学欧文分校的Steven Potkin博士领导的fBIRN财团于2005年12月1日开始运营。《国家研究进展报告》介绍了fBIRN的部分年度工作，fBIRN进展报告也介绍了fBIRN进展情况。MBIRN项目有一份独立的进度报告，这里不直接涉及。NAC努力的这一核心，以前被称为BIRN核心，从今以后将被称为NAC工程核心。NAC工程努力-NAC工程努力中心围绕支持NAC研究人员、合作者和用户的研究活动所需的软件环境的创建和维护。这一活动的很大一部分体现在3D Slicer应用软件中。Slicer软件为NeuroImage分析和相关成像应用程序提供了一个完全开源、跨平台、“点击”的终端用户应用程序软件环境。在NAC的工作中，Slicer是协作的关键媒介；需要一种通用的使用模式，才能将新算法作为Slicer模块实现，并交付给临床和应用科学合作者，以“与他们的现有数据和相同的应用程序一起使用”。这一过渡模式是持续努力的结果，目的是确保算法开发人员在使用中心的常见软件实践时得到教育和支持。这种过渡模式的另一个重要方面是共享计算基础设施，其中包括高性能图形工作站、多CPU计算服务器、万亿级磁盘存储和千兆网络。这种共享的基础设施使算法开发人员能够控制对临床和研究数据的访问，以开发和测试新的方法。这样开发的新软件很容易被在相同软件环境中运行的最终用户测试。开发人员和用户之间的这种快速交流对于有效的开发至关重要。在本报告所述期间，国家咨询委员会感激地接受了一项设备补充，允许购买和安装70个新的高端工作站。这一亟需的升级使该中心能够从Sun Solaris操作系统迁移到位的Linux环境。与所有重大升级一样，致力于确保平稳过渡，特别是在Slicer及其支持软件包方面。我们很高兴地报告，这一过渡是以最小的干扰实现的，这在很大程度上要归功于Slicer所依赖的软件包(VTK、ITK、TCL/TK)所代表的卓越工程。预计进一步增加一套16中央处理器计算服务器和200个节点计算集群将产生更多的软件维护和移植需求，以促进进一步的高级研究。南汽工程努力的一个持久特征是与国家级财团持续和丰富的合作。特别是，mBIRN和fBIRN的工作有助于定义和开发图像获取、校准、数据共享和数据库/信息学的最佳实践；NAC工程核心继续积极参与这些研究工作，技术和效益双向流动。国家医学图像计算联盟(NA-MIC)在算法开发和软件工程方法领域有着类似的协同关系。NA-MIC提供了与Insight Software Toolkit(ITK)的架构师、开发人员和维护者直接交互的重要机制，近年来，ITK已成为NAC许多算法开发工作的平台。