Maciejewski Mark W, Schuyler Adam D, Gryk Michael R, Moraru Ion I, Romero Pedro R, Ulrich Eldon L, Eghbalnia Hamid R, Livny Miron, Delaglio Frank, Hoch Jeffrey C
Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut.
Department of Cell Biology, UConn Health, Farmington, Connecticut.
Biophys J. 2017 Apr 25;112(8):1529-1534. doi: 10.1016/j.bpj.2017.03.011.
Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users.
计算技术的进步推动了核磁共振(NMR)在生物分子应用方面的诸多最新进展。由于NMR应用的广泛多样性,用于处理和分析NMR数据的软件包数量众多且种类繁杂,各个实验室依赖着数十个甚至数百个软件包。发现、获取、安装和维护所有这些软件包是一项繁重的任务。由于大多数软件包源自学术实验室,当开发者毕业、资金停止或研究人员转向其他项目时,软件的持续性就会受到影响。为了简化生物分子NMR软件的获取和使用,促进软件的持续性,并提高计算工作流程的可重复性,我们开发了NMRbox,这是一个用于NMR软件和计算的共享资源。NMRbox采用虚拟化技术提供一个预先配置了数百个软件包的综合软件环境,可作为可下载的虚拟机或由专用计算云支持的平台即服务提供。正在进行的开发包括一个元数据收集器,用于规范、注释和保存工作流程,促进并加强向生物磁体库(BioMagResBank)的数据存档,以及用于贝叶斯推理的工具,以增强计算分析的稳健性和可扩展性。除了便于使用和保存丰富且动态更新的生物分子NMR软件环境外,NMRbox还促进了一类新型元软件包的开发和部署。NMRbox对非营利用户免费提供。