NMRbox: A Resource for Biomolecular NMR Computation

被引：336

作者：

Maciejewski, Mark W. ^{[1
]}

Schuyler, Adam D. ^{[1
]}

Gryk, Michael R. ^{[1
]}

Moraru, Ion I. ^{[2
]}

Romero, Pedro R. ^{[3
]}

Ulrich, Eldon L. ^{[3
]}

Eghbalnia, Hamid R. ^{[3
]}

Livny, Miron ^{[4
]}

Delaglio, Frank ^{[5
,6
]}

Hoch, Jeffrey C. ^{[1
]}

机构：

[1] UConn Hlth, Dept Mol Biol & Biophys, Farmington, CT 06030 USA

[2] UConn Hlth, Dept Cell Biol, Farmington, CT USA

[3] Univ Wisconsin, Dept Biochem, 420 Henry Mall, Madison, WI 53705 USA

[4] Univ Wisconsin, Dept Comp Sci, 1210 W Dayton St, Madison, WI 53706 USA

[5] NIST, Inst Biosci & Biotechnol Res, Rockville, MD USA

[6] Univ Maryland, Rockville, MD USA

来源：

BIOPHYSICAL JOURNAL | 2017年 / 112卷 / 08期

基金：

美国国家卫生研究院;

关键词：

SOFTWARE; REPRODUCIBILITY;

D O I：

10.1016/j.bpj.2017.03.011

中图分类号：

Q6 [生物物理学];

学科分类号：

071011 ;

摘要：

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.

引用

页码：1529 / 1534

页数：6

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