NMRbox: A Resource for Biomolecular NMR Computation

Abstract

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.

Figure 1

Schematic overview of the NMRbox PaaS infrastructure. The NMRbox hardware is located in a state-of-the-art high performance computing facility with UPS-backed power, a backup generator, and redundant cooling along with a 40 GbE dark-fiber connection to an off-site disaster recovery location. The networks inside the datacenter are fully redundant with 40 GbE bandwidth with redundant 10 GbE connections to the VM host servers along with an 80 GbE-capable firewall. The HPC networks are connected to the world via a 100 GbE network to Internet2 and our ISP. There are currently five VM host servers with dual Intel Xeon E5 v4 processors (Intel, Santa Clara, CA) with a combined 196 cores and 2.3 TB of RAM and 10 TB of local RAID 10 storage. Users’ home folders and VM datastores are located on a Qumulo QC24 scale-out network-attached storage (qumulo.com) with 96 TB of capacity. Backups and additional storage for users is provided on a University-owned 3.8 PB AmpliStor on-premise cloud storage appliance (http://amplidata.com/himalaya/) with a dedicated NMRbox bucket. User data and authentication is decentralized from the NMRbox VMs allowing seamless transitions between NMRbox VM versions. Users access the NMRbox PaaS VMs through Real VNC Viewer with a full graphical user interface or via secure shell (shown by arrows). Data can be transferred between users’ local computers and their NMRbox accounts (shown by arrows) via scp/sFTP, and a Globus NMRbox institutional endpoint that allows easy and efficient transfers, including the ability to sync data, and which resolves many issues with firewalls. Expansion of the VM hosts hardware and storage is ongoing.

Figure 2

Component software making up the metapackage COMPASS (15). COMPASS requires interaction among multiple software packages, mediated by Python scripts (https://www.python.org). NMRbox greatly simplifies deployment of COMPASS in all its complexity by providing all the programs preinstalled and configured. Figure was adapted from Fenwick et al. (10), with permission.