BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

Abstract

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/.

Figure 1.

Global outline of the database platform and data flow.

Figure 2.

Details of screenshots of the BIGNASim portal. (A) Details of the three search options. (B) Browser table. Column selectors and top search box allow filtering contents. (C) Portal to available analyses, after trajectory selection. Also available for global database analyses. Each bullet leads to analyses of the indicated molecular fragment. Number in parentheses indicates the available data items on each option. Full screenshots are available in the Supplementary Material examples

Figure 3.

Screenshots of the BIGNASim portal. Example of navigation in the analysis structure for obtaining the twist parameter of CG bp-steps. (i) Selection of series of analysis based on curves. (ii) Selection of helical parameters. (iii) Selection of the twist parameter calculated for CG steps on all individual frames. Numbers in parentheses indicate the amount of available data items on each option. Raw histogram data are available for downloading. Full screenshots are available in the Supplementary Material examples.