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http://hdl.handle.net/2445/114795
Title: | BIGNASim: A NoSQL database structure and analysis portal for nucleic acids simulation data |
Author: | Hospital Gasch, Adam Andrio, Pau Cugnasco, Cesare Codo, Laia Becerra, Yolanda Dans, Pablo D. Battistini, Federica Torres, Jordi Goñi Macià, Josep Ramon Orozco López, Modesto Gelpí Buchaca, Josep Lluís |
Keywords: | Àcids nucleics Bases de dades Simulació per ordinador Nucleic acids Databases Computer simulation |
Issue Date: | 4-Jan-2016 |
Publisher: | Oxford University Press |
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 120s 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 metatrajectories 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/. |
Note: | Reproducció del document publicat a: https://doi.org/10.1093/nar/gkv1301 |
It is part of: | Nucleic Acids Research, 2016, vol. 44, p. D272-D278 |
URI: | http://hdl.handle.net/2445/114795 |
Related resource: | https://doi.org/10.1093/nar/gkv1301 |
ISSN: | 0305-1048 |
Appears in Collections: | Articles publicats en revistes (Bioquímica i Biomedicina Molecular) Publicacions de projectes de recerca finançats per la UE Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona)) |
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