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

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10.1093/nar/gkv1301
 
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Hospital, Adam
Andrio, Pau
Cugnasco, Cesare
Codó, Laia
Becerra Fontal, YolandaMés informacióMés informacióMés informació
Dans, Pablo D.
Battistini, Federica
Torres, Jordi
Goni, Ramón
Orozco, Modesto
Gelpí, Josep Lluís
Document typeArticle
Defense date2016-01-04
PublisherOxford Journals
Rights accessOpen Access
Attribution-NonCommercial-NoDerivs 4.0 Spain
Except where otherwise noted, content on this work is licensed under a Creative Commons license : Attribution-NonCommercial-NoDerivs 4.0 Spain
ProjectESTUDIO DE FORMAS INUSUALES O TENSIONADAS DE LOS ACIDOS NUCLEICOS DE POTENCIAL INTERES BIOMEDICO O BIOTECNOLOGICO (MINECO-BIO2012-32868)
SIMDNA - Advanced multiscale simulation of DNA (EC-FP7-291433)
ELIXIR-EXCELERATE - ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences. (EC-H2020-676559)
BioExcel - Centre of Excellence for Biomolecular Research (EC-H2020-675728)
MuG - Multi-Scale Complex Genomics (EC-H2020-676556)
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 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/.
CitationHospital, Adam [et al.]. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.. "Nucleic Acids Research", 04 Gener 2016, vol. 44, núm. D1, p. D272-D278. 
URIhttp://hdl.handle.net/2117/84242
DOI10.1093/nar/gkv1301
ISSN0305-1048
Publisher versionhttp://nar.oxfordjournals.org/content/44/D1/D272.long
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