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dc.contributor.authorHospital, Adam
dc.contributor.authorAndrio, Pau
dc.contributor.authorCugnasco, Cesare
dc.contributor.authorCodo, Laia
dc.contributor.authorBecerra Fontal, Yolanda
dc.contributor.authorDans, Pablo D.
dc.contributor.authorBattistini, Federica
dc.contributor.authorTorres Viñals, Jordi
dc.contributor.authorGoñi, Ramon
dc.contributor.authorOrozco, Modesto
dc.contributor.authorGelpi, Josep Lluis
dc.contributor.otherUniversitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors
dc.date.accessioned2017-03-28T09:03:27Z
dc.date.available2017-03-28T09:03:27Z
dc.date.issued2016-01-04
dc.identifier.citationHospital, A., Andrio, P., Cugnasco, C., Codo, L., Becerra, Y., Dans, P., Battistini, F., Torres, J., Goñi, R., Modesto, O., Gelpi, J.L. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. "Nucleic acids research", 4 Gener 2016, vol. 44, núm. D1, p. D272-D278.
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/2117/102934
dc.description.abstractMolecular 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 mu s 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/.
dc.language.isoeng
dc.rightsAttribution 3.0 Spain
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/es/
dc.subjectÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
dc.subject.lcshNucleic acids
dc.subject.lcshGenomics
dc.subject.otherMetadata
dc.subject.otherBenchmarking
dc.subject.otherChest pain units
dc.subject.otherDatasets
dc.subject.otherBioinformatics
dc.titleBIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data
dc.typeArticle
dc.subject.lemacÀcids nucleics
dc.subject.lemacGenòmica
dc.contributor.groupUniversitat Politècnica de Catalunya. CAP - Grup de Computació d'Altes Prestacions
dc.identifier.doi10.1093/nar/gkv1301
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttps://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1301
dc.rights.accessOpen Access
drac.iddocument19786656
dc.description.versionPostprint (published version)
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/675728/EU/Centre of Excellence for Biomolecular Research/BioExcel
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/676556/EU/Multi-Scale Complex Genomics/MuG
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/676559/EU/ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences./ELIXIR-EXCELERATE
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/FP7/291433/EU/Advanced multiscale simulation of DNA/SIMDNA
upcommons.citation.authorHospital, A., Andrio, P., Cugnasco, C., Codo, L., Becerra, Y., Dans, P., Battistini, F., Torres, J., Goñi, R., Modesto, O., Gelpi, J.L.
upcommons.citation.publishedtrue
upcommons.citation.publicationNameNucleic acids research
upcommons.citation.volume44
upcommons.citation.numberD1
upcommons.citation.startingPageD272
upcommons.citation.endingPageD278


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Except where otherwise noted, content on this work is licensed under a Creative Commons license: Attribution 3.0 Spain