title: 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/.
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
authors.forename: Adam
authors.initials: A
authors.lastname: Hospital
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain.
authors.forename: Pau
authors.initials: P
authors.lastname: Andrio
authors.affiliation: Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Dept. Computer Architecture, Technical University of Catalonia (UPC-BarcelonaTech), 08034 Barcelona, Spain.
authors.forename: Cesare
authors.initials: C
authors.lastname: Cugnasco
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain.
authors.forename: Laia
authors.initials: L
authors.lastname: Codo
authors.affiliation: Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Dept. Computer Architecture, Technical University of Catalonia (UPC-BarcelonaTech), 08034 Barcelona, Spain.
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Becerra
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Dans
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
authors.forename: Federica
authors.initials: F
authors.lastname: Battistini
authors.affiliation: Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Dept. Computer Architecture, Technical University of Catalonia (UPC-BarcelonaTech), 08034 Barcelona, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Torres
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain.
authors.forename: Ramón
authors.initials: R
authors.lastname: Goñi
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain modesto.orozco@irbbarcelona.org.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain gelpi@ub.edu.
authors.forename: Josep Ll
authors.initials: JL
authors.lastname: Gelpí
mesh_terms: D030561:Databases, Nucleic Acid; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000737:chemistry*
chemical_list: D009696:Nucleic Acids