A FAIR-Compliant Management Solution for Molecular Simulation Trajectories.

Abstract

Simulation studies of molecules primarily produce data that represent the configuration of the system as a function of the progress variable, usually time. Because of the high-dimensional nature of these data, which grow very quickly, compromises are often necessary and achieved by storing only a subset of the system's components, for example, stripping solvent, and by restricting the time resolution to a scale significantly coarser than the basic time step of the simulation. The resultant trajectories thus describe the essentially stochastic evolution of the molecules of interest. Maintaining their interpretability through metadata is of interest not only because they can aid researchers interested in specific systems but also for reproducibility studies and model refinement. Here, we introduce a standard for the storage of data created by molecular simulations that improves compliance with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. We describe a solution conceived in PostgreSQL, along with reference implementations, that provides stringent links between metadata and raw data, which is a major weakness of the established file formats used for storing these data. A possible structure for the logic of SQL queries is included along with salient performance testing. To close, we suggest that a PostgreSQL-based storage of simulation data, in particular when coupled to a visual user interface, can improve the FAIR compliance of molecular simulation data at all levels of visibility, and a prototype solution for accomplishing this is presented.