ParmBSC1 forcefield Nucleotide MD Simulations Database

ParmBSC1 Portfolio, a BigData approach to efficiently manage large nucleic acids simulation data.


ParmBSC1 portfolio is a comprehensive database system and analysis portal holding all the MD trajectories prepared during the development and validation of the ParmBSC1 forcefield. The database allows direct access to trajectory data and information about the structure and MD simulation together with a complete set of analyses performed. Additionally, the database is provided with a flexible NAFlex-based engine allowing users to perform their own analysis pipelines.

ParmBSC1 portfolio uses state-of-the-art technology to deal with BigData management. Two well-known noSQL databases (Cassandra and Mongo) are used to store trajectory coordinates and analyses, respectively. These noSQL databases are queried using REST web services and php drivers.

 To facilitate the access to all information stored, we built a web portal on top of the database system, allowing several ways of accessing the data. The final scheme of the ParmBSC1 portfolio is shown in the next figure. Information about how to access data and how to use the portal can be found in these help pages, divided in 5 sections (left column in this page).