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BioSimGrid Biomolecular Simulation Database
Abstract
BioSimGrid is a distributed biomolecular simulation database. It is a general-purpose database for trajectories from molecular dynamics simulations. Though initially designed as a distributed data grid, BioSimGrid allows for installation as a stand-alone instance. This can later be integrated into a wider, networked system. This presentation of BioSimGrid follows a scenario in biological research to demonstrate how to install the system, and how to deposit, query, and analyze trajectories in this system, with real Python code examples for each step. What then follow are explanations of the underlying concepts in the implementation of BioSimGrid: relational database, distributed computing, and the input/output (deposit and analysis) modules. Finishing the presentation is a discussion of the emerging trends and concerns in the further development of BioSimGrid and similar biological databases. This discussion touches on quality-assurance issues and the use of BioSimGrid as a back-end for other speciality databases. The experience of developing BioSimGrid compels the conclusion: In the development and maintenance of biomolecular simulation databases, it is essential that sustainability be asserted as a key principle.
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