Project description
Molecular dynamics simulation for biology and chemistry research
Molecular dynamics (MD) simulations are widely used and have resulted in great advances in many scientific disciplines. Millions of supercomputer hours are devoted to collecting trajectories to produce amounts of simulation data. However, the community cannot analyse them properly due to the poor tradition of data sharing and the lack of appropriate infrastructure. The result of the limited analysis is the loss of data. In this context, the EU funded MDDB project will design a European-scale repository of MD simulation (and associated analysis tools) to integrate into mainstream biology and chemistry research. The project will optimise computational resources, favour the analysis (and meta-analysis) of trajectories for several perspectives and fields, and guarantee a fast and efficient information exchange between groups.
Objective
After decades of development and a Nobel prize, Molecular Dynamics (MD) has reached maturity. It is no longer an exotic technique used by a small group of theoreticians but rather a method extensively used by a very large community of users. Millions of supercomputer hours are devoted to collecting trajectories, thus producing a deluge of simulation data that the community is unable to handle. A poor tradition of data sharing and the lack of appropriate infrastructures to do so lead to the loss of data after limited analysis that most likely revealed only a small fraction of the information contained. Sparse initiatives to build trajectory repositories have encountered difficulties related to: i) the lack of trust of the community in the reliability of the data deposited; ii) the lack of interoperable standards and simulation ontologies; iii) uncertainties regarding the database technology required; v) difficulties of the users to interact in an open manner with the data; and vi) disconnection of the MD-field with neighboring communities. The MDDB projects intends to design a European-scale repository of MD simulation (and associated analysis tools), which will: i) optimize computational resources; ii) favor the analysis (and meta-analysis) of trajectories for many different perspectives and fields; iii) guarantee a fast and efficient interchange of information between groups; and iv) facilitate the integration of the MD simulation field into neighboring communities. The overall result will be a more efficient use of MD and the integration of the MD field into mainstream biology and chemistry research.
Fields of science
Keywords
Programme(s)
Funding Scheme
HORIZON-RIA - HORIZON Research and Innovation ActionsCoordinator
08028 Barcelona
Spain