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MDAnalysis: Faster, Extensible Molecular Analysis for Reproducible Science

Project MDAnalysis

Oliver Beckstein (Arizona State University, NumFOCUS)

Funding Cycle 4

Proposal Summary

To improve and maintain high-performance tools for analysis of biological systems at the molecular scale and incentivize scientists to drive transparent and reproducible research.



MDAnalysis, as one of the most widely used libraries for the analysis of biomolecular simulations and structures, has established a mature core functionality that underpins analysis workflows in academia and industry. This proposal is focused on two areas of strategic growth: (1) improving the performance of essential core components by rewriting Python code in Cython; and (2) broadening the user and developer base by separating non-core modules into “MDAKits” (MDAnalysis Toolkits, akin to SciPy’s SciKits) to enable the rapid development and dissemination of new components and tools that can be released independently of the main package.

Key Personnel

Irfan Alibay
Oliver Beckstein
Richard Gowers
Fiona Naughton
Lily Wang