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PEDS Advance Access originally published online on April 14, 2008
Protein Engineering Design and Selection 2008 21(6):369-377; doi:10.1093/protein/gzn012
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations

Andrew M. Simms1, Rudesh D. Toofanny2, Catherine Kehl1, Noah C. Benson1 and Valerie Daggett1,2,3

1Biomedical and Health Informatics Program, University of Washington, Seattle, WA 98195, USA 2Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA

3 To whom correspondence should be addressed. E-mail: daggett{at}u.washington.edu

Dynameomics is a project to investigate and catalog the native-state dynamics and thermal unfolding pathways of representatives of all protein folds using solvated molecular dynamics simulations, as described in the preceding paper. Here we introduce the design of the molecular dynamics data warehouse, a scalable, reliable repository that houses simulation data that vastly simplifies management and access. In the succeeding paper, we describe the development of a complementary multidimensional database. A single protein unfolding or native-state simulation can take weeks to months to complete, and produces gigabytes of coordinate and analysis data. Mining information from over 3000 completed simulations is complicated and time-consuming. Even the simplest queries involve writing intricate programs that must be built from low-level file system access primitives and include significant logic to correctly locate and parse data of interest. As a result, programs to answer questions that require data from hundreds of simulations are very difficult to write. Thus, organization and access to simulation data have been major obstacles to the discovery of new knowledge in the Dynameomics project. This repository is used internally and is the foundation of the Dynameomics portal site http://www.dynameomics.org. By organizing simulation data into a scalable, manageable and accessible form, we can begin to address substantial questions that move us closer to solving biomedical and bioengineering problems.

Keywords: data warehouse/database/Dynameomics/OLAP/protein dynamics

Received March 3, 2008; revised March 3, 2008; accepted March 4, 2008.


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