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BioSimGrid: grid-enabled biomolecular simulation data storage and analysis

By Muan Hong Ng, Steven Johnston, Bing Wu, Stuart E. Murdock, Kaihsu Tai, Hans Fangohr, Simon J. Cox, Jonathan W. Essex, Mark S.P. Sansom and Paul Jeffreys

Abstract

In computational biomolecular research, large amounts of simulation data are generated to capture the motion of proteins. These massive simulation data can be analysed in a number of ways to reveal the biochemical properties of the proteins. However, the legacy way of storing these data (usually in the laboratory where the simulations have been run) often hinders a wider sharing and easier cross-comparison of simulation results. The data is commonly encoded in a way specific to the simulation package that produced the data and can only be analysed with tools developed specifically for that simulation package. The BioSimGrid platform seeks to provide a solution to these challenges by exploiting the potential of the Grid in facilitating data sharing. By using BioSimGrid either in a scripting or web environment, users can deposit their data and reuse it for analysis. BioSimGrid tools manage the multiple storage locations transparently to the users and provide a set of retrieval and analysis tools for processing the data in a convenient and efficient manner. This paper details the usage and implementation of BioSimGrid using a combination of commercial databases, the Storage Resource Broker and Python scripts, gluing the building blocks together. It introduces a case study of how BioSimGrid can be used for better storage, retrieval and analysis of biomolecular simulation data

Topics: ZA4450, QH301, QA76
Year: 2006
OAI identifier: oai:eprints.soton.ac.uk:65004
Provided by: e-Prints Soton

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  1. (1998). [16] International Organization for Standardization Codes for the representation of names of countries and their subdivisions — Part 2: Country subdivision code, http://www.iso.org/iso/en/prods-services/iso3166ma/
  2. (2001). [17] An Open Source Project Numerical Python, http://numeric.scipy.org/ numpy.pdf,
  3. (1997). [7] The Molecular Modeling Toolkit,
  4. (2005). [9] SDSC Storage Resource Broker,
  5. (2004). A Web/Grid portal implementation of BioSimGrid: A biomolecular simulation database (abstract),
  6. (2006). Active-site dynamics of hydrolases: comparative analysis of molecular-dynamics simulations via the BioSimGrid database, Biochemistry
  7. (1981). AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions,
  8. (2004). BioSimGrid: towards a worldwide repository for biomolecular simulations,
  9. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations,
  10. (1998). He received a B.Sc. in theoretical physics
  11. (1992). is a Reader in the School of Chemistry at the University of Southampton. He received his undergraduate degree in chemistry from the University of Oxford in 1989, and his doctorate from the same institution in 1992. He then worked at Yale University from
  12. (2005). M.H. Ng is a research fellow at the Southampton Regional e-Science Centre. She received her B.Eng.
  13. (1996). NAMD — A parallel, object-oriented molecular dynamics program,
  14. (2003). Protein simulation and drug design,
  15. (2001). The anatomy of the Grid: Enabling scalable virtual organizations.
  16. (2005). The globus striped GridFTP framework and Server, in:
  17. (1999). The Grid: Blueprint for a New Computing Infrastructure,
  18. (1998). The SDSC storage resource broker, in:

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