Parameter optimization in 3D reconstruction on a large scale grid

  • Authors:

  • J. R. Bilbao-Castro;A. Merino;I. García;J. M. Carazo;J. J. Fernández

  • Affiliations:

  • Biocomputing Unit, Centro Nacional de Biotecnología, Universidad Autónoma, 28049 Madrid, Spain and Dept. Arquitectura de Computadores y Electrónica, Universidad de Almería, 041 ...;Biocomputing Unit, Centro Nacional de Biotecnología, Universidad Autónoma, 28049 Madrid, Spain;Dept. Arquitectura de Computadores y Electrónica, Universidad de Almería, 04120 Almería, Spain;Biocomputing Unit, Centro Nacional de Biotecnología, Universidad Autónoma, 28049 Madrid, Spain;Dept. Arquitectura de Computadores y Electrónica, Universidad de Almería, 04120 Almería, Spain

  • Venue:
  • Parallel Computing
  • Year:
  • 2007

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Abstract

Reaching as high structural resolution as possible in 3D electron microscopy of biological specimens is crucial to understanding their function and interactions. Technical and biological limitations make electron microscopy projections of such specimens quite noisy. Under those circumstances, the broadly used Weighted Back-Projection algorithm presents some limitations for 3D reconstruction. Iterative tomographic reconstruction algorithms are well suited to provide high resolution 3D structures under such noisy conditions. Nevertheless, these iterative algorithms present two major challenges: computational expensiveness and some free parameters which need to be correctly tuned to obtain the best possible resolution. This work applies global optimization techniques to search for the optimal set of parameters and makes use of the high-throughput capabilities of grid computing to perform the required computations. Fault tolerance techniques have been included in our application to deal with the dynamic nature and complexity of large scale computational grids. The approach for parameter optimization presented here has been successfully evaluated in the European EGEE grid, obtaining good levels of speedup, throughput and transfer rates.