Effects of the downsampling scheme on three-dimensional electron microscopy of single particles

Three-dimensional electron microscopy allows scientists to study biological specimens and to understand how they behave and interact with each other depending on their structural conformation. Electron microscopy projections of the specimens are taken from different angles and are processed to obtain a virtual three-dimensional reconstruction for further studies. Nevertheless, the whole reconstruction process, which is composed of many different subtasks from the microscope to the reconstructed volume, is not straightforward nor cheap in terms of computational costs. Different computing paradigms have been applied in order to overcome such high costs. While classic parallel computing using mainframes and clusters of workstations is usually enough for average requirements, there are some tasks which would fit better into a different computing paradigm – such as grid computing. Such tasks can be split up into a myriad of subtasks, which can then be run independently using as many computational resources as are available. This chapter explores two of these tasks present in a typical three-dimensional electron microscopy reconstruction process. In addition, important aspects like fault-tolerance are widely covered; given that the distributed nature of a grid infrastructure makes it inherently unstable and difficult to predict.

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Grid Computing in 3D Electron Microscopy Reconstruction

Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare ◽

10.4018/978-1-60566-374-6.ch020 ◽

2011 ◽

pp. 392-409

Author(s):

J.R. Bilbao Castro ◽

I. Garcia Fernandez ◽

J. Fernandez

Keyword(s):

Electron Microscopy ◽

Grid Computing ◽

Three Dimensional ◽

Dimensional Electron ◽

Reconstruction Process ◽

Computing Paradigm ◽

Structural Conformation ◽

Reconstructed Volume ◽

Dimensional Reconstruction ◽

Computational Resources

Three-dimensional electron microscopy allows scientists to study biological specimens and to understand how they behave and interact with each other depending on their structural conformation. Electron microscopy projections of the specimens are taken from different angles and are processed to obtain a virtual three-dimensional reconstruction for further studies. Nevertheless, the whole reconstruction process, which is composed of many different subtasks from the microscope to the reconstructed volume, is not straightforward nor cheap in terms of computational costs. Different computing paradigms have been applied in order to overcome such high costs. While classic parallel computing using mainframes and clusters of workstations is usually enough for average requirements, there are some tasks which would fit better into a different computing paradigm – such as grid computing. Such tasks can be split up into a myriad of subtasks, which can then be run independently using as many computational resources as are available. This chapter explores two of these tasks present in a typical three-dimensional electron microscopy reconstruction process. In addition, important aspects like fault-tolerance are widely covered; given that the distributed nature of a grid infrastructure makes it inherently unstable and difficult to predict.

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26S Proteasome Structure Revealed by Three-dimensional Electron Microscopy

Journal of Structural Biology ◽

10.1006/jsbi.1998.3958 ◽

1998 ◽

Vol 121 (1) ◽

pp. 19-29 ◽

Cited By ~ 137

Author(s):

Jochen Walz ◽

Annette Erdmann ◽

Mary Kania ◽

Dieter Typke ◽

Abraham J Koster ◽

...

Keyword(s):

Electron Microscopy ◽

Three Dimensional ◽

26S Proteasome ◽

Dimensional Electron

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