Web portal to an image database for high-resolution three-dimensional reconstruction

Web portal to an image database for high-resolution three-dimensional reconstruction The exponential increase of image data in high-resolution reconstructions by electron cryomicroscopy (cryoEM) has posed a need for efficient data management solutions in addition to powerful data processing procedures. Although relational databases and web portals are commonly used to manage sequences and structures in biological research, their application in cryoEM has been limited due to the complexity in accomplishing the dual tasks of interacting with proprietary software and simultaneously providing data access to users without database knowledge. Here, we report our results in developing web portal to SQL image databases used by the Image Management and Icosahedral Reconstruction System (IMIRS) to manage cryoEM images for subnanometer-resolution reconstructions. Fundamental issues related to the design and deployment of web portals to image databases are described. A web browser-based user interface was designed to accomplish data reporting and other database-related services, including user authentication, data entry, graph-based data mining, and various query and reporting tasks with interactive image manipulation capabilities. With an integrated web portal, IMIRS represents the first cryoEM application that incorporates both web-based data reporting tools and a complete set of data processing modules. Our examples should thus provide general guidelines applicable to other cryoEM technology development efforts. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Structural Biology Elsevier

Web portal to an image database for high-resolution three-dimensional reconstruction

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Publisher
Elsevier
Copyright
Copyright © 2003 Elsevier Inc.
ISSN
1047-8477
eISSN
1095-8657
DOI
10.1016/j.jsb.2003.09.035
Publisher site
See Article on Publisher Site

Abstract

The exponential increase of image data in high-resolution reconstructions by electron cryomicroscopy (cryoEM) has posed a need for efficient data management solutions in addition to powerful data processing procedures. Although relational databases and web portals are commonly used to manage sequences and structures in biological research, their application in cryoEM has been limited due to the complexity in accomplishing the dual tasks of interacting with proprietary software and simultaneously providing data access to users without database knowledge. Here, we report our results in developing web portal to SQL image databases used by the Image Management and Icosahedral Reconstruction System (IMIRS) to manage cryoEM images for subnanometer-resolution reconstructions. Fundamental issues related to the design and deployment of web portals to image databases are described. A web browser-based user interface was designed to accomplish data reporting and other database-related services, including user authentication, data entry, graph-based data mining, and various query and reporting tasks with interactive image manipulation capabilities. With an integrated web portal, IMIRS represents the first cryoEM application that incorporates both web-based data reporting tools and a complete set of data processing modules. Our examples should thus provide general guidelines applicable to other cryoEM technology development efforts.

Journal

Journal of Structural BiologyElsevier

Published: Oct 1, 2003

References

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    Grundy, W.N.; Bailey, T.L.
  • Finding and using local symmetry in identifying lower domain movements in hexon subunits of the herpes simplex virus type 1 b capsid
    He, J.; Schmid, M.F.; Zhou, Z.H.; Rixon, F.; Chiu, W.
  • Alignment error envelopes for single particle analysis
    Jensen, G.J.
  • IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database
    Liang, Y.; Ke, E.Y.; Zhou, Z.H.
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    Martone, M.E.; Gupta, A.; Wong, M.; Qian, X.; Sosinsky, G.; Ludascher, B.; Ellisman, M.H.
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    Metoz, F.; Sherman, M.B.; Schmid, M.F.

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