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EMEN2: An Object Oriented Database and Electronic Lab Notebook

  • Ian Rees (a1), Ed Langley (a2), Wah Chiu (a1) (a2) and Steven J. Ludtke (a1) (a2)
Abstract
Abstract

Transmission electron microscopy and associated methods, such as single particle analysis, two-dimensional crystallography, helical reconstruction, and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source.

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*Corresponding author. E-mail: sludtke@bcm.edu
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C. Allan , J.M. Burel , J. Moore , C. Blackburn , M. Linkert , S. Loynton , D. Macdonald , W.J. Moore , C. Neves , A. Patterson , M. Porter , A. Tarkowska , B. Loranger , J. Avondo , I. Lagerstedt , L. Lianas , S. Leo , K. Hands , R.T. Hay , A. Patwardhan , C. Best , G.J. Kleywegt , G. Zanetti & J.R. Swedlow (2012). OMERO: Flexible, model-driven data management for experimental biology. Nat Methods 9, 245253.

T. Berners-Lee , J. Hendler & O. Lassila (2001). The semantic web. Sci Am 284, 2837.

D. Blankenberg , G. Von Kuster , N. Coraor , G. Ananda , R. Lazarus , M. Mangan , A. Nekrutenko & J. Taylor (2010). Galaxy: A web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol Chapter 19, Unit 19.10.1-Unit 19.1021.

B. Giardine , C. Riemer , R.C. Hardison , R. Burhans , L. Elnitski , P. Shah , Y. Zhang , D. Blankenberg , I. Albert , J. Taylor , W. Miller , W.J. Kent & A. Nekrutenko (2005). Galaxy: A platform for interactive large-scale genome analysis. Genome Res 15, 14511455.

J. Goecks , A. Nekrutenko , J. Taylor & Galaxy Team (2010). Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11, R86.

I. Goldberg , C. Allan , J.M. Burel , D. Creager , A. Falconi , H. Hochheiser , J. Johnston , J. Mellen , P. Sorger & J. Swedlow (2005). The Open Microscopy Environment (OME) Data Model and XML file: Open tools for informatics and quantitative analysis in biological imaging. Genome Biol 6, R47.

K. Kvilekval , D. Fedorov , B. Obara , A. Singh & B.S. Manjunath (2010). Bisque: A platform for bioimage analysis and management. Bioinformatics 26, 544552.

G.C. Lander , S.M. Stagg , N.R. Voss , A. Cheng , D. Fellmann , J. Pulokas , C. Yoshioka , C. Irving , A. Mulder , P.W. Lau , D. Lyumkis , C.S. Potter & B. Carragher (2009). Appion: An integrated, database-driven pipeline to facilitate EM image processing. J Struct Biol 166, 95102.

D.N. Mastronarde (2005). Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 152, 3651.

N. Shadbolt , W. Hall & T. Berners-Lee (2006). The semantic web revisited. IEEE Intell Syst 21, 96101.

G. Stocker , M. Fischer , D. Rieder , G. Bindea , S. Kainz , M. Oberstolz , J.G. McNally & Z. Trajanoski (2009). iLAP: A workflow-driven software for experimental protocol development, data acquisition and analysis. BMC Bioinformatics 10, 390.

C. Suloway , J. Pulokas , D. Fellmann , A. Cheng , F. Guerra , J. Quispe , S. Stagg , C.S. Potter & B. Carragher (2005). Automated molecular microscopy: The new Leginon system. J Struct Biol 151, 4160.

G. Tang , L. Peng , P.R. Baldwin , D.S. Mann , W. Jiang , I. Rees & S.J. Ludtke (2007). EMAN2: An extensible image processing suite for electron microscopy. J Struct Biol 157, 3846.

J. Zhang , N. Nakamura , Y. Shimizu , N. Liang , X. Liu , J. Jakana , M.P. Marsh , C.R. Booth , T. Shinkawa , M. Nakata & W. Chiu (2009). JADAS: A customizable automated data acquisition system and its application to ice-embedded single particles. J Struct Biol 165, 19.

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Microscopy and Microanalysis
  • ISSN: 1431-9276
  • EISSN: 1435-8115
  • URL: /core/journals/microscopy-and-microanalysis
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