Hostname: page-component-586b7cd67f-vdxz6 Total loading time: 0 Render date: 2024-11-22T10:09:39.925Z Has data issue: false hasContentIssue false
  • English
  • Français

EMEN2: An Object Oriented Database and Electronic Lab Notebook

Published online by Cambridge University Press:  29 January 2013

Ian Rees ,
Ed Langley ,
Wah Chiu  and
Steven J. Ludtke
Ian Rees
Affiliation:
Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
Ed Langley
Affiliation:
Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Wah Chiu
Affiliation:
Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Steven J. Ludtke*
Affiliation:
Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
*
*Corresponding author. E-mail: [email protected]
Get access

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.

Keywords

TEMcryo-EMdatabaseelectronic notebooksoftwareweb interface
Type
Software, Techniques and Equipment Development
Information
Microscopy and Microanalysis , Volume 19 , Issue 1 , February 2013 , pp. 1 - 10
Copyright
Copyright © Microscopy Society of America 2013

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Allan, C., Burel, J.M., Moore, J., Blackburn, C., Linkert, M., Loynton, S., Macdonald, D., Moore, W.J., Neves, C., Patterson, A., Porter, M., Tarkowska, A., Loranger, B., Avondo, J., Lagerstedt, I., Lianas, L., Leo, S., Hands, K., Hay, R.T., Patwardhan, A., Best, C., Kleywegt, G.J., Zanetti, G. & Swedlow, J.R. (2012). OMERO: Flexible, model-driven data management for experimental biology. Nat Methods 9, 245–253.CrossRefGoogle ScholarPubMed
Berners-Lee, T., Hendler, J. & Lassila, O. (2001). The semantic web. Sci Am 284, 28–37.Google Scholar
Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A. & Taylor, J. (2010). Galaxy: A web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol Chapter 19, Unit 19.10.1-Unit 19.1021. Google Scholar
Crockford, D. (2006). The application/json Media Type for JavaScript Object Notation (JSON). IETF Request for Comments 4627. CrossRefGoogle Scholar
Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W.J. & Nekrutenko, A. (2005). Galaxy: A platform for interactive large-scale genome analysis. Genome Res 15, 1451–1455.CrossRefGoogle ScholarPubMed
Goecks, J., Nekrutenko, A., Taylor, J. & Galaxy Team (2010). Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11, R86. Google Scholar
Goldberg, I., Allan, C., Burel, J.M., Creager, D., Falconi, A., Hochheiser, H., Johnston, J., Mellen, J., Sorger, P. & Swedlow, J. (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. CrossRefGoogle ScholarPubMed
Kvilekval, K., Fedorov, D., Obara, B., Singh, A. & Manjunath, B.S. (2010). Bisque: A platform for bioimage analysis and management. Bioinformatics 26, 544–552.Google Scholar
Lander, G.C., Stagg, S.M., Voss, N.R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P.W., Lyumkis, D., Potter, C.S. & Carragher, B. (2009). Appion: An integrated, database-driven pipeline to facilitate EM image processing. J Struct Biol 166, 95–102.Google Scholar
Ludtke, S.J., Nason, L., Tu, H., Peng, L. & Chiu, W. (2003). Object oriented database and electronic notebook for transmission electron microscopy. Microsc Microanal 9, 556–565.Google Scholar
Mastronarde, D.N. (2005). Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 152, 36–51.Google Scholar
Olson, M.A., Bostic, K. & Seltzer, M. (1999). Berkeley DB. In Proceedings of the FREENIX Track: 1999 USENIX Annual Technical Conference, pp. 183–192. Monterey, CA: USENIX Association.Google Scholar
Shadbolt, N., Hall, W. & Berners-Lee, T. (2006). The semantic web revisited. IEEE Intell Syst 21, 96–101.Google Scholar
Stocker, G., Fischer, M., Rieder, D., Bindea, G., Kainz, S., Oberstolz, M., McNally, J.G. & Trajanoski, Z. (2009). iLAP: A workflow-driven software for experimental protocol development, data acquisition and analysis. BMC Bioinformatics 10, 390.CrossRefGoogle ScholarPubMed
Suloway, C., Pulokas, J., Fellmann, D., Cheng, A., Guerra, F., Quispe, J., Stagg, S., Potter, C.S. & Carragher, B. (2005). Automated molecular microscopy: The new Leginon system. J Struct Biol 151, 41–60.CrossRefGoogle ScholarPubMed
Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I. & Ludtke, S.J. (2007). EMAN2: An extensible image processing suite for electron microscopy. J Struct Biol 157, 38–46.Google Scholar
Winer, D. (1999). XML-RPC specification. Available at http://xmlrpc.com (accessed November 19, 2011).Google Scholar
Zhang, J., Nakamura, N., Shimizu, Y., Liang, N., Liu, X., Jakana, J., Marsh, M.P., Booth, C.R., Shinkawa, T., Nakata, M. & Chiu, W. (2009). JADAS: A customizable automated data acquisition system and its application to ice-embedded single particles. J Struct Biol 165, 1–9.CrossRefGoogle ScholarPubMed
Supplementary material: PDF

Ian Rees Supplementary Material

Appendix

Download Ian Rees Supplementary Material(PDF)
PDF 1.4 MB