Microscopy and Microanalysis

Software, Techniques and Equipment Development

EMEN2: An Object Oriented Database and Electronic Lab Notebook

Ian Reesa1, Ed Langleya2, Wah Chiua1a2 and Steven J. Ludtkea1a2 c1

a1 Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA

a2 Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA

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.

(Received April 04 2012)

(Accepted August 19 2012)

Key words

  • TEM;
  • cryo-EM;
  • database;
  • electronic notebook;
  • software;
  • web interface

Correspondence:

c1 Corresponding author. E-mail: sludtke@bcm.edu