EMEN2: An object oriented database and electronic lab notebook

Microscopy and Microanalysis

Volumn 19, Issue 1, 2013, Pages 1-10

  Rees, Ian ^a   Langley, Ed ^a   Chiu, Wah ^a   Ludtke, Steven J ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

cryo EM; database; electronic notebook; Key words TEM; software; web interface

Indexed keywords

ARTICLE; BIOLOGY; CHEMICAL DATABASE; COMPUTER PROGRAM; CRYOELECTRON MICROSCOPY; ELECTRON TOMOGRAPHY; INFORMATION PROCESSING; INTERNET; METHODOLOGY;

AUTOMATIC DATA PROCESSING; BIOLOGY; CRYOELECTRON MICROSCOPY; DATABASES, CHEMICAL; ELECTRON MICROSCOPE TOMOGRAPHY; INTERNET; SOFTWARE;

EID: 84873402386     PISSN: 14319276     EISSN: 14358115     Source Type: Journal    
DOI: 10.1017/S1431927612014043     Document Type: Article

References (18)

1. 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
2. Berners-Lee, T., Hendler, J. & Lassila, O. (2001). The semantic web. Sci Am 284, 28-37
3. 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
4. Crockford, D. (2006). The application/json Media Type for Java- Script Object Notation (JSON). IETF Request for Comments 4627
5. 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
6. 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
7. 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
8. Kvilekval, K., Fedorov, D., Obara, B., Singh, A. & Manjunath, B.S. (2010). Bisque: A platform for bioimage analysis and management. Bioinformatics 26, 544-552
9. 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
10. 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
11. Mastronarde, D.N. (2005). Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 152, 36-51
12. 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
13. Shadbolt, N., Hall,W. & Berners-Lee, T. (2006). The semantic web revisited. IEEE Intell Syst 21, 96-101
14. 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
15. 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
16. 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
17. Winer, D. (1999). XML-RPC specification. Available at http://xmlrpc.com (accessed November 19, 2011)
18. 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