Project management system for structural and functional proteomics: Sesame
- 152 Downloads
A computing infrastructure (Sesame) has been designed to manage and link individual steps in complex projects. Sesame is being developed to support a large-scale structural proteomics pilot project. When complete, the system is expected to manage all steps from target selection to data-bank deposition and report writing. We report here on the design criteria of the Sesame system and on results demonstrating successful achievement of the basic goals of its architecture. The Sesame software package, which follows the client/server paradigm, consists of a framework, which supports secure interactions among the three tiers of the system (the client, server, and database tiers), and application modules that carry out specific tasks. The framework utilizes industry standards. The client tier is written in Java2 and can be accessed anywhere through the Internet. All the development on the server tier is also carried out in Java2 so as to accommodate a wide variety of computer platforms. The database tier employs a commercial database management system. Each Sesame application module consists of a simple user interface in the client tier, corresponding objects in the server tier, and relevant data stored in the centralized database. For security, access to stored data is controlled by access privileges. The system facilitates both local and remote collaborations. Because users interact with the system using Java Web Start or through a web browser, access is limited only by the availability of an Internet connection. We describe several Sesame modules that have been developed to the point where they are being utilized routinely to support steps involved in structural and functional proteomics. This software is available to parties interested in using it and assisting to guide its further development.
- 1.Edwards, A.E., Arrowsmith, C.H., Christendat, D., Dharamsi, A., Friesen, J.D., Greenblatt, J.F., and Vedadi, M. (2000) Nature Struct. Biol. 7supplement, 970–972.Google Scholar
- 2.Orfali, R., and Harkey, D. (1998) Client/Server Programming with JAVA and CORBA, 2nd edn., John Wiley and Sons, New York, NY.Google Scholar
- 3.Fogh, R., Ionides, J., Ulrich, E., Boucher, W., Vranken, W., Linge, J.P., Habeck, M., Rieping, W., Bhat, T.N., Westbrook, J., Henrick, K., Gilliland, G., Berman, H., Thornton, J., Nilges, M., Markley, J., and Laue, E. (2002) Nature Struct. Biol. 9, 416–418.Google Scholar
- 4.Bertone, P., Kluger, Y., Lan, N., Zheng, D., Christendat, D., Yee, A., Edwards, A. M., Arrowsmith, C. H., Montelione, G.T., and Gerstein, M. (2001) Nucleic Acids Res. 29, 2884–2898.Google Scholar
- 5.Berman, H.M. Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. (2000) Nucleic Acids Res. 28, 235–242.Google Scholar