Web-Ice

Web-Ice is a platform to optimize automated data collection at macromolecular crystallography beamlines. A programming interface allows the beamline control software (e.g., Blu-Ice/DCS) to trigger data analysis automatically. Results are organized based on a list of samples that the user provides, and are examined within a Web page, viewed either locally by the user or remotely by collaborators.

Web-Ice currently provides tools for:

Rapid analysis and display of diffraction images
Choice of proper experimental parameters to optimize the collection of the full data set.
Inspection of data analysis results within a Web-browser interface.
Initiating data collection or export a data collection strategy to the Blu-Ice interface.
Access to the beamline log messages and the beamline video system.

Reference: A. González, P. Moorhead, S. E. McPhillips, J. Song, K. Sharp, J. R. Taylor, P. D. Adams, N. K. Sauter and S. M. Soltis "Web-Ice: integrated data collection and analysis for macromolecular crystallography." J. Appl. Cryst. 41, 176-184 (2008).

For instructions on installing Web-Ice, pleasew consult the developers' wiki.

Web-Ice Software design

The Web-Ice front end runs on a Tomcat web server installed on a Linux server. In addition Web-Ice makes use of a network of software applications and application servers such us:

The Authentication Server, a common authentication protocol for Blu-Ice and web applications. This allows users to access and switch between all these applications without authenticating multiple times. It also restricts access to beamline control features to users who are enabled at the beamline.
Executable programs and shell scripts are run by Web-Ice on behalf of the user via the Impersonation Daemon. The Impersonation Daemon accepts commands via the HTTP protocol. After verifying the authentication information with the Authentication Server, it enables Web-Ice to run background jobs with the actual rights of the Unix user account.
The Crystal Analysis Server is an application running on a web server (Tomcat). Like Web-Ice, it runs programs and scripts via the impersonation server, but at the request of DCSS or Web-Ice, rather than the user. The Crystal Analysis Server allows the data analysis results to be available to both Web-Ice and Blu-Ice.
The Crystal Server, an interface to the database containing the information about the users samples (provided in an Excel spreadsheet). Selected results from sample analysis by Web-Ice and the Crystal Analysis Server are written to the Crystal Server for permanent storage in the database.

Web-Ice also uses the following established programs for crystallographic data analysis and data collection strategy calculations:

LABELIT. N. K. Sauter, R. W. Grosse-Kunstleve, and P. D. Adams. J. Appl. Cryst.37, 399-409. (2004)
DISTL. Z. Zhang, H. van den Bedem, N. K. Sauter, G. P. Snell and A. Deacon J. Appl. Cryst. 39, 112-119. (2006)
MOSFLM. A. G. W. Leslie; in Crystallographic Computing, Oxford University Press. (1990)
BEST. A. N. Popov and G. P. Bourenkov. Acta Cryst. D59, 1145-1153. (2003)
RADDOSE. J. W. Murray, E. F. Garman and R. B. G. Ravelli. J. Appl. Cryst. 37, 513-522. (2004)

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[Up] Start Web-Ice Users' documentation Web-Ice Developers' Wiki	Web-Ice Web-Ice is a platform to optimize automated data collection at macromolecular crystallography beamlines. A programming interface allows the beamline control software (e.g., Blu-Ice/DCS) to trigger data analysis automatically. Results are organized based on a list of samples that the user provides, and are examined within a Web page, viewed either locally by the user or remotely by collaborators. Web-Ice currently provides tools for: Rapid analysis and display of diffraction images Choice of proper experimental parameters to optimize the collection of the full data set. Inspection of data analysis results within a Web-browser interface. Initiating data collection or export a data collection strategy to the Blu-Ice interface. Access to the beamline log messages and the beamline video system. Reference: A. González, P. Moorhead, S. E. McPhillips, J. Song, K. Sharp, J. R. Taylor, P. D. Adams, N. K. Sauter and S. M. Soltis "Web-Ice: integrated data collection and analysis for macromolecular crystallography." J. Appl. Cryst. 41, 176-184 (2008). For instructions on installing Web-Ice, pleasew consult the developers' wiki. Web-Ice Software design The Web-Ice front end runs on a Tomcat web server installed on a Linux server. In addition Web-Ice makes use of a network of software applications and application servers such us: The Authentication Server, a common authentication protocol for Blu-Ice and web applications. This allows users to access and switch between all these applications without authenticating multiple times. It also restricts access to beamline control features to users who are enabled at the beamline. Executable programs and shell scripts are run by Web-Ice on behalf of the user via the Impersonation Daemon. The Impersonation Daemon accepts commands via the HTTP protocol. After verifying the authentication information with the Authentication Server, it enables Web-Ice to run background jobs with the actual rights of the Unix user account. The Crystal Analysis Server is an application running on a web server (Tomcat). Like Web-Ice, it runs programs and scripts via the impersonation server, but at the request of DCSS or Web-Ice, rather than the user. The Crystal Analysis Server allows the data analysis results to be available to both Web-Ice and Blu-Ice. The Crystal Server, an interface to the database containing the information about the users samples (provided in an Excel spreadsheet). Selected results from sample analysis by Web-Ice and the Crystal Analysis Server are written to the Crystal Server for permanent storage in the database. Web-Ice also uses the following established programs for crystallographic data analysis and data collection strategy calculations: LABELIT. N. K. Sauter, R. W. Grosse-Kunstleve, and P. D. Adams. J. Appl. Cryst.37, 399-409. (2004) DISTL. Z. Zhang, H. van den Bedem, N. K. Sauter, G. P. Snell and A. Deacon J. Appl. Cryst. 39, 112-119. (2006) MOSFLM. A. G. W. Leslie; in Crystallographic Computing, Oxford University Press. (1990) BEST. A. N. Popov and G. P. Bourenkov. Acta Cryst. D59, 1145-1153. (2003) RADDOSE. J. W. Murray, E. F. Garman and R. B. G. Ravelli. J. Appl. Cryst. 37, 513-522. (2004)

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