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Remote Collaboration Environment for Protein Crystallography

A solution to allow a team of researchers distributed anywhere in the world to perform a complete crystallographic experiment, from data collection to structure publication.

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Remote Collaboration Environment for Protein Crystallography

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  1. General Goal:Allow a team of researchers distributed anywhere in the world to perform a complete crystallographic experiment, from data collection to structure publication. A Remote Collaboration Environment for Protein CrystallographyHEPiX-HEPNT Conference, 8 Oct 1999 User at SSRL Team Member at Home Lab Remote Collaborator Internet Local Area Network Collaboratory Manager Nicholas Sauter, Stanford Synchrotron Radiation Laboratory http://smb.slac.stanford.edu sauter@stanford.edu Equipment Control Data CPU

  2. Protein crystal Diffraction data Electron density Molecular model of Cholera toxin X-ray Diffraction Experiments Give the Detailed Atomic Structure of Protein Molecules

  3. Protein Diffraction Work Bears Several Similarities to the High Energy Physics Field • Experiments performed at National facilities • Large user base • ~4 users per group • ~90 groups per year at each beamline • Big datasets • Current detectors: ~0.6 Terabyte/year • CCD next generation: ~20 Tb/year • Acquisition software must perform well since each group has ~50 hours experimental time • No downtime is possible • Very little time for data backup • Graphical user interface • Users need shared access to data during an extended analysis period SSRL Synchrotron Source

  4. Designing a Modern System from the Ground Up • High Performance Computing Environment at the Beamline • Distributed Architecture • Cross Platform Compatibility • GUI’s Implemented in Tcl/Tk • Extending this System for Remote Access • Viewing the Data from a Remote Platform • Live Video Feed from the Experimental Floor • Remote File Access and Data Archiving • General Security Considerations • Delivering X-window Legacy Applications with Terminal Server

  5. The Problem of Multiple, Simultaneous User Interfaces

  6. The Problem of Multiple Hardware Hosts

  7. Solution: Distributed Control System (DCS)

  8. A Peek Inside the DCS Server

  9. Cross-Operating System Library (XOS) Features • Supports portable, multithreaded, distributed programs • Network communication using simplified socket objects. • Thread creation and synchronization with mutexes and semaphores. • Memory mapped files and hash tables. • Inter-thread communication with message queues and Win32-style messages. • Compile-time approach • Header file xos.h loads appropriate, system-dependent include files. Advantages • Portability • Compile code on Digital Unix, IRIX, OpenVMS, Windows NT/95. • Easy to port to new platforms similar to any of the above. • Reliability • Simpler APIs leads to more reliable code. • Less need to study different platforms; easy for novice programmers. • Performance • Native system calls on each platform for maximum performance • No runtime overhead for platform independence. • Open Source

  10. Tcl / Tk for GUI Development • Rapid Development • GUI needs only a fraction of the code necessary in C, C++ or Java. • Easy for the novice programmer! • Quick coding & easy maintenance is essential for rapidly changing beamline environment. Source: John Ousterhoust, IEEE Computer, March 1998

  11. Other Advantages of Tcl /Tk Platform Independence • Unix, VMS, Mac, and Win32. • Scripts can be distributed without compilation and run on any computer Tcl/Tk has been installed on. • Or…scripts can be bundled with Tcl/Tk binaries and distributed as a single executable file. Extensible in C/C++ • Tcl was designed to be extended readily in C or C++. • High performance code, multiple threads, etc., best implemented as extensions. XOS library is used for sockets. Object Orientation • The [Incr Tcl] extension to Tcl provides object-oriented features such as classes. • The [Incr Widgets] extension provides an object oriented framework for building complex widgets from built-in Tcl widgets.

  12. Data Collection GUI written in Tcl/Tk

  13. Adding a JPEG Compressor to the System

  14. A Web-based Data Viewer at https://smb.slac.stanford.edu:8100

  15. Video Feeds from the Experimental Floor Sample Manipulation Beamline Instruments Videoconference

  16. Architecture for Remote Video

  17. Transparent File Access For Remote Collaborators

  18. Metadata for Diffraction Images File Header • File Parameters • Creation date • Access control list • Tape archive status • User annotation • Annotation by data processing software • Move, rename, and copy tracking Thumbnail View Larger JPEG View Larger JPEG View

  19. Architecture for Remote Archiving

  20. General Security Architecture

  21. Legacy Applications Can Run Within X-window on Metaframe WRQ Reflection-X Showing SGI Desktop at SSRL Data Analysis Application Running at SSRL SGI Desktop at home lab Windows Terminal Server at SSRL Seen Through ICA Connection

  22. Summary: Four Platforms for Remote Access

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