CLS Beamline Remote Access Project

CLS has undertaken a project with major funding from CANARIE and additional funding from CLS, Surface Science Western (at the University of Western Ontario), IBM Canada and Big Bangwidth to develop a remote access system for the CMCF, CMCF2 and VESPERS beamlines. The development team also includes the Alberta Synchrotron Institute at the University of Alberta.

Project Description

The vision for this project is to move towards a single User Interface for all End User applications and systems for the CLS, even systems residing in different locations and organizations through a common web interface. This is accomplished using emerging web-services technologies.

Project Partners

	CANARIE Inc ( www.canarie.ca ) CANARIE, Canada’s advanced Network development organization, is a not-for-profit corporation supported by its members, project partners and the Federal Government. Since 1993, CANARIE has received more that $350 million from the Government of Canada. That funding has been used for the research and implementation of advanced networks and applications that stimulate economic growth and increase Canada’s international competitiveness. CAnet 4 is the fourth generation of Canada’s research and education network. CANARIE’s mission is to accelerate Canada’s advanced network development and use by facilitating the widespread adoption of faster, more efficient networks and by enabling the next generation of advanced products, applications and services to run on them. This project received financial support for the CANRIE R&D program.
	Canadian Light Source ( www.lightsource.ca ) The CLS facility, operated by Canadian Light Source Inc., is a national science research laboratory for the production of high brightness synchrotron light from the infrared, visible, and ultraviolet to x-ray region of the electromagnetic spectrum. CLS is a third-generation light source facility, established as Canada’s National Synchrotron Laboratory, and is accessible to researchers from the academic, government, and private sectors. The Canadian Light Source worked on requirements definition, system design, implementation and deployment.
	From the 1970’s Western began to establish two related themes in its science programs that have helped it to take an important role in this proposed activity. One of these was synchrotron science and its applications. UWO took the lead in building Canada’s first national beamlines at Madison USA, and since then has trained more highly qualified personnel (HQP) in synchrotron science than any other university in Canada. From the earliest concepts of the CLS, UWO scientists haven taken major roles in developing government and industrial support for the facility, in managing the growing facility and in continuing to submit a number of the research ideas for study on CLS beamlines. In short, UWO and its scientists form a strong pole of synchrotron expertise in Canada. A second theme instituted in the 70’s was the creation of a laboratory specialized in the applications in surface science with a strong mandate to develop connections with industry. Over the subsequent 24 years, Surface Science Western (SSW) has grown into a consulting organization known across North America for its reliable and imaginative responses to process problems in industries with products ranging from automobiles to minerals to electric power. SSW has continually promoted the development of new analytical techniques and protocols both for industrial and academic use. Quite recently, the concept of the VESPERS beamline was developed by SSW scientists and received funding approval by CFI and OIT. Surface Science Western worked on requirements development and integration and system testing.
	The Alberta Synchrotron Institute, located at the University of Alberta, is a partnership of the three research universities of the province and funded by provincial funding agencies (Alberta Science and Research Authority, Alberta Innovation and Science, Alberta Heritage Foundation for Medical Research, Alberta Ingenuity Fund) and Western Economic Diversification. Its mandate is to represent Alberta’s scientists in the development of the experimental facilities at the CLS, to facilitate access at other synchrotrons until the commissioning of the CLS is completed and to develop and provide expertise in synchrotron science for academic and industrial research in the province. The scientists of the Alberta synchrotron institute are actively involved in the development of the experimental facilities of the CLS, including the protein crystallography beamlines. The Alberta Synchrotron Institute worked on requirements development.
	IBM Canada is a key contributor to the Canadian economy through significant R&D investment, job creation, use of Canadian suppliers and extensive participation in university research programs. IBM Canada is one of the country's largest R&D investors, contributing $334 million dollars (Cdn) in 2004. Our export revenue for the same year was $1.7 billion (Cdn). At year end 2004, IBM Canada and its wholly-owned subsidiaries employed some 20,000 regular full-time and part-time people across the country. IBM worked on requirement development, system design and software implementation.
	BigBangwidth is 100% Canadian owned SME that began operations in 2000. The company has had substantial financial backing from one of Canada’s leading Venture Capitalists – TechnoCap Inc. To date, the company has raised over $5 000 000 in investment and continues to be strongly supported. The company is in the early revenue stage having customers in both the research markets as well as the commercial markets. The company is highly supportive of the project and has the financial and human resources necessary to complete the project and support it going forward. For the past 3.5 years, the company has developed and refined world-class optical switches. The technology, BigBangwidth Lightpath Accelerator™, is an ideal solution for individual access to research networks. Unlike IP and Ethernet packet switches, Lightpath Accelerator™ employs single mode fiber optic NanoPhotonic™ devices at its core to supply secure protocol-independent data transfers at virtually any data rate. Data rates up to 10 Gigabit Ethernet can be achieved to the desktop to enable high performance applications. BigBangwidth worked on networking hardware deployment and switch interface software development.

Project Details – Protein Crystallography

Macromolecular crystallography is a method for determining the structures of biological large molecules, specifically proteins and nucleic acids, by X-ray diffraction studies of three-dimensional crystals. It has made enormous contributions to our understanding of all aspects of life sciences including that critical to research on health, the environment and agriculture. The processes of life depend fundamentally on the atomic and geometrical structure and interactions of the molecules in the living cell, therefore structural information at the atomic level increasingly contributes to the detailed understanding of complex biological processes in basic scientific fields ranging from cell biology, biochemistry, genetics, infectious diseases and immunology to the more applied medical, pharmaceutical and biotechnology/protein engineering research sectors. The increasing importance of structural information is reflected in the explosive growth of the field in the past decade as is documented in the number of deposition of macromolecular structures in the Protein Data Bank (PDB). More than five thousand structures had been deposited in year 2004 resulting in the total of 32,000 structures deposited so far.

Today, many important biological processes can be understood at the level of the precise molecular interactions, because crystal structures of key proteins involved have been determined by X-ray crystallography. Examples of these include the recognition of foreign antigens by antibodies and lymphocyte receptors of the immune system, the binding of viruses, such as HIV, to specific cellular receptors in the human host, the interactions between critical hormone and hormone receptors such as estrogen and insulin, the altered structures of key proteins that promote tumour formation in specific cancers, and binding of antibiotics to the receptor site of the bacterial ribosome.

The basis of structure-based, rational drug development is the availability of co-crystal structures of target proteins, complexed with chemically synthesized small molecule drug candidates. These co-crystal structures are used to help define the critical interactions of designed inhibitors on target molecules in the most efficient manner and at the highest resolution possible. The structural information is then used by medicinal chemists to plan and execute the synthesis of new compounds with improved properties; these are then subjected to structural analysis in subsequent rounds of drug design cycles. It is usually necessary to analyze dozens or hundreds of co-crystal structures of lead compounds bound to a protein target in order to be able to develop rationally an effective inhibitor (potential drug) against the protein target. This translates into a need for the analysis of thousands of crystals. Arguably, the largest single project of this kind was the development of the inhibitors of the HIV protease and HIV reverse transcriptase that led to revolutionary new treatments for HIV infections and AIDS. Other prominent examples of drugs that have evolved from structure-based drug design methods include those to fight influenza (neuraminidase inhibitors), hypertension (renin inhibitors), arthritis (Cox2 inhibitors), prostrate cancer (thymidylate synthase inhibitors) and carbonic anhydrase II inhibitor dorzolamide, the first topical treatment for glaucoma.

Today the high-intensity X-rays available at modern synchrotron sources have become an indispensable tool for protein crystallography. Virtually all crystallographic experiments on proteins and other biological macromolecules are conducted at synchrotron facilities. The resulting data are of superior quality and the experiments can be performed much faster. At present synchrotron data collection requires travel by the researchers to the synchrotron facility which is cumbersome, results in time delay between the conception and the execution of the experiment and leads to inefficient use of the valuable time at the synchrotron facility. The plan of the Canadian structural biology community is to develop experimental facilities at the CLS that can be accessed via dedicated research networks allowing researchers to submit their crystals to the CLS via FedEx, screening them, planning experiments, downloading the resulting diffraction data on their home computers and in special cases performing remote data collections.

The Canadian structural biology community is developing experimental facilities at the Canadian Light Source (CLS) synchrotron in Saskatoon. The current End-to-end Lightpaths to Synchrotrons CANARIE project AAP-29 delivers greatly improved access to CLS for researchers in Alberta by leveraging CANARIE User Controlled Lightpaths (UCLP), regional ORANs Netera and SRnet, and BigBangwidth's products. AAP-29 allows researchers to see their research data as it is collected and control experiments from a distance. This reduces their need to travel to the synchrotron, and results in better access and more efficient use of the CLS facility.

The new project will:

1. Extend UCLP Lightpath access to the Canadian Light Source (CLS) protein crystallography beamlines to more researchers across Canada. This first goal is an extension of AAP-29 to other provinces by UCLP and to replace the loaned equipment at CLS with permanent equipment.

2. Provide an SOA-based Synchrotron Collaboration and Scheduling System to aid with resource scheduling and file sharing for protein crystallography beamline users and shared infrastructure with CIIP-15. The second goal compliments the first by allowing remote researchers to use the synchrotron as efficiently and effectively as possible. Synchrotron Collaboration and Scheduling System, "SCSS" Currently, access to synchrotron beamlines is governed by a manual system of proposals, review committees, and time scheduling. Researchers typically gather data at a beamline during intensive sessions that may last 2 or 3 24-hour days. SCSS is a web-services based workflow system that automates the submission and tracking of beamline time requests. SCSS does not replace human involvement in granting beamline time, but it automates the manual flow of paper. SCSS also manages opportunistic beamline requests. This mode of beamline scheduling is not possible if researchers have to fly to the synchrotron, but networked remote beamline access would make it possible. It will also become feasible for a remote researcher to use one or two spare hours of beamline time. The result is that more science can be done, and the synchrotron is used more efficiently. Finally, SCSS automates collaborative file sharing by automatically synchronizing data between collaborating researchers. Researchers can graphically drag-and-drop data repository icons to indicate a collaborative relationship, and the SCSS system will keep the data in those repositories synchronized across UCLP even though they may contain terabytes of data.

VESPERS

VESPERS (VEry Sensitive Elemental and Structural Probe Employing Radiation from a Synchrotron) is an X-ray microscope that is slated for opening at CLS in late 2006. This instrument will have the power to detect the most minute changes in the crystal structure of solid materials; in addition, the microscope can simultaneously reveal the elemental compositions of these structures with detection sensitivities usually extending to parts per million concentrations or less. A VESPERS facility offers immense possibilities for application in fields such as metallurgy, materials science and geochemistry. In particular, we see clear applications in important Canadian industrial sectors of mining and mineral recovery, power generation and specialty metals production. We need VESPERS to be accessible, remotely, in real time, for a significant portion of its operating time. This objective is almost without parallel in the synchrotron community; if achieved, it could profoundly change the culture by which science is delivered to its practitioners by synchrotrons worldwide. Until now, almost all synchrotron users needed to physically be in place at a synchrotron end station in order to carry out an experiment. Therefore, most individual experimental sessions are measured in numbers of days and are booked weeks in advance. In a country like Canada, geography is a particularly strong limitation to the type of access that a facility of this investment needs.

The proposed project has several stages, beginning with the bootstrap design of all software to control a hard x-ray fluorescence and diffraction beamline, called VESPERS now under design at the CLS. This software would be written to allow control of the beamline using the same protocols whether the user is in a remote locale or is stationed right at the CLS itself. The finished system would be first tested off-line using many of the experimental control devices that would be later employed in the actual synchrotron beamline experiments. Following these simulation tests, actual remote beamline control experiments would then be established through a laboratory site at the University of Western Ontario that would serve as a central locale for users wishing to control experiments at CLS from western Ontario. Subsequently, remote control from facilities in Canada and Australia would be demonstrated. The University of Adelaide, as part of this project, would concentrate on developing on-line data analysis and 3-D visualization software. To support remote operation a series of web services needs to be developed that permit the tracking and management of beamline user samples and experiment by experiment scheduling. For more advanced users who have the experience to be able to define experiment setup procedures in advance, the system would be designed to accommodate the queuing of experiments that are then run when the beamline is otherwise idle.

This remote access capability will not only involve remote control of the facilities for designated users, but also the instant sharing of data and results between members of an academic experimental team or within a group of industrial specialists. By adding integration with the beamline scheduling and workflow software, the added benefit that beam-time can be more efficiently allocated results in more effective use of time on the beamline. Many of the benefits associated with this solution are not solely dependent on making the actual instrumentation available remotely, but also through the benefits of removing travel requirements, more efficient scheduling and collaboration, and lower costs for the experiment team.

Service Oriented Architectures

Service oriented architectures (SOA) enable flexible, modular applications to be constructed from heterogeneous systems. The key to this flexibility is the creation of coarse-grained building blocks known as services. These self-describing groupings of data and/or function can be combined and recombined in multiple configurations as business requirements change. The standard abstractions used within an SOA mean that the underlying programming language, operating system, geographical location and organizational ownership are not important. Web services are an example of an SOA. The key interaction in a SOA is the binding of a service requester to a service provider. This may be supported by publication of the service description to a directory by the service provider, and a discovery of the service by the service requester.

WebSphere Application Server provides excellent support for Web services. WebSphere Business Integration Server Foundation adds to this capability by providing the powerful service composition and dynamic invocation capabilities of WebSphere Process Choreographer. This can be used as a service integrator to combine a series of diverse existing services as a single service which is of use in the modernized systems.

WebSphere Studio Application Developer Integration Edition provides visual tools to create business processes. This allows business users and developers to collaborate when creating business processes, enabling rapid prototyping, development and deployment of code that fits the needs of the business.

Contact Elder Matias to learn more about control and instrumentation at the Canadian Light Source.

Last modified: 2009-10-05 14:10:23