Status as of December, 2004 / Quarterly report (cumulative since June 30 2004)

Project Staff

James Myers, Tara Talbott, Jens Schwidder, Al Geist, Mike Peterson, Alan Chappell, Carina Lansing

Progress

Since the last report, the SAM team has delivered a SAM 2.0 release incorporating key enhancements including

• single sign-on capabilities,
• simplified administration,
• increased notebook/portal integration,
• web-service-based metadata extraction and data translation capabilities, and
• enhanced performance.

In addition, work to internationalize the Electronic Laboratory Notebook (ELN) client has been completed as part of a subcontract from the NSF-sponsored George E. Brown, Jr. National Earthquake Engineering and Simulation Grid (NEESgrid) project. The ELN now supports locale-dependent labels in menus and on buttons and allows entry of textual notes in any desired language.

Additional capabilities, in particular, an extended grammar for the DAV Searching and Locating (DASL) protocol allowing semantically scoped searches, and support for upload of specific byte ranges within resources (versus replacing the entire file), have been developed in this period and are being pilot tested within the Collaboratory for Multiscale Chemical Science.

Complementing this work were a large number of community interactions at major conferences and workshops including the DOE National Collaboratories Workshop Series, SuperComputing 2004, and the W3C "Semantic Web for Life Sciences" Workshop.

Design/Development Activities

• Semantic Grid: Work is continuing on the detailed design of SAM's Semantic Services (SS) layer and Semantic Grid concepts. A semantically-scoped search capability accessible via WebDAV's Distributed Searching and Locating (DASL) search mechanism has been developed. It is anticipated that the CMCS project will begin using this capability to provide flexible provenance-based queries in the next quarter. At the conceptual level, the work in this area is feeding into activities such as the DOE Data Management Workshop series, DOE COllaboratory Workshops, the GGF Semantic Grid Research Group, and proposal development. The RDF pedigree/provenance property, which includes reified information concerning the software used to generate derived data, has been temporarily ported to the SAM 2.0 framework (based on Jakarta Slide 2.0). The provenance capability is currently being generalized and incorporated into SAM's extension of the DASL basic grammar.

• Data Format Description Language (DFDL):Work is continuing to design a standard for a language that can describe the content of arbitrary data files. The Grid Forum DFDL working group is very active and is currently developing an XML Schema-related syntax for the DFDL language. Examples forming a set of 'unit tests' and 'integration tests' have been developed and will drive the specification. The SAM team is very involved in crafting the standard and is contributed significant concepts that derive from the developed of the BFD language and its extensions within the SAM project. As the language nears standardization, the SAM team will be investigating design options for building a DFDL parser. Interest in DFDL is growing - as a technology for persistent archiving of arbitrary data, and as a grid data virtualization mechanism.

• SAM Notebook Services Layer: Building on work to refactor the transitional ELN notebook support within SAM to create a high-level notebook services API, ORNL has migrated the DOE2000 eNote notebook to use SAM services. Over the next few months, work will be done to generalize the existing notebook service layer and data model which will provide a migration path for eNote users and will be leveraged in the development of web-based SAM annotation and notebook interfaces.

Community Outreach

SAM team members participated in a wide range of meetings, workshops, reviews, and collaboration discussions during this quarter:

• Presentations

  • The Scientific Annotation Middleware Project, James Myers, DOE National Collaboratories PI Meeting, Aug. 9-12, 2004, Argonne, IL
  • Fine-grained References into Binary Data and Data Virtualization Services, James Myers, W3C Semantic Web for Life Sciences Workshop, October 26-28, 2004, Cambridge, MA
  • Middleware for Scientific Portals, Jens Schwidder, Al Geist, James Myers, Tara Talbott, Michael Peterson, InterLab 2004, October 27-29, 2004, Oak Ridge, TN
  • Standardizing Format Descriptions, James Myers, Partnerships in Innovation - Serving a Networked Nation Workshop, November 15-16, 2004, National Archives and Records Administration, College Park, MD

• Conferences/Workshops/Meetings

  • DOE Data Centers: Preparing for the Future Workshop, July 14-15, 2004, Oak Ridge, TN - Complimenting the earlier DOE Data Management Workshop series, which focused on data management R&D, this workshop focused on policy and funding issues related to the growing number of DOE funded persistent data repositories.
  • DOE National Collaboratories PI Meeting, Aug. 9-12, 2004, Argonne, IL - This meeting focused on identifying new areas for collaboratory research where requirements for next generation science aligned with promising collaboratory R&D directions. SAM and CMCS team members contributed to the discussion and the published workshop report.
  • NSF Chemistry Division Workshop on Cyber-Enabled Chemistry, October 3-5, Washington, DC - The workshop provided recommendations to the NSF Chemistry Division on the promises and challenges in harnessing cyberinfrastructure in the chemistry community. CMCS and SAM, and the Virtual NMR Facility were discussed and cited in the workshop report.
  • W3C's Semantic Web for Life Sciences Workshop, October 27-28, 2004, Cambridge, MA - This meeting featured a wide ranging discussion of current and planned uses of Semantic Web technologies in the life sciences as well as discussion of ways to promote adoption/remove barriers to semantic web use in the life sciences. In his talk and through discussion, Jim Myers presented the Data Format Description Language as a potential mechanism for extending naming schemes inside files, e.g. making it possible to name a particular cell in an file containing data from a whole microarray with a persistent name such that the cell could be referenced in semantic statements. Further, the ability of webDAV to associate metadata with any URL was used to argue for a similar protocol-level capability in the Semantic Web. The latter in particular is relevant to the larger discussion at the workshop of the pros and cons of the Life Science Identifier (LSID) protocol. (The LSID discussion continues on the public-semweb-lifesci@w3.org mailing list.) Position papers submitted to the workshop are available from the workshop website, as is the workshop report.
  • SuperComputing ’04, November 7-12, 2004, Pittsburg, PA - The SAM project was represented in posters, presentations, and demonstrations in the Argonne, Oak Ridge, and Pacific Northwest National Laboratory booths.
  • Partnerships in Innovation - Serving a Networked Nation Workshop, November 15-16, 2004, National Archives at College Park, MD - Jim Myers presented the Data Format Description Language (DFDL) as a mechanism for data preservation, allowing data to be read and interpretted without requiring a working copy of the originating program, as part of a panel on Grid Technologies: Foundations for Preservation Environments.
  • Opportunities for Distributed Science: A National Collaboratories Program Workshop, December 1-3, 2004, Boulder, CO - This workshop connected goals of next-generation research across many scientific disciplines to underlying information technology requirements and began organizing these into a potential plan for future collaboratory and grid research and development.
  • Data Format Description Language (DFDL) Working Group Meeting, December 6-7, 2004, Los Gatos, CA - Jim Myers and Alan Chappell attended to present work towards defining the DFDL syntax and to participate in moving the standard forward.

• Publications

  • National Collaboratories Horizons Report of the August 10-12, 2004, National Collaboratories Program Meeting Conducted by the Office of Advanced Scientific Computing Research of the U.S. Department of Energy Office of Science
  • CHE Cyber Chemistry Workshop Report, Washington, DC, October 3-5, 2004

• Collaborations/Community Activities

  • Collaboratory for Multiscale Chemical Science (CMCS): An ongoing collaboration related to the use of SAM as the primary CMCS data/metadata management system. CMCS and SAM are currently collaborating on performance enhancements, porting CMCS to SAM 2.0/2.1, adopting semantic search capabilities, and general hardening.

  • Network for Earthquake Engineering and Simulation (NEES) Grid: PNNL has completed a subcontract from the NEESgrid project. This effort focused on integration of the ELN and SAM with the NEESgrid portal, security mechanism, and metadata/data repository, and internationalization of the ELN (support for alternate languages for the labels used within the ELN user interface, and the ability to enter textual notes in alternate languages). All software from this project has been incorporated in to the standard SAM and ELN distributions. The ELN and SAM have been incorporated into the NEESGrid 3.2 Release.

  • Web Downloads Registrations to download SAM and notebook software are continuing at a pace of 1-2 per day.

  • International Conference on Semantics for a Networked World, with a focus on Grid Databases: Jim Myers was invited to serve on the Program Committee for this conference, which was held July 17-19, 2004, Paris, France.

  • GridSem 2004, 1st International Workshop on the Semantic Grid, Jim Myers was invited to serve on the program committee for this conference, which was held August 23-24, Valencia, Spain.