Scientific Annotation Middleware (SAM)

Principal Investigator:

Jim Myers, National Center for Supercomputing Applications

Co-Investigators:

Tara Talbott, Pacific Northwest National Laboratory,

Jens Schwidder, Oak Ridge National Laboratory

Michael Peterson, Pacific Northwest National Laboratory,

Al Geist, Oak Ridge National Laboratory

Abstract

We propose the creation of a Scientific Annotation Middleware (SAM) system that will provide the significant advances in research documentation and data pedigree tracking required for effective management and coordination of the complex, collaborative, cross-disciplinary, compute-intensive research enabled through the Scientific Discovery through Advanced Computing (SciDAC) initiative. The proposed system presents researchers, applications, problem-solving environments (PSE), and software agents with a layered set of components and services that provide successively more specialized capabilities for the creation and management of metadata, the definition of semantic relationships between data objects, and the development of electronic research records. Researchers will access the system through a notebook interface, available via desktop computers and mobile devices, as well as through SAM components embedded in other software systems. SAM will support manual and programmatic queries across entries generated by these multiple sources. This research, performed by the same team that created the very successful DOE2000 electronic notebook project, will lead to fundamentally new and more complete, effective, and efficient ways to document the scientific work performed in SciDAC and across DOE.

Additional Project Information:

Executive Summary

Technical Overview

Project Management Plan

Coordination With Other Projects

Software Engineering Plan

Deliverables

Current Status - March 2005 Quarterly Report

SAM version 2.1 Release March 28, 2005 - the fourth public release of SAM software incorporates improved search capabilies using DAV, optional fully web-based ELN client and migration to Jakarta Slide 2.1 codebase. (see link for details and download)

SAM version 2.0 Release September 1, 2004 - the third public release of SAM software incorporating data/metadata and enhanced electronic notebook functionality as well as preview capabilitiesrelates to provenance, security, and notarization (see link for details and download)

NEW: Adapting the Electronic Laboratory Notebook for the Semantic Era, CTSPresentation2005.ppt, Tara Talbott, Michael Peterson, Jens Schwidder, and James D Myers, Proceedings of the 2005 International Symposium on Collaborative Technologies and Systems (CTS 2005), May 15-20, 2005, St. Louis, MO

NEW: Bootstrapping to a Semantic Grid, Jens Schwidder, Tara Talbott, and James D Myers, Proceedings of the Semantic Infrastructure for Grid Computing Applications Workshop at IEEE/ACM International Symposium on Cluster Computing and the Grid CCGRID 2005 May 9-12, 2005, Cardiff, UK

A Collaborative Informatics Infrastructure for Multi-scale Science (pdf), James D. Myers, Thomas C. Allison, Sandra Bittner, Brett Didier, Michael Frenklach, William H. Green, Jr., Yen-Ling Ho, John Hewson, Wendy Koegler, Carina Lansing, David Leahy, Michael Lee, Renata McCoy, Michael Minkoff, Sandeep Nijsure, Gregor von Laszewski, David Montoya, Carmen Pancerella, Reinhardt Pinzon, William Pitz, Larry A. Rahn, Branko Ruscic, Karen Schuchardt, Eric Stephan, Al Wagner, Theresa Windus, Christine Yang, Proceedings of the Challenges of Large Applications in Distributed Environments (CLADE) Workshop, June 7, 2004, Honolulu, HI, pp. 24-33

Electronic Notebooks: An Interface Component for Semantic Records Systems (ppt), James D. Myers, Michael Peterson, K Prasad Saripalli, Tara Talbott, 227th American Chemical Society (ACS) National Meeting, Anaheim, CA, March 28-April 1, 2004

Adaptive Informatics Infrastructure for Multi-scale Chemical Science (ppt), James D. Myers, Larry Rahn, David Leahy, Carmen Pancerella, Gregor von Laszewski, Branko Ruscic, William H. Green, Jr., 227th American Chemical Society (ACS) National Meeting, Anaheim, CA, March 28-April 1, 2004

Re-Integrating The Research Record, James D. Myers, Alan R. Chappell, Matthew Elder, Al Geist, Jens Schwidder, Computing in Science and Engineering, May/June 2003, pp 44-50

Multi-Scale Science:Supporting Emerging Practice with Semantically Derived Provenance, James D. Myers, Carmen Pancerella, Carina Lansing, Karen L. Schuchardt, and Bret Didier, Proceedings of the Semantic Web Technologies for Searching and Retrieving Scientific Data Workshop, Sanibel Island, FL, Oct 20, 2003

Binary Format Description (BFD) Language and Tools

Draft/Evolving Requirements and Implementation Plan for public comment

Overview Presentation (.ppt)