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CIENTIFIC NNOTATION IDDLEWARE. S A M. Client API. ELN API. Subscriber. DAV/DASL. Notebook Services. JMS. Metadata generation/ translation. BFD. Configurable security framework. Processing. SOAP. Web Service. External Security. Security. XSLT. Java Storage Interface. JDBC.

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Client API
















Java Storage Interface





Web-based standards make tools and resources available to collaborators

  • Browser accessible graphical user interface for access to resources and visualization
  • Community tools – group formation, announcements, chat, threaded discussion, calendar, task list management
  • Portlet structure accommodates knowledge management too, research applications, and other specialized portal functions

Text Whiteboard Sound Equations

SAM APIs/Interfaces/Components

This diagram represents the major conceptual elements of the CMCS Informatics Infrastructure. A portal serves as the web interface for scientists and is powered by the CHEF Architecture shown on the left. Other web interfaces enable remote web services as well as direct access to data from desktop clients. The shared data services infrastructure takes advantage of a variety of standards and open-source technologies. This infrastructure is powered by the Scientific Annotation Middleware also shown to the left.

  • Extends Jakarta Slide, uses OpenJMS, Jaxen, JDOM, COG
  • Supports WebDAV protocol standards for data/metadata access, search, …
  • Supports external authentication and authorization mechanisms
  • Data Store interface allows data/metadata to be stored in files, relational DBs, DataGrids, …
  • Client-side protocol, API, and component-level interfaces

Collaboratory for Multi-scale Chemical Science

Chemical Science Application Areas

The Multi-scale Challenge

  • Impact of Chemical Science relies upon flow of information across many physical scales
    • Data from smaller scales supports models at larger scales
    • New knowledge is assimilated from different data and toolsat each scale
    • Critical science lies at scale interfaces
      • Molecular properties, transport
      • Validated chemical mechanisms, reduced mechanisms
      • Chemistry - turbulence interactions
    • Impact through industrial application is mostlyat larger scales, but industrial R&D draws on all scales
  • Multi-scale information is complex and its pedigree matters
    • The propagation of data pedigree across scales is difficult
    • Data is validated and annotated in post-publication processes
  • Multi-scale science faces barriers
    • Normal publication route is slow
    • Data and meta-data are not easily available
    • Incompatible data formats and undocumented metadata thwart information exchange
    • The researchers and facilities involved are distributed geographically and among multiple disciplines
    • Complexity of multi-scale science can lead to unnecessary duplication and impede investment of research dollars


Thomas C. Allison,6 Sandra Bittner,3 Brett Didier,2 Michael Frenklach,8William H. Green, Jr.,7 Darrian Hale,1 Mihael F. Hategan-Marandiuc,3Carina Lansing,3Gregor von Laszewski,3 David Leahy,1 James D. Myers,2 Michael Minkoff, 3 David Montoya,5 Luwi Oluwole,7Carmen Pancerella,1 Reinhardt Pinzon,3 William Pitz,4 Larry Rahn,1 Jane Riese,5 Branko Ruscic,3Karen Schuchardt,2 Albert F. Wagner,3 Theresa Windus,2 Christine Yang,1 and Ginger Young5

SciDAC Reacting Flow Simulations

  • Detection and tracking of features in large-scale simulation data sets for BES SciDAC reacting flow simulations
  • Contact: David Leahy, SNL

Chemical Model Reduction

  • Web-service hosted for computational reduction of chemical models against specific ranges of validity
  • Contact: Bill Green, MIT

1Sandia National Laboratories, Livermore, CA

2Pacific Northwest National Laboratory, Richland, WA

3Argonne National Laboratory, Argonne, IL

4Lawrence Livermore National Laboratory, Livermore, CA

5Los Alamos National Laboratory, Los Alamos, NM

6NIST, Gaithersburg, MD

7Massachusetts Institute of Technology, Cambridge, MA

8University of California, Berkeley, CA

PrIMe: Process Informatics Model

  • International collaboration for generation of predictive kinetic models based on the best current experimental and theoretical data
  • Contact: Michael Frenklach, UCB



The goal of the CMCS project is to enable chemical scientists to conquer barriers to rapid sharing of validated information and open new paradigms for multi-scale science. The emerging vision for meeting these requirements is a chemical science ‘knowledge grid,’ which incorporates advances being made in semantic web, informatics, collaboratory, and grid communities. This is being accomplished by developing and publicly deploying an adaptive informatics infrastructure that integrates a set of key collaboration tools, chemistry-specific applications, data resources, and services, such as a Chemical Science Portal enabling data-centric project- and community-level collaboration, XML data/metadata management services enabling annotation and data discovery, and tools for security, notification, and collaboration. The CMCS environment is currently used by several pilot groups in the combustion research community and other areas of chemistry. The capabilities of CMCS, together with several new scientific results enabled by CMCS were showcased at SC02 and SC03.

HCCI Consortium

  • A Multi-University Consortium formed to address Homogenous Charge Compression Ignition (HCCI) Engines
  • Contact: Bill Pitz, LLNL

Real Fuels Chemistry

  • NIST project on chemistry of realistic fuels
  • Contact: Tom Allison, NIST

CMCS Objectives

  • Architect and build an adaptive informatics infrastructure enabling multi-scale science
    • XML data/metadata management services
    • Chemical Science Portal enabling data-centric project- and community-level collaboration
    • Middleware and tools for security, notification, collaboration
  • Pilot project within combustion research community
    • Enable rapid exchange of multi-scale data/pedigree
    • Integrate chemical science tools that generate, use and archive metadata
  • Demonstrate the power of adaptive infrastructure to existing and new areas as CMCS evolves
    • Development environment for an evolving set of collaborative cross-scale science tools
    • Develop collaborative data pedigree/annotation tools
    • Explore and develop a prototype ‘knowledge grid’ capability
  • Gain adoption and continued support by science community participation
  • Document success and continuation path


  • International Union of Pure & Applied Chemistry Task Group on Thermochemistry of Radicals
  • Contact: Branko Ruscic, ANL

Quantum Chemistry

  • BES SciDAC Chemistry, EMSL Chemistry Program, NW Chem, ECCE
  • Contact: Theresa Windus, PNNL

Chemical Science Informatics Architecture

CMCS Metadata Structure


Resource Name: CH3OOqueryResult.xml

Title: ATcT Thermochemistry Data Table for Methylperoxy radical

Creation Date: 2003-11-10

Creator: Branko Ruscic

Contributors: Reinhardt Pinzon, Albert F. Wagner, Melita L.Morton, Gregor von Laszewski, Sandra Bittner, Sandeep Nijsure

Keywords: Thermodynamics, molecule, species

MIME Type: text/xml-activetables-thermochemistry







O Atom Reference – ATcT AtomicLexicon in MainLibrary (1.027)

Plot View (text/html)

ATcT Bibliography in Main Library (1.027)

JANAF format (text/plain)

ATcT PolyatomicRRHOLexicon



ATcT NetworkEncyclopedia

ATcT SpeciesDictionary



ATcT PreferredEnthalpiesCompendium


CMCS Development Partnerships

CMCS is Funded by

SciDAC PI MeetingCharleston, SC March 22-24, 2004

National Collaboratory Program