Collaboratory for Multi-scale Chemical ScienceCollaboratory for Multi-scale Chemical Science

Abstract

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.

SciDAC PI MeetingCharleston, SC March 22-24, 2004

CMCS TeamThomas C. Allison,6 Sandra Bittner,3 Brett Didier,2

Michael Frenklach,8 William H. Green, Jr.,7 Darrian Hale,1

Mihael F. Hategan-Marandiuc,3 Carina Lansing,3 Gregor von Laszewski,3 David Leahy,1 James D. Myers,2

Michael Minkoff, 3 David Montoya,5 Luwi Oluwole,7 Carmen Pancerella,1 Reinhardt Pinzon,3 William Pitz,4

Larry Rahn,1 Jane Riese,5 Branko Ruscic,3 Karen Schuchardt,2 Albert F. Wagner,3 Theresa Windus,2

Christine Yang,1 and Ginger Young5

X (cm)

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Chemical Science Application AreasSciDAC Reacting Flow Simulations

Detection and tracking of features in large-scale simulation data sets for BES SciDAC reacting flow simulations

Contact: David Leahy, SNL

PrIMe: Process Informatics ModelInternational collaboration for generation

of predictive kinetic models based on the best current experimental and theoretical data

Contact: Michael Frenklach, UCB

Chemical Model ReductionWeb-service hosted for computational

reduction of chemical models against specific ranges of validity

Contact: Bill Green, MIT

HCCI Consortium A Multi-University Consortium formed to

address Homogenous Charge Compression Ignition (HCCI) Engines

Contact: Bill Pitz, LLNL

IUPAC 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, ECCEContact: Theresa Windus, PNNL

Real Fuels Chemistry NIST project on chemistry of realistic fuelsContact: Tom Allison, NIST

http://cmcs.org

CMCS ObjectivesArchitect and build an adaptive informatics

infrastructure enabling multi-scale scienceXML data/metadata management servicesChemical Science Portal enabling data-centric project- and

community-level collaborationMiddleware and tools for security, notification, collaboration

Pilot project within combustion research communityEnable 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 toolsDevelop collaborative data pedigree/annotation toolsExplore and develop a prototype ‘knowledge grid’ capability

Gain adoption and continued support by science community participation

Document success and continuation path

The Multi-scale ChallengeImpact of Chemical Science relies upon flow of

information across many physical scalesData from smaller scales supports models at larger scalesNew knowledge is assimilated from different data and tools

at each scaleCritical science lies at scale interfaces

Molecular properties, transportValidated chemical mechanisms, reduced mechanismsChemistry - 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 mattersThe propagation of data pedigree across scales is difficultData is validated and annotated in post-publication

processes

Multi-scale science faces barriersNormal publication route is slowData and meta-data are not easily available Incompatible data formats and undocumented metadata

thwart information exchangeThe researchers and facilities involved are distributed

geographically and among multiple disciplinesComplexity of multi-scale science can lead to unnecessary

duplication and impede investment of research dollars

REACTIONLAB

1Sandia National Laboratories, Livermore, CA 2Pacific Northwest National Laboratory, Richland, WA 3Argonne National Laboratory, Argonne, IL4Lawrence Livermore National Laboratory, Livermore, CA5Los Alamos National Laboratory, Los Alamos, NM6NIST, Gaithersburg, MD7Massachusetts Institute of Technology, Cambridge, MA8University of California, Berkeley, CA

CMCS Development PartnershipsCIENTIFIC

NNOTATION

IDDLEWARE

SAM

CMCS is Funded by

National Collaboratory Program

Java Storage Interface

JDBC FilesystemXML conf.

JDBCGridFTP

DAV/DASLNotebookServices

JMS

ExternalSecuritySecurity

BFD

SOAP

XSLT

Processing

Client API ELN API Subscriber

WebService

Metadatageneration/translation

Configurablesecurity

framework

SAM APIs/Interfaces/Components

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

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

Resource Name: CH3OOqueryResult.xmlTitle: ATcT Thermochemistry Data Table for Methylperoxy radicalCreation Date: 2003-11-10 Creator: Branko Ruscic Contributors: Reinhardt Pinzon, Albert F. Wagner, Melita L.Morton, Gregor von Laszewski, Sandra Bittner, Sandeep NijsureKeywords: Thermodynamics, molecule, species MIME Type: text/xml-activetables-thermochemistry

Text Whiteboard Sound Equations

Plot View (text/html)

JANAF format (text/plain)

O Atom Reference – ATcT AtomicLexicon in MainLibrary (1.027)

ATcT Bibliography in Main Library (1.027)

ATcT NetworkEncyclopedia

ATcT SpeciesDictionary

hastranslations

hasinputs

IUPAC

issanctionedby

references

ATcT PolyatomicRRHOLexicon

pitzNotesBibliography

references

ATcT PreferredEnthalpiesCompendium

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.

Web-based standards make tools and resources available to collaborators

Annotations

CMCS Metadata Structure

ProvenanceRelationships

Content

Metadata

Chemical Science Informatics Architecture