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
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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
