Collaboratory for Multiscale Chemical Sciences CMCS New Informatics Capabilities for CHEMKIN users

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Collaboratory for Multi-scale Chemical Sciences
(CMCS) New Informatics Capabilities for CHEMKIN
users

• David Leahy and Larry Rahn
• Sandia National Laboratories
• Combustion Symposium 2004
• University of Illinois at Chicago
• July 25, 2004
• http//cmcs.org

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Outline

• Multi-Scale, Multi-Domain Science Challenges
• The Collaboratory for Multi-Scale Sciences
  (CMCS)
• An adaptive informatics infrastructure
• Data and Metadata Services
• Examples
• Related projects
• Conclusions and Future Work

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Combustion is a Multi-scale Chemical Science
Challenge

• Science relies upon validated of information
  shared across physical scales
• New knowledge is assimilated from different data,
  tools, and disciplines at each scale
• Critical science lies at scale interfaces
• Impact through industrial application is mostly
  at larger scales
• Multi-scale scientific collaboration faces
  barriers
• Normal publication route is slow and excludes
  much important data
• Multi-scale information is complex and its
  pedigree associated metadata matters
• New approaches to developing and sharing
  trustworthy data are needed
• Community resources are highly distributed
• Complexity of multi-scale science can lead to
  unnecessary duplication and impede investment

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Challenge Multi-scale science takes too long
Industrial researcher
Peer Reviewed Publication
Autoignition not predicted by chemical mechanism
NIST review Publish in data base
Evaluation Need Thermochemistry for new radical
New Mechanism developed, validated
Read paper
Peer Reviewed Publication
Conference Presentation
Evaluation Need computational data, collaborate
with Quantum Chemist
Peer Reviewed Publication of new radical
thermochemistry
Peer Reviewed Publication of computation
1 year
Time
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Shared repository speeds multi-scale communication
Industrial researcher accesses new mechanism
Peer Reviewed Publication
NIST review, Publish in data base
Annotation autoignition not predicted by
chemical mechanism
Notification New Mechanism developed, validated
Notification Results in decision to develop new
mechanism
Peer Reviewed Publication
Publicly Shared Data Repository
Parsers Translators Annotators
NIST Repository
Conference Presentation
Peer Reviewed Publication of new radical
thermochemistry
Evaluation Need computational data, collaborate
with Quantum Chemist
Peer Reviewed Publication of computation
1 year
Time
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Collaboratory for Multi-scale Chemical Science
(CMCS)

• A collaboration of 8 national labs and
  universities
• Chemical scientists spanning the scales from
  electronic structure of molecules to simulations
  of reacting flow
• Computer and information scientists expert in
  emerging web-based technologies
• Funded by DOE/SC MICS office
• Part of the National Collaboratory Program
• Pilot project within DOE combustion research
  community
• In our third year, renewed through 2008
• Targets Chemical Science Community and BES SciDAC
  projects with much broader goals in the longer
  term

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Multi-disciplinary CMCS Team
SNL - Larry Rahn, Christine Yang, Carmen
Pancerella, David Leahy, Darrian Hale PNL -
Brett Didier, James D. Myers, Karen Schuchardt,
Theresa Windus, Carina Lansing ANL - Al Wagner,
Branko Ruscic, Gregor von Laszewski, Reinhardt
Pinzon, Kaizar Amin LLNL- William
Pitz LANL- David Montoya, Rick Knight NIST-
Thomas C. Allison MIT - William H. Green, Jr.
, Luwi Oluwole UCB - Michael Frenklach
denotes Institutional Point of
Contact CMCS Development Partnerships
SAM
National Collaboratory Program
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Goal of CMCS
New forms of data sharing, pedigree
annotation New Paradigms for collaborative
research

• Enhance chemical science research by
  providing an adaptive informatics infrastructure
  with an integrated set of collaboration tools,
  data management tools, and chemistry-specific
  applications, data resources.

Increased access to state-of-the-art research
knowledge More rapid and efficient multi-scale
scientific progress
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CMCS Approach

• Pilot in combustion science to enable
  data-centric collaboration knowledge grid
• Develop Portal supporting collaboration,
  community evaluation, knowledge management, and
  research tools
• Innovate approaches to capture and present
  metadata, annotation, and semantic information
• Enable data translation and data interoperability
• Emphasize lightweight just-in-time integration,
  aspect-oriented design, open source, Web/grid
  standards, technologies

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Reacting Flow Modeler
Thermo-chemist
Thermo-dynamics Application
CHEMKIN Application
XML-based Web technologies enable data
interoperability, metadata capture, annotation
Thermo- dynamics Data base
Thermo data
Kinetics data
Parsers Annotators Translators
Parsers Annotators
Shared Data Repository Distributed Authoring and
Versioning (WebDAV) protocol
Annotation
Annotation
Annotation

XML Thermo- dynamics Data Set
XML Kinetics Data Set
XML Transport Data Set
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CMCS Informatics

• Infrastructure Capabilities
• Collaboration
• Data/metadata management
• Annotation
• Translation
• Visualization
• Notification
• Search
• Security

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CMCS Pilot User Groups

• HCCI University Consortium Bill Pitz (LLNL)
• DNS Feature Tracking Detection David Leahy
  and Larry Rahn (SNL)
• Reduced Chemical Mechanisms Bill Green (MIT)
• PrIMe led by Michael Frenklach (UCB)
• NIST/PrIMe Data Warehouse
• PrIMe Library of on-demand chemistry models
• IUPAC led by Branko Ruscic (ANL)
• Develop and publish validated thermochemical data
• Real Fuels Project Wing Tsang and Tom Allison
  (NIST)
• Lead real fuels chemistry at NIST
• Quantum Chemistry Theresa Windus (PNNL)

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CMCS Pilot Databases, Applications

• LLNL Chemistry Database Bill Pitz (LLNL)
• Computational Result Database David Feller
  (PNNL)
• RIOT Reduced Chemical Mechanisms Bill Green
  (MIT)
• ReactionLab Michael Frenklach (UCB)
• Development and publishing chemical reaction
  models, interfaced with NIST/PrIMe Data Warehouse
• ATcT Active Thermochemistry Tables Branko
  Ruscic (ANL)
• Optimizes networks of thermochemical data
• Chemical Kinetics and Thermochemistry Database
  for High-Temperature Materials Synthesis Mark
  Allendorf (SNL)

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Integration of Applications Enabled by Flexible
Infrastructure
Browser
Active Table
Command line applications
Portlet API
Web service
Web service
CMCS/DAV API
XML/SOAP
Java Parser of ASCII data
Web service
XML/SOAP
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Translations in CMCS

• Extensible Stylesheet Language Transformation
  (XSLT)
• XML ? HTML for web viewing
• XML ? HTML for interactive applet tools
• XML ? ASCII formats for other programs
• Web Service Interface
• Command line web services, e.g. OpenBabel for
  Geometry translations
• Java interfaces for parsing ASCII or binary
  files, e.g. Chemkin ? XML

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Application Integration in CMCS

• Portlets interfaced to web services via XML/SOAP
• Active ThermoChemistry Tables (ATcT) Branko
  Ruscic (ANL)
• Range Identification Optimization Tool (RIOT)
  Bill Green (MIT)

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Shared Applications for Collaborative Data
Analysis
Thermochemical Active Tables (ATcT) functionality
available as a Web service accessible from an
enabled Project Team workspace in the CMCS
Portal.
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RIOT -- Reduced Kinetic Models Significantly
Reduce Cost Of Reacting Flow Simulations
11 reduced models plus the full model (model 0)
cover the 12,000 finite volumes
4x speed-up in 2-d laminar methane flame
simulation without loss of accuracy (Lu,
Bhattacharjee, Barton, Green, 2003)
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Disk-like Access to Data Using Desktop Clients
Example Lab View Application on Windows Desktop
LabView writes to Webdrive DAV Client
(http//www.southrivertech.com/) which deposits
data directly in CMCS archive.
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Shared Applications for Collaborative Data
Analysis
Thermochemical Active Tables (ATcT) functionality
available as a Web service accessible from an
enabled Project Team workspace in the CMCS
Portal.
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Data Translation and Visualization
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Summary

• CMCS provides a public data sharing collaborative
  workspace for chemists
• Modern XML technologies provide better ways for
  scientists to share knowledge
• Web-based interfaces for data and applications
• Metadata management
• Translations
• Visualization
• CMCS Pilot Groups are providing valuable feedback
  to the CMCS iterative development cycle

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CMCS Data/Metadata Philosophy

• Scientific metadata has meaning across chemical
  science domains
• Scientific data is generally opaque and can be
  somewhat meaning-free outside of a discipline
• Metadata must be understood and manipulated and
  formatted in a machine-comprehensible way
• We are not enforcing standards
• There is no schema that spans the scales the CMCS
  addresses
• Enforcing standards across multiple chemistry
  communities would not be pragmatic
• Enforcing standards would alienate scientists
• When and if standards exist
• CMCS provides a technological framework for
  standard adoption
• We encourage the community to develop, review and
  adopt standards
• We can map our scientific content to and from
  standards, as needed

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Chemical Science Data and metadata
?Hatomiz ( )
0

kcal/mol
CH3OOH
calculated, G3//B3LYP, T. Windus, more at
http//...
value and uncertainty
data
units kcal/mol
quantity enthalpy of atomization
species methylhydroperoxide, CAS 3031-73-0
temperature 0 K
calculated G3//B3LYP creator T. Windus using
Ecce more info http//avatar.emsl.pnl.gov8080/Ec
ce/.../CH3OOH/.../GxEnergy
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Scientific Data Provenance

• Data provenance (or data pedigree) -- where a
  piece
• of data came from and the process by which it
  arrived
• in the data repository is essential for the
  sharing of
• scientific or technical data
• Data provenance is the metadata that describes
  the
• datas context and provides a traceable path to
  its origin
• Provenance captures the identification of the
  data, the traceability of the data, possibly
  across scales and/or domains, as well as
  information about accuracy and sensitivity
• Provenance metadata is associated with CMCS
  resources (WebDAV protocol, XML annotation
  standards), and is browsable and searchable from
  the CMCS portal
• Pedigree may include the series of steps
  necessary to reproduce the data ? generalized
  workflow development, or virtual data
• Data is linked to projects, references, inputs,
  and outputs

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Metadata Title Active Tables Thermochemistry
Data Table for Methyl peroxy Contributors
Reinhardt Pinzon, Albert F. Wagner, Melita
L.Morton, Gregor von Laszewski, Sandra
Bittner, Sandeep Nijsure, Kaizar Amin, Baoshan
Wang Creation Date 2003-11-10 Creator
Branko Ruscic Keywords Thermodynamics,
molecule, species MIME Type text/xml-activetab
les-thermochemistry
Text
Whiteboard
Sound
Equations
CH3OOqueryResult.xml
references
hastranslations
O Atom Reference NASA7ElementsLexicon in
MainLibrary 0.004
Plot View (text/html)
JANAF format (text/plain)
Active Tables Bibliography in Main Library
(0.001)
hasinputs
PolyatomicRRHOLexicon
references
NetworkEncyclopedia
pitzNotesBibliography
FixedEnthalpiesCompendium
SpeciesDictionary
issanctionedby
Data Provenance Relationships as Graph
IUPAC
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Key Data/Metadata Management Components

• WebDAV -- Web Digital Authoring and Versioning
• Extension to HTTP for file management and
  collaborative file sharing on remote web servers
• Files/collections and properties (data about
  data)
• Methods GET, POST, PUT, COPY, MOVE, DELETE,
  MKCOL, PROPFIND, PROPPATCH , LOCK/UNLOCK, ACLs
• DASL (DAV Searching and Locating) -- search
  extension for DAV
• http//www.webdav.org
• SAM -- Scientific Annotation Middleware
• Built on top of WebDAV, in particular Jakarta
  Slide
• Automatic annotation and translation services
• Notifications (tied to email daemon in CMCS)
• Supports multiple perspectives, workflows, goals
• Different users and different applications
• Event enabled data/metadata repository
• Jim Myers, PNNL, P.I. http//www.scidac.org
  /SAM

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Sample Metadata from XML Data file

• ltdctitlegtActive Tables Elements
  Cookbooklt/dctitlegt
• ltdcdescriptiongtThis document contains standard
  thermochemical reference states for
  elements/isotopes.lt/dcdescriptiongt
• ltdccreatorgt
• ltrdfBaggtltrdfligtBranko Rusciclt/rdfligtlt/rdf
  Baggt
• lt/dccreatorgt
• ltdctermscreatedgt2003-04-06lt/dctermscreatedgt
• ltcmcsispartofprojectgt
• ltrdfBaggtltrdfligt
• ltcmcshref xlinktype"simple"
  xlinktitle"methylperoxyNotes (0.001)
  xlinkhref"/slide/files/projects/primeThermo/meth
  ylperoxyNotes"/gt
• lt/rdfligtlt/rdfBaggt
• lt/cmcsispartofprojectgt
• ltcmcshasinputsgt
• ltrdfBaggtltrdfligt
• ltcmcshref xlinktype"simple"
  xlinktitle"Active Tables Bibliography in Main
  Library (0.001)" xlinkhref"/slide/files/public/A
  ctiveTables/MainLibrary/"/gt
• lt/rdfligtlt/rdfBaggt
• lt/cmcshasinputsgt
• ltcmcsspeciescasgt
• ltrdfBaggtltrdfligt183748-02-9lt/rdfligtlt/rdfB
  aggt
• lt/cmcsspeciescasgt

Dublin Core Metadata Elements and Terms
CMCS Metadata Properties
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Related Projects Expanding CMCS

• Reacting Flows Feature Tracking in Numerical
  Simulation Datasets
• Feature detection and tracking is a data mining
  approach with the motivation to extract further
  scientific understanding from valuable DNS data
  sets. CMCS is working with BES/SciDAC projects
  here at the CRF towards adopting new standard
  formats for feature data/metadata.

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Related Projects Leveraging CMCS

• DART Metadata
• CMCS teams experience with metadata management
  was relevant to the DTA team successfully
  reaching its Material Transparency Milestone.
• DHS Data Integration
• An integrated Rad/Nuc Countermeasures System
  requires the well-organized and efficient flow of
  data.
• C-MS3D (Outstanding NIH Proposal)
• Structure and function of biological
  macromolecules is central problem in biology.
  MS3D, an emerging approach, uses intra-molecular
  chemical cross-linking followed by mass
  spectrometric analysis to gain insights into the
  structure of these macro-molecules. C-MS3D would
  be a data-centric collaboration infrastructure
  for the leaders of the MS3D research community.

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CMCS Explorer Search of CMCS Metadata
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Metadata at Work Data Viewer Registered With SAM
Data translations provided automatically by SAM
for this file type.
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CMCS Metadata Stored as WebDAV Properties
DAV property is a keyword/value pair
namespacetag, and a well-formed XML value.
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CMCS Metadata Use

• Metadata provides identification and
  documentation to scientific data.
• Example Attaching an owner, creation date,
  abstract, type to data.
• Example Tracking data to program versions, and
  possibly bugs for that version.
• Metadata documents the context and value of the
  data.
• Example The theoretical atomization energy of
  methylhydroperoxide (and its uncertainty) from
  Ecce (used as input to ATcT) contains information
  identifying the species and the quantity, units,
  the theoretical method used, vibrational
  frequencies and geometry, reference to source
  file, creator, etc.
• Metadata facilitates cross-scale transfer of
  data.
• Example Can show a chain of inputs, including
  input parameters and configuration files, across
  scales.
• Example Can retrieve literature references which
  describe this data.
• Metadata allows users to comment on the data and
  its quality.
• Example CMCS infrastructure can be used for
  scientific peer review of data.
• Metadata is necessary for effective
  collaboration.
• Example Scientific data becomes more usable to
  others when it is documented.

Metadata, also referred to as data annotation,
converts scientific data into knowledge.
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CMCS Metadata Elements

• Using Dublin Core for some basic pedigree
  properties creator, dates, publisher,
  is-referenced-by, references, replaces,
  is-replaced-by, has-version, etc.
• Dublin Core Element Set and Qualified Dublin Core
• Use of both XML and RDF to encode metadata values
• Use of XLink to express values of hyperlinks
• CMCS properties for chemical science to enable
  searching species name, CAS, chemical
  properties, and chemical formula.
• CMCS properties for defining scientific data
  has-inputs, has-outputs, and is-part-of-project.
• CMCS properties for scientific publication and
  peer review annotations is-sanctioned-by.
• Currently defined 36 elements in the core CMCS
  pedigree.
• Flexible infrastructure for addition of new
  metadata. As new metadata is added to
  infrastructure,current apps will not break!

CMCS metadata is strongly encouraged, though not
required, for all CMCS data, and CMCS metadata is
extensible.