Collaboratory for Multiscale Chemical Science CMCS: A Knowledge Grid Adaptive Informatics Infrastruc

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Collaboratory for Multi-scale Chemical Science
(CMCS)A Knowledge Grid/ Adaptive Informatics
Infrastructure

• Jim Myers, Carmen Pancerella

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CMCS Enabling New Forms of Research and
Communication

• Distributed Research Groups
• Chemical Databases
• Rich Publication
• Community Annotation
• Informatics Analysis
• Cross-scale Communication
• Peer Data Review
• Pedigree Analysis
• Automated informatics
• Automated monitoring/analysis

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Adaptive Informatics Infrastructure

• Infrastructure a well designed, scalable,
  reusable, flexible set of tools, middleware, and
  services
• Informatics the emerging use of semi-automated
  means to derive new knowledge from the analysis
  of (large amounts of) heterogeneous data,
  annotating existing data with its newly
  discovered meaning
• Adaptive able to dynamically change to
  incorporate new knowledge and support new
  activities
• Low Barriers
• Many access points
• Storage of data in original formats with dynamic
  metadata extraction and translation
• Powerful
• Arbitrary formats (binary, ASCII, XML)
• Integrated data, metadata, pedigree across
  internal and external tools
• Evolvable
• Schema can be changed/extended as needed
• Metadata, translations, viewers, portal, etc. can
  be dynamically configured

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SAM Architecture
Notebook Services
Semantic Services
DAV, DASL, JMS, SAM Extensions
DAV, JDBC, GridFTP
Metadata Services
DataGrid
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SAM Metadata Services Layer

• Jakarta Slide DAV server plus configurable
• Mime Type Assignment
• CMCS default Based on dcformat tag within .xml
  file
• Property Generation from binary/ASCII/XML files
• 12 types ? standard CMCS properties
• Resource Translation
• 12 Viewers/Translators for CMCS including
  Interactive Applets
• Mapping to Data Store(s)
• NIST Kinetics DB
• JMS Events for access and changes
• Feeds events to CMCS NED Email Notification
  daemon
• Authentication/Authorization model
• (single sign-on with CMCS Portal
  username/password or GridCert)

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Extensible Scientific Interchange Language (XSIL)
/ Binary Format Description (BFD) language

• XSIL (Roy Williams, CalTech) - XML Encoding and
  Java code for scientific data
• Ints, floats, vectors, arrays, time series,
• Can describe the byte structure of external data
  files/streams (encoding, byte order,)
• Can have link(s) to external data
• BFD (Alan Chappell, Jim Myers, PNNL) XML Encoding
  and Java code for describing binary/ascii files
• Bug fixes, removed ambiguities
• Parameterized logic (if, while, for)
• Parameterized Stream interface
• Being used as input for Grid Forum Data Format
  description Language (DFDL) standard

ltXSILgt ltParam Name"date" Type"String" /gt
ltParam Name"Program Version" Type"float" /gt
ltParam Name"numColumns" Type"int" /gt ltArray
Name"data" Type"float"gt ltDimgt
ltXBFDvalue-of select "/XSIL/Param_at_Name
'numColumns'" /gt lt/Dimgt ltDimgt6lt/Dimgt
lt/Arraygt ltStream Encoding"Binary"
Type"Remote XBFDstreamnumber"0" /gt
lt/XSILgt
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Demo
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Example

• Binary ? XML ? Properties
• Translation of Chemistry Data
• SAM-based Electronic Notebook
• CMCS Portal/Pedigree Browser

ELN
DAV
Fortran Application
SAM
DAV
JMS
Local Disk
DataGrid
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CMCS Provenancede-facto standards

• Cmcshasinputs workflow
• Cmcshasoutputs workflow
• Samhastranslations virtual workflow
• Cmcsispartofproject hierarchy
• Elnchildren hierarchy
• (Davcollection) hierarchy
• Dctermsreferences scientific pedigree
• Dctermsisreferencedby scientific pedigree
• Elnreferences informal/private scientific
  pedigree

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Applications/Chemistry Services

• Extensible Computational Chemistry Environment
• Export to CMCS with pedigree/metadata
• Active Thermochemical Tables
• Portlet/web service using CMCS data store
• RIOT adaptive mechanism reduction
• Portlet/web service using CMCS data store
  asynchronous invocation mechanism

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Standard Protocol and API

• WebDAV An early web service (XML commands over
  HTTP)
• A widely adopted standard for metadata/data
  transport
• Put/Get data with arbitrary properties (dynamic)
• Properties can be discovered and accessed
  independently
• DASL, Versioning, Transactions,
• JSR 170 Java Content Repository
• An API for working with nodes with properties
  (versioning, queries, typing, notification, )

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Path Forward

• Pilot groups doing real chemistry
• Exploring new practice
• Peer-Review / Endorsement Mechanisms/Interfaces
• Digital publication, third party annotation
• Activity Reporting tools
• Scoping Searches, Notifications
• Based on user-defined notion of
  provenance/hierarchy
• Notebook Views of Other Hierarchies
• E.g. A notebook sharing a computational chemistry
  project hierarchy
• Validation of Chemical networks
• E.g. Active Thermo-chemical Tables
• Workflow by Example
• Informatics Data File Assembly Tool

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URLs/Team Members

• http//cmcs.org/
• http//www.scidac.org/SAM/

CMCS Team Members Thomas C. Allison, Kaizar
Amin, 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, James D. Myers, Sandeep Nijsure, Gregor
von Laszewski, David Montoya, Carmen Pancerella,
Reinhardt Pinzon, William Pitz, Larry Rahn,
Branko Ruscic, Karen Schuchardt, Eric Stephan, Al
Wagner, Baoshan Wang, Theresa Windus, Lili Xu,
Christine Yang