# Presentation: 610308

## Adaptive Informatics Infrastructure for Multi-scale Chemical Science CMCS.ORG

- _James D. Myers_: Pacific Northwest National Laboratory
- Larry Rahn, David Leahy, Carmen Pancerella: Sandia National Laboratory
- Gregor von Laszewski, Branko Ruscic: Argonne National Laboratory
- William H. Green, Jr.: Massachusetts Institute of Technology
- Division of Chemical Information, ACS National Meeting
- Anaheim, CA
- March 29, 2004

## Outline

- Multiscale Science Challenges
- What is an ‘adaptive informatics infrastructure’?
- Architecture and major components
- Combustion Science Applications
-  Status and Future Directions

## Combustion is a Multi-scale 

**New knowledge is assimilated from different data, tools, and disciplines at each scale**
**Real-time bi-directional information flow**
_**Multiple**_** applications for the same information**
**But**
**Normal publication is slow, excludes much important data, is often re-evaluated later**
**Data has different formats, hidden dependencies**
**Standardization is hard to do up-front**
**Multi-scale information is complex and its pedigree and associated metadata matters**
**Current Solutions:**
**Community Databases**
**Problem Solving Environments/Grids**
******Need lighter weight, flexible, adaptive mechanisms for sharing data                       ****	****groups ******** communities**

***Combustion is a Multi-scale ***
***Chemical Science Challenge***

## 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

## Knowledge/Semantic Grid

- A set of scalable tools, middleware, and services
- For the creation, analysis, dissemination, evaluation, and use
- Of data, information, and knowledge
- By individuals, groups, and communities
- ...A digital place for performing ‘all’ aspects of science

** ****CMCS Project Scope**

- 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

## CMCS Integrates Other Major Open Source Software Capabilities

**SAM**

**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**

**Java Storage Interface**

**JDBC**

**Filesystem**

**XML conf.****JDBC**

**GridFTP**

**DAV/DASL**

**Notebook****Services**

**JMS**

**External****Security**

**Security**

**Processing**

- Client API

- ELN API

- Subscriber

**Web****Service**

**Metadata****generation/****translation**

**Configurable****security**
**framework**

**Jetspeed, OKI**
**Standards-based Web Portal**
**Interface integration**
**Collaboration **
**Inter-portlet communication**
**JSR 168, WSRP**

**Jakarta Slide, OpenJMS, CoG**
**Layered Architecture:**
**Metadata Management Services**
**Semantic Services**
**Notebook Services**
**WebDAV**
**JSR 170 Java Content Repository API**

## CMCS Portal Interface

**CMCS Portal Interface**

**Single Sign-on**
**Group spaces**
**Customizable Panes:**
**Standard Tools ******
**Domain Tools (portlet/web service)**
**Email Notifications about new/updated data**

**Notes:**
Knowledge Management — the ability to discover and interpret data in semantically meaningful ways. Capabilities in this category include mechanisms for searching and browsing data, submitting new content, browsing provenance and other relationships, organizing and finding information based on metadata, discovering and managing vocabularies, schema, and ontologies.
Community Interaction — the ability of research groups and communities to form, organize and scope their activities and to disseminate their findings. Capabilities in this category include mechanisms for defining groups, managing membership, creating shared group data repositories, supporting real-time and asynchronous discussion, customizing the layout and mix of tools within the group’s portal view, managing group processes, assigning tasks, maintaining public data collections, and for managing broader community processes such as the review and annotation of data.
Research Support — the ability to conduct the processes of data acquisition and analysis. Capabilities in this category include mechanisms for incorporating third-party domain applications, transferring and transforming data between applications, documenting progress, automating repetitive tasks, visualizing and comparing data and metadata, and sharing results with collaborators.

## SAM Powers CMCS Knowledge Management

**Provides a node plus metadata/relationship view of underlying data sources**
**Support put/get/search/access control of arbitrary data/metadata**
**Configurable metadata extraction from binary/ASCII/XML files**
**Configurable Data Translation**
**Semantic/graph queries**
**RDF Export**
**Notebook Services (page display, signatures, timestamps, ...)**

- Fortran
- Application

- ‘Local
- Disk’

- DataGrid

- SAM

- DAV

- DAV+

- JMS

- ELN

- CMCS

## CMCS Metadata Elements

- Using Dublin Core for some basic pedigree properties: title, 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. **

## CMCS Explorer

- Browse

- Not shown:
- Search
- Metadata Entry
- Access Control

## Portal and API’s Facilitate Integration of Data & Applications

**Web service**

**Application**

**DAV**
**API**

**Notification**
**API**

**Portal**
**API**

**Notification**
**Web service**

**Fitdat, analysis**

**CMCS/DAV**
**API**

**Notification**
**API**

**DAV Client**

**Application**

**DAV/File**
**API**

**Experiment**

**Chemical**
**Mechanisms**

**Reacting**
**Flow**

***Local Services/Grid Fabric***
**Storage   Security     Event Services     Directory Services**

**Quantum**
**Chemistry**

**Kineticist**

**Thermo-**
**Chemistry**

**Kinetics**

***Scientific Annotation Middleware***
**Parsers  Translators  Annotators  Notifications  WebDAV**

**Thermochemist**

**Notification**

***CMCS***
***Portal***

**Search**

**Subscribe**

**Annotate**

**View**

**Portal and API’s Facilitate Integration of Data & Applications**

***Shared Data Repository***

**Annotation**

**XML **
**Data Set**

**Search results**

**Translator**

## CMCS Pilot Science Groups

**DNS– Jackie Chen, David Leahy**
- Feature detection & tracking in DNS data
**HCCI University Consortium – Bill Pitz**
- Homogeneous Charge Compression Ignition
**PrIMe – led by Michael Frenklach**
- Development and publishing chemical reaction models
**Real Fuels Project– Wing Tsang, Tom Allison**
- Lead real fuels chemistry at NIST
**IUPAC – led by Branko Ruscic**
- Develop and publish validated thermochemical data
**Quantum Chemistry – Theresa Windus**
- QM Reference data

## LIF Imaging LabView-based analysis application,

***LIF Imaging LabView-based analysis application,***
***ReactionLab – Matlab-based package for visualizing/comparing thermodynamic & kinetic data***

**Example:**
**LIF Imaging **
**Application**

**LabView writes to Webdrive DAV Client **

**MatLab writes DAV directly**

- ReactionLab

## ACTIVE THERMOCHEMICAL TABLES

***ACTIVE ******THERMOCHEMICAL TABLES***

*CMCS*

## RIOT Web Service

- 4x speed-up in 2-d laminar methane flame simulation
- without loss of accuracy	(Lu, Bhattacharjee, Barton, & Green, 2003)

- Range Identification
- and Optimization Toolkit

## CMCS Vision

- Short-term (Now!)
- Enable distributed expert groups to gather, evaluate, statistically analyze/validate, and publish community data
- Long-term impact envisioned from CMCS approach
- Complement scientific peer review and publication with in-depth pedigree information and new forms of collaborative data sharing and annotation
- Enable rapid start-up and evolution of collaborative multi-disciplinary science projects
- Dramatically increase accessibility of state-of-the-art research knowledge to industry and the public (a knowledge grid)
- Over-arching vision for CMCS project
**Enhance multi-scale science research by breaking down the barriers to rapid sharing of validated information and by opening new paradigms for multi-scale science.**
**Harness Semantic technologies to support distributed, interacting collaborative problem solving environments on the grid**
**An infrastructure than can ‘keep up’ with science research**

**Notes:**
Get feedback on breakout of vision into near-term (1st) and long-term (2nd)
Get feedback on content of both
Near term, high-level vision
	- right out of proposal - change any of the wording? 
	- Is there heart burn over actual content?
Long-term vision of impact
	focuses on 1) chemical science, 2) science community, 3) industry/public
	What about computer science, information science, and/or collaboration science (this one may be included in 1)

## Multi-disciplinary CMCS Team

**National Collaboratory Program**

**SNL -  Larry Rahn*, Christine Yang, Carmen Pancerella, David Leahy, Darrian Hale**
**PNL - Brett Didier*, Carina Lansing, James D. Myers, Karen Schuchardt, Eric Stephan, Theresa Windus**
**ANL - Al Wagner*, Branko Ruscic,  Michael Minkoff, Gregor von Laszewski, Reinhardt Pinzon, ****Mihael Hategan**
**LLNL-****	****William Pitz***
**LANL-****	****David Montoya*, ****Jane Riese, Ginger Young**
**NIST-**** ****	****Thomas C. Allison***
**MIT -****	****William H. Green, Jr. *, Luwi Oluwole         **
**UCB - ****	****Michael Frenklach*               **
***denotes Institutional Point of Contact**
***    ******http://cmcs .org***