A Collaborative Informatics Infrastructure for Multi-scale Science

James D. Myers,^[2]{.underline}^ Thomas C. Allison, ^[6]{.underline}^
Sandra Bittner, ^[3]{.underline}^ Brett Didier,^[2]{.underline}^ Michael
Frenklach^[8]{.underline}^, William H. Green, Jr., ^[6]{.underline}^
Yen-Ling Ho, ^[5]{.underline}^ John Hewson,^[1]{.underline}^ Wendy
Koegler,^[1]{.underline}^ Carina Lansing,^[3]{.underline}^ David
Leahy,^[1]{.underline}^ Michael Lee,^[1]{.underline}^ Renata
McCoy,^[2]{.underline}^ Michael Minkoff, ^[3]{.underline}^ Sandeep
Nijsure, ^[3]{.underline}^ Gregor von Laszewski, ^[3]{.underline}^ David
Montoya, ^[5]{.underline}^ Carmen Pancerella,^[1]{.underline}^ Reinhardt
Pinzon, ^[3]{.underline}^ William Pitz, ^[4]{.underline}^ Larry A.
Rahn,^[1]{.underline}^ Branko Ruscic, ^[3]{.underline}^ Karen
Schuchardt,^[2]{.underline}^ Eric Stephan,^[2]{.underline}^ Al Wagner,
^[3]{.underline}^ Theresa Windus,^[2]{.underline}^ Christine Yang
^[1]{.underline}^

*^1^Sandia National Laboratories, Livermore, CA 94551-0969*

*^2^Pacific Northwest National Laboratory, Richland, WA 99352*

*^3^Argonne National Laboratory, Argonne, IL 60439-4844*

*^4^Lawrence Livermore National Laboratory, Livermore, CA 94551*

*^5^Los Alamos National Laboratory, Los Alamos, NM 87545*

*^6^NIST, Gaithersburg, MD 20899-8381*

*^7^MIT, Cambridge, MA 02139*

*^8^University of California, Berkeley, CA 94720-1740*

*Jim.Myers@pnl.gov*

Abstract

The Collaboratory for Multi-scale Chemical Science (CMCS) is developing
a powerful informatics-based approach to synthesizing multi-scale
information to support a systems-based research approach and is applying
it in support of combustion research. An open source multi-scale
informatics toolkit is being developed that addresses a number of issues
core to the emerging concept of knowledge grids including provenance
tracking and lightweight federation of data and application resources
into cross-scale information flows. The CMCS portal is currently in use
by a number of high-profile pilot groups and is playing a significant
role in enabling their efforts to improve and extend community
maintained chemical reference information.

# 1. Introduction

Combustion research is, in some ways, representative of many areas that
address complex multi-scale phenomena, such as earth system studies,
fusion research, and high-energy physics. In such fields, an
understanding of environment, device, and/or system scale phenomena
requires more than simply applying one type of computation, with
increased computing power, across scales. Different physical phenomena
dominate system dynamics at these different scales, leading to a variety
of conceptual models, and associated experiments and computations,
relevant in the different regimes. However, researchers working in areas
of chemical science relevant to combustion do not consider themselves
part of a large project team to the degree seen in other fields. Rather
they see combustion as one of myriad application areas that rely on more
fundamental community reference data.

One of the major bottlenecks in multi-scale research today is in the
passing of information from one level to the next in a consistent,
validated, and timely manner. Traditionally, this information flow has
been accomplished at the community level through the research
literature. Increasingly, the literature is supplemented by community
databases. In more project oriented disciplines, collaboratory and grid
models for virtual organizations are starting to play a role. However,
these approaches do not yet scale well with respect to community,
process, and data/metadata heterogeneity \[1-3\].

Bridging these two paradigms involves numerous challenges but is
essential to the full realization of systems-science approaches. The
Collaboratory for Multi-scale Chemical Science (CMCS) \[4\] is designed
to address many of these challenges and provide rich group-level
collaboration capabilities, facile bi-directional data flow between
groups and larger communities and between communities, and
community-level review and curation mechanisms. Once communication
across scales and between projects and communities is sufficiently
transparent, the character of research can change. Researchers can use
information from multiple scales/communities to actively guide their
research and interdisciplinary efforts can form to address related data
and model requirements simultaneously across a range of scales. The
ready availability of genome and protein data and analysis tools has had
such an effect at the molecular scale in bioscience. The already
revolutionary impacts there are motivating biologists to extend, and the
broader scientific community to investigate, informatics-based
approaches across multiple scales and disciplines \[5-7\].

# 2. Combustion, and the Collaboratory for Multi-scale Chemical Science

The CMCS project was initiated in 2001 with a long-term vision of
multi-scale science enabled by modern informatics, and a commitment to
realizing this vision in support of combustion research. This focus is
motivated by the importance of the combustion problem, its classic
multi-scale nature, and the opportunities for near-term impact by such a
systems approach.

Combustion research relies on chemical information spanning more than
nine orders of magnitude in length scales. For realistic fuels, the
chemistry of combustion involves hundreds to thousands of chemical
species participating in thousands of reactions. The structural and
thermochemical properties of these species are determined from
spectroscopic experiments and, increasingly, from computational quantum
chemistry. Reaction rates as a function of temperature and pressure are
determined experimentally and by a number of computational methods using
detailed data from quantum chemistry computations. Collections of these
properties and rates are assembled into chemical mechanisms to model
chemical transformation associated with a whole suite of reactions.
These models (and often reduced forms of them) are used in detailed
simulations that investigate the coupling of reaction chemistry to fluid
dynamical processes. These interactions are then further modeled in
codes that seek to provide predictive model-based design for combustion
devices or systems.

Combustion scientists have developed numerous proven techniques, models,
and reference data that span multiple physical scales. Multiple
experimental and theoretical techniques are available to provide
complementary constraints on the values of fundamental chemical
properties. Advances in laser-based measurement methods and rapidly
advancing computational algorithms and computer technology are offering
new approaches for tackling the complexities of real-fuel chemistry,
turbulence-chemistry interactions, and multi-phase processes \[8-11\].
While the combustion community is broadly distributed today with many
stakeholders, often with conflicting priorities, researchers in the
field are recognizing that a new 'systems approach' is required. This
approach would simultaneously span disciplines, physical scales, and
geography, making data, tools, and new approaches broadly available to
significantly enhance progress towards the ultimate goal of predictive
model-based device design. Further, given the extensive base of chemical
knowledge available, an informatics-based systems approach is seen as
having the potential for immediate impacts.

The expanded role of informatics envisioned requires a new research
infrastructure and improved tools and approaches. The heterogeneity
inherent in multi-scale science requires strong support for converting
information between conceptual models and across formats. In addition,
scalable and maintainable solutions require increased abstraction of
services and resources, while researchers will need better mechanisms to
coordinate their activities within relevant groups and communities. The
emerging vision for meeting these requirements is the 'knowledge grid,'
which incorporates advances being made in semantic web, informatics,
collaboratory, and grid communities. Effective use of knowledge grids
will also require cultural changes and iterative approaches involving
long-term collaborations of domain and information researchers to fully
realize the potential of cross-scale, systems-oriented informatics.

# 3. Developing a Collaboratory for Multi-scale Chemical Science

To enable such a 'knowledge grid' approach, the CMCS project's approach
couples a multi-disciplinary team with efforts to develop a multi-scale
informatics portal toolkit, to integrate key chemistry resources, and to
develop chemistry-specific informatics applications. This is
accomplished through an iterative development and deployment process
that is driven by guiding use-cases and feedback from pilot user groups.

As depicted in Fig. 1, the CMCS portal provides its capabilities through
a multi-tiered architecture and layered services which integrate a wide
range of chemistry community data, application resources and
state-of-the-art computing technologies. In many ways, CMCS leverages
current web and grid distributed computing architectures. However, to
support the heterogeneity and rapid change inherent in multi-scale
science, CMCS places emphasis on lightweight integration supported by
aspect-oriented design \[12\].

![](media/image1.wmf)

Key to the CMCS design is the principle that application-oriented
services, middleware, and grid-level services should interact based on
aspects of information in the system, e.g. a data set's name or type,
rather than a common object model. Another key to this approach is the
elevation of data and metadata transformation and semantic
interpretation to first class operations that can be invoked by
applications and services as needed. CMCS's design leverages middleware
standards and open source toolkits related to the concepts of portals,
content management, and publish/subscribe messaging that embody these
principles. The project team, along with a number of collaborators, is
extending and evolving this base and approach to build the CMCS
combustion research portal and to further develop the concept of
lightweight, powerful knowledge grids.

In the subsections below, we first discuss the core infrastructure and
application-level services, followed by the portal itself. We group the
primary portal and data exchange interfaces into three categories for
discussion - knowledge management, community interaction, and research
support, though in use, researchers can access capabilities across these
categories as needed.

## 3.1. Core Infrastructure

The concept of portals and portlets is primarily one of integration at
the user interface layer. CMCS reviewed a number of technologies before
selecting the Apache Jetspeed \[13\] based CompreHensive collaborativE
Framework (CHEF) \[14\] as a portal engine. CHEF extends the portlet
concept to that of collaborative 'teamlets' that can communicate between
instances of themselves, e.g. to provide real-time chat capabilities.

For data and metadata management, CMCS employs the scientific content
management services developed within the DOE-funded Scientific
Annotation Middleware (SAM) project \[15\]. SAM software provides a
range of capabilities for storing and retrieving data and metadata,
searching, versioning, locking, and providing access control, as well as
extensible mechanisms for extracting metadata from files, performing
translations, and managing provenance and other data relationships. SAM,
based on the open source Jakarta Slide \[16\] content repository,
presents a Web-based Distributed Authoring and Versioning (WebDAV)
protocol \[17\] view of underlying data and metadata repositories.
WebDAV is a widely adopted Internet Engineering Task Force (IETF)
standard set of extensions to the HTTP/1.1 protocol to support basic
content management over the web. Both WebDAV and SAM support the
aspect-oriented design integral to CMCS.

The team selected the standard Java Messaging Service (JMS)
publish/subscribe protocol and the open source OpenJMS implementation
\[18\]. The publish/subscribe model maintains the independence of the
producers and consumers of notifications, allowing dynamic changes in
message routing and workflows.

For authentication and authorization, CMCS chose to initially leverage
the basic username/password and role-based access control mechanisms
available from underlying tools coupled with wire-level encryption
provided via the Secure Socket Layer (SSL). As a longer term strategy,
the team has designed the architecture to allow authentication and
authorization to be handled by separable services and to support an
incremental security model which allows anonymous access to public CMCS
resources while supporting certificate-based credentials for access to
grid resources. This plan minimizes barriers to adopting CMCS while
meeting the current and anticipated needs of users. To support
single-sign-on across the portal environment, CMCS initially modified
the CHEF user management service to synchronize user information with
the SAM repository but this is currently being updated to allow the SAM
repository to directly share the CMCS user database and authentication
service by replacing its default security module with a CMCS specific
one.

CMCS has implemented a number of web services based on Apache's Axis
\[19\] toolkit. CMCS has used Axis to wrapper several tools as noted
below and has simplified the tasks of launching and monitoring web
services through the development of a higher-level programming
interface. The Commodity Grid (CoG) toolkit \[20\] has also been used to
demonstrate the ability to run applications as web or grid services as
desired.

## 3.2. Application-Level Service Interfaces 

Application level services are abstractions that combine multiple low
level services to more directly support the requirements of
applications. A simple example is account creation, which, in CMCS,
involves not only creation of an identity within an authorization
service but association of that identity with portal preferences, the
creation of directories in the repository for the user, etc. Toolkits
such as CHEF and SAM provide a number of high-level service abstractions
for, for example, user/team management and collaboration, and annotation
and provenance tracking, respectively. CMCS is modifying, extending, and
integrating these services and has developed additional ones related to
messaging. In general, CMCS is aiming for a clean separation of
application-level services from both the portal engine and lower-level
services. We believe this is critical to interoperability of knowledge
grids over the longer term. While much of the development work in CMCS
to date has been focused on immediate needs for practical integration,
defining appropriate abstractions for such services is a key longer term
goal of the project that is being pursued with collaborating projects.
The discussion here focuses on two areas rather than an exhaustive list
in an attempt to provide the general flavor of the changes while
avoiding details that are changing rapidly as CMCS, CHEF, SAM, and other
tools evolve.

A significant effort was made to develop a general Data Storage
Interface (DSI) providing a high-level abstraction for managing metadata
and data access. DSI encapsulates the WebDAV-centric SAM client library,
providing higher level functionality and simplifying error handling. One
simple example is that DSI supports the submission of data and
associated metadata in a single call, hiding the fact that this requires
two separate WebDAV operations. DSI is used within many CMCS developed
tools and is also available to third party developers as an integration
point. Another service abstraction that has been created is an
annotation mechanism generalized from SAM's electronic laboratory
notebook (ELN) and now available as a service that can be invoked from
within a portlet.

CMCS has also developed new services that monitor JMS events and use
these events to trigger email notifications and simple workflows to
produce derived data. Currently, the events published in CMCS are
limited to those from the repository indicating changes to data and
metadata. We anticipate additional message sources including other
services and portlet-based tools. The Notification Email Daemon (NED)
service allows users to register interest in events based on data's
location, type, and metadata values and to request individual or
digested email notification of data creation, modification, and/or
access. NED monitors the events from the repository, applies appropriate
filters, generates digests, and sends email. A simple workflow engine
uses similar methodology to trigger third party applications to analyze
data and produce derived data sets.

## 3.3. The CMCS Portal / Community Data Exchange

The most visible parts of the CMCS infrastructure development effort are
the specific portlets providing the knowledge management, community
interaction, and research support capabilities. These portlets appear
within the overall CMCS portal interface of the user's web browser and
interact with portal engine, high-level and base services, and each
other as needed. These portlets appear in the overall portal view
coordinated by CHEF and Jetspeed. When a user logs in to the CMCS
portal, the teams to which he belongs appear as tabs across the top of
the portal workspace. Within each team space, multiple pages showing
customized aggregations of portlets are available.

**3.3.1. Knowledge Management.** Due to the very flexible and powerful
data and metadata capabilities being developed in CMCS and given work
being conducted within CHEF on group collaboration tools and within
other Grid and collaboratory projects on research support tools (e.g.
grid job launching), CMCS placed an early emphasis on developing
data-centric tools supporting knowledge management activities. Knowledge
management is defined here as the general ability to discover and
interpret data in semantically meaningful ways. Capabilities in this
category include mechanisms for searching and browsing data, organizing
and finding information based on metadata, submitting new content,
browsing provenance and other relationships, and discovering and
managing vocabularies, schema, and ontologies.

Given the capabilities of the CMCS infrastructure, it was not possible
to directly leverage data interfaces developed in other portal projects.
The Explorer portlet was designed as the default CMCS data and metadata
browsing tool providing a full set of basic content management
operations including file upload, copy, move, and delete, and the
creation of hierarchical directory structures. The Explorer supports
traversing directories, viewing files sorted by different criteria (e.g.
creation date, author), creating bookmarks, and setting access controls.
It also allows users to create, view, and edit arbitrary key/value
metadata (i.e. WebDAV properties) associated with files and directories.
Metadata can describe a variety of aspects of data including its type
and format, its owner and creators, the type of measurement represented
by the data, its categorization, judgments of its quality, and its
relationships to other data. Different metadata are relevant in
different scientific tasks. The CMCS Explorer makes all of the metadata
available through a common interface and provides filtering mechanisms
to limit the metadata shown in the current view. For example, the CMCS
has defined a relatively small set of common metadata \[21\] based in
part on the Dublin Core \[22\] that is shown by default, but groups may
define their own standards and customize their Explorer view to
highlight their metadata.

The Explorer interprets some metadata, versus simply displaying it, to
provide live links to related data including 'virtual'
derived/translated formats, and to support viewing data within the
portal. The Explorer creates links for any metadata including an Xlink
\[23\] to other data within the repository that will refocus the
Explorer on the link target, providing an alternative to browsing via
directory hierarchies. The Explorer provides a similar mechanism to
trigger the creation of derived/translated data. This capability relies
on a dynamically generated "hastranslations" property generated by SAM
based on the capabilities of registered translators. Translated data can
be downloaded or directly copied to user-specified locations in the
repository. When translations are available that produce output viewable
within a browser (e.g. HTML or JPEG images), Explorer creates a "View
As" list that can be used to trigger popup windows with the specified
view(s) of the data. Since views generated via translation can include
interactive applets, the Explorer can be used not only as a way to
quickly discover and evaluate data, but as a means to then explore the
data interactively.

Several additional tools are associated with the Explorer and can be
launched from its interface. These tools share state, and changes in one
tool can trigger changes in the others. This capability is being
developed as a prototype for a more general mechanism to support
inter-portlet communication. Specific tools include:

**[Provenance Graph Tool]{.underline}** --- provenance (or pedigree)
\[24\] is a broad term describing the history of a piece of data. The
CMCS Provenance Graph tool \[25\] displays a node-and-arc graph of data
relationships, providing a powerful alternative to the tabular metadata
view in the Explorer. The Provenance Graph is fully configurable and can
be used to show any set of relationships. This is critical in allowing
researchers to focus on workflow provenance (data processing history) or
scientific provenance (e.g. association with refereed papers), or to
highlight or hide annotations and project relationships.

**[Advanced Search Tool]{.underline}** --- search is an essential tool
for data discovery. Search involves finding data based on comparisons
with metadata patterns specified by the user. Due to CMCS's rich
metadata capabilities, very complex searches are possible. To support a
range of user needs, the CMCS Search tool was designed with multiple
interfaces. For the simplest cases, a Google-like search box allows
users to specify words to be matched across all metadata properties. A
second configurable interface allows search based on specified values
for multiple metadata properties. These interfaces are built upon a
search programming interface which is also accessible to integrate
search capabilities directly into portlets and applications.

**[Annotation Tool]{.underline}** --- annotation is the attachment of
free-form information to existing data. The Annotation tool supplements
the simple metadata creation capability of the Explorer with a much
richer model derived in part from the SAM-based electronic laboratory
notebook (ELN) \[26\]. The Annotation tool allows data owners and third
parties to associate text, sound, images, equations, or whiteboard
drawings with existing data. Annotations are stored as independent files
linked via metadata to the specified data and can have their own
metadata and additional relationships. Thus annotations can be protected
with access controls and threaded to organize related topics of
discussion.

The Explorer and associated knowledge management tools continue to
evolve in response to user feedback and as other parts of the
infrastructure mature and make new capabilities possible.

**3.3.2. [Community Interaction.]{.underline}** The CMCS portal provides
a variety of portlets and tools to support community interactions. In
general, these tools provide research groups and communities the ability
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(s), managing group
processes, assigning tasks, maintaining public data collections, and
managing broader community processes such as the review and annotation
of data. In some sense, they bridge between the public-oriented
knowledge management capabilities and the small-group oriented
research/project-oriented capabilities.

Many CMCS capabilities in this area are provided by tools, or minor
modifications of tools within CHEF. Examples include Chat, Discussion,
and Calendar portlets. CMCS has developed a number of additional tools,
some in response to specific user needs and others to begin to explore
longer term issues for knowledge grids. Examples of the former include
an email subscription tool for managing the event-driven notification
service discussed above and a sophisticated task management portlet. The
subscription portlet can be used to set up notifications for teams,
sub-teams, or individuals triggered by a range of conditions from new
files appearing in a given directory to matches to persistent queries
based on the CMCS search capability. The task management portlet allows
tasks to be categorized, prioritized, and filtered by priority, status,
category, assignee, and milestone/version.

The prototype capabilities include the annotation tool described above,
which is an initial step towards support for peer review. The team also
created a mechanism for "expert discovery" that allows users to publish
requests for additional data (i.e. at other scales) that are compared
with advertised expertise and interest profiles. When a match is found,
the system forwards the request by email providing an introductory
contact. Additional capabilities, including application and schema
registries and associated management tools are in development.

CMCS has also modified and extended the basic user and team management
capabilities provided by CHEF. In addition to automating the creation of
access-restricted and publicly readable data areas in the repository for
users and groups, modifications were also made to expose user and team
definitions outside the portal and to allow users more control over
individual and group profiles. A New User portlet allows an individual
to create an account on CMCS and provide information about her
combustion-related interests and expertise. The Teams portlet allows any
CMCS user to create a team, thereby becoming its administrator. The
administrator can then add and remove members, promote other members to
the administrator role, set descriptive metadata about the team, and
specify an (internal or external) team web page. Further modifications
including, for example, an email invitation mechanism allowing team
administrators to invite/include people who have not yet registered with
CMCS, are planned.

**3.3.3. [Research Support.]{.underline}** The tools discussed under the
topics of knowledge management and community interaction clearly provide
some support for research, but they address only part of the
requirements. To perform detailed experiments, calculations, and
modeling runs, researchers need access to domain applications and ways
to transfer and transform data, automate repetitive tasks, visualize and
compare data and metadata, and document their progress. Thus, research
support in the CMCS infrastructure is primarily in the form of
interfaces supporting inclusion of domain resources. These are described
here, with examples of resources that have been integrated to support
multi-scale chemistry given in the following section.

CMCS's use of WebDAV provides a number of possibilities for data
integration. WebDAV-based file system drivers exist for most platforms
allowing applications to view the CMCS repository as a file system and
to directly upload and download information without any modification to
the application itself \[27,28\]. WebDAV libraries exist in a number of
languages \[17,29,30\], and the CMCS DSI library provides a higher-level
interface in Java. To support integration of external data sources, CMCS
relies on capabilities within SAM to map relational databases, GridFTP
stores, and other sources into the WebDAV namespace using Java or
XML-based interfaces.

WebDAV also plays a role in CMCS support for metadata integration.
Supplementing the manual metadata entry available within the Explorer,
CMCS supports direct metadata submission and retrieval via WebDAV
clients and DSI. Thus, WebDAV-aware applications have full access to
CMCS metadata. To support applications that interact through file system
drivers, CMCS provides a SAM-based metadata extractor mechanism that can
pull information from within arbitrary (e.g. binary) files and populate
WebDAV properties, converting to any schema desired.

As noted previously, CMCS has developed mechanisms to enact simple
workflows based on JMS triggers and to manage interactions with
long-running remote web services. However, to date, CMCS has emphasized
mechanisms to document and view workflow-based relationships over
traditional workflow enactment services. The metadata extraction
mechanism discussed above and WebDAV/DSI interfaces allow applications
to contribute workflow documentation that is then available within the
Explorer and Provenance Graph Tool. CMCS also has internal mechanisms to
track provenance, adding metadata to specify the source of copies and
translations requested via the Explorer or the data interfaces. The team
continues to track more powerful grid workflow mechanisms and is relying
on feedback from the pilot communities to prioritize inclusion of a
general computational gateway in the system.

The standard portal/portlet mechanism is the primary display integration
mechanism available in CMCS. CHEF provides a richer model that supports
interacting portlets including server-mediated communication between
portlets and a mechanism for portlets to invoke other portlets. As
noted, CMCS also has a lightweight mechanism to allow portlets to share
state information, making it possible, for example, for an application
to control independently developed data viewer portlets to display its
results. Combined with the mechanism to register translations capable of
producing browser-viewable renderings of data, these mechanisms provide
sufficient capabilities to allow portal environments to approach the
richness of more traditional problem solving environments.

CMCS's design allows very powerful integration of all information
related to an experiment. The repository can store data and associated
notes, images, documents, and other material in any format and store all
relationships between them. In addition to the tools for managing data
and metadata, and for adding annotations that were mentioned in previous
sections, CMCS provides an electronic laboratory notebook application
that can be launched from the portal and stores its output directly in
the CMCS repository \[26\]. The notebook can be extended with additional
'editors' supporting entry of new types of annotation and can be
configured to use any translators registered with CMCS to render data on
notebook pages.

## 3.4. Combustion Resources 

A wide range of existing combustion data collections and applications
have been integrated with CMCS using these mechanisms. A number of
leading file-based collections ranging from Quantum Chemistry
calculation results \[31\] to highly annotated information on kinetic
rates with related validation experiments \[32\], chemical reaction
mechanisms for complex fuels, and feature annotations of direct
numerical simulations of hydrogen-air autoignition data have been made
available directly within with CMCS repository. These sources have been
uploaded manually via the portal or directly via applications supporting
WebDAV. Other sources, of which the NIST Kinetics Database \[33\] is the
first, will be maintained at their home institutions and mapped into the
CMCS repository namespace via SAM.

Applications have been integrated with CMCS using WebDAV and via
wrapping as data translators or as part of event-triggered workflows.
For example, the Extensible Computational Chemistry Environment
(Ecce)\[34, 35\], a state-of-the-art problem solving environment
supporting a growing number of quantum chemistry codes, has been
modified to export molecular scale data to CMCS including full
provenance information. Additional modifications include a new mechanism
to combine multiple quantum mechanical calculations to directly produce
thermodynamic information used as input to higher-scale computations. As
another example, Fitdat, which converts between different community
standards for parameterization of the temperature dependence of
thermodynamic information, has been wrapped and can be triggered as part
of a simple workflow to automatically produce alternate
parameterizations of new data that are then stored in CMCS with links to
the original data

The CMCS metadata and translator/viewer capabilities provide some of the
most striking demonstrations that rich, lightweight integration is
possible. Extractors have been created that populate the core CMCS
metadata types (the default metadata displayed in the Explorer) based on
information within numerous file types. Translators have been created
across the range of combustion scales to convert between popular
community file formats. For example, OpenBabel \[36\], a tool for
converting between molecular geometry file formats, has been integrated
via a web service wrapper registered with the CMCS repository to provide
on-demand translations of molecular geometry files. Sophisticated
viewers generate interactive displays of molecular structures and
XY-graphs from a variety of molecular geometry and tabular data files
respectively. Overall, the CMCS production server currently has 25
metadata extractors and 40 translations/views configured.

## 3.5. Chemical Informatics Applications

Three new informatics based applications have been developed which take
advantage of the CMCS structure and capabilities. They, and the pilot
communities they are enabling, represent a new level of sophistication
in combustion research that is directly enabled by the ability to
integrate large amounts of heterogeneous data and coordinate group
analysis of the entire corpus provided by CMCS.

**[Active Thermochemical Tables (ATcT)]{.underline}** --- ATcT \[37\] is
a new approach to evaluating thermodynamic data in which fundamental
data representing a network of related measurements are statistically
analyzed to calculate the most accurate estimate of species enthalpy
given current information and to explore the impact of additional
measurements. CMCS developed an Active Tables portlet and associated web
service to allow users to import and export data to ATcT from their CMCS
workspace and to interactively run analyses and perform queries against
the ATcT chemical network.

The IUPAC (International Union of Pure and Applied Chemistry,
http://www.iupac.org) Task Group \"Selected Free Radicals and Critical
Intermediates: Thermodynamic Properties from Theory and Experiment\"
\[38\] is using ATcT and related tools, and CMCS' team coordination
capabilities, to critically evaluate data for a number of radicals
important in combustion and atmospheric chemistry and produce
recommended thermochemical values. This data will be subsequently used
by the chemical community at large to create accurate models of relevant
chemical reactions for complex systems such as flames or the atmosphere.
The 13 members of this Task Group have been selected by IUPAC from among
the most prominent scientists in the field. They will be working across
as many as ten time zones to analyze data related to 30+ ephemeral
chemical species.

**[ReactionLab]{.underline}** --- ReactionLab is a Matlab-based open
source software package for modeling reaction kinetics. ReactionLab
addresses key issues related to the efficient evaluation and validation
of kinetics data and models and provides a suite of tools for exploring
and comparing experimental data and model results. ReactionLab has been
extended using DSI to directly store and retrieve information from CMCS
workspaces.

**[Range Identification and Optimization Toolkit (RIOT)]{.underline}**
--- RIOT provides optimal reduced kinetics models that produce results
with specified error tolerances over user-defined ranges of conditions
while minimizing the overall number of reactions in the model, and
consequently the computational resources required to run it. RIOT is
integrated into CMCS via a portlet and remote web service, using the
CMCS messaging system to support monitoring of long-running RIOT
calculations.

The PrIMe (Process Informatics Model) group is a research team of about
40 international scientists, including kineticists, thermodynamicists,
quantum chemists, experimenters, and modelers. PrIMe has formed to
assemble thermodynamic, chemical kinetic, and transport data for use in
developing a curated public multi-scale library and associated tools
that can mine the library to produce, for example, customized optimal
kinetics models. The PrIMe group will use ReactionLab, ATcT, RIOT, and
numerous other CMCS capabilities to coordinate activities, evaluate
data, and interact with the larger community.

# 4. Conclusion

The CMCS team, guided by feedback from pilot users and in collaboration
with other software development projects, has developed a powerful
multi-scale combustion portal and underlying informatics toolkit. A
variety of chemistry data resources have been integrated and innovative
informatics applications have been developed and made available within
the portal. International teams of scientists have formed more than half
a dozen pilot groups tackling important open issues in combustion
chemistry.

The portal allows researchers to work naturally, accessing heterogeneous
data, working within community groups, and performing research that
directly integrates community data, tools, and processes. The
infrastructure provides the multiple information pathways necessary to
integrate tools and allow researchers to maintain a focus on their
science rather than the mechanics of data transfer. Community data
exchange (including translation and extraction mechanisms) and standard
programming interfaces are designed into the portal, underlying
services, and the data/metadata repository to make it simple to
integrate third-party data and application resources without requiring
modifications that would prohibit these resources from continued
independent development.

These are all issues that will present challenges to future knowledge
grids spanning virtual organizations. Although not discussed directly in
this paper, CMCS is also helping to elucidate other knowledge grid
related issues such as licensing of community data from myriad sources,
procedures for direct community data review, and mechanisms for
assessing community contributions independent of the scientific
literature. As knowledge grids lower barriers to discovering, analyzing,
and generating chemical information, technologies and research processes
will need to co-evolve. Researchers will need to easily participate in
multiple communities, and sub-communities will need to be able to
independently develop and evolve their domain resources while
contributing to multi-scale goals. We believe the approaches taken
within CMCS are advancing our ability to meet these goals.

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# 11. Acknowledgements

This work was supported as part of the Collaboratory for Multi-Scale
Chemical Science (CMCS) project within the National Collaboratories
Program sponsored by the U.S. Department of Energy\'s Office of
Mathematical, Information, and Computational Sciences. Sandia National
Laboratories is operated by the Sandia Corporation under Contract No.
DE-AC04-94-AL85000 with the U.S. Department of Energy. Pacific North
Pacific Northwest National Laboratory is operated by Battelle for the
U.S. Department of Energy under Contract No. DE-AC06-76RLO 1830.

The authors wish to acknowledge members of the CompreHensive
collaborativE Framework (CHEF) and Scientific Annotation Middleware
(SAM) projects, and the researchers involved in CMCS pilot groups, for
helpful discussions related to CMCS' design and contributions to
hardening the CMCS software. Baoshan Wang and Kaizar Amin are also
acknowledged for contributions to the CMCS project.