pervasive.iu.edu

A commitment to research.A catalyst for economic development.

Produced by the Office of the Vice President for Information Technology and CIOCopyright 2007, The Trustees of Indiana University

Pervasive Technology Labs Program R

eport 2007

Report to the Lilly Endowment, Inc.Grant Number 1999 2280-000

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TABLE OF CONTENTs

I. ExecutiveSummaryandIntroduction

II. LabReports

II.1 Open Systems Lab

II.2 Advanced Network Management Lab

II.3 Community Grids Lab

II.4 Visualization and Interactive Spaces Lab

II.5 Scientific Data Analysis Lab

II.6 Knowledge Acquisition and Projection Lab

III. CollaborativeandLeveragedActivities

IV. EconomicDevelopment

V. OutreachActivities

VI. OperationalActivities

VII. Appendices

Appendix 1: Patents Filed by Pervasive Technology Labs

Appendix 2: Technology Disclosures by Pervasive Technology Labs

Appendix 3: Publications by Pervasive Technology Labs Since Inception

LabAdministrationandContactInformation

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I. ExECuTIvE summAry ANd INTrOduCTION

The first half of 2007 has been a time of significant accomplishment for Pervasive Technology Labs

(PTL). Scientific and scholarly accomplishment reflects several years of effort by PTL as intellectual

developments and software products created by PTL scientists reach a level of maturity. During the

reporting period PTL leaders, staff, and affiliates published more than 60 peer-reviewed scientific papers or

technical reports, disclosed three new inventions to the IU Research and Technology Corporation (IURTC),

and released 17 new open source software packages. PTL also added three new online services during the

reporting period. In addition, one new patent for important software technology is being pursued.

Since its inception, PTL and affiliates have produced 686 peer-reviewed scholarly publications and technical

reports, given hundreds of talks and presentations, released 64 open source software packages, disclosed 40

inventions to the IURTC, and now deliver a total of 95 online services. Software and other tools developed

by PTL scientists now comprise mission-critical components of some of the nation’s most advanced and

innovative information technology systems.

The scientific innovation and intellectual output of PTL is translating into strong grant success. During

the first six months of 2007, PTL was collectively awarded a total of $532,272 in new grants. New grants

received by other units of Indiana University working in collaboration with PTL total $16,834,579 for the

reporting period. Most notably, the Community Grids Lab received notice that they have been awarded

a prestigious and highly competitive grant totaling $1,964,049 from the National Science Foundation in

support of their Polar Grid polar science project. Grants totaling $8,282,819 have been submitted during

the reporting period or are under continuing review from prior reporting periods. To date PTL has received

$696,906 in grant funding toward FY 2007–08 activities. The total funding brought into IU directly by PTL,

or by other units of IU working in collaboration with PTL, totals $100,598,579.

The Pervasive Technology Labs have achieved the tremendous milestones of more than $100,000,000 in

funding and more than 1,000 publications and presentations. The support of the Lilly Endowment has

transformed the scholarly achievement and grant competitiveness of IU’s information technology and

computer science fields.

Because grants bring jobs, talented professionals, and money into the State of Indiana, they are an

important aspect of PTL’s economic impact. But this impact extends far beyond the millions of dollars of

federal grant and contract money brought into the state. PTL is working directly with the private sector to

help create a vibrant twenty-first-century economy. The Haelan Group, a company partly owned by IU as

a result of investments by the PTL Capital Investment Fund, has been purchased by another company, and

Indiana University expects to receive a significant return on its investment. During the last reporting period,

PTL and its related spin-off companies received a total of $1,041,000 in grants related directly to economic

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development (particularly Small Business Innovation Research and Small Business Technology Transfer

grants). Anabas, Inc., and the Community Grids Lab received SBIR and STTR funding in the amount

of $941,000. This funding included an SBIR Phase II award of $742,000. Getting a Phase II award is

particularly notable, and this reflects the early success of prior funding.

Businesses related to PTL and the PTL Capital Investment Fund are also reaching important turning

points. The vast majority of new startup companies fail, and PTL-related companies are not immune from

the risk of failure inherent in starting new companies. Two companies related to PTL have suspended

their activities. With lessons learned from the cessation of activities of one company, paired with new

innovations, the Open Systems Lab has developed White River Labs, a new company started during this

reporting period.

Another sign of the ongoing maturity of initiatives aided by the IPCRES grant from the Lilly Endowment

is the recent “changing of the guard” at the IU School of Informatics. Founding Dean Mike Dunn

has retired, and Robert Schnabel has assumed leadership of the school. In many ways this signals the

successful completion of the startup phase of the School of Informatics and its maturity as part of

Indiana University.

Collaborations between PTL and the rest of IU have achieved new heights in importance and impact

—both within Indiana and with other national and international research and educational groups.

Pervasive Technology Labs teamed up with Oklahoma University, the National Center for Supercomputer

Applications, and other national research labs to put on a national competition of weather science

students. The WxChallenge pitted 64 teams against each other in an NCAA-style playoff to determine

which team could do the best job forecasting the weather using IU’s Big Red supercomputer and Science

Gateway software developed under the leadership of PTL Science Director Dennis Gannon. This is just

one example of more than 15 events that collectively exposed hundreds of students to new frontiers in

cyberinfrastructure thanks to PTL outreach efforts. PTL has also been exceedingly active in providing

information to residents of the State of Indiana. More than 35 press releases or articles related to PTL

activities were published in the popular media, and several outreach events were held to educate Hoosier

children and families. The Community Grids Lab has also enjoyed tremendous success in outreach to

faculty and students at minority-serving institutions, particularly the Navajo Nation. As a result, faculty

and students alike at minority-serving institutions are better able to take advantage of new information

technology developments. The involvement of the Community Grids Lab is expected to transform the

way the Navajo Nation uses Web 2.0 tools as community-building mechanisms, enabling communication

across large distances in sparsely populated areas of the U.S. West.

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Particularly notable accomplishments of the Pervasive Technology Labs are summarized below on a

lab-by-lab basis:

· TheOpenSystemsLab(OSL)had a successful period, with the launching of the lab’s second

spin-off company, White River Labs, LLC, this spring. The OSL research team also received two

new grant awards, completed one new Ph.D., and had nine new software and version releases,

including Version 1.2 of its highly regarded Open MPI software library (the software that runs many

of the most powerful supercomputers in the world). In March new technologies for enabling Open

MPI to continue running applications even when part of a supercomputer fails were incorporated

into Open MPI project and will be included in Version 1.3 when released in late 2007. This is

particularly important given that as supercomputers get larger and larger, with tens of thousands of

processors, it is simply unavoidable that components will fail as programs are executed. Open MPI

is the best solution yet to address this fundamental problem in the evolution of supercomputers.

Programming such supercomputers is a notoriously difficult challenge. OSL researchers continue

to pursue several projects to modernize and simplify supercomputer programming, including

the development of a library of programming tools called the Boost MPI Library. OSL is working

directly with many of IU’s domain scientists as well. For example, OSL is working with IU’s

Biocomplexity Institute to bring improved computational methods and resources to the analysis of

electrical activity in the brain, thus supporting one of IU’s key strategic priorities in its Life Sciences

Strategic Plan.

· TheAdvancedNetworkManagementLab(ANML) received two new grant awards during the

period and made significant progress in its wireless research. ANML filed for expanded patent

protection of its wireless locator technology and is engaged in discussions with an Indianapolis-

based company to explore possible venture capital investment in commercialization of this

technology. ANML researchers remain focused on cybersecurity and have released a second version

of “Hflow,” a forensic data synthesis tool that provides unique capabilities for tracking “bad actors”

through the Internet. The ANML deepened its involvement with Indiana’s ChaCha Search, Inc.,

helping the company to identify potential security risks and educating it on available methods of

risk mitigation. ANML researchers also engaged in extensive community outreach during the period,

helping educate young Hoosiers on technology and related careers.

· TheCommunityGridsLab(CGL)saw five students earn Ph.D.’s during the spring semester,

bringing to 51 the total number of students to successfully defend a Ph.D. thesis under the

supervision of CGL Director Geoffrey Fox over the course of his distinguished career. With CGL,

Fox is also enjoying one of the most successful periods of his career in obtaining external funding.

CGL received two additional grant awards during the period, bringing total funding received by

CGL since inception to more than $9,000,000. As mentioned previously, the CGL recently received

notification that they have been awarded a nearly $2 million grant from the National Science

Foundation that will begin in August 2007 to support their Polar Grid project. The lab continues

its core research in grid and Web services architecture and has recently begun to focus on mixing

Web 2.0 with grid/Web services. One highlight of CGL activities is a new collaborative polar grid

cyberinfrastructure development effort for the modeling and remote sensing of ice sheets used to

study climate change. CGL is also currently in discussions with ChaCha Search, Inc., to explore

integrating ChaCha capability into a minority-serving institution/research scientist “match-making”

portal under development by CGL scientists. CGL hopes to submit Small Business Innovation and

Research (SBIR) and Small Business Technology Transfer (STTR) grant proposals with ChaCha in

the near future. The lab is currently involved in other successful SBIR and STTR projects.

· TheVisualizationandInteractiveSpacesLab(VISLab)continues its commitment to science and

technology education in Indiana, making significant progress on its Discovering the Science of

the Environment (DSE) program with partners at the IUPUI Center for Earth and Environmental

Science. The DSE team conducted a weeklong environmental science workshop for Indiana science

educators and took delivery of a 20-foot mobile science education trailer during the reporting

period. The program recently received additional funding from several major companies and

foundations. The VIS Lab also advanced its VisPort visualization portal project and continued

research in the area of health monitoring—specifically, the use of mobile devices to support

individuals with kidney disease, an National Institutes of Health-funded collaborative effort

with the IU School of Nursing led by Kay Connelly. Connelly, whose affiliation within PTL was

transferred to the VIS Lab during the reporting period, received an IU Outstanding Junior Faculty

Award and the IU Trustees Teaching Award for 2006–07.

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· TheScientificDataAnalysisLab(SDALab) has continued to collaborate with researchers at

Indiana University and Purdue University. SDA Lab Associate Director Randy Heiland is presently

on leave from Pervasive Technology Labs and is working within the Research Technologies Division

of University Information Technology Services. While the future path for the SDA Lab is unclear,

and though its affiliations and organization may change, it is clear that the important activities of

the Scientific Data Analysis Lab will continue within Indiana University.

· TheKnowledgeAcquisitionandProjectionLab(KAPLab)had an active period, with two

students receiving Ph.D.’s and KAP Lab researchers launching a project with Purdue astronomers

to develop remote access capability to a 20-inch robotic telescope used for teaching students from

junior high through college. KAP Lab researchers also assumed a leadership role in the National

Science Foundation-funded CrystalGrid Framework crystallography project as an extension of

their work on the Common Instrument Middleware Applications (CIMA) project. This project will

create unprecedented possibilities for research collaborations of scientists who study the structure

of chemical compounds within the United States. Other notable activities during the reporting

period include participation in the previously mentioned PolarGrid project with the CGL and a

collaborative effort with the IU School of Informatics to develop next-generation performance

support systems for disaster management. This reporting period the KAP Lab also established a

relationship with the P-16 Center in the IU School of Education to participate in a project aimed at

helping Hoosier teachers and strengthening Indiana schools.

II. LAB rEpOrTs

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II.1 OpEN sysTEms LAB

AndrewLumsdaine, Director

LabMission

The mission of the Open Systems Lab (OSL) is to develop science and technology

for computing with large-scale and pervasive hardware and software systems,

to enable more productive computing and software development, and to foster

economic development in the State of Indiana. Work in the OSL is motivated

by the changing nature of modern information technology systems. The OSL

advocates open standards and open source software as technologies

for enabling modern pervasive systems to seamlessly interoperate.

SummaryofKeyLabActivities

Current research projects at the OSL remain focused in five core areas:

Parallelanddistributedcomputing. Most of the world’s largest supercomputers depend on use of a

Message Passing Interface software library to enable communication among the thousands of processors

within such computers. The OSL is currently spearheading several efforts in high-performance parallel and

distributed computing to improve reliability, availability, and scalability of these environments, including

the Open MPI and OSCAR projects.

Scientificsoftware. As computation becomes an increasingly important tool for science and informatics,

the OSL is developing tools, practices, and curricula to allow scientists and informaticians to effectively

develop software while maintaining a primary focus on their research.

Next-generationprogrammingtoolsandlanguages. One of the major stumbling blocks to the use of

supercomputers is that they are simply too hard to program. The OSL is creating tools to enable large-scale

pervasive software applications that will make it qualitatively more straightforward to harness the power

of modern supercomputers. Key OSL activities in this area include continued research into the theory of

generic programming as well as its practical application in programming languages, software libraries, and

software applications.

Automaticdeviceconfiguration. Recognizing the increasing number of mobile devices in use, the OSL is

developing technologies for these devices to be able to automatically configure themselves based on context

and user preferences.

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Applications. The OSL is collaborating with several research groups at IU and elsewhere to apply its

research results to other scientific projects. Collaborators include the IU BioComplexity Institute, the

School of Informatics, the School of Library and Information Science, and University Information

Technology Services.

ResearchandDevelopmentActivity

The Message Passing Interface (MPI) library standard defines the most critical tools in existence for

programming supercomputers. Without MPI, it would be impossible to run today’s largest supercomputers.

The OSL’s Open MPI project remains at the forefront of the high performance computing community in

research and development of a production-quality, open source version of this important standard. In

addition, Open MPI provides many new research-produced features and performance enhancements not

previously available in an open source MPI implementation. Open MPI enables robust scientific computing

across thousands of computers, allowing scientists and engineers to focus on their work rather than the

mechanics of parallel computing.

Version 1.2 of Open MPI was released in March 2007, incorporating many major performance

improvements over previous releases, as well as new features derived from recent research. One of the

major problems in managing large supercomputers is the problem of component failure. With thousands

of processors and tens of thousands of individual parts in a modern supercomputer, something breaks, on

average, more than once a day. Many calculations running on large supercomputers take days or weeks to

complete. This means that it is essential to create tools that enable large applications to run successfully

even when part of the supercomputer on which they are running fails. The traditional method of dealing

with this problem—saving intermediate results and restarting calculations each time there is a failure—

simply will not work when it takes hours to write the data required for a restart and a failure can be expected

every few hours. The OSL has developed a fault tolerance framework for Open MPI that enables programs to

continue running even in the event of a hardware failure.

This facility was incorporated into the current development code base for the Open MPI project and will

be included in version 1.3 of Open MPI when released in late 2007. Demonstrating the commitment to a

production-quality and feature-complete implementation of the MPI 2.0 standard, a variety of maintenance

and bug-fix releases were also made in the first half of 2007, including versions 1.1.4, 1.1.5, 1.2.1, 1.2.2,

and 1.2.3. The MPI Testing Tool (MTT) continued to be used and enhanced during this period, performing

automatic regression testing of the Open MPI code base on several computer clusters at Indiana University.

The OSL is pursuing several projects that modernize and simplify parallel programming interfaces in

mainstream languages, particularly for multi-core computing and cluster computing. The Boost.MPI

library provides a high-level, high-performance C++ approach to the Message Passing Interface (MPI, as

implemented by Open MPI) that drastically simplifies many common parallel-programming tasks in a

cluster computing environment. By building Boost.MPI on top of the industry-standard MPI interface and

subjecting it to the rigorous Boost peer-review process, the Open MPI team can make cluster computing

more accessible to researchers and professional programmers alike. Additionally, the Boost.MPI library

has become the foundation upon which the project team is building next-generation, parallel scientific

computing libraries for linear algebra (the Matrix Template Library) and graph/network processing

(the Parallel Boost Graph Library).

With multi-core home and desktop computers becoming commonplace, the OSL is applying programming

techniques that have been successful in cluster computing to multi-core computing. OSL researchers

have initiated a three-pronged approach to simplify the parallelization of existing programs on multi-

core computers. The first direction involves parallelizing existing software libraries—in particular, the

C++ Standard Library that is used by a large number of desktop applications in industry—so that existing

applications can immediately benefit from multi-core computers.

The second direction the OSL is

pursuing for multi-core computing

involves simplifying and

modernizing OpenMP, an industry

standard for evolving existing

sequential programs into parallel

programs optimized for multi-core

computers. Like Boost.MPI, the

OSL research team’s extensions

to OpenMP aim to provide a

simpler interface that will enable

the parallelization of many more

existing applications than OpenMP

supports today while using a more

intuitive, lightweight mechanism.

OSL researchers are working with

the OpenMP Architecture Review

Board (ARB) to introduce their

Software being developed in the OSL enables researchers to meet the intense computing requirements of modern science by harnessing the power of hundreds or even thousands of processors that comprise modern supercomputers like IU’s Big Red. Photo by Chris Eller.

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OpenMP extensions into the OpenMP standard, making them available to a much larger audience in

industry and academia.

The OSL research team’s newest innovation may be one of the most important advances in programming

for high-performance computing in several years. Called CorePy, this new programming environment

makes it dramatically easier to program new types of processors, such as the Cell processor from Sony,

Toshiba, and IBM. Application developers write their applications in Python, a common and widely used

scripting language. Based on the new paradigm of “synthetic programming” developed in the OSL, CorePy

bypasses the traditional compiler-based tool chain and instead uses a runtime code synthesis engine to let

developers construct high-performance computational kernels without using compiled languages such as C

or C++. Research conducted using CorePy demonstrates how synthetic programming can be used to create

applications that achieve excellent performance on a given platform without the use of compiled languages.

In collaboration with the IU Biocomplexity Institute, the OSL is

working to bring improved computational methods and resources

to analyze the electrical activity of living brain tissue. Understanding

this electrical activity is critical to understanding how the brains of

animals work, and thus is critical to gaining a better understanding

of the human brain. However, even the most basic analysis of data

about the electrical activity of animal brains typically takes many days.

Using CorePy, OSL researchers have been able to provide tools that

perform analysis of neural activity within minutes, rather than days.

These tools will improve scientists’ productivity because they can very

quickly analyze data in many different ways, making it possible to analyze the larger data sets that will be

produced by tomorrow’s denser, more accurate neural activity sensors. The IU Life Sciences Strategic Plan

has identified neurosciences as a key area of strategic focus for IU, and the OSL is aiding IU accomplishment

in this area.

The OSL has been working to transfer the benefits of generic programming and metaprogramming from

the realm of research computing to everyday usage by professional programmers in industry. Generic

programming refers to techniques that allow computer programs to be written in a very general grammar

and then turned into executable computer programs. This programming paradigm has produced greatly

improved software libraries that offer high performance along with high-level, flexible, and intuitive

interfaces that integrate well with existing applications. Working with the ANSI/ISO C++ committee, the

OSL team has introduced extensions into the C++ language to bring these software methodologies into

the mainstream and benefit the millions of programmers already using C++. Two extensions in particular,

variadic templates and concepts, are expected to be in the upcoming ISO C++ standard, due in 2009.

IntellectualAccomplishmentsandExternalFundingActivity

• Nine new packages of open source software were distributed by OSL during the reporting period,

including: Open MPI v1.1.4, Open MPI v1.1.5, Open MPI v1.2, Open MPI v1.2.1, Open MPI v1.2.2,

Open MPI v1.2.3, Boost 1.34.0, Concept GCC version 4.3.0 alpha 6, CorePy Research Release.

• OSL has distributed, to date, 31 open source software packages.

• The lab now delivers 13 online services.

• Sixteen new OSL peer-reviewed publications appeared in print during the reporting period.

• The lab had one new Ph.D. dissertation completed.

• OSL researchers gave a total of 20 presentations during the reporting period.

• Two grant awards totaling $323,000 were made to the lab during the reporting period.

• Four additional grant proposals totaling $1,850,527 were submitted and are under continuing review.

For a complete listing of all Pervasive Technology Labs disclosures, online services, hardware applications,

publications, and presentations, please visit www.pervasive.iu.edu.

EducatingtheResidentsofIndianaandBeyond

Research results from OSL-based projects are being directly incorporated into classroom education,

training, and outreach in a number of ways. For example, research results from OSL’s work on generic

programming have been directly incorporated into courses currently being offered at Indiana University,

Texas A&M University, and Rensselaer Polytechnic Institute. As the OSL contributions to C++ and other

programming languages become standardized parts of these languages, they will be incorporated into the

basic programming curriculum at numerous institutions.

The OSL was instrumental in organizing and supporting the inaugural Boost Libraries Conference

(BoostCon ‘07), held May 14–18, 2007, in Aspen, Colorado. Devoted to the development and use of next-

generation generic C++ libraries, BoostCon ‘07 attracted nearly 100 attendees from around the world. The

conference was extremely successful and planning is under way to make it an annual event.

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Google’s Summer of Code is the open source equivalent of an internship program. Students apply to work

on an established open source software project, and each is paired with a mentor from that project who

will help the student learn skills for software development and collaboration in the open source world.

From the Open Systems Laboratory, Douglas Gregor is mentoring a student working on the Boost project,

and DongInn Kim is mentoring a student working on the Globus/Condor Package for OSCAR.

AcceleratingEconomicGrowth

White River Labs, LLC, is a new spin-off of the OSL created during the current reporting period to

commercialize technology based on synthetic programming. Synthetic programming is a novel paradigm

for creating high-performance applications from scripting languages, enabling a high level of developer

productivity without sacrificing runtime performance. CorePy, the first programming package created

for synthetic programming, uses the Python programming language to provide a synthetic programming

environment for IBM’s PowerPC and Cell/B.E. processors. Research conducted in the OSL led to the

development and validation of CorePy and synthetic programming. White River Labs’ founders are

Christopher Mueller, a recent Ph.D. graduate of IU, and Andrew Lumsdaine, the director of the OSL.

BringingDistinctiontoIndianaUniversityandtheStateofIndiana

The OSL’s Open MPI implementation of the Message Passing Interface (MPI) specification remains

OSL’s highest-profile project, helping IU’s Big Red Supercomputer achieve the greatest parallel processing

efficiency. Open MPI was created by an international consortium of several major research labs, including

the OSL. Big Red remains among the world’s fastest supercomputers and positions Indiana University

among national leaders in cyberinfrastructure capabilities. It allows Indiana scientists to conduct leading-

edge research in the life sciences and a variety of disciplines. The OSL’s work on Open MPI has been

instrumental to IU’s continuing advancement in the area of supercomputing.

As evidenced elsewhere in this report, the OSL has a strong track record in developing and releasing high-

quality software, some of which has become quite widely used. In addition, the OSL actively participates in

a number of software-related standardization efforts, including the ISO/IEC JTC1/SC22/WG21 international

working group for the programming language C++, ECMA TC39/TG2, TC39/TG3, TC39/TG5 (C\#, CLI,

and C++), and OpenMP. Much of the work with these bodies has been in support of improved support for

generic programming for the C\# and C++ programming languages, as well as contributions of components

to the Standard Library for C++. The OSL’s work in programming language and software development has

contributed to IU’s reputation as an international leader in these areas.

LabOutlook,July–December2007

Throughout the next six months, the OSL will continue efforts to simplify parallel programming tasks for

multi-core and cluster computers by releasing their parallel programming libraries as open source. OSL

researchers are also initiating a collaborative project with Microsoft to bring their high-level MPI interface

onto the .NET platform to be released as open source. They anticipate that during this time-frame, their

work to bring generic programming support into the C++ language will be completed, with the inclusion

of concepts in the ISO C++0x Working Draft.

The OSL anticipates both future Open MPI maintenance releases and new research initiatives in the areas of

fault tolerance, one-sided communications, additional high-performance transport technologies, collective

communication algorithms, and enhanced run-time systems support. Open MPI version 1.3 is expected to

be released by the end of 2007, incorporating significant work from the OSL in the area of fault tolerance.

The OSL will continue development on its OSCAR project. It will also work to create libraries of software

for supercomputers and continue work in synthetic programming to include important emerging

hardware platforms. The research team will apply the synthetic programming approach to applications in

bioinformatics and network analysis and will seek new application areas. During the next year the OSL will

continue to increase the scope of its interactions with other research groups. The OSL team hopes to expand

collaborations in application areas and to aggressively grow existing collaborations.

II.2 AdvANCEd NETwOrk mANAgEmENT LAB

StevenWallace,Director

Gregory Travis, Assistant Director

LabMission

The mission of the Advanced Network Management Lab (ANML) is to perform

research in the fields of network performance, management, and security; to use

this research to develop new high-tech business opportunities in Indiana; and

to contribute to IU’s mission by collaborating with the School of Informatics,

the Research and Education Networking Information Sharing and Analysis

Center (REN-ISAC), the Center for Applied Cybersecurity Research (CACR), and the Global Research

Network Operations Center (Global NOC). ANML provides support for facility research, including

partnering on grant applications, network security education in support of CACR, network forensics

assistance to REN-ISAC, and the development of new tools for Global NOC. ANML meets this mission

with a combination of basic research, applied research and development, education, and entrepreneurial

development.

SummaryofKeyLabActivities

The Advanced Network Management Lab began 2007 with an all-hands retreat at the Stone Age Institute

in Bloomington. The goal of the event was to identify the lab’s strengths in terms of intellectual capacity,

collaborative capacity, and physical infrastructure.

Key areas identified for further development, given lab strengths, were:

• Corporate partnerships

• Network anomaly detection, including fraud detection

• Wireless development

• Facilities development, particularly as a data repository

• Research publications

• Software development

Moving forward on priorities identified during the retreat, the ANML subsequently initiated a new program

of external outreach and education, as well as a new program and infrastructure for the sharing of lab-

collected and produced network data. The ANML’s existing programs in the fields of cybersecurity and

wireless infrastructure were redefined and refocused.

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ANML is currently involved in several corporate collaborations

detailed below. It partners with the University of Michigan on a

Department of Homeland Security-funded project for the study

of “Botnets”—collections of software robots, or “bots,” that

work together, often for malicious purposes. ANML researchers

are also collaborating with the IU School of Informatics

on a Web site-ranking project. The lab has a new initiative

with Hewlett-Packard to jointly develop software and course

materials. And finally, the lab has grown an active relationship

with ChaCha Search, Inc., founded by Indiana entrepreneur

Scott Jones, collaborating and assisting the company with

service development.

ResearchandDevelopmentActivity

WirelessResearch

ANML continues to develop its wireless device location system

designed to pinpoint wireless devices such as laptops,

Personal Digital Assistants (PDAs), and cell phones for

purposes such as emergency response, incident handling,

and cybersecurity.

The research team filed for patent protection

for various aspects of the technology and,

during this quarter, expanded that patent

protection with a filing for a worldwide

patent. The lab is collaborating with the

University of California, San Diego (UCSD)

on this work and has been integrating

UCSD’s open-access, open-source “CalRadio”

technology into their hardware.

The wireless locator project team is currently

working on a second generation of the

system. Second-generation features include a

fast multiplexer operating at radio frequency,

a new tuner and integrated signal strength

ANML’s custom-designed and built wireless locator antenna.

ANML developed software code for the ANML wireless locator.

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meter, and custom Field Programmable Gate Array (FPGA)-based control circuitry. Together these new

features should allow the wireless locator antenna to identify the source of a wireless network transmission

on the basis of just one packet—the smallest possible unit of wireless computer communication.

Cybersecurity

ANML researchers have been analyzing user web-surfing behavior by examining “click data”—information

on which sites are visited from a given site—off of IU’s network. This has resulted in the development of a

system that performs automatic discovery of non-obvious relationships between Web sites. This discovery

is based on the use of Mutual Information (MI)—specifically, information known about both Web sites—

as opposed to the traditional approach of constructing a model of the relationship and empirically testing

that model.

Precision of future predictions made using single-hour segments of web traffic data.

The figure on the previous page shows values of precision derived by trying to use a single hour of Web

traffic data to predict (1, 2, ...) hours into the future. In this case, precision is a measure of the proportion

of predicted Web clicks that actually took place; true positives contribute to the score and false negatives

detract from it. The data show a strong daily cycle to Web traffic in that one hour of data is more effective

at predicting user behavior at the same time of day tomorrow than just a few hours in the future. The data

also show that over a third of Web traffic is basically static: users follow links between the same pairs of sites

again and again, regardless of the time of day.

ANML has made presentations on its predictive systems at the IU School of Informatics, and several

publications on the research are undergoing peer review.

ANML researchers continue their relationship with the Honeynet Alliance, a federation of universities and

corporate researchers engaged in research and development of cyberforensic tools. ANML’s significant

contributions include the Sebek system, which facilitates the capture of malicious computer activity

even when the intruder has employed sophisticated technologies in an attempt to elude detection and

reconstruction by hiding or encrypting his operations.

ANML also develops the “Hflow” portion of the Honeynet software suite. Hflow is an integrated data

synthesis component that takes forensic information from a number of sources such as Sebek, network flow

records, operating system identification, and others to produce a single set of records detailing each activity

on a computer system that can be used for later recall and analysis. Such comprehensive views are essential

for tracking malicious activities on the Internet, since it is now possible to use several types of programs to

disguise malicious activities.

ANML recently released a second version of the Hflow system, a set of tools used to catch and identify

bad actors on the Internet, and presented a paper on its work at the Institute of Electrical and Electronic

Engineers (IEEE) Information Assurance Workshop, held in June 2007 at the U.S. Military Academy in West

Point, New York.

ANML researchers are also developing, in association with the IU School of Informatics, a system called

“Nettrust,” which allows a group of peer individuals to rank Web pages in two simple directions: badness/

untrustworthiness and goodness.

Badness or goodness is determined by individuals based on their perception of the site’s value, placing

special emphasis on the site’s trustworthiness. To that end, Nettrust employs technologies that allow

not only for the ranking of sites, but also provide tools to help the user determine if sites representing

themselves as online financial services (banks or portfolio management services, for example) are truly who

or what they claim to be.

2�

Above are two figures showing the Nettrust software “plug-in” installed on the Firefox browser platform.

The first image shows Nettrust on the popular eBay Web site, and the second shows it on Indiana

University’s Bloomington Web site. Users can see peer rankings of the sites on the red and green bars under

the address bar and can view the system’s confidence that the site represents a legitimate online banking

service by looking at the icon to the right of the word “Bank?”

ANML is a partner in a successful grant proposal with the University of Michigan and the Michigan

Educational and Research Information Triad (MERIT). The work is funded by the Department of Homeland

Security, and ANML received funding and began formal work on the project in June 2007. Technologies

being developed under the grant include an incident correlation and detection system for the United States

Computer Emergency Readiness Team (US-CERT). This system correlates activities known to be associated

with “Botnets” (networks of infected or otherwise compromised computers under the control of an

unauthorized individual or individuals) and merges them into a daily report of suspected compromised

systems so that further human action can be taken in the cases. Botnets are problematic because they are

used to launch “denial of service” attacks against important hosts such as network nameservers, popular

search engines, and other critical aspects of cyberinfrastructure. They can also be used as illegitimate sources

of e-mail “spam” and other similar disruptions.

The Nettrust browser plug-ins

AdvancedNetworkManagement

ANML conducted two major activities related to network management during the reporting period.

First is the development of a national map showing the emerging regional networks, such as

Indiana’s Ilight network, and suggesting ways in which the regional network infrastructure can be

leveraged for national gain.

Regional research and education networks in the United States

ANML’s new four-terabyte research data repository will make security-related data available to the research community.

25

ANML has also purchased and is building a data repository to store network traffic data about the activities

of ILight and Abilene. ILight is the high-speed research and education network linking universities and

colleges throughout the United States. Abilene is the United States’ fastest network supporting research

activities. A database of the activity patterns of these networks is being assembled by ANML, which will

prove a treasure trove for network researchers throughout the United States. ANML’s database currently

resides on four terabytes of online disk and will be made available to network researchers worldwide for

use in their experiments, research, and operational testing.

ANML’s data repository will fill two needs. First, it will act as an aggregator for global network information,

such as Internet2 NETFLOW records, that ANML is positioned to collect. Second, it will provide the

platform for aggregated, summary, and value-added data about network activity—including network security

threats—that are produced by ANML’s cybersecurity analysis research systems. Examples of the latter include

outputs from ANML’s “darknet” detectors, the lab’s network graph correlators, Border Gateway Protocol

(BGP) monitors, and other value-added data products.

The research team plans to develop a system in which the network will be made available to all researchers in

the security community. Researchers who wish to access data from the repository can sign in via a simple Web

interface and be presented with a catalog of available data products. In turn, the system will require attribution

to ANML and IU in any research products, papers, or other intellectual output resulting from accessed data.

The pace and capabilities of U.S. networking performance and security research will be enhanced, new research

capabilities will be created, and the role of IU and the PTL will be highlighted as well.

IntellectualAccomplishmentsandExternalFundingActivity

• One patent held by the lab was upgraded to a worldwide patent during the reporting period.

• The lab distributed two new packages of open source software.

• The lab gave a total of five presentations during the reporting period.

• Two new grant awards totaling $298,307 were made to the lab.

For a complete listing of all Pervasive Technology Labs disclosures, online services, hardware applications,

publications, and presentations, please visit www.pervasive.iu.edu.

EducatingtheResidentsofIndianaandBeyond

To support strategic goals identified in its winter retreat, ANML has initiated an expansive public

outreach and education program. During the winter several ANML staff members traveled the state

giving presentations to middle and high school students interested in technology and networking

topics (see Outreach section).

In addition to travel, ANML has initiated a program of monthly network security tips, internally called

“Security Sam.” The lab presents topics of general interest such as home wireless security, password

protection, and other issues important to Hoosiers in an increasingly wired and interconnected world.

“Security Sam” tips have appeared so far in IU’s Living Well publication (see Appendix 10).

ANML has also conducted two on-site summer workshops for Hoosier high school students. The first,

conducted in conjunction with the IU School of Informatics, was done during IU’s annual Informatics

Summer Camp. The second, hosted entirely by Pervasive Technology Labs staff, was held in both ANML

and University Information Technology Services (UITS) facilities.

Both workshops involved hands-on activities by the students in which they learned to identify their

computers on the Internet, recognize when their computers were under attack by others on the Internet,

and decide on the appropriate response from a moral, technical, and legal perspective. Both workshops

were well-attended, and the lab plans to conduct similar workshops on a different topic next summer.

AcceleratingEconomicGrowth

ANML continues to be involved in technology transfer and technology consulting with Indiana

corporations. During the reporting period ANML deepened its relationship with ChaCha Search, Inc.,

a company founded by Indiana entrepreneur Scott Jones.

During the reporting period ANML researchers collaborated with ChaCha, helping the company identify

circumstances under which the “gaming” of their system by unscrupulous individuals might occur and

educating them on possible methods of mitigation. ANML also participated in an Indiana 21st Century

Research and Technology Fund grant submission with ChaCha in which the company proposes to bring its

technology to mobile devices such as PDAs and cell phones. ANML’s role in the grant, should it be awarded,

would be to help Cha Cha address the unique security considerations of mobile computing and to develop

voice recognition capability for mobile devices.

Also during the reporting period, ANML team members conducted talks with Booksource, an Indianapolis-

based IT company, to explore possible venture capital investment in ANML’s radiolocator technology.

27

BringingDistinctiontoIndianaUniversityandtheStateofIndiana

ANML staff members continue to travel to industry and academic conferences, reporting on the lab’s

progress and research. In the reporting period ANML presented on cybersecurity topics at the eighth

annual IEEE Information Assurance Workshop, held at the U.S. Military Academy. ANML also presented

on infrastructure and cybersecurity at the EDUCAUSE 2007 annual conference in Denver, Colorado.

Finally, ANML presented on its wireless technology at the IEEE International Conference on Portable

Information Devices.

ANML staff is also highly involved in merger planning activities between the national Internet2 research

and education network backbone and the NLR network.

LabOutlookJuly–December2007

During the next six months ANML plans to focus on the following:

• Continued development of botnet detection with the University of Michigan, leading to a Phase II

proposal to the Department of Homeland Security for a next-generation botnet detection system.

• Ongoing development of ANML’s unique wireless radiolocation system.

• Further research and development of advanced network anomaly detection, specifically the use of graph

theory as a replacement for traditional signature and rate detection of cyber attacks.

• Increased collaboration with outside entities for both research and development and economic

development purposes.

• Continued and expanded public outreach and education programs.

In addition to these ongoing activities, ANML researchers are beginning the prototype phase of a new

type of cybersecurity simulation and monitoring system based on a Department of Homeland Security

requirement recently transmitted in a Broad Agency Announcement (BAA). ANML hopes to combine

its knowledge of computer networks and cybersecurity with the work of Pervasive Technology Labs’

Visualization Lab to create a unique system of network visualization, attack simulation, and attack

scenario war-gaming. The lab anticipates this will be a major development effort.

ANML will also expand its nascent data repository, both in depth of data available as well as

value-added services.

II.3 COmmuNITy grIds LAB

GeoffreyFox,Director

Marlon Pierce, Assistant Director

LabMission

The mission of the Community Grids Lab (CGL) is to create the technology that

will enable grid computing to help solve important scientific problems. In creating

new global communities, grid computing will open the way to new possibilities for

e-business and e-science. CGL focuses on creating new technology infrastructure and

applications that will enable distributed business enterprises and cyberinfrastructure

for distributed science and engineering. Computers and networks are getting faster; the distinction between

computers and the network is blurring. This points to a future where individuals and corporations interact

with grid-based applications without needing to explicitly manage the underlying technological details.

CGL’s focus on applications has spawned much cross-disciplinary collaboration in research and development

of scientific and business applications. A current major emphasis is in earth science and particle physics, with

other projects in education, biocomplexity, chemistry, apparel design, digital film production, and sports

informatics.

SummaryofKeyLabActivities

Established in 2001, CGL includes Director Geoffrey Fox, Assistant Director Marlon Pierce, four senior (post-

doctoral) research associates, three software engineers, and 14 Ph.D. candidates. CGL has an international

visitors program that hosted three Chinese, one Japanese and one Korean scholar in the 2006–07 academic

year. Visiting scholars were supported by their governments to collaborate with the Community Grids Lab

for periods ranging from three months to one year. Visiting students participate in IU’s academic program

while performing research in the laboratory. Fifteen CGL students have received their Ph.D.’s since the lab’s

inception, and the lab expects approximately six more students to graduate in the coming year.

CGL is devoted to the combination of excellent technology and its application to important scientific

problems. Director Geoffrey Fox has been committed to this method since he established the Caltech

Concurrent Computation Program (C3P) nearly 25 years ago. Technologies used by CGL researchers have

changed along with the field. Fox started with parallel computing from 1983 until 1995, and then moved

to Web-based computing and education with collaborative technologies. Starting in 2000, Fox and his

research team began to focus on grids as broadly defined to include communities and collaboration.

Recently CGL’s focus has been on multi-core programming and applications, while their grid work

continues with a Web 2.0 flavor. CGL, PTL, and IU in general expect to benefit greatly from the very early

recognition of the importance of Web 2.0 technology as a pervasive and transformational force in society

and computer science.

29

Individual project activities are described in the following section.

ResearchandDevelopmentActivity

GridArchitecture

CGL continues its core research in grid and Web services architecture, which acts as a backdrop to all its

projects. It finished a general analysis of services with Dennis Gannon to identify areas in which further work

is needed by the global community. This activity identified data and metadata federation as a critical area

in which some approaches exist, but no consensus has been reached on the appropriate architecture. CGL’s

research in grid management was received well in international conferences last year, and lab researchers

now believe practical systems will inevitably mix Web 2.0 with grid/Web services, so this has become a

recent research focus. CGL researchers are also exploring the integration of coarse grain parallel computing

with grid workflow, looking for possible unified approaches. This work benefits greatly from CGL’s close

involvement with the Open Grid Forum, in which CGL members lead e-Science and study groups.

ParallelismandMulti-CoreChips

The computer industry will be revolutionized by new chip architectures with multiple cores (processing

units) on the same chip. This is illustrated by the Cell processor that has been developed by IBM for gaming

and is highlighted in their new Indianapolis center. Moreover, even commodity Intel chips now have four

and will have more than 100 cores in the next five years. These designs require less power and potentially

offer huge performance increases. However, this functionality requires an individual to learn how to take

parallel computing expertise largely confined to the science and engineering domain and apply it to the

broad range of applications that run on commodity clients and servers. CGL is just starting a major effort in

this area funded by industry in collaboration with Rice University and the University of Tennessee. Initial

project work is focused on studying a range of Advanced Micro Devices (AMD) and Intel and Sun multi-

core architectures and evaluating their performance. CGL researchers are looking into a possible universal

runtime for the different forms of parallelism and are also exploring parallel data-mining algorithms for

multi-core chips.

CGL is currently researching the use of data-mining and clustering techniques as an important application

for multi-core technology. CGL scientists are applying the technology to problems in geographical

information systems (census clustering) and chemical informatics (chemical space clustering).

SemanticScholarGrid

Semantic Scholar Grid is a new project that started in 2006, exploring futuristic models for scientific

publishing by developing Web 2.0 social networks to support the sharing, annotating, and semantic analysis

of scientific data and papers. CGL researchers are building Web service tools that allow capability integration

of key systems such as del.icio.us and Google Scholar.

ChemicalInformaticsandCyberinfrastructureCollaboratory(CICC)

The NIH-funded CICC project is building the Web services, Web portals, databases, and workflow tools

that can be used to investigate the abundance of publicly available data on drug-like molecules contained

in the National Institutes of Health (NIH) PubChem and Developmental Therapeutics Program (DTP)

databases. As part of this effort, the CGL team has developed numerous services, including online services,

for accessing statistical packages, data services, and user interfaces that allow users to search for full three-

dimensional chemical structures of the one million drug-like molecules currently in PubChem. These data

can be used as inputs in many other calculations. A prominent example includes an online docking results

service that CGL also developed that calculates the ability of drug-like molecules to attach themselves to

much larger proteins. The initial versions of these calculations were used in the inaugural run of IU’s Big

Red supercomputer. CGL has also developed Web services in collaboration with Cambridge University for

performing chemistry-specific document mining. This text mining tool (OSCAR) can be used to extract

chemical information and other

metadata from abstracts and journal

articles available from the NIH Entrez

PubMed system. CGL researchers

have used this information to drive

simulations (such as structural

calculations described above) on Big

Red, but they also see many other

potential applications.

The NSF CI-TEAM Minority-Serving Institutions Cyberinfrastructure Empowerment Coalition (MSI-CIEC) has enabled some initial MSIs to partner with CI projects and resources to enhance education and research needs of MSI faculty and students to be competitive in the global, knowledge-based economy and society of the twenty-first century.

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Minority-ServingInstitutionsCyberinfrastructureOutreachProjects

The Minority-Serving Institutions Cyberinfrastructure Outreach Projects initiative will help ensure that a

diverse group of scientists, engineers, and educators from historically underrepresented minority institutions

are actively engaged in the development of new Cyberinfrastructure (CI) tools, strategies, and processes.

The key strategy is not to identify particular universities with which to collaborate, but rather to interact

with the Alliance for Equity in Higher Education. This consortium is formed by AIHEC (American Indian

Higher Education Consortium), HACU (Hispanic Association of Colleges and Universities) and NAFEO

(National Association for Equal Opportunity in Higher Education) and ensures our efforts will have

systemic impact on at least 335 minority-serving institutions. CGL’s current flagship activity is MSI-CIEC,

Minority-Serving Institution Cyberinfrastructure (CI) Empowerment Coalition, which builds on the success

of our initial Minority-Serving Institutions Cyberinfrastructure Institute (MSI CI2) project. Activities include

workshops, campus visits, and pro-active linkage of MSI faculty with cyberinfrastructure researchers.

EarthquakeCrisisManagementinaGridofGridsArchitecture

This U.S. Department of Defense (DoD) Phase II Small Business Innovation Research (SBIR) project

is led by Pervasive Technology Labs seed-fund recipient Anabas, Inc., with CGL and Ball Aerospace as

subcontractors. The project team is creating an environment to build and manage net-centric grids from

services and component grids. CGL technologies, including Geographic Information System (GIS) and

NaradaBrokering systems, will be used, and CGL will also supply non-military applications including

earthquake crisis management.

ParticlePhysicsAnalysisGrid

This Department of Energy Phase I SBIR project aims to develop an interactive grid using streaming

data optimized for the physics analysis stage of Large Hadron Collider (LHC) data grids. This approach

differs from the mainstream work of the Open Science Grid and Enabling Grids for e-Science (EGEE),

which concentrate on the initial batch processing of the raw data. CGL has developed a novel concept

called “Rootlets” that provides a distributed collaborative implementation of the important European

Organization for Nuclear Research (CERN) Root analysis package.

PolarGrid

Polar Grid is a new activity stemming from CGL’s collaboration with Elizabeth City State, a historically black

university in North Carolina. CGL researchers are working with the Center for Remote Sensing of Ice Sheets

(CReSIS), a National Science Foundation Science and Technology Center led by the University of Kansas, to

define and implement cyberinfrastructure used to support the modeling and remote sensing of ice sheets.

The recent dramatic evidence of the impact of climate change on the polar regions makes this an urgent

project of global importance. CGL recently received notification that it and its partners have been awarded a

grant from the National Science Foundation totaling $1,964,049 to support the Polar Grid project. Project

work under this grant will begin in September 2007.

QuakeSimandGISGridProject

The QuakeSim project (formerly known

as SERVOGrid) was re-funded through

the National Aeronautics and Space

Administration’ (NASA) Advanced Information

Systems Technology (AIST) and Achieving

Competence in Computing, Engineering, and

Space Science (ACCESS) programs. The AIST

funding continues work led by Dr. Andrea

Donnellan at NASA Jet Propulsion Laboratory

(JPL) to build the distributed computing

infrastructure (i.e., cyberinfrastructure) begun

under previous NASA AIST and Computational

Technologies (CT) program grants. CGL’s

focus in this project will be to convert the

QuakeSim portal and services into a National

Science Foundation (NSF) TeraGrid Science Gateway. CGL researchers are updating the QuakeSim portal

to be compliant with current Java and Gateway standards. They are also developing workflow and planning

services that will enable QuakeSim codes such as GeoFEST and Virtual California to run on the best

available NSF and NASA supercomputers.

The NASA ACCESS project is a

joint venture that combines team

members from the QuakeSim project

with the NASA Research, Education

and Applications Solution Network

(REASoN) project. CGL’s goal in this

project is to develop and exchange

portal components and Web services

with the REASoN team. Exchanged

components include GRWS, a GPS

data service developed by University

of California, San Diego/Scripps;

Analyze_tseri, portlets and services

developed by CGL and adopted by

the REASoN team; and Regularized

Polar Grid showing linking of participating institutions to cyberinfrastructure at ECSU, IU, TeraGrid, and multiple base and field camps associated with scientific observation expeditions.

The QuakeSim Portal being used to select and analyze Southern California Global Positioning System.

��

Deterministic Annealing Expectation-maximizing Algorithm for Fitting Hidden Markov Models (RDAHMM),

GPS data-mining services developed by CGL using JPL codes and adopted by the REASoN team.

CGL’s work during this period was dominated by a complete redevelopment of the QuakeSim portal and

several of its Web services for GPS station analysis and seismic deformation analysis. These included major

revisions to the Geophysical Finite Element Simulation Tool (GeoFEST), Disloc, Simplex, Analyze_tseri, and

RDAHMM services in an effort to make them more self contained and independent of the portal clients.

This means they can be easily used by other client applications such as the Taverna workflow composer.

CGL scientists build portlet Web interfaces that combine Java Server Faces and Ajax/Google Maps. They have

also recently developed a plotting service that produces Google Keyhole Markup Language (KML) markups

of grids and vector points, useful for representing the results of applications such as Disloc and Simplex.

OpenGridComputingEnvironments(OGCE)

The OGCE project provides generic portal software suitable for building scientific Web portals and gateways.

This NSF-funded project operates as a consortium of several universities, led by the Community Grids

Lab. The OGCE is currently in a no-cost extension phase after the formal project ended in August 2006.

The project will be continued through a new grant award from the NSF Office of Cyberinfrastructure.

A significant milestone for the project was the release of version 2.1 of the core portal software, which

included a Condor-G portlet interface. The interface can be used to submit jobs to Globus through the

Condor interface and thus inherit Condor’s matchmaking capabilities. The project team is also completing

an evaluation of the Sakai project as a container for the OGCE grid portlets, eventually replacing the current

Gridsphere-based container. The OGCE’s other major release was the beta version of Grid Tag Libraries

and Beans (GTLAB), an XML markup language that extends Java Server Faces and greatly simplifies the

development of Grid portlets using reusable tag libraries.

The OGCE project will be undergoing a very large shift towards Web 2.0 technologies. The first step in this

process was a major survey and tutorial (see publication lists in appendices).

Also under the OGCE banner, CGL continued a collaboration with Rick McMullen’s Knowledge Acquisition

and Projection Lab on their Common Instrument Middleware Architecture (CIMA) portal. A CGL graduate

student is currently completing the development of a set of instrument Atom news feeds—Web-based

content feeds of CIMA instrument metadata that can be integrated with popular news readers such as

iGoogle and Sage.

NaradaBrokeringProject

The NaradaBrokering project had three new releases (version 1.3.2, 2.0.1 and 2.0.2) during the reporting

period. These releases incorporated support for the major feature of Graphical User Interface-based

deployment of distributed broker networks. This capability significantly reduces the complexity of setting

up and managing broker networks in various topologies.

During this timeframe the NaradaBrokering team presented its research for securely tracking the availability

of entities in distributed systems, typically a precursor to any fault tolerance scheme attempting to mask

failures in distributed components. This research was presented at the 21st IEEE International Parallel and

Distributed Processing Symposium in Long Beach, California.

Because failures often take place in distributed

settings, the NaradaBrokering researchers have

developed a framework for incorporating fine-

tunable redundancies in their reliable delivery

scheme. Their algorithm allows them to guarantee

reliable delivery of streams in the presence of

multiple failures within the system. This work

was presented at the 2007 Institute of Electrical

and Electronics Engineers (IEEE) Conference on

Autonomic Computing in Jacksonville, Florida.

The Clarens effort by the High Energy Physics

Group at the California Institute of Technology has

developed a framework for wrapping capabilities

within ROOT—a powerful particle physics analysis

software suite from CERN—as distributed services. As part of a collaborative effort between IU and the

California Institute of Technology, CGL is developing a loosely coupled framework using NaradaBrokering

to discover and load-balance accesses to services available to physicists for analyzing and collaborating

over data produced in particle physics experiments. This included a site visit in March 2007 to lay the

groundwork for the algorithms and use cases.

OMIISoftware

CGL was funded by the UK Open Middleware Infrastructure Institute (OMII) to develop core Web service

(grid) support for reliable messaging (FIRMS) and notification (FINS). Both software packages have been

successfully deployed within the latest version of the OMII Container. These projects are complete.

CGL’s work on the Clarens project with the California Institute of Technology, which uses Narada Brokering, is funded by an STTR with Deep Web Technologies.

�5

CollaborationGrids:GlobalMMCS(MultiMediaCollaborationSystem)

The Collaboration Grids project generated important input for the audio/video transport component

of NaradaBrokering, and CGL researchers are focusing on improving the core infrastructure and the

application to e-Sports for sharing and annotating real-time video between trainers and athletes. They are

exploring collaborations with China on the 2008 Olympics with a project entitled e-Sports.

e-Sports

E-Sports is a new effort (spun off from GlobalMMCS and working closely with NaradaBrokering

development) that CGL started very recently to enable the following capabilities:

• Managing streams: Play multiple streams while eliminating network-induced effects through the use of

services for ordering, buffering, and jitter reduction.

• Enable active replays: This is the ability to play back certain sections of a live stream while retaining the

ability to revert to the live streams at any time.

• Streams annotation: This refers to the ability to annotate streams and be able to record these annotated

streams at a later time. These annotations can be based on text or graphics. This newly modified stream

would be then be made available for playback or further annotations.

IntellectualAccomplishmentsandExternalFundingActivity

• CGL distributed three new packages of open source software during the reporting period.

• The lab now delivers 55 online services.

• Thirty-five new peer-reviewed publications appeared in print during the reporting period.

• The lab gave 55 presentations during the reporting period.

• Six lab employees earned Ph.D.’s during the reporting period, bringing Director Geoffrey Fox’s career

total of Ph.D. students graduated to more than 50.

• Two new grant awards totaling $75,599 were made to the lab.

• The lab received notice of one additional National Science Foundation award totaling more than

$1,960,000 to begin in August 2007.

• Total external funding received by CGL since its inception topped $9,000,000 for the reporting period

and will exceed $11,000,000 with the newly received NSF award beginning next period.

• Six grant proposals totaling $3,123,924 were submitted during the reporting period.

For a complete listing of all Pervasive Technology Labs disclosures, online services, hardware applications,

publications, and presentations, please visit www.pervasive.iu.edu.

EducatingtheResidentsofIndianaandBeyond

CGL has major activities in outreach to faculty and students at minority-serving institutions. These efforts

are motivated by the observation of Richard Tapia, Rice University professor and distinguished Hispanic

American scientist: “No first-world nation can maintain the health of its economy or society when such a large

part of its population remains outside all scientific and technological endeavors.” CGL has been successful in

four proposals related to these efforts, three from the National Science Foundation and one from the

Lumina Foundation in Indianapolis. CGL’s work hinges on the observation that cyberinfrastructure and its

underlying grid technology inherently bridge the digital divide and can broaden participation in science and

provide better education and business opportunities. Currently CGL’s activities are focused with the Navajo

Nation in providing education and health applications for their grid and with historically black universities

Elizabeth City State University and Jackson State University. The lab is hosting an undergraduate student

this summer from Jackson State as part of IU’s university-wide historically black colleges and universities

initiative. There are clear ways that this work could be extended to K–12 education, but proposals in this

area have thus far been unsuccessful.

AcceleratingEconomicGrowth

CGL partners with several small business ventures that were detailed in previous sections of this report:

• CGL, with partners Anabas, Inc., and Ball Aerospace, won a Department of Defense Phase II SBIR to

dynamically build and manage grids.

• The lab is working on a Department of Energy Phase I STTR with the California Institute of Technology

and Deep Web Technologies.

• Anabas and CGL have recently won an additional Department of Energy Phase I STTR for collaborative

systems.

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BringingDistinctiontoIndianaUniversityandtheStateofIndiana

CGL Director Geoffrey Fox continues as vice president responsible for e-Science for the Open Grid Forum.

He is chair of two major conferences this year: the annual e-Science conference in Bangalore, India, in

December and the next Open Grid Forum event in Seattle this October. In 2007 Fox reached a significant

milestone in his career, having supervised students in the successful defense of more than 50 Ph.D. theses.

Hasan Bulut, who defended this spring, marked the fifty-first Ph.D. earned by a student working under Fox.

Fox has also been given courtesy positions at the University of Southampton (United Kingdom, renewal),

the University of Houston, and the Alliance for Equity in Higher Education to recognize the importance of

collaborative work.

LabOutlookJuly–December2007

GridArchitecture

CGL continues this fundamental activity, focusing on interaction of grid, Web 2.0, and digital

library technology.

ParallelismandMulti-CoreChips

CGL researchers expect this activity to grow in importance with a focus on applications that are likely on

future multi-core clients. This application work will be in conjunction with research in new runtime systems.

SemanticScholarGrid

This flagship Web 2.0 activity will be augmented by a broader range of projects looking at ways of using

Web 2.0 approaches in file transfer, document sharing, and people networking in science and education.

ChemicalInformaticsandCyberinfrastructureCollaboratory(CICC)

Grid computing, and more specifically high-throughput grid computing, is an essential component for

conducting and managing structure and docking calculations that populate database services. CGL scientists

have been investigating problems in grid workflow matchmaking and are implementing a job management

system for the TeraGrid, which should ultimately also work across multiple grid sites. This will be generally

applicable to computing problems (including those in QuakeSim), but the team will concentrate on the

CICC high-throughput problems as the primary implementation of its ideas over the next six months.

CICC also provides a significant opportunity for investigations in applying Web 2.0 techniques to e-Science.

CGL is evaluating the use of Yahoo Pipes as a sample workflow/mashup building tool that can be used

to encode scientific use cases combining several CICC RSS feeds. CGL researchers are also investigating

problems in adapting Start Pages such as Netvibes and iGoogle to support ecosystems of user interface

widgets to CICC gadgets. Finally, the important new area of microformatting for metadata expression and

management will be investigated.

OpenGridComputingEnvironments(OGCE)

The OGCE project has recently been awarded its second National Science Foundation grant from the Office

of Cyberinfrastructure. CGL scientists will be preparing several new components for release this year at

Supercomputing 2007, with a focus on providing components and services to support TeraGrid science

gateways. These will include logging, reporting, and accounting tools; batch queue wait time predictors;

and computational science management tools.

Also at Supercomputing 2007, CGL staff will host the third annual GCE workshop. Paper proceedings will

be published in the journal Concurrency and Computation: Practice and Experience.

The OGCE will also undergo several significant software engineering upgrades, including a major upgrade

to its build system, system-build testing on the NSF build and test facility, and upgrades to its unit and

system tests.

Minority-ServingInstitutionsCyberinfrastructureOutreachProjects

CGL’s recent awards give it plenty to do with a Web 2.0 portal for MSI faculty and students as a major focus.

One challenge is identifying those scientists at minority-serving institutions who are good candidates for

collaborating on e-Science projects. CGL plans to promote self-identification (bottom-up) using Web 2.0,

rather than traditional top-down approaches that tend to always locate the same small group of outreach

candidates.

The lab is currently completing a prototype portal that combines various Web 2.0 approaches, including

AJAX, shared bookmarking, profile building, researcher matchmaking, and community building. CGL

researchers are working to complete the prototype in July and will enter an early user phase during the next

six months.

EarthquakeCrisisManagementinaGridofGridsArchitecture

This work will continue with a focus on sensor grids.

PolarGrid

CGL will continue to help Elizabeth City State University (ECSU) bring up a prototype Polar Grid and

Science Gateway. Marlon Pierce will spend a week at ECSU in July instructing students and research staff

on grid computing and establishing requirements for their science gateway.

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NaradaBrokeringandParticlePhysicsAnalysisGrid

During this timeframe the project team is planning a major release (version 3.0) that will incorporate

support for the production version of its scheme for repository redundancy and fault tolerance. Intermediate

releases in this reporting scheme would focus on simplifying the recording and replay of streams and

the users that are authorized to initiate such actions. Another focus of their efforts will be to develop an

algorithm that will make recommendations about repository placements within the broker network. This

placement scheme would enable the reduction of overheads related to reliable delivery at the producers and

consumers of a given stream.

CGL researchers also plan to release a prototype version of the framework, using NaradaBrokering, which

can be used within Clarens to discover and load-balance accesses to services that are available to physicists

for analyzing and collaborating over data produced in particle physics experiments.

QuakeSimandGISWork

CGL plans to complete internal testing of the QuakeSim portal and services and make the portal available

to the geophysical community at the American Geophysical Union meeting in December 2007. The project

team also plans several enhancements to existing portlets and services for better integration with GPS

analysis applications.

One of their goals is to extend the current portal into a TeraGrid Science Gateway for selected codes,

particularly GeoFEST. This will allow them to use the much larger high-performance computing resources

that the TeraGrid provides. They will be using their Grid Tag Libraries and Beans (GTLAB) project (from the

OGCE work) to provide these new capabilities.

e-Sports:CGL researchers expect to do a prototype release of the e-Sports software during this reporting

period. This software will harness the distributed repository capability available within NaradaBrokering

to facilitate the recording and replay of multimedia streams.

II.4 vIsuALIzATION ANd INTErACTIvE spACEs LAB

M.PaulineBaker,Director

LabMission

The mission of the Visualization and Interactive Spaces Lab (VIS Lab) is to create

new capabilities for access to information and to embed these capabilities into

environments for exploration and learning. This goal is accomplished through

advanced computer-generated graphics and novel sensor-based user interfaces to

create innovative environments for data exploration, learning, and visualization of

data. The lab’s research agenda includes work on user interfaces, display innovations, graphics software,

and visualization functionality over the Web. The VIS Lab is especially interested in taking a collaborative

approach, where technology solutions can contribute to applications that affect people’s lives now.

SummaryofKeyLabActivities

The VIS Lab made significant progress during the reporting period with Discovering the Science of the

Environment (DSE). The purpose of the DSE program is to improve environmental education and

understanding of our environment by providing professional development for educators and activity-based

opportunities for middle school students that enhance environmental awareness and understanding. This

program is conducted in collaboration with IUPUI’s Center for Earth and Environmental Science. To date

the DSE team has:

• Conducted its first weeklong institute for educators. The workshop was offered as a continuing

education course through the IUPUI School of Education. Teams of 2-4 educators from 10 different

schools participated. The institute was held in the new Earth Discovery Center at Eagle Creek Park.

• Taken delivery of a 20-foot mobile science education trailer. The trailer has its own generator and

will be equipped with an Internet satellite and a variety of probes, hand-held computers, and

display technologies. It will visit schools in the nine-county region surrounding Indianapolis

starting in the fall. DSE also hired a specialist in environmental education who will deliver trailer-

based programs to the schools.

• Received funding from several agencies, including Veolia Water, Nina Mason Pulliam Charitable

Trust, Lilly Foundation, Dow AgroSciences, and Duke Energy. DSE has also reached the finalist stage

for an Impact1000 award.

41

The Lab also advanced VisPort, a

visualization portal tailored for specific

communities. VisPort emphasizes custom

visualizations and interfaces, introduces

the notion of visualization informatics,

and uses Web services to support

access to remotely hosted visualization

functionality. VisPort was introduced at

the annual Supercomputing conference

in November and the TeraGrid meeting in

June. Current efforts with VisPort include

customizing the visualizations to provide

convenient access to the vast array of

environmental data available on the Web.

In health monitoring, VIS Lab researchers

continued their research on the use of

mobile devices to support individuals

with kidney disease. This work, led by Kay

Connelly, is conducted in conjunction

with researchers from the IU School of

Nursing and is supported by a grant from

the National Institutes of Health.

Finally, the VIS Lab juggled a number of shifts in personnel. Randy Heiland, associate director for the

Scientific Data Analysis Lab, is on leave from Pervasive Technology Labs. Heiland is currently on assignment

managing the High-Performance Applications group within University Information Technology Services of

IU. As a result of this shift, David Milsho, an IUPUI informatics graduate who had been working with the

SDA Lab, is presently working in the VIS Lab. In another PTL re-assignment, the affiliation of Kay Connelly

within PTL was transferred from the Open Systems Lab (OSL) to the VIS Lab. Connelly joined PTL very

early and was affiliated with the first lab that formed. However, her work is much closer in spirit to the VIS

Lab agenda. For example, Connelly and VIS Lab Director M. Pauline Baker are working together on the DSE

program. Finally, the VIS Lab also said goodbye to Ed Bachta, who left the lab to join the technology team

at the Indianapolis Museum of Art. Bachta joined the VIS Lab in 2003 and was a productive and valued

member of the team.

In the Indiana Watershed Explorer, users can view Indiana counties, basins, and sub-basins.

ResearchandDevelopmentActivity

DiscoveringtheScienceoftheEnvironment. The DSE program

consists of a number of components, including information

delivery over the Web, in-the-field experiences focused on data

collection and analysis, a mobile environmental science trailer,

an equipment loan program, and a professional development

program. The VIS Lab’s goals are to encourage authentic, inquiry-

based opportunities for learning about science. Recognizing that

today’s learners are growing up in a completely digital and media-

rich world, the program makes significant use of technology to

entice, engage, and empower. During this reporting period, VIS

Lab staff researched possibilities for probes that could be used

by students to measure physical and chemical properties of

water and soil. They designed, developed, and tested a prototype

software application that guides students through a structured learning exercise in making and testing

hypotheses about water quality. The team also designed a series of “interactivities”—small multimedia

components that explore a concept related to water and watersheds. They worked extensively with the U.S.

Geological Survey archives to make data about water quality accessible in a teacher- and student-friendly

way. Finally, DSE researchers planned and conducted a weeklong workshop for 36 educators. Participants

included educators from Indianapolis Public Schools, Pike and Carmel-Clay Townships, a rural school from

Green County, and naturalists from Indy Parks.

VisPort. A portal for visualization functionality, VisPort was originally designed and developed as part of

our scientific visualization collaborations with high-performance computing research teams. VisPort has

demonstrated value as an easy-to-use tool for generating visualizations. In its current VisPort development,

Baker’s team is concentrating on environmental science data. Using various Web protocols, they have

developed the functionality to query the National Oceanic and Atmospheric Administration collection of

coastal ocean buoys to get real-time updates on water level information or meteorological conditions. In

a similar manner, VisPort can query the U.S. Geological Survey collection of sites that monitor Indiana’s

streams and rivers to access and display information about water flow and water chemistry. The goal of this

work is to give Indiana teachers access to data about sites that are close to their schools and perhaps familiar

to their students.

The DSE program includes use of mobile computing technologies to support learning about the environment.

4�

HealthEducationontheGo. Connelly’s team

continued development of the Dietary Intake

Monitoring Application (DIMA) for dialysis

patients under National Institues of Health grant

R21 EB007083. Two studies with dialysis patients

were conducted. The first study investigated input

mechanisms for food items, comparing voice and

barcode scanning as input channels. The second

study is the first phase of a two-part plan to examine

different navigation styles and complexities for the

icon interface portion of DIMA. The first phase tested

all of the standard mobile Graphical User Interface

(GUI) components to examine correlations between

participants—Mini Mental State and ability to use the

various graphical interfaces. Planning for the second

phase of the study is now under way, which will test

participants’ ability to navigate the application. In a

separate effort, Connelly’s research group performed

a three-week field trial of Chick Clique with teenage

girls. The data is currently being analyzed and should

provide insights into the ability of technologies to

encourage physical activity with this age group.

UsableSecurity. Connelly’s team finished the analysis

of a user study performed in the fall, examining a

typical user’s mental model for how an operating

system is configured and comparing the Windows NT interface with an interface they designed. The results

identified key issues regarding users’ lack of understanding of how programs, services, and the operating

system interact, leading to an inability to securely configure their machines. Their work has suggested

guidelines for how to improve these configuration interfaces to assist typical users. This study also compared

two different methods for performing a user study on security interfaces, showing that the use of a joint

explorer (i.e., a researcher pretending to be another study subject who is partnered with the participant)

provides much more valuable information than simply asking the participant to think aloud.

VisPort makes it easy for teachers and their students to access and graph U.S.G.S. water quality data.

IntellectualAccomplishmentsandExternalFundingActivity

• The VIS Lab now delivers 10 online services.

• The lab has created three hardware applications that are in use in educational settings in central Indiana.

• The lab had three new publications appear in print during the reporting period.

• The lab gave two presentations during the reporting

period.

• Two students earned master’s degrees during the

reporting period.

• One grant proposal totaling $67,359 was submitted

during the reporting period.

For a complete listing of all Pervasive Technology Labs

disclosures, online services, hardware applications,

publications, and presentations, please visit

www.pervasive.iu.edu.

EducatingtheResidentsofIndianaandBeyond

As described above, DSE is aimed squarely at educating

Indiana students and their teachers.

Additionally, Connelly received an Alliances for Graduate

Education in the Professoriate (AGEP) award from the

National Science Foundation, as well as other funds, to

organize a three-day workshop for students and faculty

of IU’s regional campuses. Participants will learn how

to develop a K–12 outreach program that debunks the

“geeks” stereotype and encourages children to consider

careers in technology.

In a recent workshop, 36 Indiana educators learned how to establish outdoor classrooms at their schools and use technology to explore environmental science.

The DSE program will utilize a mobile science education lab. The PTL logo is on the back.

45

As always, the VIS Lab had the pleasure of showing off the gallery to numerous visitors to the ICTC building.

The lab estimates that it was visited by 189 people in the last six months. Its guests included people

attending the New Media Consortium, staff from the Indiana Commission on Higher Education, and the

CIC IT Training Conference. It also had guests from local elementary schools, as well as high-ranking officials

from the National Cancer Institute. Guests came from as far away as Sun Yat Sen University in China.

AcceleratingEconomicGrowth

VIS Lab work with DSE is designed to contribute to Indiana’s economic well-being. Indiana has chosen

to make the life sciences a priority and is having reasonable success at creating new jobs in this sector.

Long-term success of the initiative will depend on availability of a workforce that is scientifically and

technologically prepared for these jobs. Among its goals, DSE aims to encourage Indiana youth towards

the interests and skills needed for these careers.

The VIS Lab also helps, in its way, to change perceptions about Indiana as a technology-savvy state, which

is another factor affecting economic growth. The VIS Lab recently scored a hat trick with the placement of

Ed Bachta at the Indianapolis Museum of Art. At the museum, Ed joins Rob Stein and Charlie Moad, also

former members of the VIS Lab. The departure of this talented trio is certainly a big loss for the VIS Lab.

However, the museum is one of the institutions that help shape public perceptions about the community,

especially for visitors to Indiana, and showcasing innovative technology at the museum raises Indiana’s

technology profile. Positioning these three talented individuals at the museum would not have happened

without the Pervasive Technology Labs program and the VIS Lab collaboration with the museum.

BringingDistinctiontoIndianaUniversityandtheStateofIndiana

Kay Connelly received two awards for her work in 2006–07. These are the Indiana University Outstanding

Junior Faculty Award and the Indiana University Trustees Teaching Award.

M. Pauline Baker was invited to participate as a panel member on an National Science Foundation site

visit to the Engineering Research Center (ERC) for Biomedical Engineering Education, headquartered at

Vanderbilt University. This is the fifth time that Baker has served on this panel, and this marks the final year

for this ERC.

LabOutlookJuly–December2007

Over the next six months the VIS Lab will concentrate on researching the use of multimedia and mobile

computing for applications in health and environmental science education. VIS Lab researchers will also

continue efforts towards encouraging Indiana youth, including our own students, to consider graduate

study and careers in science and technology.

RandyHeiland,Associate Director

LabMission

The mission of the Scientific Data Analysis Lab (SDA Lab) is to develop and

deploy software tools and applications that contribute to improved science

understanding and education. The lab actively seeks academic researchers and

educators who have challenging problems in scientific data management,

analysis, and visualization. While the lab is interested in tackling problems

in many scientific domains, the staff is currently focused on challenges in the

life sciences—an area of rapid growth in the State of Indiana. The lab is also committed to science and

mathematics education in its K–12 outreach efforts.

SummaryofKeyLabActivities

The SDA Lab has been led since its inception in 2003 by Associate Director Randy Heiland. Starting in

May, Associate Director Heiland is on leave from Pervasive Technology Labs and on assignment within the

Research Technologies Division of University Information Technology Services.

During the reporting period the SDA Lab continued its collaborations with a number of groups. In

each case, the SDA Lab has worked to define, develop, and demonstrate data management, analysis,

and visualization functionality that can enhance the team’s ability to conduct its research. The lab’s

collaborations have been with:

• Chemical Informatics and Cyberinfrastructure Collaboratory (CICC), with faculty in the IU School of

Informatics and the IU Bloomington Department of Chemistry

• Tissue Simulation Toolkit group, with faculty in the IU Bloomington Department of Physics

• Nonlinear Optical Properties of Molecules, with faculty in the Purdue University School of Chemistry

ResearchandDevelopmentActivity

ChemicalInformaticsandCyberinfrastructureCollaboratory(CICC). The SDA Lab continued its

collaboration with researchers in the CICC. In this work, they were able to leverage and expand earlier

software development of molecular visualization clients that communicated with the CICC Web Services.

In addition, SDA researchers shared with them the potential role that the VisPort visualization portal might

provide for their community of cheminformatics researchers. In February Heiland delivered a guest lecture

in Informatics 573, Programming for Chemical and Life Science Informatics at IU Bloomington. The

II.5 sCIENTIFIC dATA ANALysIs LAB

47

lab also made a major investment of time and energy working with the CICC team to develop strategies

and prepare materials for seeking additional external funding to continue and expand the research.

The High-Performance Applications team will continue to work with the Chemical Informatics and

Cyberinfrastructure Collaboratory in the future.

TissueSimulationToolkit(TST).The SDA Lab continued to provide high-performance computing and

scientific visualization support for the Tissue Simulation Toolkit project. Last year’s proposal to the

National Institutes of Health for funding this work was not successful, but was very valuable in helping

the team to reshape a modified proposal that was submitted in May. A Tissue Simulation Toolkit

workshop is planned for August at IU. In the future, the High-Performance Applications team will work

with the Tissue Simulation Toolkit researchers, adding the ability to run parameter study simulations on

IU supercomputers.

A molecular visualization client accessing the CICC Web Services.

Simulating vasculature using the Tissue Simulation Toolkit.

NLOPredict. The lab continued its collaboration with Garth

Simpson in the School of Chemistry at Purdue University in

support of researching nonlinear optical properties of molecules

at biological interfaces. The lab’s visualization software has been

of such value to the effort that Simpson requested and received

approval from his program manager at the National Science

Foundation to fund Heiland’s efforts.

IntellectualAccomplishmentsandExternalFundingActivity

• The SDA Lab released one new package of open source software during the period.

• The lab now delivers 11 online services.

• Two new peer-reviewed publications appeared in print during the period.

• One new grant proposal totaling $67,359 was submitted during the period. This proposal was

successful and is slated to begin in the following reporting period.

For a complete listing of all Pervasive Technology Labs disclosures, online services, hardware applications,

publications, and presentations, please visit www.pervasive.iu.edu.

CreatingtheTwenty-First-CenturyWorkforce

• The SDA Lab currently employs one full-time lab staff member and supports no additional graduate

students, affiliated faculty, or part-time employees.

• During the reporting period the following changes in lab personnel occurred:

o Associate Director Randy Heiland went on leave from Pervasive Technology Labs. He is currently on

assignment leading activities of the High-Performance Applications Group of UITS.

o David Milsho’s affiliation within PTL has shifted to the VIS Lab.

• During the reporting period students affiliated with the lab have achieved the following degrees:

o No degrees were earned during the reporting period.

Two visual representations of molecular tensors available in NLOPredict.

49

EducatingtheResidentsofIndianaandBeyond

In March and April the SDA Lab conducted its eighth and ninth evening computer workshops at the

Girl Scouts Math and Science Center in Indianapolis. These workshops are designed to introduce girls to

programming and mathematical concepts using some very creative and fun projects. To date this series of

workshops has reached more than 150 girls.

AcceleratingEconomicGrowth

During this reporting period Heiland revisited Cummins, Inc., in Columbus, Indiana, to identify potential

collaborations between the High-Performance Applications group and Cummins engineers.

BringingDistinctiontoIndianaUniversityandtheStateofIndiana

Staff from the SDA and VIS Labs delivered a presentation on the VisPort system at the annual TeraGrid

conference, held in June in Madison, Wisconsin.

LabOutlookJuly–December2007

In May Heiland accepted a new challenge as manager for the High-Performance Applications group within

the Research Technologies division of IU’s University Information Technology Services (UITS). This is a

key position in IU’s continuing emergence as a national player in high-performance computing. No final

decision has been reached yet, but it may turn out that in the future some of the SDA Lab activities migrate

permanently to the VIS Lab, while others migrate to UITS.

II.6 kNOwLEdgE ACquIsITION ANd prOjECTION LAB

DonaldF.“Rick”McMullen,Director

LabMission

The mission of the Knowledge Acquisition and Projection Lab (KAP Lab) is

to develop new insights about how knowledge is created, managed, and used

within organizations and to use this knowledge to develop advanced information

technology systems that will create new possibilities for management, delivery,

and use of institutional knowledge. Some application areas for the technology

developed by the KAP Lab include:

• Managing the data and information produced by arrays of sensors, such as ocean buoys

• Creating tools to enhance problem solving in distributed and virtual organizations

• Knowledge management for innovation in virtual organizations

• Just-in-time information delivery systems for distributed organizations, such as delivery of

information needed to repair the highly technical infrastructure and equipment on board

Navy ships

The KAP Lab is currently unique among Pervasive Technology Labs in that it is almost entirely self-funded.

SummaryofKeyLabActivities

During the reporting period the KAP Lab participated in several key activities:

• KAP Lab researchers continued to develop the lab’s expertise in sensor networks and their semantic

interoperability through National Science Foundation-sponsored research and participation in

workshops and conferences. The lab was invited to speak at “INGRID 2007—Instrumenting the Grid,”

the second International Workshop on Distributed Cooperative Laboratories. A related project started

to develop a Web 2.0 approach to remote access and use of instruments and sensors. This project

is motivated by the intense activity in social and commercial worlds to develop and apply Web 2.0

technologies and APIs to construct relevant, responsive, and reconfigurable services.

• The KAP Lab assumed a leadership role in the CrystalGrid Framework (CGF) project. CGF is funded by

the National Science Foundation to develop an integrated approach to e-Science for crystallography.

The outcomes of this project will include an end-to-end approach to experiment design and execution,

data acquisition, analysis using codes accessible through a service-oriented architecture and Web 2.0

APIs, publication of results, and a repository approach to archiving experimental observations and

publications to support verification of results and reuse of data.

51

• KAP Lab researchers participated in the development of a proposal for a Polar Exploration Grid with

the Community Grids Lab and University Information Technology Services. This project aims to build

and field portable high-performance nodes for processing Synthetic Aperture Radar (SAR) data about

ice sheets to determine their exact thickness. The field-processed data will be made available through a

satellite communications network to remote collaborators in the United States for real-time consulting.

The proposed polar exploration grid will provide a deeper understanding of the impact of global

climate change on polar ice sheets and will allow real-time interaction of scientists with new data,

rather than waiting weeks to see and analyze data from a campaign.

• Lab staff continued collaborations with IU School of Informatics researchers in socio-technical

systems for disaster management and development of next-generation performance support systems.

The lab supported and participated in a local training workshop to teach volunteers to use a system

(the Bloomington Emergency Community Information System, BECIS) for coordinating citizen-based

disaster response. This work has resulted in a proposal, entitled ICE-IS: Indiana Collaborative Emergency

Information System, solicited by the Indiana Department of Homeland Security to fund the further

development of the BECIS concept and plans for integration with state disaster management systems

and propagation to other Indiana counties.

• Researchers from the KAP Lab started a new internal project with the head of the IU Imaging Center:

an advanced capability microscopy service center supported by the National Science Foundation and

IU Office of the Vice President for Research. The objective is to improve throughput and utility of the

facility and to develop a model that can be applied to other service laboratories at IU and elsewhere.

• KAP Lab researchers worked with a group in Australia on a project to develop an advanced instrument

control process based on the CIMA instrument ontology and associated software tools. The process

will be used as a remote access methodology for the Australian Synchrotron.

• Conference, workshop and symposia committees:

o Technical Program Committee for the Third IEEE International Conference on Intelligent Sensors

and Information Processing (ISSNIP 2007), to be held in Melbourne, Australia, December 2007

o Workshop Chair, Second International Workshop on Scientific Instruments and Sensors on the

Grid, to be held in conjunction with ISSNIP 2007

o Program Committee for CCGrid 2007

o Organizing Committee for the International e-Science in Crystallography workshop, April 2007

o Organizing Committee, Mini-Symposium in Honor of John C. Huffman, April 2007

ResearchandDevelopmentActivity

This reporting period the KAP Lab initiated a project with astronomers

at Purdue University Calumet to develop remote access capability

to a 20-inch robotic telescope. This telescope will be used for teaching

astronomy to undergraduates and junior high school students, for

research, and as a community resource for informal science education.

It will be located away from the city of Calumet for better observation

and will combine informal observation directed by an instructor with a

queue of observations requested by researchers. It will also be possible

for several groups at different locations to observe simultaneously and

share control of the telescope, and for casual observers to “tune in”

to see what is being observed.

Work continued on the CIMA National Science Foundation

Middleware project. The network of research facilities using this

software has added three new members during the reporting period.

As a result of this project, a network of research and service labs that

do crystallography was established. CIMA provides the

mechanism for acquiring data from instruments and sensors

in these labs and sending these data streams to remote data

management systems. A key component of the services that

support this network of labs is the IU Data Capacitor (DC), a

very large network-attached disk cache for streaming data. The

CIMA group participated in demonstrations of the DC at the

SC06 supercomputing expo and continues to work as a “friendly

user” application in its development.

The lab assisted with the organization and execution of The

Second International Workshop for Crystallographic Data

Management in April. This workshop gathered approximately

50 crystallographers, computational scientists, and data

management experts to discuss the future of data management in crystallography and in e-Science

in general. One outcome of the meeting was a research agenda for data management and federated

repositories. This agenda will be aired in several upcoming meetings and venues, and an effort will

be made to make funding agencies aware of the needs.

These small appliances turn a wide variety of sensing and measuring devices into “smart,” network-accessible sensors and instruments. These are currently used in laboratory or field settings for scientific research but could be used to provide home health telemetry or similar embedded monitoring applications.

The CIMA instrument middleware project addresses the need for a consistent mechanism for communicating with and controlling scientific instruments and sensors.

5�

The KAP Lab’s collaboration with the Open Grid Computing Environments group is continued and

expanded. This effort was originally started to develop novel multi-user interfaces to remote instruments

and sensors. During this reporting period it was expanded to include a project to develop Web 2.0 interfaces

that provide instrument data and control functions. This is a new approach, extending previous work to use

portlets communicating with Web services, and will support leveraging a broad range of existing and future

Web 2.0-based services for communication, computing, and storage.

The lab continued research on using anomalous

microwave propagation effects to enhance network

range in marine sensor networks. A proposal was

submitted to the National Science Foundation

during the reporting period to provide funding to

expand and enhance this work.

The lab continued a collaboration with IU School of

Informatics researchers on context-aware systems and

the use of context to improve human performance

in problem-solving environments. This work brings

together several important concepts in Artificial

Intelligence (AI) and performance support. Context

in work or learning situations is a powerful determinant of what actions are necessary and appropriate for

achieving individual and group goals. Performance Support Systems (PSS) bridge the gap between a user’s

personal knowledge and that needed to complete a task successfully, but they do not routinely take into

account context (it is usually assumed as the domain of the PSS). This project is about developing and

applying theories of context, user, and task in reasoning about situations. This core approach is used to

find and provide information in real time to assist humans in performing tasks as individuals and in groups

under a variety of situations.

The KAP Lab continued development work on the SAGE3 sensor agent software system. This system is a

National Science Foundation-sponsored research collaboration on auto-scaling of sensor networks for

environmental research. SAGE3 is a distributed, agent-based signal-processing and condition-monitoring

system that can be used to produce, capture, process and monitor real-time data streams, and to create

value-added, real-time signal products from existing streams in an open, easily accessible way. The SAGE3

software was modified to support multiple related instances of the agent execution server and to improve

reliability and manageability. The servers will be distributed across many labs and research groups yet

function as a single data acquisition, signal processing, and event detection and response system, so high

reliability is a key requirement.

The KAP Lab is developing software to automatically configure and maintain wireless sensor networks used for monitoring freshwater lakes and other environmental monitoring tasks.

Collaboration was continued with Virginia Tech to research and model coordination in policy making and

priority setting regarding basic research between the National Science Foundation and its cognate agencies

in other countries. The primary aim is to understand how funding agencies in different countries interact to

support international scientific collaborations. A grant proposal to continue this work is in preparation.

KAP Lab scientists continued to develop the Diagnostic Workbench (DWB) and issued an invention

disclosure to the IU intellectual property unit. The DWB is a problem-solving environment for

troubleshooting electronic and mechanical components that brings together ambient intelligence,

machine reasoning, and collaboration technologies to create a shared workspace with memory. The

memory is used to suggest solutions for future problems based on past events and to locate expertise

based on who participated in prior activities and what they contributed to solutions.

IntellectualAccomplishmentsandExternalFundingActivity

• The KAP Lab had two new technology disclosures during the reporting period.

• Two new packages of open source software were distributed.

• The lab had two students earn Ph.D.’s during the reporting period.

• The lab had two new peer-reviewed publications appear in print during the reporting period.

• The KAP Lab submitted two grant proposals totaling $3,132,718 during the reporting period.

For a complete listing of all Pervasive Technology Labs disclosures, online services, hardware applications,

publications, and presentations, please visit www.pervasive.iu.edu.

The KAP Lab Diagnostic Workbench (DWB) leverages our research in Ambient Intelligence and performance support systems to produce an environment that is an active partner and assistant in diagnosing and repairing electronics and electro-mechanical systems. Here two researchers in different locations collaborate with the DWB’s diagnostic system to repair an electronic component.

55

EducatingtheResidentsofIndianaandBeyond

This reporting period the lab established a relationship with the P-16 Center in the School of Education

through the development of an initial joint project. The expert system envisioned by the project team will

strengthen Indiana Schools by allowing teachers to locate scholars within the P-16 Center and the School

of Eduction or on the IU Bloomington campus who can offer consultation on classroom or educational

challenges and develop outreach partnerships. The following projects and activities continued during the

reporting period:

• Continued work on two research projects: “ReefScope: An International Research and Education

Partnership in Curriculum and Cyberinfrastructure Development for Teaching Secondary and Higher

Education Students about Coral Reef Ecology, Sensor Networks and the Impact of Global Climate

Change” and “International System Development and Education Center (ISDEC): Developing

Information and Instructional Systems for a Global High-Tech Workforce.” At this stage the project

team is seeking non-governmental organization (NGO) and foreign government support for these

international projects.

• Completed a collaboration with the Ubiquitous Society of Korea to prototype an education program

to inform chief executive officers and chief information officers of high-tech manufacturing and

logistics companies about applications and impact of ubiquitous computing technologies. The next

step is to redevelop the content for distribution through distance education channels available in the

United States.

AcceleratingEconomicGrowth

The KAP Lab collaborated with an Indiana-based defense contractor in the development and submission

of a Small Business Innovative Research (SBIR) proposal entitled “Expedited Transition of Propulsion

Modeling and Simulation Capability.”

BringingDistinctiontoIndianaUniversityandtheStateofIndiana

As mentioned in more detail elsewhere, the lab contributed heavily to the organization and execution of an

international e-Science meeting. A number of prominent crystallographers and computer scientists from as

far away as Australia attended the meeting.

LabOutlookJuly–December2007

The KAP Lab expects all projects described above to continue (except where noted) during the upcoming

reporting period. In addition to these ongoing activities, the lab expects to expand its relationship with the

IU School of Education. Interactions started with joint development of Science, Technology, Engineering

and Mathematics (STEM) teaching and workforce development projects and are expected to branch out into

other areas, including effectively leveraging expertise in the School of Education to support the development

of school and district enhancement projects.

III. COLLABOrATIvE ANd LEvErAgEd ACTIvITIEs

Pervasive Technology Labs continues to be very effective in collaborating

with Indiana University as a whole and University Information Technology

Services (UITS) in particular. To date the total impact of PTL on grant

successes by Indiana University totals $100,598,579. This includes grants won by

PTL, grants won by PTL in collaboration with other units of IU, and grants won

by other subunits of IU leveraging and drawing upon the expertise of PTL. The

impact of PTL on IU competitiveness cannot be overstated. For example, there are

now a total of nine universities participating in the TeraGrid—the National Science

Foundation’s largest national cyberinfrastructure project. Of the nine partners, only

four received new national facility funding during this century. Indiana University

and Purdue University are two of those four who became part of the TeraGrid.

The joint IU-Purdue proposal was funded primarily on the basis of the strength

of researchers brought to IU by Pervasive Technology Labs and the strength of

IU’s University Information Technology Services. That success in 2003 began a

sea change in the depth and extent of collaborations between PTL and UITS and

increased collaborative activities between PTL and the university as a whole.

Highlights of recent key collaborative and leveraged activities are presented below:

GrantandContract-RelatedActivity

Ongoing grants

TeraGrid. The TeraGrid is the National Science Foundation’s flagship effort to

create a national cyberinfrastructure to accelerate innovation and enhance productivity of U.S. researchers.

(“Cyberinfrastructure” refers to high-performance computers, massive data storage systems and data resources,

advanced instruments, visualization systems, and people all interconnected by high-speed networks.)

2007 has been a turning point in IU’s role within the TeraGrid. With IU’s Big Red in production as part

of the TeraGrid, for a period of time IU had the largest supercomputer integrated within the TeraGrid.

Big Red remains today the third-largest supercomputer within the TeraGrid and is a major computational

resource for the national research community. PTL is responsible for the LEAD Science Gateway—a Web-

based interface used for predicting weather. LEAD is particularly important because it dramatically lowers

the barriers to using the TeraGrid and supports interactive prediction of severe weather such as tornadoes

in response to weather conditions that make severe weather more likely. Because IU now has a major

TeraGrid computational resource, it is possible for UITS to collaborate much more intensively with PTL,

57

PTL COO Craig Stewart

PTL Science Director Dennis Gannon

shortening the research and development cycle for further enhancement of LEAD’s capabilities. As described

in the Outreach Activities section of this report, PTL and UITS collaborated with several other universities

to support one of the largest and most important cyberinfrastructure outreach activities ever done at IU or

around the world—the WxChallenge. The WxChallenge was a competition, styled after the NCAA basketball

playoffs, in which teams of college students competed to produce the best weather forecasts using the LEAD

portal, Big Red, the IU Data Capacitor, and other supercomputer facilities that are part of the TeraGrid.

Multi-CoreParallelProgramming.Judy Qui continues to work for UITS on the development of new tools

for multi-core processors, funded by a grant to the Community Grids Lab.This relationship takes advantage

of many synergies between CGL and UITS that relate to this particular activity, and both organizations will

be more effective as a result.

59

Results of major collaborative grants submitted during last reporting period

NationalScienceFoundation“High-PerformanceComputingSystemAcquisition:TowardsaPetascale

ComputingEnvironmentforScienceandEngineering”Solicitation. Indiana University, again with

Purdue University as a partner, submitted a $30,000,000 proposal to the second round of this competition

on November 30, 2006. With key PTL personnel named as project co-investigators and providers of

specialized technical expertise, this proposal depends heavily on the collaboration between PTL and UITS,

as well as the IU collaboration with Purdue University. This grant program, which has a total of four

rounds, is one of the largest grant programs in the United States, and it is extremely competitive. Both the

quality of the proposal and matching contributions (university, state, and private) play strong roles in this

competition. This proposal remains under continuing review.

NationalScienceFoundationHigh-PerformanceComputingOperations. The National Science

Foundation held a one-time grant competition to provide high-performance computing capacity to the

nation for the period from 2007 to 2009. Purdue University led the development of a $5,000,000 proposal

in response to this solicitation, with IU as a partner. This proposal was submitted on November 28, 2006,

with named IU participants drawn from PTL and UITS. This proposal solicitation is highly unusual in that

the majority of the funds available are targeted at a specific group of institutions that have received past

support from the National Science Foundation for particular supercomputing activities. The Purdue/IU

proposal remains under continuing review.

New Grant Activities

PTL and UITS participated in two major collaborative grant projects during the reporting period:

• PlantCyberinfrastructure. PTL and UITS together collaborated with Yale University, Carnegie

Mellon University, and Florida State University to submit a $50,000,000 grant to the National

Science Foundation for a major plant cyberinfrastructure facility. The Florida/Yale/CM/IU grant

proposal was one of two finalists chosen by the NSF, though it ultimately was not the proposal

selected for funding by the NSF. However, IU’s success in reaching the finalist stage seems to have

been heavily dependent upon the collaboration between PTL and UITS, and in particular on the

joint ability of these two organizations to promote “Web 2.0” social networking tools that would be

used for support of scientific research. While this particular effort was not successful, we believe that

there is a clear message for IU in its future grant activities: leverage the CGL expertise with Web 2.0

technologies to create new capabilities for scientific research.

• PolarGrid. The Polar Grid project was mentioned earlier, in the Community Grids Lab report.

A particular grant activity related to this project involved PTL and UITS. With CGL Director Geoffrey

C. Fox as principal investigator and PTL Chief Operating Officer Craig Stewart as one of the

co-principal investigators, IU submitted a grant for $2,000,000 in computer hardware to support

polar ice sheet research. A particularly innovative aspect of this proposal is the use of military-spec

field equipment powered by solar cells intended for deployment in the polar regions of the United

States. The computer hardware specifications for this proposal were developed by UITS Research

Technologies Director Matt Link and High Performance Systems Manager David Hancock. This

proposal remains under continuing review.

New collaborative research and development activities

IEDC. As part of its collaborative work with the Indiana Economic Development Corporation, IU’s Big

Red supercomputer was upgraded to 30 TFLOPS during the reporting period. That is, its ability to do

mathematical calculations is now 30 trillion calculations per second—up from 20 trillion before. As a result,

Big Red moved up from thirty-first place to thirtieth place on the list of the 500 fastest supercomputers in

the world. The 10 TFLOPS addition to Big Red, along with an additional 10 TFLOPS of capability formally

owned by Purdue University but integrated with Big Red, are intended to provide capabilities for economic

development within the State of Indiana. UITS and PTL have worked together to solicit interest from the

private sector. Repeated meetings have taken place between representatives of IU and two large Indiana-

based companies, along with one small Indiana-based startup. As a result of PTL-developed technologies

and UITS expertise in managing Big Red, IU expects some of the largest companies in Indiana to enhance

their national and international competitiveness by using Big Red.

SIDGrid. The Social Informatics Data Grid (https://sidgrid.ci.uchicago.edu/) is creating new capabilities for

researchers in the social sciences—particularly psychologists, sociologists, and neural scientists. Specifically,

SIDGrid “enables researchers to collect real-time multimodal behavior at multiple time scales. Multimedia

data (voice, video, images, text, numerical) is stored in a distributed data warehouse that employs Web and

Grid services to support data storage, access, exploration, annotation, integration, analysis, and mining

of individual and combined data sets.” These are fundamentally new capabilities for social scientists and

are being developed through a grant to Bennett Bertenthal, IU’s recently appointed Dean of the College

of Arts and Sciences. Bertenthal received funding for this project while at the University of Chicago. Dean

Bertenthal’s move to IU has opened up a new area of collaborations between PTL, UITS, social scientists at

IU, and social and computer scientists at the University of Chicago. IU expects that dramatic advances in the

capabilities provided for social scientists will result from these efforts, as well as additional grant funding to

IU. An “all hands” meeting for the SIDGrid project was recently concluded at IU, and the team is continuing

to put collaborations into operation to produce concrete benefits for social scientists.

61

Major conferences, events, and awards

InternationalSupercomputerConference. PTL Chief Operating Officer Craig Stewart presented a paper

at the International Supercomputer Conference about the deployment and first year of operations of IU’s

Big Red supercomputer. Stewart was one of just a handful of Americans to speak at this conference. This

paper highlighted in particular the aspects of Big Red’s deployment that take advantage of software facilities

developed by PTL. In addition, IU’s Data Capacitor team (involving UITS and PTL), with partners from

Technische Universitaet Dresden, demonstrated impressive performance on a distributed transatlantic Lustre

file system designed to move large amounts of scientific data quickly and easily.

Tutorials.As a result of collaborations between PTL and UITS, along with researchers funded through

INGEN and METACyt, IU put on a tutorial about use of Big Red at the Indy07 Bioinformatics conference.

Big Red is proving to be particularly valuable for researchers studying protein function, so this tutorial will

help build up the Indiana user base of life scientists using Big Red.

MiraAwards. Indiana University and PTL were again prominent at the 2007 Mira Awards (http://www.

techpoint.org/Mira/nominees.htm). PTL Seed Fund recipient The Haelan Group was a nominee in the

“Health & Life Sciences Company” category, while PTL-affiliated faculty Kay Connelly and Bradley C.

Wheeler were nominees in the category of “Education Contribution to Technology–Individual.” University

Information Technology Services, the School of Informatics, and Pervasive Technology Labs at Indiana

University (the Data Capacitor Team) were nominees in the Education Contribution to Technology–

Department/Program/Team category. Being selected as a nominee for the Mira Awards is a high honor, and

participating in the Mira Awards ceremony helps increase the appreciation that Indiana’s business leaders

have for the value of PTL, UITS, and IU.

Iv. ECONOmIC dEvELOpmENT

Pervasive Technology Labs is working directly with the private sector of the State of Indiana to help

create a vibrant twenty-first-century economy.

During the last reporting period PTL and its related spin-off companies received a total of $1,041,000 in

grants related directly to economic development (particularly Small Business Innovation Research and Small

Business Technology Transfer grants). Anabas, Inc., and the Community Grids Lab received SBIR and STTR

funding in the amount of $941,000. This funding included an SBIR Phase II award of $742,000. Qualifying

for a Phase II award is challenging and is based on the early success of prior funding. Anabas’s and CGL’s

receipt of a Phase II award is especially notable for this reason.

Indiana University is also beginning to experience returns on its investments. The Haelan Group, a company

partly owned by IU as a result of investments by the PTL Capital Investment Fund, has been successfully

acquired by another company, and IU expects to receive a significant return on its investment. Many of the

businesses related to PTL and the PTL Capital Investment Fund are also reaching important turning points.

The vast majority of new startup companies fail, and PTL-related companies are not immune from the risk

of failure inherent in the formation of new companies. Two companies related to PTL have suspended

their activities. With lessons learned from the cessation of activities of one company, paired with new

innovations, the Open Systems Lab has developed White River Labs, a new company started during this

reporting period.

The following sections of this report summarize the status of companies in which the Pervasive Technologies

Labs have played some role.

Companies not affiliated with PTL in which the PTL Capital Investment Fund has made investments:

TheHaelanGroup. The Haelan Group was successfully acquired by CareGuide Corporation in 2006, and

the investment fund holds stock in CareGuide as a result of the sale. The position of the company has

remained essentially unchanged since the last report, though the company continues to thrive under new

ownership and was recently a finalist in the 2007 Mira Awards. The Haelan investment is currently valued at

$480,000. There is also an anticipated earn-out over the next three years as Haelan reaches new milestones

that will yield additional funds beyond the initial stock payout. Given an initial investment of $450,000 in

the Haelan Group, this means that the return to the PTL Capital Investment Fund will exceed $30,000.

Chartlogix,Inc.(wasDynomed,Inc.).The status of Chartlogix remains the same as the previous report.

Following the successful sale of Dynomed, Inc., to Chartlogix in 2006, the investment remains at the given

value of $300,000. Chartlogix has indicated they are contemplating a sale of the Dynomed unit. If the

Dynomed unit is sold, the investment fund will attempt to sell the stock with the sale of the unit.

6�

Companies affiliated with PTL in which the PTL Capital Investment Fund has made investments:

Anabas,Inc.(affiliatedwiththeCommunityGridsLab). Last year Anabas reported substantial success

with funding obtained from a phase II SBIR, an Indiana 21st Century Research and Technology matching

fund, and a small project funded by Science Applications International Corporation (SAIC). Much of the

effort in the last six months has gone into delivering on the SAIC project by analyzing grid implications of

the Air Force Focused Long Term Challenges (FLTCs). The company also focused on long-term challenges

while continuing work on the phase II SBIR that is a joint project with CGL and Ball Aerospace in Dayton,

Ohio. Anabas had its third successful project review on this SBIR. It just obtained a $100,000 U.S.

Department of Energy Small Business Technology Transfer (STTR) award on Collaborative Visualization

with CGL and a nuclear fusion group at General Atomic in San Diego, California. Anabas is continuing

activities in Hong Kong, developing a collaborative tool for the textile industry. It is piloting its new product

with a large apparel manufacturing company, the Crystal Group. Anabas continues to note that its most

difficult current challenge is recruiting employees. The company is eager to hire but is having trouble

locating qualified candidates

SGCTechnologies,LLC(affiliatedwiththeAdvancedNetworkManagementLab).SGC Technologies,

LLC, (www.sgctech.com) continues to develop and market its enterprise file- and data-sharing tool,

FileShare. Activity in the period has included several maintenance and upgrade releases to the software.

SGC now counts five institutional installations of its software (including license-free installations by entities

related to Indiana University) and is currently working on three additional installation prospects.

EnVizableLLC(affiliatedwiththeVisualizationandInteractiveSpacesLab). During the current reporting

period EnVizable, LLC, has continued conversations with museums interested in the PercepTable-based

etx exhibit. In addition to the museums that have expressed interest earlier, the company is working

with a representative who sees potential for a placement in a cultural history museum in Korea. These

conversations have not yet generated a firm sale or contract, but they confirm the interest within the

museum community in these types of exhibit technologies.

Veterisoft,Inc.(createdbyandaffiliatedwiththeOpenSystemsLab). Veterisoft’s position remains

essentially unchanged from the previous report. The company has had insufficient sales to continue

operations at full strength. Veterisoft did manage to extend its operations into 2007 as a result of a contract

with Indiana University. However, the full-time staff member has now stopped drawing a paycheck. The Web

site remains in place, and Veterisoft’s software products remain available for sale. Veterisoft is contemplating

a contract with a person to sell software on contract—a way that would keep activities going in absence of

operating cash, and which could bring in some money and enable activities to be reinvigorated if a larger

market for their products emerges.

65

Companies affiliated with PTL but operating without investment from the PTL Capital Investment Fund:

WhiteRiverLabs,LLC(affiliatedwiththeOpenSystemsLab).Founded in summer 2007, White River

Labs is the newest PTL spin-off company and is still in the earliest stages of development. Founded by

Christopher Mueller, a recent IU graduate, and Andrew Lumsdaine, director of OSL, the company’s goal

is to commercialize technology based on synthetic programming—a novel paradigm for creating high-

performance applications from scripting languages, enabling a high level of developer productivity without

sacrificing run-time performance. CorePy, the first programming package created for synthetic programming,

uses the Python programming language to provide a synthetic programming environment for IBM’s

PowerPC and Cell/B.E. processors. Research conducted in the OSL led to the development and validation of

CorePy and synthetic programming.

AcquiredScience,LLC(affiliatedwiththeScientificDataAnalysisLab). Acquired Science, LLC, has been

performing pro bono consulting work for a nonprofit consortium of businesses in Columbus, Indiana.

Attendees have included representatives from the local arts council, philharmonic, museums, and private

schools. The goals of the consortium are to improve the interconnectedness of these member institutions, as

well as the greater community, and to seek new funding opportunities.

v. OuTrEACh ACTIvITIEs

67

The Pervasive Technology Labs Community Outreach Program had a successful first year, meeting its goals

of conducting an average of 12 outreach events per year and forming important outreach partnerships with

IU departments and community science educators. The program has already been invited back to several

schools to conduct future career talks and activities.

The Community Outreach Program capped off its first year with its largest and most ambitious program to

date, a summer technology workshop for Indiana teens hosted by the Advanced Network Management Lab.

ANML invited high school students with an interest or aptitude in technology to visit PTL and participate

in a hands-on network security simulation exercise. The goal of the program was to introduce Hoosier

students to technology careers available in their home state. The teens also visited the Indiana University

machine room and learned about IU’s Big Red supercomputer and its role in the national TeraGrid network

of supercomputers. Networking and systems professionals from PTL and University Information Technology

Services talked about their own jobs and other careers related to technology at IU and across the state.

The Summer Technology Workshop was a success, with full attendance and several students on the waiting

list. Feedback on the program from both students and parents was positive, and the labs hope to have a

similar workshop on a new topic next summer.

69

Students receiving instructions for a hands-on network security simulation exercise conducted during the June Summer Technology Workshop.

Dan Miller of University Information Technology Services leads a tour of the IU machine room during the Summer Technology Workshop given by the PTL Community Outreach Program.

ANML researchers also conducted a network security simulation exercise for Indiana students from largely

underrepresented groups in the technology industry who attended the School of Informatics weeklong

summer camp in June. In addition, the PTL Community Outreach Program sponsored “camperships” for

two students with financial need to attend the Informatics Summer Camp free of charge.

The Community Outreach Program is excited to announce that they are meeting in July and August with the

leadership of Wonderlab, a popular science and technology museum for children located in Bloomington,

to discuss a potential partnership for the coming school year. The proposed program would offer classes on

site at Wonderlab, taught by PTL staff on various technology topics.

The labs also participate in several exciting outreach projects outside of the PTL Community Outreach

Program. One highlight of the current period was the testing in April of a robotic vehicle developed by a

team from the IU School of Informatics and the Advanced Network Management Lab. The vehicle is a GPS-

equipped golf cart used as a teaching tool for computer science students. The Visualization and Interactive

Spaces Lab also continued its successful Discovering the Science of the Environment outreach program.

Kay Connelly received an Alliances for Graduate Education in the Professoriate (AGEP) award from the

National Science Foundation, as well as other funds, to organize a workshop in which participants will

learn how to develop their own technology-related K–12 outreach program (see details in VIS Lab report).

The Community Grids Lab also continues to expand its partnership on various projects designed to bring

minority-serving institutions (MSIs) into the cyberinfrastructure. This summer CGL also hosted visiting

student researchers from MSIs (see CGL Report for more details).

71

Community Outreach Program events for the period are listed below:

February9,2007—HASTIIndianaTeachersofScienceConference,Indianapolis,Indiana

PTL staff talks with Hoosier science teachers about science outreach needs and opportunities at a booth

sponsored by the IU School of Informatics.

February22,2007—ScienceandTechnologyCareersTalk

Talk by Danko Antolovic of the Advanced Network Management Lab at 21st Century Charter School,

Indianapolis, Indiana.

February26,2007—ScienceFairJudging

Scientists from the Open Systems Lab, Community Grids Lab, and Advanced Network Management Lab

serve as judges for the Saint Susanna School Annual Science Fair, Plainfield, Indiana.

March22,2007—TechnologyCareersTalkat21stCenturyCharterSchoolatFountainSquare,

Indianapolis,Indiana

Talk given by PTL-affiliated scientist Ed Balas.

June14,2007—2007SchoolofInformaticsSummerCamp

IT professionals from the Advanced Network Management Lab conduct a hands-on network security

simulation exercise for campers at the 2007 IU School of Informatics Summer Camp. The Community

Outreach Program is a proud sponsor of two student “camperships” for the weeklong event.

June28,2007—SummerTechnologyWorkshopattheAdvancedNetworkManagementLab,

Bloomington,Indiana

Hands-on workshop and IU machine room tour for Indiana high school students who are considering

careers in computer programming, networking, or technology.

vI. OpErATIONAL ACTIvITIEs

7�

The central management and support structure of Pervasive Technology Labs is functioning extremely well.

Central support activities have operated during the last year better than ever before in the history of PTL.

The central operational and support staff includes the following individuals:

Therese Miller manages all central supporting staff within PTL, and that centralization has resulted in

excellent operational support for the labs overall, including improved management of data needed to

track and report on PTL activities.

Daphne Siefert-Herron has been tremendously successful as PTL information manager. Siefert-Herron has

been particularly effective in achieving excellent press coverage of PTL activities. The increased effectiveness

of PTL’s outreach efforts is largely the result of Siefert-Herron’s expertise.

PTL Operations Manager Therese Miller (right) and Information Manager Daphne Siefert-Herron

75

Deana Forrest serves as the PTL office services assistant and supports the

Bloomington labs. Jennifer Browning serves as PTL services coordinator in

Indianapolis, aiding the activities of the VIS and SDA Labs.

Jacque Whaley has left her support role in the PTL to join the private sector.

We thank her for her years of dedicated and expert assistance to PTL and wish

her well in the future.

The streamlining of PTL operational activities achieved during the past two

years has allowed Chief Operating Officer Craig Stewart to focus more on

strategic planning for PTL. IU Vice President for Information Technology

and Chief Information Officer Bradley Wheeler, PTL Science Director

Dennis Gannon, and Stewart communicate regularly to set and coordinate

achievement of PTL strategic goals.

IUPUI Services CoordinatorJennifer Browning

Office Services Assistant Deana Forrest

vII. AppENdICEs

77

AppENdIx 1: pATENTs FILEd By pErvAsIvE TEChNOLOgy LABs

79

Appendix 1: Patents filed by Pervasive Technology Labs

**Items in bold indicate new for the reporting period 1/07 to 6/07.

TechNo. TechName PTLDirector Description Status Comments

For a complete listing of all Pervasive Technology Labs disclosures, online services, hardware applications, publications, and presentations please visit www.pervasive.iu.edu.

05021

SecondGenerationWi-FiRadiolocator:

Wi-Fi Test Hardware

Compression scheme for improved efficiency of sparse matrix computations.

Wallace

Wallace

Lumsdaine

Wirelessnetworkradiolocationapparatuses,systems,andmethods.

An integrated circuit board incorporating this technology has been built and is being further developed.

Encoding scheme that reduces memory requirements necessary to store and access matrices.

Active

Active

Active

UpgradedtoPCTapplicationfiledwithU.S.PatentandTrademarkOffice

Provisional Patent Filed

Provisional Patent Filed

81

AppENdIx 2: TEChNOLOgy dIsCLOsurEs FILEd By pErvAsIvE TEChNOLOgy LABs

8�

Appendix2:TechnologyDisclosuresbyPervasiveTechnologyLabs

**Items in bold indicate new for the reporting period 1/07 to 6/07.

TechNo. TechName PTLDirector Description Status Comments

NotYetAssigned

NotYetAssigned

07030

07028

DiagnosticWorkbench

CommonInstrumentMiddlewareArchitecture(CIMA)forLaboratoryInstruments

SecondGenerationWi-FiRadiolocator:

VariadicGCC

Synthetic Programming Environment for PowerPC/AltiVec

McMullen

McMullen

Wallace

Lumsdaine

Lumsdaine

Assiststechniciansofvariouslevelsofexpertisetorepairandmaintainelectronicandmechanicalsystems

Softwareprovidesremoteaccessandstreamingdatacapabilitiesforawiderangeoflaboratoryinstruments.

Wirelessnetworkradiolocationapparatuses,systems,andmethods.

Compiler for C++ “variadic templates” extension

Runtime system for synthesizing and executing high-performance machine instruction sequences directly from scripting languages.

New

New

UpgradedtoPCTapplicationfiledwithU.S.PatentandTrademarkOffice

Completed

Active Seeking patent protection

85

Appendix2:TechnologyDisclosuresbyPervasiveTechnologyLabs

(continued)

TechNo. TechName PTLDirector Description Status Comments

07015

05099

05097

05095

05091

LibNBC

Wi-Fi Test Hardware

Web services and applications for structural visualization of mutation data

Information Visualization Cyberinfrastructure Database

Information Visualization Cyberinfrastructure Software Framework

MutDB

Lumsdaine

Wallace

Heiland/Mooney (PTL Fellow) collaboration

Borner (PTL Fellow)

Borner (PTL Fellow)

Mooney (PTL Fellow)

Non-blocking collective operation library

An integrated circuit board incorporating this technology has been built and is being further developed.

Software providing Web services functionality to access and display genetic mutation data.

Database of scholarly work that aims to serve researchers and technologists interested in the large-scale analysis, modeling, and visualization of literature data sets.

Framework designed to facilitate the integration of data analysis, modeling, and visualization algorithms into a unified system.

Database, software, and Web site suitable for genome annotation.

Open Source

Provisional Patent Filed

Active

Open Source

Open Source

Active

Appendix2:TechnologyDisclosuresbyPervasiveTechnologyLabs

(continued)

TechNo. TechName PTLDirector Description Status Comments

05090

05085

05056

05052

06218

07003

S-BLEST, structure- based local environment search tool

Parallel Boost Graphic Library

Indiana University Case-Based Reasoning Framework (IUCBRF)

Traffic-Based Mechanism for Ordering Search Results

NaradaBrokering

SMEApp

Mooney (PTL Fellow)

Lumsdaine

McMullen

Wallace

Fox

McMullen

Software that rapidly finds structurally similar sites in protein structures within a database and identifies structural environments associated with a given function.

Library for parallel computation of graph (or network) data structures.

Framework to facilitate the development of case-based reasoning (CBR) systems.

Tool to analyze traffic on a data network to determine the requested and referring URLs for HTTP requests on the World Wide Web.

A CGL Open-Source project that researches fundamental issues pertaining to distributed middleware systems.

Diagnostic software that learns from expert actions.

Active

Open Source

Open Source

Complete

Open Source

New (at RTC intake stage)

Copyright Application

87

Appendix2:TechnologyDisclosuresbyPervasiveTechnologyLabs

(continued)

TechNo. TechName PTLDirector Description Status Comments

06163

06088

06020

05119

05118

Single-Packet Radiolocation of 802.11 Wireless Sources

ArtXplore, Location Tracking System

ConceptGCC

Navigating New Spaces

PhotoBoard

Wallace

Baker

Lumsdaine

Baker

Baker

Apparatus consists of a set of 16 directional antennas, a radio receiver, a power-measuring device, and data collection equipment.

Location tracking system for ArtXplore, a Digital Museum Experience, and some of the overall system architecture and data design.

Extends the existing O/S GNU C++ compiler with language support generic programming.

Application allowing Indianapolis Museum of Art (IMA) visitors to browse the IMA collection on the PercepTable. Prototype application for examining large groups of digital images and assigning them to categories.

Non-exclusive license

Non-exclusive license

Completed

Non-exclusive license

Non-exclusive License

Appendix2:TechnologyDisclosuresbyPervasiveTechnologyLabs

(continued)

TechNo. TechName PTLDirector Description Status Comments

05105

05101

05021

05009

04074

Type checker prototype for extended generic C#

Open MPI

Compression scheme for improved efficiency of sparse matrix computations.

Make a Meal Auto-Sensing Interface for Nutrition Education

Matrix Template Library version 1-2, Iterative Template Library versions 1-4

Lumsdaine

Lumsdaine

Lumsdaine

Baker

Lumsdaine

Prototype implementation of a type checker and translator to standard Generic C# for some extended features we propose for that language.

Parallel run-time environment and message-passing system that is an implementation of the Message Passing Interface (MPI) standard.

Encoding scheme that reduces memory requirements necessary to store and access matrices.

Computer interface that uses physical objects for teaching about food nutrient values by detecting what food items are present on a tray.

Generic library written in C++ for basic linear algebra computations.

Active

Open Source

Active

Hold

Open Source

Provisional Patent Filed

89

Appendix2:TechnologyDisclosuresbyPervasiveTechnologyLabs

(continued)

TechNo. TechName PTLDirector Description Status Comments

04073

04072

04067

04020

04009

Boost Graphic Library

Slashtmp: Method to convey authorization to one outside of the party’s administrative domain

Boost MultiArray

Boost enable if

MPI.NET (P/Invoke Bindings Subset)

Lumsdaine

Wallace

Lumsdaine

Lumsdaine

Lumsdaine

Provides algorithms and data-structures concerning graphs (nodes and edges).

Method to create a unique Uniform Resource Locator (URL) that can be used to authorize a specific web-based action for a party outside the user’s administrative domain.

Generic library of multi-dimensional arrays.

General purpose tool for controlling template function overloading and class template specializations in C++.

Set of bindings from C# to the MPI standard allowing high-performance parallel communications from programs written in C# and other CLI languages.

Open Source

Non- Exclusive License

Open Source

Open Source

Open Source

Appendix2:TechnologyDisclosuresbyPervasiveTechnologyLabs

(continued)

TechNo. TechName PTLDirector Description Status Comments

0397

0383

0361

0360

Narada Brokering

Distributed Shared Memory with Just-In-Time Compilation

MUTT (Multi-User Tool Tracking)

PercepTable ™

Fox

Lumsdaine

Baker

Baker

Distributed middleware to handle a large number of clients. Also supports a variety of interactions such as centralized, distributed, and P2P.

Just-in-time compilation to affect distributed, shared memory functionality in a distributed memory (cluster) virtual machine.

Software to track and decode user interaction with physical objects used in a user interface without wires, mouse, or keyboard.

Device for display and interaction with computer-generated graphics. Graphics are projected onto a horizontal table and users interact with display using tools tracked by video camera.

Open Source

Hold

Active

Non-exclusive License

91

Appendix2:TechnologyDisclosuresbyPervasiveTechnologyLabs

(continued)

TechNo. TechName PTLDirector Description Status Comments

For a complete listing of all Pervasive Technology Labs disclosures, online services, hardware applications, publications, and presentations, please visit www.pervasive.iu.edu.

0352

0349

0314

0313

LAM-MPI

SourceGrid

Spoofwatch

Tsunami

Lumsdaine

Lumsdaine

Wallace

Wallace

MPI programming environment and development system for heterogeneous computers on a network.

Portal for software project managers that is a collection of compatible development and testing portlets.

SNORT plug-in that detects IP packets using spoofed source addresses.

Implementation of file transfer protocol of the same optimized to transfer large files over long distance network links where there may be packet loss due to errors.

Open Source

Exclusive License

Open Source

Open Source

AppENdIx 3: puBLICATIONs By pErvAsIvE TEChNOLOgy LABs — sINCE INCEpTION

9�

OpenSystemsLabPublications

Abrahams, D., & Siek, J. (2001, October). Policy Adaptors and the Boost Iterator Adaptor Library. Paper

presented at the Second Workshop on C++ Template Programming.

Abrahams, D., Siek, J., & Witt, T. (2003). Iterator Façade and Adaptor (No. N1455-03-0038, ISA/IEC JTC 1):

Information Technology Subcommittee SC22 Programming Language C++.

Abrahams, D., Siek, J., & Witt, T. (2003). New Iterator Concepts (No. N1477-03-0060, ISO/IEC JTC 1):

Information Technology Subcommittee SC22 Programming Language C++.

Albrecht, A., Gottschling, P., & Naumann, U. (2003). Markowitz-Type Heuristics for Computing Jacobean

Matrices Efficiently. Paper presented at the International Conference on Computational Science, St.

Petersburg, Russia.

Albrecht, A., Gottschling, P., & Naumann, U. (2002). Logarithmic Simulated Annealing for Optimal

Derivative Code (No. 372). United Kingdom: University of Hertfordshire.

Barrett, B. (2004). Return of the MPI Datatypes. Cluster World Magazine, MPI Mechanic Column, 2(6), 34–36.

Barrett, B., Squyres, J., & Lumsdaine, A. (2003, May). Integration of the LAM/MPI Environment and the

PBS Scheduling System. Paper presented at the 17th Annual International Symposium on High

Performance Computing Systems and Applications, Quebec, Canada.

Barrett, B., Squyres, J., & Lumsdaine, A. (2005). Implementation of Open MPI on Red Storm (No. LA-UR-05-

8307). Los Alamos, NM: Los Alamos National Laboratories.

Barrett, B., Squyres, J., Lumsdaine, A., Graham, R., & Bosilca, G. (2005, September). Analysis of the

Component Architecture Overhead in Open MPI. Paper presented at the 12th European PVM/MPI

Users’ Group Meeting, Sorrento, Italy.

Blackford, L., Demmell, J., Dongarra, J., Duff, L., Hammarling, S., Heroux, M., et al. (2002). An Updated

Set of Basic Linear Algebra Subprograms (BLAS). ACM Transactions on Mathematical Software, 28(2),

135–151.

Breuer, A., Gottschling, P., Gregor, D., & Lumsdaine, A. (2006, April). Effecting Parallel Graph Eigensolvers

Through Library Composition. Paper presented at the Performance Optimization for High-Level

Languages and Libraries (POHLL), Rhodes Island, Greece.

Castain, R., Woodall, T., Daniel, D., Squyres, J., Barrett, B., & Fagg, G. (2005, September). Open Run-

Time Environment (OpenRTE): A Transparent Multi-Cluster Environment for High-Performance

Computing. Paper presented at the 12th European PVM/MPI Users’ Group Meeting, Sorrento, Italy.

Cheng, J., Morris, J., Tran, J., Lumsdaine, A., Giordano, N., & Pyrak-Nolte, L. (2004). Single Phase Flow

in a Fracture: Micro-Model Experiments & Network Flow Simulation. International Journal of Rock

Mechanics, 41(4), 687–693.

Debasis, D., Mueller, C., Chen, K., & Glazier, J. A. (2005). Solving the Advection-Diffusion Equations in

Biological Contexts Using the Cellular Potts Model. Physical Review E, 72(041909).

95

Dimov, P., Gregor, D., Järvi, J., & Powell, G. (2003). A Proposal to Add an Enhanced Binder to the

Library Technical Report (No. N1455-03-0038): Information Technology Subcommittee SC22

Programming Language C++.

Douglas, G., Järvi, J., Kulkarni, M., Lumsdaine, A., Musser, D., & Schupp, S. (2005). Generic Programming

for High-Performance Libraries. 3(2).

Edmonds, N., Breuer, A., Gregor, D., & Lumsdaine, A. (2006, November). Single-Source Shortest Paths with

the Parallel Boost Graph Library. Paper presented at the Ninth DIMACS Implementation Challenge:

The Shortest Path Problem, Piscataway, NJ.

Friedman, D., Ghuloum, A., Siek, J., & Winebarger, L. (2003). Improving the Lazy Krivine Machine (No.

581). Bloomington, IN: Indiana University Department of Computer Science

Gabriel, E., Fagg, G., Bosilca, G., Angskun, T., Dongarra, J., Squyres, J., et al. (2004, September). Open MPI:

Goals, Concept, and Design of a Next Generation MPI Implementation. Paper presented at the 11th

European PVM/MPI Users’ Group Meeting, Budapest, Hungary.

Garcia, R., Järvi, J., Lumsdaine, A., Siek, J., & Willcock, J. (2003, October). A Comparative Study of Language

Support for Generic Programming. Paper presented at the Proceedings of the 2003 ACM SIGPLAN

Conference on Object-Oriented Programming, Systems, Languages, and Applications (OOPSLA ‘03).

Garcia, R., Järvi, J., Lumsdaine, A., Siek, J., & Willcock, J. (2005). An Extended Comparative Study of

Language Support for Generic Programming. Journal of Functional Programming.

Garcia,R.,Järvi,J.,Lumsdaine,A.,Siek,J.,&Willcock,J.(2007).ComparativeStudyofLanguage

SupportforGenericProgramming.Journal of Functional Programming,17(2),145–205.

Garcia, R., & Lumsdaine, A. (2005). MultiArray: A C++ Library for Generic Programming with Arrays.

Software: Practice and Experience, 35(2), 159–188.

Garcia, R., & Lumsdaine, A. (2005, September). Type Classes Without Types. Paper presented at the 2005

Workshop on Scheme and Functional Programming.

Gerlach, J., Gottschling, P., & Der, U. (2001). A Generic C++ Framework for Parallel Mesh Based Scientific

Applications. Paper presented at the 6th International Workshop on High-Level Parallel

Programming Models and Supportive Environments, San Francisco, CA.

Gottbrath, C., Barrett, B., Gropp, B., Lusk, E., & Squyres, J. (2006, September). An Interface to Support the

Identification of Dynamic MPI 2 Processes for Scalable Parallel Debugging. Paper presented at the

13th European PVM/MPI Users’ Group Meeting, Bonn, Germany.

Gottschling, P. (2004). Angel—An Extensible Library for Jacobean Accumulation. Paper presented at the

Fourth International Conference on Automatic Differentiation, Chicago, IL.

Gottschling, P. (2006). Fundamental Algebraic Concepts in Concept-Enabled C++ (No. 638). Bloomington,

IN: Indiana University Open Systems Lab.

Gottschling, P., Gräber, M., & Ralf, M. (2003, May). Numerical Simulation of Degassing Processes from

Glass Powders (in German). Paper presented at the 77th Conference of German Society of Glass

Technology, Leipzig, Germany.

Gottschling, P., Gräber, M., & Ralf, M. (2004). Finite Difference Calculation of Degassing from Glass Powders

(in German). Paper presented at the 78th Conference of German Society of Glass Technology,

Germany.

Graham, R., Barrett, B., Shipman, G., & Woodall, T. (2006, September). Open MPI: A High Performance,

Flexible Implementation of MPI Point-To-Point Communications. . Paper presented at the Clusters

and Computational Grids for Scientific Computing, Flat Rock, North Carolina.

Graham, R., Shipman, G., Barrett, B., Castain, R., & Bosilca, G. (2006, September). Open MPI: A High

Performance, Heterogeneous MPI. Paper presented at the Fifth International Workshop on

Algorithms, Models and Tools for Parallel Computing on Heterogeneous Networks, Barcelona, Spain.

Graham, R., Woodall, T., & Squyres, J. (2005, September). Open MPI: A Flexible High Performance MPI.

Paper presented at the 6th Annual International Conference on Parallel Processing and Applied

Mathematics, Poznan, Poland.

Gregor, D. (2004). High-Level Static Analysis for Generic Libraries. Rensselaer Polytechnic Institute.

Gregor, D. (2006). A Brief Introduction to Variadic Templates. Technical report N2087=06-0157, ISO/IEC JTC

1, Information Technology, Subcommittee SC 22, Programming Language C++. Bloomington, IN:

Indiana University.

Gregor, D. (2006). Concepts. Berlin, Germany: ANSI/ISO C++ Standard Committee, Evolution Working

Group.

Gregor, D. (2006). Concepts for the C++0x Standard Library: Containers. Technical report N2085=06-

0155, ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language C++.

Bloomington, IN: Indiana University.

Gregor, D. (2006). Conceptualizing the Range-Based for Loop (No. N2049-06-0119, ISO/IEC JCT 1):

Information Technology Subcommittee SC22 Programming Language C++.

Gregor, D. (2006). Large-Scale Network Analysis with the Boost Graph Libraries. Networks and Complex

Systems Talk Series.

Gregor, D. (2006). Signals and Slots for Library TR2. Bloomington, IN: Indiana University Open Systems Lab.

Gregor, D. (2006). Signals and Slots for Library TR2. Technical report N2086=06-0156, ISO/IEC JTC 1,

Information Technology, Subcommittee SC 22, Programming Language C++. Bloomington, IN:

Indiana University.

Gregor,D.,&Järvi,J.(2007).VariadicTemplatesforC++.Object-Oriented Programming Languages and

Systems:ACMPress.

97

Gregor,D.,&Järvi,J.(2007).VariadicTemplatesfortheC++0xStandardLibrary(Revision1),Technical

reportN2192=07-0052,ISO/IECJTC1,InformationTechnology,SubcommitteeSC22,

ProgrammingLanguageC++.Bloomington,IN:IndianaUniversity.

Gregor,D.,&Järvi,J.(2007).VariadicTemplatesfortheC++0xStandardLibrary.Technicalreport

N2151=07-0011,ISO/IECJTC1,InformationTechnology,SubcommitteeSC22,Programming

LanguageC++.Bloomington,IN:IndianaUniversity.

Gregor, D., Järvi, J., Kulkarni, M., Lumsdaine, A., Musser, D., & Schupp, S. (2005). Generic Programming

and High Performance Libraries. International Journal of Parallel Programming, 33(2).

Gregor,D.,Järvi,J.,Maurer,J.,&Merrill,J.(2007).ProposedWordingforVariadicTemplates.

TechnicalReportN2152=07-0012,ISO/IECJTC1,InformationTechnologySubcommitteeSC22,

ProgrammingLanguageCPP.Bloomington,IN:IndianaUniversity.

Gregor,D.,Järvi,J.,Maurer,J.,&Merrill,J.(2007).ProposedWordingforVariadicTemplates(Revision

1),TechnicalreportN2191=07-0051,ISO/IECJTC1,InformationTechnology,SubcommitteeSC

22.Bloomington,IN:IndianaUniversity.

Gregor, D., Järvi, J., & Powell, G. (2006). Variadic Templates (Revision 3). Technical report N2080=06-

0150, ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language C++.

Bloomington, IN: Indiana University.

Gregor, D., Järvi, J., Siek, J., Stroustrup, B., Dos Reis, G., & Lumsdaine, A. (2006, October). Concepts:

Linguistic Support for Generic Programming in C++. Paper presented at the 2006 ACM SIGPLAN

Conference on Object-Oriented Programming, Systems, Languages, and Applications (OOPSLA ‘06).

Gregor,D.,&Järvi,J.(2007).DecltypefortheC++0xStandardLibraryTechnicalreportN2194=07-0054,

ISO/IECJTC1,InformationTechnology,SubcommitteeSC22,ProgrammingLanguageC++.

Bloomington,IN:IndianaUniversity.

Gregor, D., & Lumsdaine, A. (2005, October). Lifting Sequential Graph Algorithms for Distributed-Memory

Parallel Computation. Paper presented at the 2005 ACM SIGPLAN Conference on Object-Oriented

Programming, Systems, Languages, and Applications (OOPSLA ‘05).

Gregor, D., & Lumsdaine, A. (2005). The Parallel BGL: A General Library for Distributed Graph

Computations. Parallel Object-Oriented Scientific Computing (POOSC).

Gregor, D., & Lumsdaine, A. (2006, February). Parallel Boost Graph Library. Paper presented at the SIAM

Conference on Parallel Processing, San Francisco, CA.

Gregor, D., Powell, G., & Järvi, J. (2003). Typesafe Variable-Length Function and Template Argument Lists

(No. N1483-03-0066, ISO/IEC JTC 1): Information Technology Subcommittee SC22 Programming

Language C++.

Gregor, D., & Schupp, S. (2002, July). Making the Usage of STL Safe. Paper presented at the Generic

Programming, IFIP TC2/WG2.1 Working Conference on Generic Programming.

Gregor, D., & Schupp, S. (2003). Retaining Path-Sensitive Relations across Control-Flow Merges (No. 03-15):

Rensselaer Polytechnic Institute.

Gregor, D., & Schupp, S. (2006). STLlint: Lifting Static Checking from Languages to Libraries. Software:

Practice and Experience, 36, 225–254.

Gregor, D., Schupp, S., & Musser, D. (2001). Base Class Injection. Third International Conference on

Generative and Component-Based Software Engineering (2186), 106–117.

Gregor, D., Schupp, S., & Musser, D. (2001). Design Patterns for Library Optimization. Paper presented at

the International Conference on Parallel/High-Performance Object-Oriented Scientific Computing

(POOSC’01), Tampa, FL.

Gregor, D., Schupp, S., & Musser, D. (2003). Design Patterns for Library Optimization. Scientific

Programming, 11(4), 309–320.

Gregor, D., & Siek, J. (2005). Explicit Model Definitions Are Necessary (No. N1798-05-0058, ISO/IEC JTC

1): Information Technology Subcommittee SC22 Programming Language C++.

Gregor, D., & Siek, J. (2005). Implementing Concepts (No. N1848-05-0108, ISO/IEC JTC 1): Information

Technology Subcommittee SC22 Programming Language C++.

Gregor, D., Siek, J., Willcock, J., Järvi, J., Gardia, R., & Lumsdaine, A. (2005). Concepts for C++Ox: Revision 1

(No. N1849-05-0109, ISO/IEC JTC 1): Information Technology Subcommittee SC22 Programming

Language C++.

Gregor, D., & Stroustrup, B. (2006). Concepts (No. N2042-06-0112, ISO/IEC JTC1): Information Technology

Subcommittee SC22 Programming Language C++.

Gregor, D., & Stroustrup, B. (2006). Concepts (Revision 1) (No. N2080=06-0150, ISO/IEC JCT 1).

Bloomington, IN: Information Technology Subcommittee SC22, Programming Language C++.

Gregor, D., & Stroustrup, B. (2006). Concepts (Revision 1). Technical report N2081=06-0151, ISO/IEC JTC

1, Information Technology, Subcommittee SC 22 Programming Language C++. Bloomington, IN:

Indiana University.

Gregor,D.,&Stroustrup,B.(2007).ProposedWordingforConcepts.TechnicalreportN2193=07-0053,

ISO/IECJTC1,InformationTechnology,SubcommitteeSC22,ProgrammingLanguageC++.

Bloomington,IN:IndianaUniversity.

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++Ox Standard Library: Utilities

(Revision 1) (No. N2082+06-0152, ISO/IEC JCT 1). Bloomington, IN: Information Technology

Subcommittee SC 22, Programming Language C++.

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++0x Standard Library: Algorithms

(Revision 1). Technical report N2084=06-0154, ISO/IEC JTC 1, Information Technology,

Subcommittee SC 22, Programming Language C++. Bloomington, IN: Indiana University.

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++0x Standard Library: Iterators

(Revision 1). Technical report N2083=06-0153, ISO/IEC JTC 1, Information Technology,

Subcommittee SC 22, Programming Language C++. Bloomington, IN: Indiana University.

99

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++OX Standard Library: Algorithms

(No. N2040-06-0110, ISAO/IEC JCT 1): Information Technology Subcommittee SC22, Programming

Language C++.

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++OX Standard Library: Approach

(No. N2036-06-0106, ISO/IEC JTC1): Information Technology Subcommittee SC22 Programming

Language C++.

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++OX Standard Library: Introduction

(No. N2037-06-0107, ISA/IEC JTC 1): Information Technology Subcommittee SC22 Programming

Language C++.

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++OX Standard Library: Iterators (No.

N2039-06-0109, ISO/IEC JCT1): Information Technology Subcommittee SC22 Programming

Language C++.

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++OX Standard Library: Numerics:

Information Technology Subcommittee SC22 Programming Language C++

Gregor, D., Willcock, J., & Lumsdaine, A. (2006). Concepts for the C++OX Standard Library: Utilities (No.

N2038-06-0108, ISO/IEC JCT 1): Information Technology Subcommittee SC22, Programming

Language C++.

Hoefler, T., Gottschling, P., Rehm, W., & Lumsdaine, A. (2006, September). Optimizing a Conjugate

Gradient Solver with Non-Blocking Collective Operations. Paper presented at the ParSim 2006

Workshop.

Hoefler, T., Gottschling, P., Rehm, W., & Lumsdaine, A. (2006, September). Optimizing a Conjugate

Gradient Solver with Non-Blocking Collective Operations in Recent Advantages in Parallel Virtual

Machine and Message Passing Interface. Paper presented at the 13th European PVM/MPI User’s

Group Meeting.

Hoefler, T., Janisch, R., & Rehm, W. (2006, November). Parallel Scaling of Teter’s Minimization for Ab Initio

Calculations. Paper presented at the HPC Nano Workshop in conjunction with SC ‘06.

Hoefler,T.,Lichei,A.,&Rehm,W.(2007,March).Low-OverheadLogGPParameterAssessmentfor

ModernInterconnectionNetworks.Paperpresentedatthe21stIEEEInternationalParallel&

DistributedProcessingSymposium.

Hoefler, T., & Lumsdaine, A. (2006). Design, Implementation, and Usage of LibNBC. Technical Report,

Open Systems Lab. Bloomington, IN: Indiana University.

Hoefler, T., Reinhardt, M., Mietke, F., Mehlan, T., & Rehm., W. (2006). Low Overhead Ethernet

Communication for Open MPI on Linux Clusters. Technical Report 06, TU Chemnitz. Bloomington,

IN: Indiana University.

Hoefler,T.,Siebert,C.,&Rehm,W.(2007).APracticallyConstant-TimeMPIBroadcastAlgorithmfor

Large-ScaleInfiniBandClusterswithMulticast.FirstIEEEInternationalParallel&Distributed

ProcessingSymposium,232.

Hoefler, T., Squyres, J., Bosilca, G., Fagg, G., Lumsdaine, A., & Rehm, W. (2006). Non-Blocking Collective

Operations for MPI-2. Technical Report, Open Systems Lab. Bloomington, IN: Indiana University.

Hoefler, T., Squyres, J., Fagg, G., Bosilca, G., Rehm, W., & Lumsdaine, A. (2006, September). A New

Approach to MPI Collective Communication Implementations. Paper presented at the Sixth

Austrian-Hungarian Workshop on Distributed and Parallel Systems.

Hoefler, T., Squyres, J., Mehlan, T., Mietke, F., & Rehm, W. (2005, November). Implementing a Hardware-

Based Barrier in Open MPI. Paper presented at the KiCC ‘05, Chemnitzer Informatik Berichte.

Hoefler, T., Squyres, J., Rehm, W., & Lumsdaine, A. (2006, December). Case for Non-Blocking Collective

Operations. Paper presented at the Frontiers of High Performance Computing and Networking—

ISPA 2006 Workshops.

Hoefler, T., Viertel, C., Mehlan, T., Mietke, F., & Rehm, W. (2006, September). Assessing Single-Message and

Multi-Node Communication Performance of InfiniBand. Paper presented at the IEEE Inernational

Conference on Parallel Computing in Electrical Engineering, PARELEC 2006.

Hursey, J., Squyres, J., & Lumsdaine, A. (2006). A Checkpoint and Restart Service Specification for Open

MPI. Technical Report TR635. Bloomington, IN: Indiana University.

Hursey,J.,Squyres,J.,Mattox,T.,&Lumsdaine,A.(2007,March).TheDesignandImplementationof

Checkpoint/RestartProcessFaultToleranceforOpenMPI.Paperpresentedatthe21stIEEE

InternationalParallelandDistributedProcessingSymposium.

Izaguirre, J. A., Ma, Q., Matthew, T., Willcock, J., Slabach, T., Moore, B., et al. (2002). Overcoming

Instabilities in Verlet-l/r-RESPA with the Mollified Impulse Method. In T. Schlick & H. H. Gan

(Eds.), Proceedings of Third International Workshop on Methods for Macromolecular Modeling (Vol. 24,

pp. 146–174). Berlin, New York: Springer-Verlag.

Järvi, J. (2001). Tuple Types and Multiple Return Values. C/C++ Users Journal, 19, 24–35.

Järvi, J. (2002). Proposal for Adding Tuple Types into the Standard Library (No. N1403-02-0061):

Information Technology Subcommittee SC22 Programming Language C++.

Järvi, J., Gregor, D., Willcock, J., Lumsdaine, A., & Siek, J. (2006). Algorithm Specialization in Generic

Programming: Challenges of Constrained Generica in C++. Paper presented at the 2006 ACM

SIGPLAN Conference on Programming Language Design and Implementation (PDLI ‘06), New

York, NY.

Järvi, J., Lumsdaine, A., Gregor, D., Kulkarni, M., Musser, D., & Schupp, S. (2004, April). Generic

Programming and High-Performance Libraries. Paper presented at the Workshop on Next

Generation Software at IPDPS 2004, Sante Fe, NM.

Järvi, J., Lumsdaine, A., Siek, J., & Willcock, J. (2003, October). An Analysis of Constrained Polymorphism

for Generic Programming. Paper presented at the Multiparadigm Programming 2003: Proceedings

of the MPOOL Workshop at OOPSLA ‘03, Anaheim, CA.

101

Jarvi, J., Lumsdaine, A., & Wise, D. (Eds.). (2002). MSPLS 2002: Proceedings of the Workshop of the Midwest

Society for Programming Languages and Systems (No. TR560). Bloomington, IN: Indiana University

Department of Computer Science.

Järvi, J., & Powell, G. (2001, October). The Lambda Library: Lambda Abstractions in C++. Paper presented at

the Second Workshop on C++ Template Programming (TMPW ‘01).

Järvi, J., & Powell, G. (2001). Side Effects and Partial Function Application in C++. Paper presented at the

Multiparadigm Programming with OO Languages Workshop (MPOOL ‘01).

Järvi, J., Powell, G., & Lumsdaine, A. (2003). The Lambda Library: Unnamed Functions in C++. 33, 259–291.

Järvi, J., & Stroustrup, B. (2003). Mechanisms for Querying Types of Expressions: Decltype and Auto

Revisited (No. N1527-03-0110, ISO/IEC JTC1): Information Technology Subcommittee SC22

Programming Language C++.

Järvi, J., Stroustrup, B., Gregor, D., & Siek, J. (2003). Decltype and Auto (No. N1478-03-0061, ISO/IEC JTC

1): Subcommittee SC 22 Programming Language C++.

Järvi, J., Willcock, J., & Lumsdaine, A. (2005, January 19). Associated Types and Constraint Propagation

for Mainstream Object-Oriented Generics. Paper presented at the 20th annual ACM SIGPLAN

Conference on Object-Oriented Programming Systems Languages and Applications (OOPSLA ‘05)

New York, NY.

Järvi, J., Willcock, J., Hinnant, H., & Lumsdaine, A. (2003). Function Overloading Based on Arbitrary

Properties of Types. C/C++ Users Journal, 21(6), 25–32.

Järvi, J., Willcock, J., & Lumsdaine, A. (2004). Associated Types and Constraint Propagation for Mainstream

Object-Oriented Generics (No. 2004-12-3): Texas A&M University Department of Computer

Science.

Järvi, J., Willcock, J., & Lumsdaine, A. (2003). Concept-Controlled Polymorphism. Generative Programming

and Component Engineering, 2830, 228–244.

Järvi, J., Willcock, J., & Lumsdaine, A. (2004, April). Algorithm Specialization and Concept Constrained

Genericity. Paper presented at the Concepts: A Linguistic Foundation of Generic Programming at

Adobe Tech Summit, San Jose, CA.

Järvi, J., Willcock, J., & Lumsdaine, A. (2005, December). Associated Types and Constraint Propagation

for Mainstream Object-Oriented Generics. Paper presented at the 20th Annual ACM SIGPLAN

Conference on Object-Oriented Generics (OOPSLA ‘05), New York, NY.

Kambadur,P.,Gregor,D.,&Lumsdaine,A.(2007,May).ParallelizationofGenericLibrariesbasedon

TypeProperties.PaperpresentedattheSeventhInternationalConferenceonComputational

Science(LNCS),Beijing,China.

Kambadur, P., Gregor, D., Lumsdaine, A., & Dharurkar, A. (2006, September). Modernizing the C++

Interface to MPI. Paper presented at the 13th European PVM/MPI Users’ Group Meeting, Bonn,

Germany.

Kim, D., Squyres, J., & Lumsdaine, A. (2005, May). Revamping the OSCAR Database: A Flexible Approach to

Cluster Configuration Data Management. Paper presented at the 19th International Symposium on

High Performance Computing Systems and Applications, Guelph, Ontario, Canada.

Kim, D., Squyres, J., & Lumsdaine, A. (2006, May 14–17). Introduction of the OSCAR Database API (ODA).

Paper presented at the 20th International Symposium on High-Performance Computing in an

Advanced Collaborative Environment (HPCS’06).

Lee, L.-Q. (2002). Generic Programming for High-Performance Scientific Computing. University of Notre

Dame, South Bend, IN.

Lee, L.-Q., & Lumsdaine, A. (2002). Generic Programming for High Performance Scientific Applications.

Paper presented at the 2002 Joint ACM Java Grande-ISCOPE Conference.

Lee, L.-Q., & Lumsdaine, A. (2003, April). Generic Message Passing Framework. Paper presented at the

Proceedings of the International Parallel and Distributed Processing Symposium (IPDPS).

Lee, L.-Q., & Lumsdaine, A. (2005). Generic Programming for High Performance Scientific Applications.

Concurrency and Computation: Practice and Experience, 17(7–8), 941–965.

Lumsdaine, A., Barrett, B., Brightwell, R., & Squyres, J. (2006, May). Implementation of Open MPI on the

Cray XT3. Paper presented at the Cray Users Group 2006, Lugano, Switzerland.

Lumsdaine,A.,Gregor,D.,Hendrickson,B.,&Berry,J.(2007).ChallengesinParallelGraphProcessing.

ParallelProcessingLetters,17(1),5–20.

Lumsdaine, A., & Wu, D. (2003). Krylov-Subspace Acceleration of Waveform Relaxation. SIAM Journal on

Numerical Analysis, 41(1), 90–111.

Mehlan, T., Strunk, J., Hoefler, T., Mietke, F., & Rehm, W. (2006, September). RS—A Portable Interface

for Reconfigurable Systems. Paper presented at the IEEE International Conference on Parallel

Computing in Electrical Engineering, PARELEC 2006.

Mietke, F., Baumgartl, R., Rex, R., Mehlan, T., Hoefler, T., & Rehm, W. (2006). Analysis of the Memory

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Mueller, C., Dalkilic, M., & Lumsdaine, A. (2005, April). High-Performance Direct Pairwise Comparison of

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Mueller, C., Dalkilic, M., & Lumsdaine, A. (2005, February 14). Implementing Data Parallel Algorithms

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Mueller, C., Dalkilic, M., & Lumsdaine, A. (2006). High-Performance Direct Pairwise Comparison of Large

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Mueller, C., & Lumsdaine, A. (2006, October). Runtime Synthesis of High-Performance Code from Scripting

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Mueller,C.,Martin,B.,&Lumsdaine,A.(2007,February).InterpretingLargeVisualSimilarityMatrices.

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Ralf, M., Gaber, M., & Gottschling, P. (2003, July). Water Release and Crystallization of Glass Powders. Paper

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Ralf, M., Gaber, M., & Gottschling, P. (2004). Volatile Concentration and Diffusivity Determined by Vacuum

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Rasmussen, C., & Squyres, J. (2005, September). A Case for New MPI Fortran Bindings. Paper presented at

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Sankaran, S., Squyres, J., Barrett, B., & Lumsdaine, A. (2003). Checkpoint-Restart Support System Services

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Sankaran, S., Squyres, J., Barrett, B., Lumsdaine, A., Duell, J., Hargrove, P., et al. (2005). LAM-MPI

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Squyres, J. (2003, December). Definitions and Fundamentals—The Message Passing Interface (MPI). Cluster

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Squyres, J. (2004, April). Everything You Wanted to Know About Groups and Communicators. Cluster World

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Squyres, J. (2004, May). How to Succeed in Datatypes Without Really Trying. Cluster World Magazine, MPI

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Squyres, J. (2004, July). In Parallel, Everyone Hears You Scream. Cluster World Magazine, MPI Mechanic

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Squyres, J. (2004, August). In Parallel, Everyone Hears You Scream II. Cluster World Magazine, MPI Mechanic

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Squyres, J. (2004, September). The Joys of Asynchronous Computing. Cluster World Magazine, 2, 36–38.

Squyres, J. (2004, October). More Joys of Asynchronous Communication. Cluster World Magazine, MPI

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Squyres, J. (2004, December). MPI Debugging-Can You Hear Me Now? Cluster World Magazine, MPI

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Squyres, J. (2004, November). MPI_Reduce: Introducing Open MPI. Cluster World Magazine, 2, 20–28.

Squyres, J. (2004, January). Processes, Processors, and MPI, Oh My. Cluster World Magazine, MPI Mechanic

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Squyres, J. (2004, February). What Really Happens During MPI_INIT. Cluster World Magazine, MPI Mechanic

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Squyres, J. (2004, March). Zen and the Art of MPI Collectives. Cluster World Magazine, MPI Mechanic

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Squyres, J. (2005, January). Debugging in Parallel (in Parallel). Cluster World Magazine, 3, 34–37.

Squyres, J. (2005). Doing More With Less. Cluster World Magazine, MPI Mechanic Column, 3(6), 32–34, 50.

Squyres, J. (2005). Is Your Application Spawnworthy? Cluster World Magazine, MPI Mechanic Column, 3(3),

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Squyres, J. (2005, May). Progress is the Opposite of Congress. Cluster World Magazine, 3, 32–35.

Squyres, J. (2005, February). The Spawn of MPI. Cluster World Magazine, MPI Mechanic Column, 3, 40–43.

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Squyres, J. (2006). Shared Memory Collectives and Their Consequences. Houston, TX: University of

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Squyres, J., Barrett, B., & Lumsdaine, A. (2003). Boot System Services Interface (SSI) Modules for LAM/MPI

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Squyres, J., Barrett, B., & Lumsdaine, A. (2003). MPI Collective Operations System Services Interface

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Squyres, J., Barrett, B., & Lumsdaine, A. (2003). Request Progression Interface (RPI) System Services Interface

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Squyres, J., Barrett, B., & Lumsdaine, A. (2003). The System Services Interface (SSI) to LAM/MPI (No.

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Squyres, J., & Lumsdaine, A. (2003, October). A Component Architecture for LAM/MPI. Paper presented at

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Squyres, J., & Lumsdaine, A. (2003, June). A Component Architecture for LAM/MPI. Paper presented at the

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Squyres, J., & Lumsdaine, A. (2004, July). The Component Architecture of Open MPI: Enabling Third-Party

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Veldhuizen, T. (2004). Active Libraries and Universal Languages. Indiana University, Bloomington, IN.

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Veldhuizen, T. (2005). Software Libraries and Their Reuse: Entropy, Kolmogorov Complexity, and Zipf’s Law:

Indiana University Department of Computer Science.

Veldhuizen, T. (2006, January). Tradeoffs in Metaprogramming. Paper presented at the ACM SIGPLAN

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Veldhuizen, T., & Lumsdaine, A. (2002). Guaranteed Optimization: Proving Nullspace Properties of

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Veldhuizen, T., & Lumsdaine, A. (2002). Guaranteed Optimization: Proving Nullspace Properties of

Compilers (No. TR564): Indiana University Department of Computer Science.

Veldhuizen, T., & Siek, J. (2003). Combining Optimizations, Combining Theories (No. 582). Bloomington,

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Virtanen, I., Ekholm, E., Aittokallio, T., Tähtinen, H., Salmi, J., Järvi, J., et al. (2003). State of Vigilance

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Willcock, J., & Lumsdaine, A. (2006, June). Accelerating Sparse Matrix Computations via Data Compression.

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Willcock, J., Lumsdaine, A., & Robison, A. (2002, November). Using MPI with C# and the Common

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Willcock, J., Lumsdaine, A., & Robison, A. (2002). Using MPI with C# and the Common Language

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Willcock, J., Lumsdaine, A., & Robison, A. (2005). Using MPI with C# and the Common Language

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Willcock, J., Siek, J., & Lumsdaine, A. (2001, October). Caramel: A Concept Representation System for

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AdvancedNetworkManagementLabPublications

Antolovic,D.(2007,March).DesignofaRadio-FrequencyMultilexer,UserinRadiolocationof

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Antolovic, D., Leykin, A., & Johnson, S. (2005). Vanishing Point: A Visual Road-Detection Program for a

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Antolovic, D., & Wallace, S. (2006, August). Single-Packet Radiolocation of 802.11 Wireless Source, Using an

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Balas, E. (2003, December). Sebek: Covert Glass-box Host Analysis. USENIX Login Magazine, 28.

Balas, E. (2004). Distributed Honeynets and Know Your Enemy: Learning About Security Threats. In

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Boerner, K., Penumerthy, S., Meiss, M., & Ke, W. (2006). Mapping the Diffusion of Information Among

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De Laat, C. & Steven, W. (2002, September). The Rationale of the Current Optical Networking Initiatives.

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Faber, A. M., Gupta, M., & Viecco, C. (2006, November). Revisiting Web Server Workload Invariants in the

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Meiss, M. (2006). Pandora: A Case Study in Reverse Engineering: Indiana University School of Informatics.

Meiss, M. (2006). Race Pharming. In M. Jakobsson & S. Myers (Eds.), Phishing and Counter-Measures:

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Meiss, M., Menczer, F., & Vespignani, A. (2005). On the Lack of Typical Behavior in the Global Web Traffic

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Meiss, M., & Wallace, S. (2002). Standards-Based Discovery of Switched Ethernet Topology. Bloomington,

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CommunityGridsLabPublications

Ajay, S., & Ekanayake, J. (2006, October 5–8). Analysis of the Usage Statistics of Robots Exclusion Standards

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Aktas,M.(2007).FederationinGridInformationServices.IndianaUniversity,Bloomington,IN.

Aktas, M., Aydin, G., Aysan, M. N., Balsoy, O., Fox, G., Ikibas, C., et al. (2002). Design Features and

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Aktas, M., Aydin, G., Donnellan, A., Fox, G., Granat, R., Grant, L., et al. (2004). iSERVO: Implementing the

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Aktas, M., Aydin, G., Donnellan, A., Fox, G., Granat, R., Lyzenga, G., et al. (2005, June 28–30).

Implementing Geographical Information System Grid Services to Support Computational

Geophysics in a Service-Oriented Environment. Paper presented at the NASA Earth-Sun System

Technology Conference, University of Maryland, Adelphi, MD.

Aktas, M., Aydin, G., Fox, G., Gadgil, H., Pierce, M., & Sayar, A. (2005). Information Services for Grid/Web

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Aktas, M., Fox, G., & Pierce, M. (2005). An Architecture for Supporting Information in Dynamically

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Aktas, M., Fox, G., & Pierce, M. (2005, November 27–29). Fault Tolerant High Performance Information

Services for Dynamic Collections of Grid and Web Services. Paper presented at the First

International Conference on SKG2005 Semantics, Knowledge and Grid, Beijing, China.

Aktas, M., Fox, G., & Pierce, M. (2005, November 27–29). Information Services for Dynamically Assembled

Semantic Grids. Paper presented at the First International Conference on SKG2005 Semantics,

Knowledge and Grid, Beijing, China.

Aktas, M., Fox, G., & Pierce, M. (2005, June). Managing Dynamic Metadata as Context. Paper presented at

the Istanbul International Computational Science and Engineering Conference, Istanbul, Turkey.

Aktas,M.,Fox,G.,&Pierce,M.(2007).FaultTolerantHighPerformanceInformationServicesfor

DynamicCollectionsofGridandWebServices.Future Generation Computer Systems,Special

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Beijing,China,November27–29,2005,23(3),317–337.

Aktas, M., Fox, G., & Yoo, S.-J. (2005). Data Integration Hub for a Hybrid Paper Search. Melbourne,

Australia.

Aktas, M., Oh, S., Fox, G., & Pierce, M. (2006, October 31–November 3). XML Metadata Services. Paper

presented at the Second International Conference on Semantics, Knowledge, and Grid (SKG 2006),

Guilin, China.

Aktas, M., Oh, S., Fox, G., & Pierce, M. (2006). XML Metadata Services and Application Usage Scenarios.

Aktas, M., Pierce, M., & Fox, G. (2004, June 10). Designing Ontologies and Distributed Resources Discovery

Services for an Earthquake Simulation Grid. Paper presented at the GGF-11 Global Grid Forum

Semantic Grid Applications Workshop, Hawaii.

Aktas, M., Pierce, M., Fox, G., & Leake, D. (2004, November 8). A Web-Based Conversational Case-Based

Recommender System for Ontology Aided Metadata Discovery. Paper presented at the Fifth IEEE/

ACM International Workshop on Grid Computing.

Alameda, J., Christie, M., Fox, G., Futrelle, J., Gannon, D., Hatgan, M., et al. (2006). The Open Grid

Computing Environments Collaboration: Portlets and Services for Science Gateways. Concurrency

and Computation: Practice and Experience—Special Issue for Science Gateways GGF14 Workshop.

Aló, R., Barnes, K., Baxter, D., Fox, G., Kuslikis, A., Lowe, C., et al. (2006, June 12–15). MSI-CIEC: MSI

Cyberinfrastructure Empowerment Coalition and the TeraGrid (Abstract) TeraGrid ‘06. Paper

presented at the Teragrid ‘06, Indianapolis, IN.

Aló,R.,Barnes,K.,Baxter,D.,Fox,G.,Kuslikis,A.,&Ramirez,A.(2007,June4–8).Advancesinthe

MSICommunityandtheMSICyberinfrastructureEmpowermentCoalition(MSI-CIEC).Paper

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Atkinson, M., DeRoure, D., Dunlop, A., Fox, G., Henderson, P., Hey, T., et al. (2004). Web Service Grids: An

Evolutionary Approach. Concurrency and Computation: Practice and Experience, 17(DOI), 377–389.

Aydin,G.(2007).AnOverviewoftheOpenGeospatialConsortiumStandardsandTheirUsein

CommunityGridsLaboratoryTechnicalReport.Bloomington,IN:IndianaUniversity.

Aydin,G.(2007).ServiceOrientedArchitectureforGeographicInformationSystemsSupportingReal

TimeDataGrids.Bloomington,IN:IndianaUniversity.

Aydin, G., Aktas, M., Fox, G., Gadgil, H., Pierce, M., & Sayar, A. (2005, November 13–14). SERVOGrid

Complexity Computational Environments (CCE) Integrated Performance Analysis. Paper presented

at the Grid Computing Conference, 6th IEEE/ACM International Workshop.

Aydin, G., Altay, H., Aktas, M., Aysan, M. N., Fox, G., Ikibas, C., et al. (2003, June 9–13). Online Knowledge

Center Tools for Metadata Management. Paper presented at the DoD HPCMP Users Group Meeting,

Seattle, WA.

Aydin, G., Fox, G., Gadgil, H., & Pierce, M. (2006, June 27–29). Streaming Data Services to Support Archival

and Real-Time Geographical Information System Grids. Paper presented at the Sixth Annual NASA

Earth Science Technology Conference, College Park, Maryland.

Aydin, G., Fox, G., Gadgil, H., & Pierce, M. (2006). Streaming Data Services to Support Archival and Real-

Time Geographical Information Systems Grids: Indiana University Community Grids Lab.

Aydin, G., Kaplan, A., Topcu, A., Yildiz, B., Balsoy, O., Pierce, M., et al. (2002, November 18–20). An XML

Based System for Dynamic Message Content Creation, Delivery, and Control. Paper presented at the

IASTED International Conference on Information and Knowledge Sharing, St. Thomas, U.S. Virgin

Islands.

Aydin, G., Pierce, M., Fox, G., Aktas, M., & Sayar, A. (2004, July 13). Implementing GIS Grid Services for

the International Solid Earth Research Virtual Observatory. Fourth ACES (APEC Cooperation for

Earthquake Simulation) Workshop.

Aydin,G.,Qi,Z.,Pierce,M.,Bock,Y.,&Fox,G.(2007,May13).BuildingaSensorGridforRealTime

GlobalPositioningSystemData.PaperpresentedattheWorkshoponPrinciplesofPervasive

InformationSystemsDesign/Pervasive2007,Toronto,Ontario,Canada.

Aydin,G.,Qi,Z.,Pierce,M.,Fox,G.,&Bock,Y.(2007).Architecture,Performance,andScalabilityofa

Real-TimeGlobalPositioningSystemDataGrid.PEPI Physics of the Earth and Planetary Interiors

(SpecialIssueonComputationalChallengesinGeosciences).

Aydin, G., Sayar, A., Gadgil, H., Aktas, M., Fox, G., Ko, S., et al. (2006). Building and Applying Geographical

Information System Grids. Concurrency and Computation: Practice and Experience (Special Issue on

Geographical Information Systems and Grids from GGF15 Workshop).

Balsoy, O., Aktas, M. S., Aydin, G., Aysan, M. N., Ikibas, C., Kaplan, A., et al. (2002). The Online Knowledge

Center: Building a Component Based Portal. Paper presented at the International Conference on

Information and Knowledge Engineering.

Balsoy, O., Jin, Y., Aydin, G., Pierce, M., & Fox, G. (2003, June 2-4). Automating Metadata Web Service

Deployment for Problem Solving Environments. Paper presented at the International Conference

on Computational Science (ICCS’03), Melbourne, Australia.

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Balsoy, O., Jin, Y., Aydin, G., Pierce, M., & Fox, G. (2005). Automating Metadata Web Service Deployment

for Problem Solving Environments. Future Generation Computer Systems, 21(6), 910-919.

Bulut,H.(2007).HighPerformanceRecordingandManipulationofDistributedStreams.Indiana

University,Bloomington,IN.

Bulut, H., Fox, G., Gannon, D., Kim, K., Ko, S.-H., Lee, S., et al. (2002, July 17). An Architecture for e-Science

and its Implications. Paper presented at the International Symposium on Performance Evaluation

of Computer and Telecommunication Systems (SPECTS ‘02).

Bulut, H., Fox, G., Pallickara, S., Uyar, A., & Wu, W. (2002, November 20). Integration of NaradaBrokering

and Audio/Video Conferencing as a Web Service. Paper presented at the IASTED International

Conference on Communications, Internet, and Information Technology, St. Thomas, U.S. Virgin

Islands.

Bulut, H., Pallickara, S., & Fox, G. (2004, June 16–18). Implementing an NTP-Based Time Service within a

Distributed Brokering System. Paper presented at the ACM International Conferences on Principles

and Practice of Programming in Java, Las Vegas, NV.

Bulut, H., Wu, W., Fox, G., Uyar, A., Pallickara, S., & Altay, H. (2004, June). A Web Services Based Streaming

Gateway for Heterogeneous A/V Collaboration. Paper presented at the Fifth International

Conference on Internet Computing, Las Vegas, NV.

Burnap, P., Bulut, H., Pallickara, S., Fox, G., Walker, D., Kaplan, A., et al. (2005, September). Worldwide

Messaging Support for High Performance Real-time Collaboration. Paper presented at the UK e-

Science All Hands Meeting.

Carpenter, B., & Fox, G. (2003, May/June). HPJava: A Data Parallel Programming Alternative. CISE Magazine.

Carpenter, B., Fox, G., Lee, H.-K., & Lim, S. (2003, October). Applications of HP Java. Paper presented at the

16th International Workshop on Languages and Compilers for Parallel Computer.

Dharurkar, A., Pallickara, S., & Fox, G. (2004, April). A Topology Viewer for Distributed Brokering Systems.

International Conference on Information Technology: Coding and Computing (ITCC ‘04), pp.

228–234.

Dong, X., Gilbert, K., Guha, R., Kim, J., Pierce, M., Fox, G., et al. (2006). Smart Mining of Drug Discovery

Information: 1. A Web Service and Workflow Infrastructure. Journal of Chemical Information and

Modeling.

Donnellan, A., Fox, G., Granat, R., Grant, L., Lyzenga, G., McLeod, D., et al. (2004, July 13). iSERVO:

Implementing the International Solid Earth Research Virtual Observatory. Fourth ACES (APEC

Cooperation for Earthquake Simulation) Workshop.

Donnellan, A., Fox, G., Rundle, J., McLeod, D., Tullis, T., & Grant, L. (2003, March). Numerical Simulations

for Active Tectonic Processes: Increasing Interoperability and Performance. Paper presented at the

Earthquake Conference, Japan.

Donnellan, A., Parker, J., Fox, G., Pierce, M., Rundle, J., & McLeod, D. (2004, June 22–24). Complexity

Computational Environment: Data Assimilation SERVOGrid. Paper presented at the 2004 Earth

Science Technology Conference, Palo Alto, CA.

Donnellan, A., Parker, J., Lyzenga, G., Granat, R., Fox, G., Pierce, M., et al. (2004, June 22–24). The

QuakeSim Project: Numerical Simulations for Active Tectonic Processes. Paper presented at the

2004 Earth Science Technology Conference, Palo Alto, CA.

Donnellan, A., Parker, J., Norton, C., Lyzenga, G., Glasscoe, M., Fox, G., et al. (2006). QuakeSim: Enabling

Model Interactions in Solid Earth Science Sensor Webs Technical Report. Bloomington, IN: Indiana

University Community Grids Lab.

Donnellan,A.,Parker,J.,Norton,C.,Lyzenga,G.,Glasscoe,M.,Fox,G.,etal.(2007,June19–21).

QuakeSim:EnablingModelInteractionsinSolidEarthScienceSensorWebs.Paperpresentedat

theNASAScienceTechnologyConferenceNSTC2007,UniversityofMaryland.

Donnellan, A., Rundle, J., Fox, G., McLeod, D., Grant, L., Tullis, T., et al. (2004). QuakeSim and the Solid

Earth Research Virtual Observatory. Pure and Applied Geophysics (Special Issue for Beijing ACES

Meeting).

Donnellan, A., Rundle, J., Ries, J., Fox, G., Pierce, M., Parker, J., et al. (2004). Illuminating Earth’s Interior

Through Advanced Computing. Computing in Science and Engineering, 6(1), 36–44.

Fox, G. (2001). Architecture and Implementation of a Collaborative Computing and Education Portal.

Bloomington, IN: Indiana University Community Grids Lab.

Fox, G. (2001). Computational Science and Information Technology: Distance Education and Training.

Bloomington, IN: Indiana University Community Grids Lab.

Fox, G. (2001, May/June). Peer-to-Peer Networks. CISE Magazine.

Fox, G. (2001). Ubiquitous Access for Computational Science and Education. Bloomington, IN: Indiana

University Community Grids Lab.

Fox, G. (2002, July/August). e-Science. CISE Magazine.

Fox, G. (2002). From Computational Science to Internetics: Integration of Science with Computer Science.

In E. H. Ronald F. Boisvert (Ed.), Computational Science, Mathematics and Software (pp. 217–236).

West Lafayette, IN: Purdue University Press.

Fox, G. (2002). Grid Services for Earthquake Science. Concurrency & Computation: Practice & Experience

(ACES Conference Special Issue).

Fox, G. (2002, September/October). Message Passing: From Parallel Computing to the Grid. CISE Magazine.

Fox, G. (2002). PDA Access to Garnet Collaboration System. Bloomington, IN: Indiana University

Community Grids Lab.

Fox, G. (2002, May/June). XML and the Importance of Being an Object? CISE Magazine.

Fox, G. (2003, September/October). Data and Metadata on the Semantic Grid. CISE Magazine.

Fox, G. (2003, January/February). Grande Applications and Java. CISE Magazine.

11�

Fox, G. (2003, March/April). Grid Computing Environments. CISE Magazine.

Fox, G. (2003, July/August). Integration of Computing and Information on Grids. CISE Magazine.

Fox, G. (2003). Messaging Systems: Parallel Computing the Internet and the Grid. In J. Dongarra, D.

Laforenza & S. Orlando (Eds.), Recent Advances in Parallel Virtual Machine and Message Passing

Interface: Lecture Notes in Computer Science from 10th European PVM/MPI User’s Group Meeting,

September 30, 2003 (Vol. 2840/2003, pp. 1–9). Venice, Italy: Springer.

Fox, G. (2003). Multiparticle Phase Shift Analysis in Peripheral Production Experiments: Lessons from the

Past. Journal of Modern Physics, 18 (Proceedings of Partial Wave Analysis Workshop, CMU June 2–4,

2002), 345–354.

Fox, G. (2003, May 16). Planning a New Generation of Multiparticle Phase Shift Analyses in Peripheral

Reactions. Paper presented at the Jefferson Laboratory Workshop on Gluonic Excitations, Newport

News, VA.

Fox, G. (2004, July/August). Grids of Grids of Simple Services. CISE Magazine.

Fox, G. (2004, March/April). The Rule of the Millisecond. CISE Magazine.

Fox, G. (2005). Community Grids Laboratory Summary. Bloomington, IN: Indiana University Community

Grids Lab.

Fox, G. (2005). Editorial for Special Issue: ACM 2002 Java Grande-ISCOPE Conference. Concurrency and

Computation: Practice and Experience, 17(5–6), 419–422.

Fox, G. (2005, May). Global Multimedia Collaboration System Tutorial. Paper presented at the IEEE

International Symposium on Collaborative Technologies and Systems, St. Louis, MO.

Fox, G. (2006, May 14–17). Collaboration and Community Grids. Paper presented at the IEEE 2006

International Symposium on Collaborative Technologies and Systems (CTS 2006), Las Vegas, NV.

Fox, G. (2006, July 24–27). Grid-Based Information Architecture for iSERVO International Solid Earth

Research Virtual Organization (abstract). Paper presented at the Western Pacific Geophysics Meeting

(WPGM), Beijing, China.

Fox, G. (2006). Some Comments on CiteULike Connotea and Related Tools. Bloomington, IN: Indiana

University Community Grids Lab.

Fox, G., Aktas, M., Aydin, G., Bulut, H., Gadgil, H., Oh, S., et al. (2005, September 11–14). Grids for Real

Time Data Applications. Paper presented at the PPAM 2005-Sixth International Conference on

Parallel Processing and Applied Mathematics, Poznan, Poland.

Fox, G., Aktas, M., Aydin, G., Bulut, H., Pallickara, S., Pierce, M., et al. (2006). Real Time Streaming

Data Grid Applications: An Invited Talk at CNIT Tyrrhenian International Workshop on

Digital Communications, July 4–6, 2005. Distributed Cooperative Laboratories: Networking,

Instrumentation, and Measurements, 2006, 253–268.

Fox, G., Aktas, M., Aydin, G., Donnellan, A., Gadgil, H., Granat, R., et al. (2005, November 27–29). Building

Sensor Filter Grids: Information Architecture for the Data Deluge. Paper presented at the IEEE First

International Conference on SKG2005 Semantics, Knowledge and Grid, Beijing, China.

Fox, G., Aktas, M., Aydin, G., Gadgil, H., Pallickara, S., Pierce, M., et al. (2005, March 13–18). Algorithms

and the Grid. Paper presented at the Algoritmy 2005 Conference on Scientific Computing, Vysoke

Tatry, Podbanske, Slovakia.

Fox, G., Aydin, G., Gadgil, H., Pallickara, S., Pierce, M., & Wu, W. (2006). Management of Real-Time

Streaming Data Grid Services. Concurrency and Computation: Practice and Experience (Special Issue

from Grid and Cooperative Computing Fourth International Conference, November 30–December

2, 2005).

Fox, G., Bulut, H., Kim, K., Ko, S.-H., Lee, S., Oh, S., et al. (2003). Collaborative Web Services and Peer-to-

Peer Grids. Paper presented at the Collaborative Technologies Symposium (CTS ‘03).

Fox, G., Gadgil, H., Pallickara, S., Pierce, M., Grossman, R. L., Gu, Y., et al. (2004). High Performance Data

Streaming in Service Architecture. Bloomington, IN; Chicago, IL: Indiana University and University

of Illinois at Chicago.

Fox, G., Gadgil, H., Pallickara, S., Pierce, M., Rundle, J., Donnellan, A., et al. (2004). Complexity

Computational Environments (CCE) Architecture: NASA.

Fox, G., & Gannon, D. (2001, May/June). Computation Grids. CISE Magazine.

Fox, G., & Gannon, D. (2006). A Survey of the Role and Use of Web Services and Service Oriented

Architectures in Scientific/Technical Grids. Bloomington, IN: Indiana University Community Grids

Lab.

Fox, G., Gannon, D., Pierce, M., & Thomas, M. (2003). Overview of Grid Computing Environments—

Proposed Global Grid Forum Information Document. Bloomington, IN: Indiana University

Community Grids Lab.

Fox, G., Gannon, D., & Thomas, M. (2002). A Summary of Grid Computing Environments. Concurrency and

Computation: Practice and Experience.

Fox, G., Gunduz, G., & Uyar, A. (2001). Audio-Video Conferencing Technology. Bloomington, IN: Indiana

University Community Grids Lab.

Fox, G., Ko, S., Kim, K., Lee, S., & Oh, S. (2003, October 20–22). Universal Accessible Collaboration

Frameworks for Ubiquitous Computing Environments. Paper presented at the International

Conference on Ubiquitous Computing (ICUC ‘03), Seoul, Korea.

Fox, G., Ko, S.-H., Kim, K., Oh, S., & Lee, S. (2002). Integration of Hand-Held Devices into Collaborative

Environments. Bloomington, IN: Indiana University Community Grids Lab.

Fox, G., Lee, S., Ko, S., Kim, K., & Oh, S. (2002). CAROUSEL Web Service: Universal Accessible Web Service

Architecture for Collaborative Application. Bloomington, IN: Indiana University Community Grids

Lab.

Fox, G., Lim, S., Pallickara, S., & Pierce, M. (2005). Message-Based Cellular Peer-to-Peer Grids: Foundations

for Secure Federation and Autonomic Services. Future Generation Computer Systems, 21(3), 401–415.

Fox, G., Mustacoglu, A., Topcu, A., & Cami, A. (2006). SRG: A Digital Document-Enhanced Service Oriented

Research Grid Technical Report. Bloomington, IN: Indiana University.

115

Fox, G., & Pallickara, S. (2002, 2002). JMS Compliance in the Narada Event Brokering System. Paper

presented at the International Conference on Internet Computing (IC-02).

Fox, G., & Pallickara, S. (2002). The Narada Event Brokering System: Overview and Extensions. Paper

presented at the International Conference on Parallel and Distributed Processing Techniques and

Applications (PDPTA ‘02).

Fox, G., & Pallickara, S. (2002). Support for Peer-to-Peer Interactions in Web Brokering Systems. ACM

Ubiquity, 3(15).

Fox, G., & Pallickara, S. (2005). Deploying the NaradaBrokering Substrate in Aiding Efficient Web & Grid

Service Interactions. Proceedings of the IEEE (Special Issue on Grid Computing), 93(3), 564–577.

Fox, G., Pallickara, S., Aydin, G., & Pierce, M. (2004). Managing in Web Service Grid with Applications to

Geographical Information Systems. In L. Grandinetti (Ed.), Grid Computing: A New Frontier of High

Performance Computing (pp. 305–331). Cetraro, Italy: Elsevier.

Fox, G., Pallickara, S., Aydin, G., & Pierce, M. (2005). Messaging in Web Service Grid with Applications to

Geographical Information Systems. In E. Grandinetti (Ed.), Grid Computing: A New Frontier of High

Performance Computing (pp. 305–331). Amsterdam.

Fox, G., Pallickara, S., & Parastatidis, S. (2004, November). Towards Flexible Messaging for SOAP Based

Services. Paper presented at the IEEE/ACM Supercomputing Conference, Pittsburgh, PA.

Fox, G., Pallickara, S., & Pierce, M. (2005). Building a Grid of Grids: Messaging Substrates and Information

Management. In M. P. Bekakos, G. A. Gravvanis & H. R. Arabnia (Eds.), Grid Technologies: Emerging

from Distributed Architectures to Virtual Organizations.

Fox, G., Pallickara, S., Pierce, M., & Gadgil, H. (2005). Building Messaging Substrates for Web and Grid

Applications. Philosophical Transactions of the Royal Society: Mathematical, Physical and Engineering

Sciences (Special Issue on Scientific Applications of Grid Computing, 363(1833), 1757–1773).

Fox, G., Pallickara, S., Pierce, M., & Walker, D. (2003). Towards Dependable Grid and Web Services. ACM

Ubiquity, 4(25).

Fox, G., Pallickara, S., & Rao, X. (2002). Scalable Event Infrastructure for Peer to Peer Grids. Paper presented

at the ACM/ISCOPE Conference on Java Grande.

Fox, G., Pallickara, S., & Rao, X. (2005). Towards Enabling Peer-to-Peer Grids. Concurrency and Computation:

Practice and Experience, 17(7–8), 1109–1131.

Fox, G., & Pierce, M. (2003). Grid Computing Environments Shells—Proposed Global Grid Forum

Information Document. Bloomington, IN: Indiana University Community Grids Lab.

Fox, G., & Pierce, M. (2003). Implications of Grids, e-Science and Cyberinfrastructure for the DoD

High Performance Computing Modernization Program. Bloomington, IN: Indiana University

Community Grids Lab.

Fox, G., & Pierce, M. (2004, October 14). Web Service Grids Paper presented at the iSERVO International

Workshop on Geodynamics: Observation, Modeling and Computer Simulation, Tokyo, Japan.

Fox, G., & Pierce, M. (2005). SERVO Earthquake Science Grid as a Summary of iSERVO Technology, October

2004. In R. Cohen (Ed.), High Performance Computing Requirements for the Computational Solid Earth

Sciences.

Fox,G.,&Sun,X.(2007).ProgressoftheKnowledgeGridEditorial.Concurrency and Computation:

Practice and Experience(SpecialIssueforFirstInternationalConferenceonSemantics,

KnowledgeandGrid(SKG2005)),Beijing,China,November27–29,2005.

Fox, G., & Walker, D. (2003). Appendix to e-Science Gap Analysis. Bloomington, IN: Indiana University

Community Grids Lab.

Fox, G., & Walker, D. (2003). e-Science Gap Analysis. Bloomington, IN: Indiana University Community

Grids Lab.

Fox, G., Wu, W., Uyar, A., Bulut, H., & Pallickara, S. (2003, June 17). Global Multimedia Collaboration

System Tutorial. Paper presented at the First International Workshop on Middleware for Grid

Computing (Co-located with Middleware 2003), Rio de Janeiro, Brazil.

Fox, G., Wu, W., Uyar, A., Bulut, H., & Pallickara, S. (2003, June 22). A Web Services Framework for

Collaboration and Videoconferencing. Paper presented at the Workshop on Advanced Collaborative

Environments (WACE ‘03), Seattle, WA.

Fox, G., & Zhuge, H. (2005). GCC 2005 Special Issue on Autonomous Grip Computing. Fourth

International Conference on Grid and Cooperative Computing.

Fox, G., & Zhuge, H. (2006). Editorial for Special Issue of the Second International Conference on

Semantics, Knowledge and Grid (SKG 2006), Guilin, China. Concurrency and Computation: Practice

and Experience.

Fox, G. C., Wu, W., Uyar, A., & Bulut, H. (2004, January 18–23). Design and Implementation of Audio/

Video Collaboration System Based on Publish/Subscribe Event Middleware. Paper presented at the

International Symposium on Collaborative Technologies and Systems (CTS ‘04), San Diego, CA.

Gadgil,H.(2007).Scalable,Fault-TolerantManagementofGridServices:ApplicationtoMessaging

Middleware.Bloomington,IN:IndianaUniversity.

Gadgil, H., Choi, J.-Y., Engel, B., Fox, G., Ko, S., Pallickara, S., et al. (2004). Management of Data Streams for

a Real Time Flood Simulation. Bloomington, IN: Indiana University Community Grids Lab.

Gadgil, H., Fox, G., & Pallickara, S. (2005, May). HP Search for Managing Distributed Services. Paper

presented at the IEEE/ACM Cluster Computing and Grid 2005 Conference, Cardiff, United

Kingdom.

Gadgil,H.,Fox,G.,&Pallickara,S.(2007,June27–29).Scalable,Fault-tolerantManagementina

ServiceOrientedArchitecturePoster.PaperpresentedattheIEEEInternationalSymposiumin

High-PerformanceDistributedComputing(HPDC),Monterey,California.

Gadgil, H., Fox, G., Pallickara, S., & Pierce, M. (2006, June 19). Managing Grid Messaging Middleware. Paper

presented at the Challenges of Large Applications in Distributed Environments (CLADE), Paris,

France.

117

Gadgil, H., Fox, G., Pallickara, S., & Pierce, M. (2006). Scalable, Fault-tolerant Management in a Service

Oriented Architecture Technical Report. Bloomington, IN: Indiana University.

Gadgil,H.,Fox,G.,Pallickara,S.,&Pierce,M.(2007).Scalable,Fault-tolerantManagementinaService

OrientedArchitectureTechnicalReport.Bloomington,IN:IndianaUniversity.

Gadgil,H.,Fox,G.,Pallickara,S.,&Pierce,M.(2007,May19).Scalable,Fault-tolerantManagementof

GridServices.PaperpresentedattheIEEECluster2007.

Gadgil, H., Fox, G., Pallickara, S., Pierce, M., & Granat, R. (2005, May). A Scripting Based Architecture for

Management of Streams and Services in Real-time Grid Applications. Paper presented at the IEEE/

ACM Cluster Computing and Grid 2005 Conference, Cardiff, United Kingdom.

Gadgil, H., Fox, G., Pierce, M., & Pallickara, S. (2005, July 21–23). HP Search: Service Management &

Administration Tool—Abstract. Paper presented at the Meeting on Virtual Lab for Earth and

Planetary Models (VLAB), Minnesota.

Gannon, D. (2001, November 12). Programming the Grid: Distributed Software Components, P2P and

Grid Web Services for Scientific Applications. Paper presented at the International Conference on

Computational Structures, Denver, CO.

Gannon, D., Alameda, J., Chipara, M., Christie, M., Dukle, V., Fang, L., et al. (2005). Building Grid Portal

Applications from a Web-Service Component Architecture. Proceedings of the IEEE March 2005,

93(3), 551–563.

Gannon, D., & Fox, G. (2005). Workflow in Grid Systems—Editorial. Concurrency and Computation: Practice

and Experience (Special Issue on GGF10 Berline Meeting).

Gil,Y.,Deelman,E.,Ellisman,M.,Fahringer,T.,Fox,G.,Gannon,D.,etal.(2007).Reportonthe2006

NSFWorkshoponChallengesofScientificWorkflowsTechnicalReport.Bloomington,IN:

IndianaUniversity.

Gong,Y.,Pierce,M.,&Fox,G.(2007).MatchmakingScientificWorkflowsinGridEnvironments

TechnicalReport.Bloomington,IN:IndianaUniversity.

Gong, Y., Xiong, Y., Zhang, Q., Zhang, Z., Wang, W., & Xu, Z. (2006, November 27–December 1). Anycast

Routing in Delay Tolerant Networks. Paper presented at the Globecom’06, San Francisco, California.

Granat,R.,Aydin,G.,Pierce,M.,&Qi,Z.(2007,April1–5).AnalysisofStreamingGPSMeasurements

ofSurfaceDisplacementThroughaWebServicesEnvironment.PaperpresentedattheIEEE

SymposiumonComputationalIntelligenceandDataMining,Honolulu,HI.

Granat, R., Aydin, G., Qi, Z., & Pierce, M. (2006, December 11–15). GPS Sensor Web Time Series Analysis

Using SensorGrid Technology. Paper presented at the American Geophysical Union AGU Fall

Meeting, San Francisco, California.

Grant, L., Donnellan, A., McLeod, D., Pierce, M., Fox, G., Chen, A. Y.-A., et al. (2005). A Web-Service Based

Universal Approach to Heterogeneous Fault Databases. Computing in Science and Engineering, 7(4),

51–57.

Guha,R.,Wiggins,G.,Wild,D.,Baik,M.-H.,Pierce,M.,&Fox,G.(2007).ImprovingUsability

andAccessibilityofCheminformaticsToolsforChemiststhroughCyberinfrastructureand

EducationTechnicalReport.Bloomington,IN:IndianaUniversity.

Gunduz, G. (2006). A Framework for Network Monitoring and Performance Based Routing in Distributed

Middleware Systems. Syracuse University, Syracuse, NY.

Gunduz, G., Pallickara, S., & Fox, G. (2003, July–August). A Framework for Aggregating Network

Performance in Distributed Brokering Systems. Paper presented at the Ninth International

Conference on Computer, Communication and Control Technologies (CCT ‘03), Orlando, FL.

Gunduz, G., Pallickara, S., & Fox, G. (2003, June). A Portal Based Approach to Viewing Aggregated

Network Performance Data in Distributed Brokering Systems. Paper presented at the International

Conference on Internet Computing, Las Vegas, NV.

Gunduz, G., Pallickara, S., & Fox, G. (2004). An Efficient Scheme for Aggregation and Presentation of

Network Performance in Distributed Brokering Systems. Journal of Systemics, Cybernetics and

Informatics.

Hayden,L.,Fox,G.,&Gogineni,P.(2007,June4–8).CyberinfrastructureforRemoteSensingofIce

Sheets.PaperpresentedattheTeraGrid2007Conference,Madison,Wisconsin.

Hey, T., & Fox, G. (2005). Grids and Web Services for e-Science. Concurrency and Computation: Practice and

Experience, 17(DOI), 317–322.

Juan, F., Fox, G., & Pierce, M. (2006, October 31–November 3). Grid Portal System Based on GPIR. Paper

presented at the SKG 2006, Guilin, China.

Kaplan, A., Topcu, A., Pierce, M., & Fox, G. (2003, June). Access Control System Using Web Services for XML

Messaging Systems. Paper presented at the Information Knowledge Engineering Conference (IKE

‘03), Las Vegas, NV.

Kim, H., Moore, L., Whalin, R., & Fox, G. (2006, July 20–23). An Experience on a Distance Education

Course over the Access Grid Nodes. Paper presented at the Fourth International Conference on

Education and Information Systems, Technologies and Applications (EISTA 2006), Orlando, FL.

Kim, J. (2005). Hybrid Search Across Peer-to-Peer Federated Data. Florida State University.

Kim, J., Balsoy, O., Pierce, M., & Fox, G. (2002, November 18–20). Design of a Hybrid Search in the Online

Knowledge Center. Paper presented at the IASTED International Conference on Information and

Knowledge Sharing, St. Thomas, U.S. Virgin Islands.

Kim, J., & Fox, G. (2004, September 22–25). A Hybrid Keyword Search Across Peer-to-Peer Federated

Databases. Paper presented at the Advances in Databases and Information Systems (ADBIS),

Budapest, Hungary.

Kim, J., & Fox, G. (2005, May 22–25). Scalable Hybrid Search on Distributed Databases. Paper presented

at the Proceedings of Third International Workshop on Autonomic Distributed Data and Storage

Systems Management, Atlanta, GA.

119

Kim, J., Fox, G., & Yoo, S.-J. (2005, September 14–16). Data Integration Hub for a Hybrid Paper Search. Paper

presented at the 9th International Conference on Knowledge-Based and Intelligent Information and

Engineering Systems, Melbourne, Australia.

Lee, H.-K. (2003). Towards Efficient Compilation of the HPJava Language for High Performance Computing.

Florida State University.

Lee, H.-K., Carpenter, B., Fox, G., & Lim, S. (2003, July 27–30). HP Java: Efficient Compilation and

Performance for HPC. Paper presented at the 7th World Multiconference on Systemics, Cybernetics

and Informatics, Orlando, FL.

Lee, H.-K., Carpenter, B., Fox, G., & Lim, S. (2003, June). HPJava: Towards Programming Support for High-

Performance Grid-Enabled Applications. Paper presented at the International Conference on Parallel

and Distributed Processing Techniques and Applications (PDPTA ‘03), Las Vegas, NV.

Lee, H.-K., Carpenter, B., Fox, G., & Lim, S. B. (2002). Benchmarking HP Java: Prospective for Performance.

Paper presented at the Sixth Workshop on Languages, Compilers, and Run-time Systems for Scalable

Computers (LCR ‘02).

Lee, H.-K., Carpenter, B., Fox, G., & Lim, S. B. (2004). HP Java: Programming Support for High-Performance

Grid-Enabled Applications. Parallel and Distributed Algorithms in Parallel Algorithms and

Applications, 19(2–3), 175–193.

Lee, S. (2003). A Modular Data Pipelining Architecture (MDPA) for Enabling Universal Accessibility in P2P

Grids. Florida State University.

Lee, S., & Fox, G. (2004, July). Wireless Reliable Messaging Protocol for Web Services (WS-WRM). Paper

presented at the IEEE Second International Conference on Web Services (ICWS 2004), San Diego, CA.

Lee, S., Ko, S., & Fox, G. (2003, June). Adapting Content for Mobile Devices in Heterogeneous Collaboration

Environments. Paper presented at the International Conference on Wireless Networks, Las Vegas, NV.

Lee, S., Ko, S., Fox, G., Kim, K., & Oh, S. (2003, June). A Web Service Approach to Universal Accessibility in

Collaboration Services. Paper presented at the First International Conference on Web Services, Las

Vegas, NV.

Lim, S. (2003). Platforms for HPJava: Runtime Support for Scalable Programming in Java. Florida State

University.

Lim, S., Carpenter, B., Fox, G., & Han-ku, L. (2003, November 3–5). A Device Level Communication Library

for the HP Java Programming Language. Paper presented at the IASTED International Conference on

Parallel and Distributed Computing and Systems (PDCS 2003), Marina del Rey, CA.

Lim, S., Fox, G., Kaplan, A., Pallickara, S., & Pierce, M. (2005). GridFTP and Parallel TCP Support in

NaradaBrokering. Proceedings of the Sixth International Conference on Algorithms and Architectures

for Parallel Processing, 3719 (DOI), 93–102.

Lim, S. B., Carpenter, B., Fox, G., & Han-ku, L. (2005). Collective Communication for the HP Java

Programming Language. Concurrency and Computation: Practice and Experience, 17(7–8), 867–894.

Lim, S. B., Carpenter, B., Fox, G., & Han-ku, L. (2005, November 2–5). Collective Communications for

Scalable Programming. Paper presented at the Proceedings of the Third International Symposium

on Parallel and Distributed Processing and Applications, Nanjing, China.

Lim, S. B., Carpenter, B., Fox, G., & Han-ku, L. (2005, June 27–30). Implementation of Collectives for

Scalable Programming in Java. Paper presented at the 2005 International Conference on Parallel

and Distributed Processing Techniques and Applications, Las Vegas, NV.

Lim, S. B., Carpenter, B., Fox, G., & Han-ku, L. (2005, October 2–5). A Low-Level Communication Library

for Java HPC. Paper presented at the Proceedings of the Sixth International Conference on

Algorithms and Architectures for Parallel Processing, Melbourne, Australia.

Lim, S. B., Fox, G., Kaplan, A., Pallickara, S., & Pierce, M. (2005). GridFTP and Parallel TCP Support in

NaradaBrokering. Journal of Future Generation Computer Systems (Special Issue of Selected Papers

from the Sixth International Conference on Algorithms and Architectures for Parallel Processing),

3719, 93–102.

Lim, S. B., Fox, G., Pallickara, S., & Pierce, M. (2004, June). Web Service Robust GridFTP. Paper presented at

the International Conference on Parallel and Distributed Processing Techniques and Applications

(PDPTA ‘04), Las Vegas, NV.

Liu, H., Fox, G., Pierce, M., & Pallickara, S. (2005). A Multi-Party Implementation of WS-Secure

Conversation. Bloomington, IN: Indiana University Community Grids Lab.

Liu, H., Pallickara, S., & Fox, G. (2005, February 3–5). Performance of Web Services Security. Paper presented

at the Thirteenth Annual Mardi Gras Conference, Baton Rouge, LA.

Liu,Z.,Pierce,M.,&Fox,G.(2007).ImplementingaCachingandTilingMapServer:AWeb2.0Case

Study.Paperpresentedatthe2007InternationalSymposiumonCollaborativeTechnologies

andSystems(CTS2007).

Mock, S., Mueller, K., Pierce, M., Youn, C., Fox, G., & Thomas, M. (2002). A Batch Script Generator Web

Service for Computational Portals. Bloomington, IN: Indiana University Community Grids Lab.

Mustacoglu,A.,&Fox,G.(2007,June25–28).AJAXIntegrationApproachforCollaborativeCalendar-

ServerWebServices.Paperpresentedatthe2007WorldCongressinComputerScience,

ComputerEngineering,&AppliedComputing,LasVegas,NV.

Mustacoglu,A.,Topcu,A.,Cami,A.,&Fox,G.(2007).ANovelEvent-BasedConsistencyModelfor

SupportingCollaborativeCyberinfrastructureBasedScientificResearch.Paperpresentedatthe

2007InternationalSymposiumonCollaborativeTechnologiesandSystems(CTS2007).

Mustacoglu, A., Wu, W., & Fox, G. (2006, May 14–17). Internet Calendaring and Scheduling Core Object

Specification (iCalendar) Compatible Collaborative Calendar-Server (CCS) Web Services. Paper

presented at the IEEE 2006 International Symposium on Collaborative Technologies and Systems

(CTS 2006), Las Vegas, NV.

Mustacoglu,F.(2007).Event-BasedModelforReconcilingDigitalEntries.Bloomington,IN:Indiana

University.

121

Nacar, M., Aktas, M., Pierce, M., Lu, Z., Erlebacher, G., Kigelman, D., et al. (2005). VLab: Collaborative Grid

Services and Portals to Support Computation Material Science. Concurrency and Computation: Practice

and Experience (Special Issue from SC ‘05 GCE ‘05 Workshop on Grid Portals).

Nacar,M.,Choi,J.,Pierce,M.,&Fox,G.(2007,June4–8).BuildingaGridPortalforTeragrid’sBigRed.

PaperpresentedattheTeraGrid2007Conference,Madison,Wisconsin.

Nacar, M., Pierce, M., Erlebacher, G., & Fox, G. (2006, November 12–13). Designing Grid Tag Libraries

and Grid Beans. Paper presented at the Second International Workshop on Grid Computing

Environments, GCE ‘06 at SC ‘06, Tampa, Florida.

Nacar, M., Pierce, M., & Fox, G. (2003, June). Designing a Grid Computing Environment Shell Engine. Paper

presented at the International Conference on Internet Computing, Las Vegas, NV.

Nacar,M.,Pierce,M.,&Fox,G.(2007).ExtendingGTLABTagLibrariesforGridWorkflowsTechnical

Report.Bloomington,IN:IndianaUniversity.

Nacar,M.,Pierce,M.,&Fox,G.(2007).GTLAB:GridTagLibrariesSupportingWorkflowswithinScience

GatewaysTechnicalReport.Bloomington,IN:IndianaUniversity.

Nacar, M. A., Pierce, M., & Fox, G. C. (2004). Developing a Secure Grid Computing Environment Shell

Engine: Containers and Service. Journal of Neural Parallel and Scientific Computations 12 (Special Issue

on Grid Computing), 379–390.

Oh, S. (2006). Optimizing Web Service Performance in Mobile Computing. Indiana University,

Bloomington, IN.

Oh, S., Aktas, M., Pierce, M., & Fox, G. (2006, May 27–29). Optimizing Web Service Messaging Performance

Using a Context Store for Static Data. Paper presented at the WSEAS International Conference on

Telecommunications and Informatics (TELE-INFO ‘06), Istanbul, Turkey.

Oh, S., Bulut, H., Uyar, A., Wu, W., & Fox, G. (2005, May). Optimized Communication Using the

SOAP Infoset for Mobile Multimedia Collaboration Applications. Paper presented at the IEEE

International Symposium on Collaborative Technologies and Systems, St. Louis, MO.

Oh, S., & Fox, G. (2005). HHFR: A New Architecture for Mobile Web Services: Principles and

Implementations. Bloomington, IN: Indiana University Community Grids Lab.

Oh, S., & Fox, G. (2006). Optimizing Web Service Messaging Performance in Mobile Computing.

Bloomington, IN: Indiana University Community Grids Lab.

Oh, S., & Fox, G. (2006). Optimizing Web Service Messaging Performance in Mobile Computing. Special

Issue in Grid Technology and Applications. Journal of Future Generation Computer Systems, Elsevier.

Oh,S.,&Fox,G.(2007).OptimizingWebServiceMessagingPerformanceinMobileComputing,July

2006.Journal Of Future Generation Computer Systems (SpecialIssueinGridTechnology)23(4),

623–632.

Oh, S., Fox, G., & Ko, S. (2003, September/October). GMSME: An Architecture for Heterogeneous

Collaboration with Mobile Devices. Paper presented at the Fifth IEEE International Conference on

Mobile and Wireless Communications Networks (MWCN 2003), Singapore.

Oh, S., Pallickara, S.-L., Ko, S., Kim, J.-H., & Fox, G. (2005, May). Cost Model and Adaptive Scheme for

Publish/Subscribe Systems on Mobile Environments. Paper presented at the Second International

Workshop on Active and Programmable Grids Architectures and Components, Atlanta, GA.

Oh, S., Pallickara, S.-L., Ko, S., Kim, J.-H., & Fox, G. (2005, May). Publish/Subscribe Systems on Node

and Link Error Prone Mobile Environments. Paper presented at the Wireless and Mobile Systems

Workshop at the International Conference on Complex Systems (ICCS ‘05), Atlanta, GA.

Pallickara, S., Gadgil, H., & Fox, G. (2005, November 13–14). On the Discovery of Topics in Distributed

Publish/Subscribe Systems. Paper presented at the 2005 IEEE/ACM GRID 2005 Workshop, Seattle, WA.

Pallickara, S., Bulut, H., Burnap, P., Fox, G., Ayar, A., & Walker, D. (2005). Support for High Performance

Real-Time Collaboration within the NaradaBrokering Substrate. Bloomington, IN: Indiana

University Community Grids Lab.

Pallickara,S.,Bulut,H.,&Fox,G.(2007,June12–15).Fault-TolerantReliableDeliveryofMessagesin

DistributedPublish/SubscribeSystems.PaperpresentedattheProceedingsoftheFourthIEEE

InternationalConferenceonAutonomicComputing,Jacksonville,Florida.

Pallickara,S.,Ekanayake,J.,&Fox,G.(2007).AScalableApproachfortheSecureandAuthorized

TrackingoftheAvailabilityofEntitiesinDistributedSystems.Paperpresentedatthe

Proceedingsofthe21stIEEEInternationalParallel&DistributedProcessingSymposium

(IPDPS2007),LongBeach,CA.

Pallickara, S., & Fox, G. (2001). An Approach to High Performance Distributed Web Brokering. ACM

Ubiquity, 2(38).

Pallickara, S., & Fox, G. (2001). An Event Service to Support Grid Computational Environments. Concurrency

and Computation: Practice & Experience, 14(13–15), 1097–1129.

Pallickara, S., & Fox, G. (2001). A Scalable Durable Grid Event Service. Bloomington, IN: Indiana University

Community Grids Lab.

Pallickara, S., & Fox, G. (2003). Efficient Support for Sophisticated Interactions Between Entities in

Distributed Brokering Systems or Lowering the Cost of Communication. ACM Ubiquity, 4(16).

Pallickara, S., & Fox, G. (2003, June). NaradaBrokering: A Distributed Middleware Framework and

Architecture for Enabling Durable Peer-to-Peer Grids. Paper presented at the ACM/IFIP/USENIX

International Middleware Conference, Rio de Janeiro, Brazil.

Pallickara, S., & Fox, G. (2004, April 4–6). An Analysis of Notification Related Specifications for Web/Grid

Applications. Paper presented at the International Conference on Information Technology: Coding

and Computing, Las Vegas, NV.

Pallickara, S., & Fox, G. (2004). Efficient Matching of Events in Distributed Middleware Systems. IEEE ITCC

2004 Track on Modern Grid and Web Systems, 2(2), 79–87.

Pallickara, S., & Fox, G. (2004, April). On the Matching of Events in Distributed Brokering Systems. Paper

presented at the IEEE ITCC Conference on Information Technology.

12�

Pallickara, S., & Fox, G. (2004, May 17–18). A Scheme for Reliable Delivery of Events in Distributed

Middleware Systems. Paper presented at the IEEE International Conference on Autonomic

Computing (ICAC ‘04), New York, NY.

Pallickara, S., Fox, G., Aktas, M., Gadgil, H., Yildiz, B., Oh, S., et al. (2006). A Retrospective on the

Development of Web Service Specifications. In P. Panos (Ed.), Securing Web Services: Practical Usage

of Standards and Specifications: Idea Group Inc.

Pallickara, S., Fox, G., & Bulut, H. (2005). Fault Tolerant Reliable Delivery of Events in Distributed

Middleware Systems. Bloomington, IN: Indiana University Community Grids Lab.

Pallickara, S., Fox, G., & Gadgil, M. (2005). On the Secure Creation, Organization and Discovery of Topics

in Distributed Publish/Subscribe Systems. International Journal of High Performance Computing

and Networking (Special issue of extended version of six best papers at the ACM/IEEE Grid 2005

Workshop).

Pallickara, S., Fox, G., & Pallickara, S.L. (2005, April 4–6). An Analysis of Reliable Delivery Specifications for

Web Services. Paper presented at the International Conference on Information Technology: Coding

and Computing, Las Vegas, NV.

Pallickara, S., Fox, G., & Pierce, M. (2003, June). Incorporating an XML Matching Engine in Distributed

Brokering Systems. Paper presented at the International Conference on Parallel and Distributed

Processing Techniques and Applications (PDPTA ‘03), Las Vegas, NV.

Pallickara, S., Fox, G., Rao, X., Uyar, A., & Walker, D. (2005). Performance of a Possible Grid Messaging

Infrastructure from UK e-Science Meeting on Grid Performance, Edinburgh, December 9, 2002.

Concurrency and Computation: Practice and Experience (Special Issue on Grid Performance), 17(2–4),

193–214.

Pallickara, S., Fox, G., Yildiz, B., Pallickara, S.L., Patel, S., & Yemme, D. (2005, December 5–8). An Analysis

of the Costs for Reliable Messaging in Web/Grid Service Environments. Paper presented at the IEEE

International Conference on e-Science and Grid Computing, Melbourne, Australia.

Pallickara, S., Fox, G., Yin, J., Gunduz, G., Liu, H., Uyar, A., et al. (2003, June). A Transport Framework for

Distributed Brokering Systems. Paper presented at the International Conference on Parallel and

Distributed Processing Techniques and Applications (PDPTA ‘03), Las Vegas, NV.

Pallickara, S., Gadgil, H., & Fox, G. (2005, September 27–30). On the Discovery of Brokers in Distributed

Messaging Infrastructures. Paper presented at the Proceedings of IEEE Cluster, Boston, MA.

Pallickara, S., Pierce, M., Fox, G., Huang, Y., & Yan, Y. (2003). A Security Framework for Distributed

Brokering Systems. Bloomington, IN: Indiana University Community Grids Lab.

Pallickara, S., Pierce, M., Gadgil, H., Fox, G., Huang, Y., & Yan, Y. (2006, June). A Framework for Secure End-

to-End Delivery of Messages in Publish/Subscribe Systems. Paper presented at the Seventh IEEE/

ACM International Conference on Grid Computing (GRID 2006), Barcelona, Spain.

Pallickara, S., Pierce, M., Gadgil, H., Fox, G., Yan, Y., & Huang, Y. (2006, September 28–29). A Framework

for Secure End-to-End Delivery of Messages in Publish/Subscribe Systems. Proceedings. Paper

presented at the Seventh IEEE/ACM International Conference on Grid Computing (GRID 2006),

Barcelona, Spain.

Perera, S., Herath, C., Ekanayake, J., Chinthaka, E., Ranabahu, A., Jayasinghe, D., et al. (2006, September 18–

22). Axis2, Middleware for Next Generation Web Services. Paper presented at the IEEE International

Conference on Web Services (ICWS ‘06), Rosemont, IL.

Pierce, M. (2006). Open Grid Computing Environments NSF NMI Project Report. Open Grid Computing

Environments (OGCE) Annual Report, June 1-May 31, 2005.

Pierce, M., & Fox, G. (2003). Federated Grids and their Security—A White Paper. Bloomington, IN: Indiana

University Community Grids Lab.

Pierce, M., & Fox, G. (2004, January/February). Scientific Applications as Web Services: A Simple Guide.

CISE Magazine.

Pierce, M., Fox, G., Aktas, M., Aydin, G., & Gadgil, H. (2006). The Solid Earth Research Virtual Observatory:

Web Services for Managing Geophysical Data and Applications. PAGEOPH Special Issue for Fifth

ACES International Workshop, Maui, HI.

Pierce, M., Fox, G., Aktas, M., Aydin, G., Gadgil, H., Qi, Z., et al. (2006). The Solid Earth Research Virtual

Observatory: Web Services for Managing Geophysical Data and Applications Unpublished draft for

PAGEOPH Special Issue for Fifth ACES International Workshop Maui, HI.

Pierce,M.,Fox,G.,Aktas,M.,Aydin,G.,Gadgil,H.,Qi,Z.,etal.(2007).TheQuakeSimProject:Web

ServicesforManagingGeophysicalDataandApplications.PAGEOPHSpecialIssueforFifth

ACESInternationalWorkshop,Maui,HI.

Pierce, M., Youn, C., Balsoy, O., Fox, G., Mock, S., & Mueller, K. (2002, November). Interoperable Web

Service for Computational Portals. Paper presented at the IEEE/ACM Supercomputing Conference

(SC ‘02).

Pierce, M., Youn, C., & Fox, G. (2002). Application Web Services. Bloomington, IN: Indiana University

Community Grids Lab.

Pierce, M., Youn, C., & Fox, G. (2002, April). The Gateway Computational Portal: Developing Web Services

for High Performance Computing. Paper presented at the International Conference on Complex

Systems (ICCS ‘02).

Pierce, M., Youn, C., & Fox, G. (2002). The Gateway Computational Web Portal. Concurrency and

Computation: Practice and Experience in Grid Computing Environments.

Pierce, M., Youn, C., & Fox, G. (2003, June). Interacting Data Services for Distributed Earthquake Modeling.

Paper presented at the ACES Workshop at ICCS, Australia.

Pierce,M.E.,Fox,G.,Yuan,H.,&Deng,Y.(2007,July4).CyberinfrastructureandWeb2.0.Paper

presentedattheHPC2006,Cetraro,Italy.

125

Qiu, X. (2004, July). Building Desktop Application with Web Services in a Message-based MVC Paradigm.

Paper presented at the IEEE Second International Conference on Web Services (ICWS 2004), San

Diego, CA.

Qiu, X. (2005). Message-based MVC Architecture for Distributed and Desktop Applications. Syracuse

University.

Qiu,X.(2007,June20–21).Multi-ParadigmRunTimeMPRforMulticoreSystems.Paperpresentedat

theMicrosoftMulticoreComputingWorkshop,Seattle,WA.

Qiu, X., Carpenter, B., & Fox, G. (2003, July). Collaborative SVG as a Web Service. Paper presented at the

SVG Open Conference, Vancouver, BC, Canada.

Qiu, X., Carpenter, B., & Fox, G. (2003). Collaborative Web Services and the W3C Document Object Model.

Bloomington, IN: Indiana University Community Grids Lab.

Qiu, X., Carpenter, B., & Fox, G. (2003, June). Internet Collaboration using the W3C Document Object

Model. Paper presented at the 2003 International Conference on Communications in Computing,

Las Vegas, NV.

Qiu, X., & Fox, G. (2004). Building Desktop Application with Web Services in a Message-based MVC

Paradigm. Bloomington, IN: Indiana University Community Grids Lab.

Qiu,X.,Fox,G.,Chrysanthakopoulos,G.,&Nielsen,H.(2007).HighPerformanceMulti-Paradigm

MessagingRunTimeonMulticoreSystemsTechnicalReport.Bloomington,IN:Indiana

University.

Qiu,X.,Fox,G.,&Ho,A.(2007).AnalysisofConcurrencyandCoordinationRuntimeCCRandDSSfor

ParallelandDistributedComputingTechnicalReport.Bloomington,IN:IndianaUniversity.

Qiu, X., & Jooloor, A. (2004). Web Service Architecture for e-Learning. EISTA 2004 International Conference

on Education and Information Systems: Technologies and Applications.

Qiu, X., & Jooloor, A. (2006). Web Service Architecture for e-Learning. Journal of Systemics, Cybernetics and

Informatics (Special Issue for EISTA 2004 International Conference on Education and Information

Systems: Technologies and Applications, 3(5)).

Qiu, X., Pallickara, S., & Uyar, A. (2004, September). Making SVG a Web Service in a Message-based MVC

Architecture. Paper presented at the SVG Open Conference 2004, Tokyo, Japan.

Rundle, J., Rundle, P., Donnellan, A., & Fox, G. (2003, June 30–July 11). Statistical Mechanics Approaches

to the Modeling of Nonlinear Earthquake Physics. Paper presented at the International Union of

Geophysics and Geodesy Conference, Sapporo, Japan.

Rundle, J. B., Rundle, P. B., Donnellan, A., & Fox, G. (2003, June 30–July 11). Gutenberg-Richter Statistics

in Topologically Realistic System-Level Earthquake Stress-Evolution Simulations. Paper presented

at the IUGG Hagiwara Symposium on Monitoring and Modeling of Earthquake and Volcanic

Processes for Prediction, Sapporo, Japan.

Sayar, A., Aktas, M., Aydin, G., Pierce, M., & Fox, G. (2005). Developing a Web Service-Compatible Map

Server for Geophysical Applications. Bloomington, IN: Indiana University Community Grids Lab.

Sayar, A., Pierce, M., & Fox, G. (2005, November 24–25). Developing GIS Visualization Web Services for

Geophysical Applications. Paper presented at the ISPRS International Society for Photogrammetry

and Remote Sensing Workshop, Ankara, Turkey.

Sayar, A., Pierce, M., & Fox, G. (2005, August 17–19). Message Exchange for Web Service-Based Mapping

Services. Paper presented at the Proceedings of GeoInformatics ‘05, Toronto, Ontario, Canada.

Sayar, A., Pierce, M., & Fox, G. (2005). OGC Compatible Geographical Information Services (No. TR610).

Bloomington, IN: Indiana University Department of Computer Science.

Sayar, A., Pierce, M., & Fox, G. (2006, February 23–25). Integration AJAX Approach into GIS Visualization

Web Services. Paper presented at the IEEE International Conference on Internet and Web

Applications and Services, Guadeloupe, French Caribbean.

Taylor, S., Fox, G., Fujimoto, R., Pullen, J., Roberts, D., & Theodoropoulos, G. (2005, October 10–12).

Revisiting Distributed Simulation and the Grid: A Penal Distributed Simulation and Real-Time

Applications, 2005. Paper presented at the Ninth IEEE International Symposium, Montreal,

Quebec, Canada.

Theimer, M., Parastatidis, S., Hey, T., Humphrey, M., & Fox, G. (2006). An Evolutionary Approach to

Realizing the Grid Vision. Bloomington, IN: Indiana University Community Grids Lab.

Thomas, M., Burress, J., Cinquini, G., Fox, G., Gannon, D., Gilbert, L., et al. (2005, June 26–30). Grid

Portal Architectures for Scientific Applications. Paper presented at the Scientific Discovery through

Advanced Computing (SciDAC 2005) Meeting, San Francisco, CA.

Thomas, M., Pierce, M., & Haupt, T. (2003). Building Interoperable Portals with Web Services: ET011 Project

Report.

Topcu,A.,Mustacoglu,A.,Fox,G.,&Cami,A.(2007).IntegrationofCollaborativeInformationSystems

inWeb2.0TechnicalReport.Bloomington,IN:IndianaUniversity.

Uyar, A. (2005). Scalable Service Oriented Architecture for Audio/Video Conferencing. Syracuse University,

Syracuse, NY.

Uyar, A., & Fox, G. (2005, May). Investigating the Performance of Audio/Video Service Architecture I: Single

Broker. Paper presented at the IEEE International Symposium on Collaborative Technologies and

Systems, St. Louis, MO.

Uyar, A., & Fox, G. (2005, May). Investigating the Performance of Audio/Video Service Architecture II: Broker

Network. Paper presented at the IEEE International Symposium on Collaborative Technologies and

Systems, St. Louis, MO.

Uyar, A., Pallickara, S., & Fox, G. (2003, June). Audio/Video Conferencing in Distributed Brokering Systems.

Paper presented at the International Conference on Communications in Computing, Las Vegas, NV.

Uyar, A., Wu, W., Bulut, H., & Fox, G. (2003, August 13–15). An Integrated Videoconferencing System for

Heterogeneous Multimedia Collaboration. Paper presented at the Seventh IASTED International

Conference on Internet and Multimedia Systems and Applications (IMSA 2003), Honolulu, HI.

127

Uyar, A., Wu, W., Bulut, H., & Fox, G. (2005, July 11–14). Service-Oriented Architecture for Building a

Scalable Videoconferencing System. Paper presented at the IEEE International Conference on

Pervasive Services, Santorini, Greece.

Uyar, A., Wu, W., Bulut, H., & Fox, G. (2006). Service-Oriented Architecture for Building a Scalable

Videoconferencing System. In Service Oriented Architecture Concepts and Cases: Institute of Chartered

Financial Analysts of India (ICFAI) University.

Uyar, A., Wu, W., & Fox, G. (2004). Service-Oriented Architecture for Building a Scalable Videoconferencing

System.

Wang, M. (2005). A Description of the Implementation of Collaborative ReviewPlus. Bloomington, IN:

Indiana University Community Grids Lab.

Wang, M. (2006). Grid-Based Collaborations. Syracuse University, Syracuse, NY.

Wang, M., Fox, G., & Pallickara, S. (2004, April 5–7). A Demonstration of Collaborative Web Services

and Peer-to-Peer Grids. Paper presented at the IEEE International Conference on Information

Technology—Methodologies, Technologies and Applications in Distributed and Grid Systems, Las

Vegas, NV.

Wang, M., Fox, G., & Pallickara, S. (2004). Demonstrations of Collaborative Web Services and Peer-to-Peer

Grids. IEEE ITCC 2004 Track on Modern Grid and Web Systems, 2(2).

Wang, M., Fox, G., & Pallickara, S. (2004, August 16–18). New Tools in Education. Paper presented at the

Seventh International Conference on Computers and Advanced Technology in Education, Kauai, HI.

Wang, M., Fox, G., & Pierce, M. (2005). General Collaboration Structures for Interactive Data Language

Applications. Bloomington, IN: Indiana University Community Grids Lab.

Wang, M., Fox, G., & Pierce, M. (2005, April 4–6). Grid-based Collaboration in Interactive Data Language

Applications. Paper presented at the International Conference on Information Technology: Coding

and Computing, Las Vegas, NV.

Wang, M., Fox, G., & Pierce, M. (2005, July 10–13). Instantiations of Shared Event Model in Grid-based

Collaboration. Paper presented at the Ninth World Multi-Conference on Systemics, Cybernetics and

Informatics, Orlando, FL.

Wang, M., Fox, G., & Pierce, M. (2006, May 14–17). Collaboration Entities on Deterministic Finite

Automata. Paper presented at the IEEE 2006 International Symposium on Collaborative

Technologies and Systems (CTS 2006), Las Vegas, NV.

Wang, M., Fox, G., & Pierce, M. (2006, February 23–25). Thin Client Collaboration Web Services. Paper

presented at the IEEE International Conference on Internet and Web Applications and Services,

Guadeloupe, French Caribbean.

Wang, M., & Geoffrey, F. (2004, November). Design of a Collaborative System for Open Office. Paper

presented at the IASTED Second International Conference on Knowledge Sharing and Collaborative

Engineering, Virgin Islands.

Wu, W., Bulut, H., Uyar, A., & Fox, G. (2003, August 13–15). A Web Services-Based Conference Control

Framework for Heterogeneous A/V Collaboration. Paper presented at the Seventh IASTED

International Conference on Internet and Multimedia Systems and Applications (IMSA 2003),

Honolulu, HI.

Wu, W., Bulut, H., Uyar, A., & Fox, G. (2005). Adapting H.323 Terminals in a Service-Oriented Collaboration

System. IEEE Internet Computing, 9(4), 43–50.

Wu, W., Fox, G., Bulut, H., Uyar, A., & Altay, H. (2004). Design and Implementation of a Collaboration

Web-Services System. Journal of Neural Parallel and Scientific Computations, 12 (Special Issue on Grid

Computing), 391–408.

Wu, W., Fox, G., Yildiz, B., Pallickara, S. L., Patel, S., & Yemme, D. (2005). An Analysis of the Costs for

Reliable Messaging in Web/Grid Service Environments. Proceedings of the 2005 IEEE International

Conference on e-Science & Grid Computing.

Wu, W., Huang, T., & Fox, G. (2006, May 14–17). Building Scalable and High Efficient Java Multimedia

Collaboration. Paper presented at the IEEE 2006 International Symposium on Collaborative

Technologies and Systems (CTS 2006), Las Vegas, NV.

Wu, W., Uyar, A., Bulut, H., & Fox, G. (2003, June). Integration of SIP VoIP and Messaging with the AccessGrid

and H.323 Systems. Paper presented at the First International Conference on Web Services, Las Vegas,

NV.

Wu, W., Uyar, A., Bulut, H., Oh, S., & Fox, G. (2005). Grid Service Architecture for Videoconferencing. In M. P.

Bekakos, G. A. Gravvanis, & H. R. Arabnia (Eds.), Grid Computational Methods.

Yan, Y., Huang, Y., Fox, G., Kaplan, A., Pallickara, S., Pierce, M., et al. (2003, June 23–26). Implementing

a Prototype of the Security Framework for Distributed Brokering Systems. Paper presented at the

International Conference on Security and Management, Las Vegas, NV.

Yildiz,B.(2007).DistributedHandlerArchitecture.IndianaUniversity,Bloomington,IN.

Yildiz, B., Pallickara, S., & Fox, G. (2005, February 23–25). Experiences for Deploying Services within the Axis

Container. Paper presented at the IEEE International Conference on Internet and Web Applications

and Services (ICIW ‘06), Guadeloupe, French Caribbean.

Yin, H., Brenes-Barahona, S., McMullen, D., Pierce, M., Huffman, K., & Fox, G. (2006, November 12–13). A

PERMIS-based Authorization Solution between Portlets and Back-end Web Services Paper presented

at the Second International Workshop on Grid Computing Environments (GCE ‘06 at SC ’06),

Tampa, FL.

Yin, H., McMullen, D. F., Nacar, M. A., Pierce, M., Huffman, K., Fox, G., et al. (2006, April 21). Providing

Portlet-Based Client Access to CIMA-Enabled Crystallographic Instruments, Sensors, and Data. Paper

presented at the Seventh IEEE/ACM International Conference on Grid Computing (GRID 2006),

Barcelona, Spain.

Youn, C. (2003). Web Services Based Architecture in Computational Web Portals. Syracuse University.

129

Youn, C., Pierce, M., & Fox, G. (2003, June). Building Problem Solving Environments with Application Web

Service Toolkits. Paper presented at the International Conference on Computational Science (ICCS

‘03), Australia.

Youn, C., Pierce, M., & Fox, G. (2003, June 23–26). Developing Secure Web Services for Computational

Portals. Paper presented at the International Conference on Security and Management, Las Vegas,

NV.

Youn, C., Pierce, M., & Fox, G. (2005). Building Problem Solving Environments with Application Web

Service Toolkits. Future Generation Computer Systems, 21(6), 856–867.

Zhai, G., Fox, G., Pierce, M., Wu, W., & Bulut, H. (2005, December 12–14). eSports: Collaborative and

Synchronous Video Annotation System in Grid Computing Environment. Paper presented at the

IEEE International Symposium on Multimedia (ISM 2005), Irvine, CA.

VisualizationandInteractiveSpacesLabPublications

Bachta, E. (2002). Manipulating Implicit Surfaces in the CAVE Using Particle Systems. University of Illinois,

Urbana, IL.

Bachta, E. (2005, May 25–27). A Case Study in the Visualization of Supernova Simulation Data. Paper

presented at the Visualization and Astrophysical Data: Bringing Together Science, Art, and

Education.

Baker, M. P. (2002). Introduction to Visualization.

Baker, M. P. (2006). Visual Representations of Covariance for the Inverse Ocean Modeling Framework.

Indianapolis, IN: Pervasive Technology Labs at Indiana University.

Baker, M. P., Bachta, E., Pietrowicz, M., Pietrowicz, S., & Stein, R. J. (2003). Riverside 2003: Multi-Media

Exploration of a Tree-Growth Database. Indianapolis, IN: Indiana University Visualization and

Interactive Spaces Lab.

Baker,M.P.,Heiland,R.,Bachta,E.,&Das,M.(2007,June5–7).VisPort:Web-BasedAccessto

Community-BasedVisualizationFunctionality.PaperpresentedattheTeraGridConference,

Madison,WI.

Camp, L. J., Connelly, K. H., Huber, L., & Shankar, K. (2006, October 17–21). Beyond Consent: User

Defined Privacy in Ubicomp. Paper presented at the Nurturing Technologies in the Domestic

Environment Workshop, UbiComp 2006, Los Angeles, CA.

Hearn, D., & Baker, M. P. (2003). Computer Graphics with OpenGL (3rd ed.). Englewood Cliffs, NJ: Prentice-

Hall.

Khalil, A., & Connelly, K. H. (2006, November). Context-Aware Telephony: Privacy Preferences and Sharing

Patterns. Paper presented at the Computer Supported Collaborative Work, Banff, Alberta, Canada.

Moad,A.,Moad,C.,Perry,J.,Wampler,R.,Goeken,G.S.,Begue,N.,etal.(2007).NLOPredict:

VisualizationandSDataAnalysisSoftwareforNonLinearOptics.Journal of Computational

Chemistry.

Pietrowicz, M., & Baker, M. P. (2003). ARBOR Data Schema and Management Tools. Indianapolis, IN:

Indiana University Visualization and Interactive Spaces Lab.

Pietrowicz, S., & Baker, M. P. (2003). A Viewer Applet for 1D Time Series Data. Indianapolis, IN: Indiana

University Visualization and Interactive Spaces Lab.

Siek,K.A.,Connelly,K.H.,Menzel,S.,&Hopkins,L.(2007).ResearchersStudyHowPatientsCanUse

PDAstoSelf-MonitorDiet.Renal Business Today.

Siek, K. A., Connelly, K. H., Rogers, Y., Rowher, P., Lambert, D., & Welch, J. L. (2006, September 18). The

Food We Eat: An Evaluation of Food Items Input into an Electronic Food Monitoring Application.

Paper presented at the UbiHealth Workshop, UbiComp 2006, Los Angeles, CA.

Stein, R. J., Bachta, E., & Baker, M. P. (2003). An XML Structure for IOM Simulation Output. Indianapolis,

IN: Indiana University Visualization and Interactive Spaces Lab.

Tennant, S., Kock, C., Palakal, M., Rogers, J., & Baker, M. P. (2003, October 15–17). Negotiating Virtual

and Physical Museum Space. Paper presented at the Virtual Systems and Multimedia Conference,

Montreal, Quebec, Canada.

Scientific Data Analysis Lab Publications

Baker,M.P.,Heiland,R.,Bachta,E.,&Das,M.(2007,June4–8).VisPort:Web-BasedAccessto

Community-BasedVisualizationFunctionality.PaperpresentedattheTeraGridConference,

Madison,WI.

Dantzer, J., Moad, C., Heiland, R., & Mooney, S. (2005). MutDB services: Interactive Structural Analysis of

Mutation Data. Nucleic Acids Research, 33.

Gannon, D., Alameda, J., Chipara, O., Christie, M., Dukle, V., Fang, L., et al. (2005). Building Grid Portal

Applications from a Web-Service Component Architecture. Proceedings of the IEEE.

Heiland, R. (2006). XML for Bioinformatics. Briefings in Bioinformatics.

Moad,A.,Moad,C.,Perry,J.,Wampler,R.,Goeken,G.S.,Begue,N.,etal.(2007).NLOPredict:

VisualizationandDataAnalysisSoftwareforNonlinearOptics.Journal of Computational

Chemistry.

Moad, C., & Plale, B. (2004). Portal Access to Parallel Visualization of Scientific Data on the Grid (No. TR-

492): Indiana University Department of Computer Science.

Peters, B., Moad, C., Youn, E., Buffington, K., Heiland, R., & Mooney, S. D. (2006). Identification of Similar

Regions of Protein Structures Using Integrated Sequence and Structure Analysis Tools. BMC

Structural Biology, 6(4).

1�1

Plale, B., Jacobs, C., Jensen, S., Liu, Y., Moad, C., Parab, R., et al. (2004, April). Understanding Grid Resource

Information Management Through a Synthetic Database Benchmark/Workload. Paper presented at

the IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004).

Plale, B., Jacobs, C., Liu, Y., Moad, C., Parab, R., & Vaidya, P. (2003). Benchmark Details of Synthetic

Database Benchmark/Workload for Grid Resource Information (No. TR-583). Bloomington, IN:

Indiana University Department of Computer Science.

KnowledgeAcquisitionandProjectionLabPublications

Atkinson, I., du Boulay, D., Chee, C., Chiu, K., Huffman, K., McMullen, D., et al. (2006, September).

Common Instrument Middleware Architecture: Extensions for the Australian e-Research

Environment. Paper presented at the UK e-Science All Hands Meeting.

Atkinson, I,. duBoulay, D., Chee, C., Chiu, K., King, T., McMullen, D., et al. (2006, December). CIMA Based

Remote Instrument and Data Access: An Extension into the Australian e-Science Environment. Paper

presented at the IEEE International Conference on e-Science and Grid Computing (e-Science 2006),

Amsterdam, the Netherlands.

Atkinson,I.,duBoulay,D.,Chee,C.,Chiu,K.,Coddington,P.,Gerson,A.,etal.(2007,January).

DevelopingCIMABasedRemoteAccessforCollaborativee-Research.Paperpresentedatthe

FifthAustralasianSymposiumonGridComputingande-Research(AusGrid2007),Ballarat,

Australia.

Bogaerts, S., & Leake, D. (2004). Facilitating CBR for Incompletely-Described Cases: Distance Metrics for

Partial Problem Descriptions (ECCBR-2004). In Advances in Case-Based Reasoning (pp. 62–76).

Berlin, Germany: Springer-Verlag.

Bramley, R., Chiu, K., Davadithya, T., Gupta, N., Hart, C., Huffman, J., et al. (2006). Instrument Monitoring,

Data Sharing and Archiving Using Common Instrument Middleware Architecture (CIMA). Journal of

Chemical Information and Modeling, 46(3), 1017–1025.

Bramley, R., Chiu, K., Huffman, J., Huffman, K., & McMullen, D. (2003). Instruments and Sensors as

Network Services: Making Instruments First Class Members of the Grid (No. TR588). Bloomington,

IN: Indiana University Department of Computer Science.

Bramley, R., Liu, F., Chiu, K., & Turner, G. (2004). A Data Stream Analysis of the MMSF Automated

Photometric Telescope. Bloomington, IN: Indiana University Department of Computer Science.

Chiu, K. (2004). XBS: A Streaming Binary Serializer for High Performance Computing. Paper presented at

the High Performance Computing Symposium 2004.

Chiu, K., & Liu, W. (2004, May 17–22). A Compiler-Based Approach to Schema-Specific XML Parsing. Paper

presented at the First International Workshop on High Performance XML Processing, New York, NY.

Crabtree, A., Evans, M., Fraser, M., Tolmie, P., & McMullen, D. (2005, September 11–15). Situating

Ubiquitous Computing in Everyday Life: Bridging the Social and Technical Divide. Paper presented

at the UbiComp 2005 International Conference, Tokyo, Japan.

Devadithya, T., Chiu, K., Huffman, K., & McMullen, D. (2005, December 5–8). The Common Instrument

Middleware Architecture: Overview of Goals and Implementation. Paper presented at the IEEE

International Conference on e-Science and Grid Computing, Melbourne, Australia.

Evans, M. (2004). A Case of Supporting Distributed Knowledge and Work in the U.S. Navy: The Challenges

of Knowledge Management to HPT. Tech Trends.

Evans, M. (2004, April 19–24). Knowledge and Performance in Context: A Case of Troubleshooting a

Complex System in the U.S. Navy. Paper presented at the International Performance Improvement

Conference and Expo, Tampa, FL.

Evans, M. (2004, April 19–23). Use Cases: A Tool for Collaborative Work Among Performance Technologists

and Software Developers. Paper presented at the International Performance Improvement

Conference and Expo, Tampa, FL.

Evans, M. (2005, July 4–6). The Effects of Institutional Elements on Knowledge and Work: A Critical-

Realistic-Inspired Analysis of Context. Paper presented at the Fourth International Critical

Management Studies Conference, Cambridge, United Kingdom.

Evans, M., Leake, D., McMullen, D., & Bogaerts, S. (2005). Context in Remote Distributed Troubleshooting:

Perspective on Socio-Technical Study. Fifth International and Interdisciplinary Conference on

Modeling and Using Context (CONTEXT-05).

Evans, M., & McMullen, D. (2004, November 6–10). Proposing an Organizational Memory to Manage

Knowledge Discovery in Scientific Collaborations. Paper presented at the ACM Conference on

Computer Supported Cooperative Work, Chicago, IL.

Evans, M., McMullen, D., Leake, D., & Bogaerts, S. (2004, September 7–10). Remote Collaborative Help:

Using Cases and Concept Maps to Coordinate and Contextualize Knowledge. Paper presented at the

UbiComp International Conference, Nottingham, United Kingdom.

Evans, M. A. (2003). The Distribution and Use of Knowledge and Performance: A Case of Virtual Work in

the U.S. Navy. Paper presented at the Association for Educational Communication Technology

International Conference, Anaheim, CA.

Evans, M. A. (2003). Knowledge and Work in Context: A Case of Troubleshooting a Complex System in the

U.S. Navy. Indiana University, Bloomington, IN.

Evans, M. A. (2003). Ubiquitous Support for Knowledge and Work. Paper presented at the UbiComp

International Conference, Seattle, WA.

Evans, M. A. (2004). Chasing a Fault across Ship and Shore: Explaining the Distribution of Knowledge and

Work in the U.S. Navy. Performance Improvement Quarterly.

Evans, M. A. (2004). Use cases: A tool for collaborative work among performance technologists and software

developers. 2004 International Performance Improvement Conference & Expo.

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Evans, M. A., McMullen, D., & Leake, D. (2004). Getting Knowledge Where It’s Needed: Building Systems

to Support Collaborative Problem Solving in Virtual Teams. Paper presented at the UbiComp

Conference.

Huffman, J., McMullen, D., & Huffman, K. (2006, July 22–27). Remote Monitoring and Access to

Instruments and Data. The CIMA Crystallography Portal. Paper presented at the 2006 Annual

Meeting of the American Crystallographic Association, Honolulu, HI.

Kratz, T., Arzburger, P., Benson, B., Chiu, C., Chiu, K., Ding, L., et al. (2006). Towards a Global Lake

Ecological Observatory Network. Publications of the Karelian Institute, 145, 51–63.

Kratz, T., Benson, B., Arzberger, P., Chiu, K., Ding, L., Fountain, T., et al. (2006, September 15). Automating

Scaling and Data Processing in a Network of Sensors: Towards a Global Network for Lake

Metabolism Research and Education. Paper presented at the Long Term Ecological Research

Network All Hands Meeting, Estes Park, Co.

Leake, D. (2003, June). Context and Experience. Paper presented at the Fourth International and

Interdisciplinary Conference on Modeling and Using Context (CONTEXT-03), Stanford, CA.

Leake, D. (2003, June). Human-Centered CBR: Integrating Case-Based Reasoning with Knowledge

Construction and Extension. Paper presented at the Fifth International Conference on Case-Based

Reasoning (CCBR-2003), Trandheim, Norway.

Leake, D., Bogaerts, S., Evans, M., & McMullen, D. (2005, October). Contextual Support for Remote

Cooperative Troubleshooting: Lessons from a Naturalistic Study. Paper presented at the

International Workshop on Cooperative Systems and Context. CEUR.

Leake, D., Bogaerts, S., Evans, M., McMullen, D., Oder, M., & Valerio, A. (2005, May 15–17). Using Cases to

Support Divergent Roles in Distributed Collaboration. Paper presented at the Eighteenth International

Florida Artificial Intelligence Research Society Conference (FLAIRS-2005), Menlo Park, CA.

Leake, D., Maguitman, A., & Reichherzer, T. (2003). Topic Extraction and Extension to Support Concept

Mapping. Paper presented at the Sixteenth International Florida Artificial Intelligence Research

Society Conference (FLAIRS-2003), Florida.

Leake, D., Maguitman, A., Reichherzer, T., Cañas, A., Carvalho, M., Arguedas, M., et al. (2003). Aiding

Knowledge Capture by Searching for Extensions of Knowledge Models. Paper presented at the

Second International Conference on Knowledge Capture (K-Cap 2003).

Leake, D., & Sooriamurthi, R. (2003). Dispatching Cases Versus Merging Case-Bases: When MCBR matters.

Paper presented at the Sixteenth International Florida Artificial Intelligence Research Society

Conference (FLAIRS-2003), Florida.

Ma, Y. (2006). A Composable Data Management Architecture for Scientific Applications. Indiana University,

Bloomington, IN.

McMullen, D. (2003, September 16–18). Case-Based Reasoning as an Enabling Technology for Next

Generation Diagnostic Systems. Paper presented at the American Society of Naval Engineers

Symposium, Bloomington, IN.

McMullen, D. (2003, June 16). Middleware for Grid-Enabling Instruments. Paper presented at the UK e-

Science Workshop on Instruments and the Grid, Daresbury, United Kingdom.

McMullen, D., Atkinson, I., Chiu, K., Turner, P., Huffman, K., Quilici, R., et al. (2006, December 4). Toward

Standards for Integration of Instruments into Grid Computing Environments. Paper presented at

the IEEE e-Science and Grid CRL Workshop, Amsterdam, the Netherlands.

McMullen, D., Devadithya, T., & Chiu, K. (2005, September 25–30). Integrating Instruments and Sensors

into the Grid with CIMA Web Services. Paper presented at the Third APAC Conference on Advanced

Computing, Grid Applications and e-Research (APAC ‘05), Gold Coast, Australia.

McMullen, D., & Huffman, K. (2005, November 18). Connecting Users to Instruments and Sensors:

Portals as Multi-User GUIs for Instrument and Sensor Facilities. Paper presented at the GCE 2005

Workshop on Grid Computing Portals in conjunction with SC ’05, Seattle, WA.

McMullen, D., & Huffman, K. (2006). Connecting Users to Instruments and Sensors: Portals as Multi-User

GUIs for Instrument and Sensor Facilities. Concurrency and Computation: Practical Experience, 18,

1–11.

McMullen, D., & Leake, D. (2002). An Architecture for Knowledge Organization and Presentation in

Distance Support of Maintenance Activities. American Society of Naval Engineers Symposium.

McMullen, D., & Reichherzer, T. (2006). Identity and Functionality in the Common Instrument Middleware

Architecture. Applied Ontology 3, IOS Press.

McMullen,D.F.(2007,April16–18).TheCommonInstrumentMiddlewareArchitecture:Experiences

andFutureDirections.PaperpresentedatInstrumentingtheGrid:SecondInternational

WorkshoponDistributedCooperativeLaboratories(INGRID2007),SantaMargheritaLigure,

Portofino,Italy.

McMullen, D. F., Atkinson, I. M., Chiu, K., Turner, P., Huffman, K., Quilici, R., et al. (2006, December).

Toward Standards for Integration of Instruments into Grid Computing Environments. Paper

presented at the IEEE International Conference on e-Science and Grid Computing (e-Science 2006),

Amsterdam, the Netherlands.

McMullen, D. F., & Reichherxer, T. (2006). Identity and Functionality in the Common Instrument

Middleware Architecture. Applied Ontology 3, IOS Press.

Parab, R., McMullen, R., & Plale, B. (2003). Comparison of Two Java Based Publish-Subscribe Systems for

Knowledge Projection Project. Bloomington, IN: Indiana University Knowledge Acquisition and

Projection Lab.

Plale, B., Jacobs, C., Jensen, S., Liu, Y., Moad, C., Parab, R., et al. (2004). Understanding Grid Resource

Information Management through a Synthetic Database Benchmark/Workload. Fourth IEEE/ACM

International Symposium on Cluster Computing and the Grid (CCGrid2004).

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Plale, B., Jacobs, C., Liu, Y., Moad, C., Parab, R., & Vaidya, P. (2003). Benchmark Details of Synthetic Database

Benchmark/Workload for Grid Resource Information (No. TR-583): Indiana University Department of

Computer Science.

Plale, B., Jacobs, C., Liu, Y., Moad, C., Parab, R., Vaidya, P., et al. (2003). Understanding Grid Resource

Information Management through a Synthetic Database Benchmark/Workload. International

Conference on High Performance Computing (HiPC).

Yin, H., Brenes-Barahona, S., McMullen, D., Pierce, M., Huffman, K., & Fox, G. (2006, November 12). A

PERMIS-based Authorization Solution Between Portlets and Back-End Web Services. Paper presented

at the GCE 2006: Workshop on Grid Computing Portals, Tampa, FL.

Yin, H., McMullen, D., Nacar, M., Pierce, M., Huffman, K., Fox, G., et al. (2006, September 28–29). Providing

Portlet-Based Client Access to CIMA Enabled Crystallographic Instruments, Sensors, and Data. Paper

presented at the Seventh IEEE/ACM International Conference on Grid Computing (Grid 2006),

Barcelona, Spain.

Publications by the Chief Executive Officer of Pervasive Technology Labs

McRobbie, M. (2002, February). Global Terabit Research Network Building Cyber Infrastructure. Paper

presented at the Pacific Rim Networking, Honolulu, HI.

McRobbie, M. (2002, May). Global Terabit Research Network Building Global Cyber Infrastructure. Paper

presented at the Internet2 Member Meeting, Arlington, VA.

McRobbie, M. (2003). The Library and Education: Integrating Information Landscapes. Emerging Visions for

Access in the Twenty-first Century Library, Council on Library and Information Resources, Washington,

D.C., 44–45.

McRobbie, M., & Antolovic, L. (2001). Implementing Life-Cycle Funding. EDUCAUSE Review, 36(5), 28–38.

McRobbie, M., Brown, M., DeFanti, T., Verlo, A., Plepys, D., McMullen, D., et al. (1999). The International Grid

(iGrid): Empowering Global Research Community Networking Using High Performance International

Internet Services. Paper presented at the INET Conference, San Jose, CA.

McRobbie, M., McMullen, D., Adams, K., Pearson, D., DeFanti, T., Brown, M., et al. (1999). The iGrid

Project: Enabling International Research and Education Collaborations Through High Performance

Networking. Paper presented at the Proceedings of Internet Workshop ‘99, Suita, Osaka, Japan.

McRobbie, M., & Palmer, J. (1999). Strategic and Financial Planning for Information Technology in Higher

Education. Paper presented at the Forum for the Future of Higher Education, Aspen, CO.

McRobbie, M., & Wallace, S. (2001). Toward a Global Terabit Research Network (GTRN). Paper presented at

the Proceedings of IWS2001, Tokyo, Japan.

Publications by the Chief Operating Officers of Pervasive Technology Labs

Arenson,A.D.,Bakhireva,L.,Chambers,T.,Deximo,C.,Foroud,T.,Jacobson,J.,etal.(2007).

ImplementationofaDistributedArchitectureforManagingCollectionandDisseminationof

DataforFetalAlcoholSpectrumDisordersResearch.InW.Dubitzky(Ed.),(Vol.LNBI4360,pp.

33–46):Springer-Verlag,BerlinHeidelberg.

Myron, S. A., Link, M. R., Knepper, R., & Stewart, C. A. (2005, November 6–9). PubsOnline: An Open Source

Database for Managing and Delivering Bibliographic Information. Paper presented at the 33rd

Annual ACM SIGUCCS Conference on User Services., Monterey, CA.

Peebles, C., Stewart, C., Voss, B., & Workman, S. (2001, October). Measuring Quality, Cost, and Value of IT

Services in Higher Education. Paper presented at the EDUCAUSE Conference, Indianapolis, IN.

Stewart, C., Mueller, M., & Lingwall, M. (2006). Progress Towards Petascale Applications in Biology.

Bloomington, IN: Indiana University.

Stewart, C. A. (2004). Bioinformatics: Transforming Biomedical Research and Medical Care. Communication

of ACM, 47(11), 31–33.

Stewart,C.A.,Mueller,M.,&Lingwall,M.(Eds.).(2007).Progress Towards Petascale Applications in

Biology: Status in 2006,LectureNotesinComputerScience:Springer-Verlag,BerlinHeidelberg.

Voss, B. (2001). Case Study: Knowledge Management Alleviates the Computing Support Crisis at Indiana

University. In G. Bernbom (Ed.), Information Alchemy: The Art and Science of Knowledge Management,

EDUCAUSE Leadership Strategies Series Volume 3: Jossey-Bass, Inc.

Voss, B. (2003). The Economic Development Case for Investment in Higher Education. EDUCAUSE Center

for Applied Research Bulletin, 2003(12).

Voss, B. (2004, September). Evolving Strategies for Campus Network Infrastructure. Syllabus Magazine, 17.

Voss, B. (2004). The Impact of Globalization on Campus Networks. EDUCAUSE Center for Applied Research

Bulletin, 2004(4).

Wang, P., Turner, G., Lauer, D. A., Allen, M., Simms, S., Hart, D., et al. (2004). One Teraflop Achieved with

a Geographically Distributed Linux Cluster. In L. T. Y. a. M. Guo (Ed.), High Performance Computing:

Paradigm and Infrastructure: Wiley Interscience.

Wang, P., Turner, G., Simms, S., Hart, D., Papkhian, M., & Stewart, C. (2005). 1 TFlops Achieved with a

Geographically Distributed Linux Cluster, Part 4. In Cluster and Grid Computing, High Performance

Computing, Paradigm and Infrastructure: John Wiley and Sons.

Wernert, E. A., Boyles, M., Huffman, J. N., Rogers, J., Huffman, J. C., & Stewart, C. A. (2005). The John-e-

box: Fostering Innovation, Inclusion, and Collaboration through Accessible Advanced Visualization.

Paper presented at the Richard Tapia Celebration of Diversity in Computing Conference

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Baden, S., Chrisochoides, N., Gannon, D., & Norman, M. (Eds.). (2000). Structured Adaptive Mesh Refinement

(SAMR) Grid Methods, Lecture Notes in Computer Science: Springer-Verlag, Berlin Heidelberg.

Foster, I., Gannon, D., Kishimoto, H., & vonReich, J. (2005). Open Grid Service Architecture Use Cases.

Global Grid Forum Document #29.

Fox, G., Gannon, D., Ko, S.-H., Lee, S., Pallickara, S., Pierce, M., et al. (2003). Chapter 18: Peer to Peer Grids.

In B. Fox, Hey (Ed.), Grid Computing: Making the Global Infrastructure a Reality: Wiley and Sons.

Fox, G., Gannon, D., & Thomas, M. (2003). Chapter 20: Overview of Grid Computing Environments. In B.

Fox, Hey (Ed.), Grid Computing: Making the Global Infrastructure a Reality: Wiley and Sons.

Gannon, D. (2003). From Web Services to Grid Services. IEEE Journal on Intelligent Systems.

Gannon, D., Ananthakrishnan, R., Krinshnan, S., Govidndaraju, M., Ramakrishnan, L., & Slominski,

A. (2003). Chapter 3: Grid Web Services and Application Factories. In B. Fox, Hey (Ed.), Grid

Computing: Making the Global Infrastructure a Reality: Wiley and Sons.

Gannon, D., Chiu, K., Govindaraju, M., & Slominksi, A. (2003). A Brief Introduction to the Open Grid

Services Infrastructure. Journal of Computing and Informatics (Special Issue on Grid Systems).

Gannon, D., Fang, L., Kandaswamy, G., Kodeboyina, D., Krishnan, S., Plale, B., et al. (2004, August).

Building Grid Applications and Portals: An Approach Based on Components, Web Services and

Workflow Tools. Paper presented at the Europar Conference, Pisa, Italy.

Gannon, D., & Fox, G. (2001). Computation Grids. IEEE Computer Science and Engineering, 3(4), 74–77.

Gannon, D., & Fox, G. (2005). Workflow in Grid Systems. Concurrency and Computation: Practice and

Experience (Special Issue on Grid Workflow).

Gannon, D., Fox, G., Pierce, M., Plale, B., vonLaszewski, G., Severance, C., et al. (2003). Grid Portals: A

Scientist’s Access Point for Grid Services (No. GCE-RG): Global Grid Forum.

Gannon, D., & Hirsch, R. (2003). Chapter Six: Programming Environments and Tools. In D. Reed (Ed.), The

Roadmap for the Revitalization of High-End Computing: CRA.

Gannon, D., Plale, B., Christie, M., Fang, L., Huang, Y., Jensen, S., et al. (2005). Service Oriented

Architectures for Science Gateways on Grid Systems. Paper presented at the International

Conference on Service Oriented Computing, Amsterdam, the Netherlands.

Gannon, D., Reed, D., Padua, D., Foster, I., & Miller, B. (1999, February). Delphi: An Integrated, Language-

Directed Performance Prediction, Measurement, and Analysis Environment. Paper presented at the

Frontiers ‘99: 9th Symposium on the Frontiers of Massively Parallel Computation, Annapolis, MD.

Gannon, D., & Reynders, J. (2001). Chapter 14: Parallel Object Oriented Libraries. In F. Dongarra, Fox,

Kennedy, Torczon, White (Ed.), CRPC Parallel Computing Handbook: Morgan-Kauffman.

Gannon, D., & Reynders, J. (2002). Parallel Object Oriented Libraries. In F. Dongarra, Fox, Kennedy,

Torczon, White (Ed.), Sourcebook of Parallel Computing: Morgan-Kauffman.

Plale, B., Gannon, D., Alameda, J., Wilhelmson, B., Hampton, S., Rossi, A., et al. (2005). Active Management

of Scientific Data. IEEE Internet Computing (Special Issue on Internet Access to Scientific Data), 9(1),

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Taylor, I., Deelman, E., Gannon, D., & Shields, M. (Eds.). (2006). Workflow for eScience: Springer-Verlag:

Berlin Heidelberg.

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Bader, D. (2004). Computational Biology and High Performance Computing. Communications of the

Association of Computers and the Humanities (ACH), 47, 34–41.

Baumgartner, J., Borner, K., Deckard, N., & Sheth, N. (2003). An XML Toolkit for an Information

Visualization Software Repository. Paper presented at the IEEE Information Visualization

Conference Poster Compendium.

Borner, K., Jun Lee, G., Penumarthy, S., & Jones, R. (2004). Visualizing the VLearn 3D. Visualization and Data

Analysis, San Jose, CA, SPIE-IS&T, 5295, 24–32.

Borner, K., & Penumarthy, S. (2005). Spatio-Temporal Information Production and Consumption of Major

U.S. Research Institutions. Paper presented at the ISSI 2005, Stockholm, Sweden.

Boyack, K., Mane, K., & Borner, K. (2004). Mapping Medline Papers, Genes and Proteins Related to

Melanoma Research. Paper presented at the IV2004, London, United Kingdom.

Chaturvedi, R., Glazier, J., Newman, S., & Alber, M. (2005). On Multiscale Approaches to Three-

Dimensional Modeling of Morphogenesis. Journal of the Royal Society Interface 2, 237–253.

Chaturvedi, R., Huang, C., Izaguirre, J., Newman, S., Glazier, J., & Alber, M. (2004, October 25–28). A

Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb. Paper presented

at the Cellular Automata: 6th International Conference on Cellular Automata for Research and

Industry (ACRI 2004), Amsterdam, the Netherlands.

Chen, J., Bai, G., Shen, Z., Li, X., & Hsu, A. (2005). Prediction of Failure Rate of Rotary Machine using

Computer Simulations. Journal of Manufacturing Science and Engineering, Transactions of the ASME,

768–772.

Cickovski, T., Huang, C., Chaturvedi, R., Glimm, T., Hentschel, H., Alber, M., et al. (2005). A Framework for

Three-Dimensional Simulation of Morphogenesis. IEEE/ACM Transactions on Computational Biology

and Bioinformatics, 2, 273–288.

Cox, S., Weaire, D., & Glazier, J. (2004). The Rheology of Two-Dimensional Forms. Rheology Acta, 43,

442–448.

Dan, D., Mueller, C., Chen, K., & Glazier, J. (2005). Solving the Advection-Diffusion Equations in Biological

Contexts Using the Cellular Potts Model. Physical Review E72, 041909.

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Dantzer, J., Moad, C., Heiland, R., & Mooney, S. (2005). MutDB Services: Interactve Stuctural Analysis of

Mutation Data. Nucleic Acids Research, 33, W311–W314.

George, H., Hentschel, E., Glimm, T., Glazier, J., & Newman, S. (2004). Dynamical Mechanisms for Skeletal

Pattern Formation in the Vertebrate Limb. Proceedings of the Royal Society London B 271, 1713–1722.

Haddad, E., & King, B. (2005). Anonymous Simple Secure M-Commerce Protocol. Paper presented at the

International Conference on Pervasive Systems and Computing.

Hu, N., Chen, R., & Hsu, A. (2006). Molecular Simulation of the Glass Transition and Proton Conductivity

of 2, 2’-Benzidinedisulfonic Acid (BDSA) and 4, 4’-Diaminodiphenylether-2, 2’-Disulfonic Acid

(ODADS) Based Copolyimides as Polyelectrolytes for Fuel Cell Applications. Polymer International.

Hu, N., Sun, X., & Hsu, A. (2005). Monte Carlo Simulations of Hydrogen Adsorption in Alkali-Doped Single-

Walled Carbon Nanotubes. Journal of Chemical Physics, 123(4), 044708.

Izaguirre, J., Chaturvedi, R., Huang, C., Cickovski, T., Coffland, J., Thomas, G., et al. (2004). CompuCell, a

Multi-Model Framework for Simulation of Morphogenesis. Bioinformatics, 20, 1129–1137.

Ke, W., Borner, K., & Viswanath, L. (2004). Analysis and Visualization of the IV 2004 Contest Dataset. Paper

presented at the IEEE Information Visualization Conference Poster Compendium.

King, B. (2004, July 13–15). Improvements to the Halving a Point Algorithm. Paper presented at the

Information Security and Privacy: Ninth Australasian Conference (ACISP 2004), Sydney, Australia.

King, B. (2004, March 1–4). A Point Compression Method for Elliptic Curves Defined over GF(2n). Paper

presented at the Workshop on Public Key Cryptography (PKC 2004), Singapore.

King, B., & Rubin, B. (2004, July 13–15). Improvements to the Halving a Point Algorithm. Paper presented at

the Information Security and Privacy: Ninth Australasian Conference (ACISP 2004), Sydney, Australia.

Kiskowski, M., Alber, M., Thomas, G., Glazier, J., Bronstein, N., Pu, J., et al. (2004). Interplay Between

Activator–Inhibitor Coupling and Cell-Matrix Adhesion in a Cellular Automaton Model for

Chondrogenic Patterning. Developmental Biology, 271, 372–387.

Koh, J., Akay, H., Liou, M., & Hsu, A. (2005). Analysis of Overall Heat Balance in Self-Heated Proton-

Exchange-Membrane Fuel Cells for Temperature Predictions. Journal of Power Sources, 144(1),

122–128.

Lambert, J., Cantat, I., Delannay, R., Renault, A., Graner, F., Glazier, J., et al. (2005). Extraction of Relevant

Physical Parameters from 3D Images of Foams Obtained by X-ray Tomography. Colloids and Surfaces A:

Physicochemical and Engineering Aspects 263, 295–302.

Mackenzie, D. (2006). Ramping up to Multiscale: Taking Biomedical Modeling to a New Level. Biomedical

Computation Review (Spring), 19–26.

Merks, R., Brodsky, S., Goligorksy, M., Newman, S., & Glazier, J. (2006). Cell Elongation is Key to in Silico

Replication of in Vitro Vasculogenesis and Subsequent Remodeling. Developmental Biology, 289, 44–54.

Merks, R., & Glazier, J. (2005). A Cell-Centered Approach to Developmental Biology. Physica, A 352, 113–130.

Merks, R., & Glazier, J. (2006). Dynamic Mechanisms of Blood Vessel Growth. Nonlinearity, 19, C1–C10.

Merks, R., Newman, S., & Glazier, J. (2004, October 25–28). Cell-Oriented Modeling of in Vitro Capillary

Development. Paper presented at the Cellular Automata: 6th International Conference on Cellular

Automata for Research and Industry (ACRI 2004), Amsterdam, The Netherlands.

Mooney, S. (2005). Bioinformatics Approaches and Resources for Single Nucleotide Polymorphism Functional

Analysis. Briefings in Bioinformatics, 6(1), 44–56.

Oiwa, N., & Glazier, J. (2004). Self-Similar Mitochondrial DNA. Cell Biochemistry and Biophysics, 41, 41–62.

Peters, B., Moad, C., Youn, E., Buffington, K., Heiland, R., & Mooney, S. (2006). Identification of Structurally

Similar Regions of Protein Structures Using the S-BLEST Web site and Services. BMC Structural Biology,

6(4).

Rogers, Y. (2006). Extending and Augmenting Scientific Enquiry Through Pervasive Learning Environments.

Children, Youth and Environments, 14(2), 67–83.

Rogers, Y., Lim, Y., & Hazelwood, W. (2006, January 5–7). Extending Tabletops to Support Flexible

Collaborative Interactions. Paper presented at the IEEE Tabletop 2006, Adelaide, Australia.

Rogers, Y., Price, S., Randell, C., Stanton-Fraser, D., Weal, M., & Fitzpatrick, G. (2005). Ubi-learning: Integrating

Outdoor and Indoor Learning Experiences. Communication of ACM, 48(1), 55–59.

Salama, P., & King, B. (2005, January). Efficient Secure Image Transmission: Compression Integrated with

Encryption. Paper presented at the SPIE Symposium on Electronic Imaging.

Salazar, K., & Tedesco, L. (2004, November). Environmental Service Learning and Community Partnerships:

Applying Science-Based Solutions to Urban Environmental Problems. Paper presented at the

Geological Society of America Annual Conference, Denver, CO.

Salazar, K., & Tedesco, L. (2005, September). Engaging Students in Urban Campus Stewardship Activities to

Address Water Quality. Paper presented at the Extending Connections: Greening of the Campus VI,

Muncie, IN.

Sheth, N., Borner, K., Baumgartner, J., Mane, K., & Wernert, E. (2003). Treemap, Radial Tree and 3D

Tree Visualizations. Paper presented at the IEEE Information Visualization Conference Poster

Compendium.

Siek, K., Rogers, Y., & Connelly, K. (2005). Fat Finger Worries: How Older and Younger Users Physically Interact

with PDAs. Paper presented at the Interact 2005.

Sooriamurthi, R., Sengupta, A., Menzel, S., Moor, K., Stamm, S., & Borner, K. (2004). Java Engagement for

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Physical Review E, 68(12), 16303.

Tedesco, L., Baker, M. P., & Hall, B. An Integrated Hydrologic Monitoring Network. American Geophysical Union

Abstracts SF31A-0719.

Tedesco, L., Baker, M. P., Rogers, Y., Hall, B., Hursey, J., Hazelwood, W., et al. (2005). RAPID: Remotely

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America Abstracts, 37(7), 408.

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and Data Analysis, San Jose, CA, SPIE-IS&T, 5295, 305–311.

Zeng, W., Thomas, G., & Glazier, J. (2004). Non-Turing Stripes and Spots: A Novel Mechanism for Biological

Cell Clustering. Physica, A 341, 482–494.

LAB AdmINIsTrATION ANd CONTACT INFOrmATION

14�

ThePervasiveTechnologyLabsarelocatedon

theBloomingtonandIndianapoliscampusesof

IndianaUniversity.

MichaelA.McRobbie,President

ofIndianaUniversity

mcrobbie@indiana.edu

CraigA.Stewart,ChiefOperatingOfficer

stewart@indiana.edu

DennisGannon,ScienceDirector

gannon@indiana.edu

ThereseMiller,OperationsManager

millertm@indiana.edu

DaphneSiefert-Herron,InformationManager

dsiefert@indiana.edu

AdministrativeOffices

Indiana University Research Park

501 N. Morton Street

Showers Complex, Suite 224

Bloomington, IN 47404

Phone: (812) 855-4810

Fax: (812) 856-7972

E-mail: ptlabs@iu.edu

OpenSystemsLab

Lindley Hall 415

150 S. Woodlawn Avenue

Bloomington, IN 47405

Director: Andrew Lumsdaine

lums@cs.indiana.edu

AdvancedNetworkManagementLab

Indiana University Research Park

501 N. Morton Street

Showers Complex, Suite 224

Bloomington, IN 47404

Director and Chief Technologist: Steven S. Wallace

ssw@indiana.edu

Associate Director: Gregory Travis

greg@iu.edu

CommunityGridsLab

Indiana University Research Park

501 N. Morton Street

Showers Complex, Suite 224

Bloomington, IN 47404

Director and Distinguished Scientist:

Geoffrey C. Fox

gcf@indiana.edu

KnowledgeAcquisitionandProjectionLab

Indiana University Research Park

501 N. Morton Street

Showers Complex, Suite 224

Bloomington, IN 47404

Director: Donald F. (Rick) McMullen

mcmullen@indiana.edu

145

VisualizationandInteractiveSpacesLab

Informatics and Communication Technology

Complex (ICTC)

535 West Street

Indianapolis, IN 46202

Phone: (317) 274-0705

Fax: (317) 278-1852

Director and Distinguished Scientist:

M. Pauline (Polly) Baker

baker@iu.edu

ScientificDataAnalysisLab

Informatics and Communication Technology

Complex (ICTC)

535 West Street

Indianapolis, IN 46202

Phone: (317) 274-0705

Fax: (317) 278-1852

Associate Director: Randy Heiland

heiland@iupui.edu

Photographers

Chris Robb, Chris Meyer, and Kendall Reeves.

Contributors

Karen Adams, M. Pauline Baker, Geoffrey Fox, Dennis Gannon, Randy Heiland, Andrew Lumsdaine, Donald

F. McMullen, Michael McRobbie, Therese Miller, Marlon Pierce, Daphne Siefert-Herron, Craig Stewart,

Gregory Travis, Steven Wallace, and Brad Wheeler.

Acknowledgements

Projects described in this report were fully or partially funded by the following grant awards:

Lilly Endowment, Inc., Award: 1999-2280-000

National Science Foundation Awards: ANI-0330620, ATM-0427264, CCF-0541335, CNS-0723054, DBI-

0446298, EAR-0446610, IIS-0536947, OCE-0341139, OISE-0505998, SCI-0330613, SCI-0537498, SCI-

0330568

National Institutes of Health Award: P20-HG003894

University of Southampton Award: GR/S90843/01

U.S. Department of Energy Awards: DE-FC02-03ER41275, DE-FC02-02ER25516

U.S. Government Award: MDA90403C1853

Los Alamos National Lab Award: W-7405-ENG-6

Thankyou

Jennifer Browning, Cheryl Combs, Harriet Fierman, Deana Forrest, Mark Long, Tim Mattox, Maria Morris,

Neal Moore, Chris Mueller, Shrideep Pallickara, David Ripley, Ellen Ware, Julie Wernert, Tina Wilson.

With sincere appreciation to Lilly Endowment, Inc., for its generous and ongoing commitment to Pervasive

Technology Labs and Indiana University.

For more information or additional copies please contact Pervasive Technology Labs’ Information Manager

Daphne Siefert-Herron at (812) 856-1242 or dsiefert@indiana.edu.

Copyright 2007, Trustees of Indiana University.