Gregory R. Madey - US grants

The waters and soils of our environment contain naturally-occurring organic matter (NOM), which helps to regulate soil fertility, pollutant toxicity, ecosystem behavior and carbon cycling. These in turn affect agricultural production, public and ecosystem health, and global climate change. However, the processes which produce NOM from plant and animal matter are poorly understood, due to the complex nature of NOM and the multitude of possible reactions in the environment. This project will combine the efforts of ecologists, geochemists and computer scientists in an attempt to model this complex system using a novel stochastic approach. In this approach, millions of individual molecules are simulated and reacted together 'in silico' to provide a computer model of the complex natural processes. The model will be developed and tested via an internet collaboration, and ultimately will be accessible to agricultural, environmental and earth scientists via a simple web browser interface.

This project examines the dynamics of the Open Source Software (OSS) movement, a genuine behavioral and technical puzzle with a far-reaching impact on the world's economy. The OSS community has developed a substantial portion of the infrastructure of the internet and has many outstanding technical achievements, without the benefit of traditional project management techniques, organizational structure, face to face interaction, and in most cases, without direct monetary compensation. We seek to understand the factors that predict developer retention and project success, and to model the growth of the OSS network over time in order to inform policy decisions regarding the OSS movement. We develop an organizational behavior/social psychological model of developer motivation and project effectiveness using a modification of Hackman & Oldham's job characteristics model and March's role identity construct, and use simulation, data mining, and agent-based modeling techniques to model how the OSS network develops over time.

A grant has been awarded to the University of Notre Dame under the direction of Dr. Mark Alber for support of establishing a Beowulf type Biocomplexity Cluster to provide computer infrastructure for The Notre Dame Interdisciplinary Center for the Study of Biocomplexity (ICSB) to meet its broad research and educational goals. The Biocomplexity Cluster will be added to the existing BoB cluster (http://bob.nd.edu) at Notre Dame. Its addition to this high performance computing facility will be embedded in the administrative structures of the Science Computation Facilities (SCF) at Notre Dame. Establishment of the Cluster will result in dramatic increase in the range and complexity of the biological computations on Notre Dame campus.

The ICSB supports the development of quantitative predictive models of biological processes ranging from subcellular to multicellular and ecological. The unique aspects of the ICSB are its interdisciplinary approach, its pursuit of complex biological systems at all scales simultaneously, and its insistence that modeling and quantitative experiments develop jointly. The Biocomplexity Cluster will help ICSB in supporting a variety of projects, which require a high-end computational environment. These projects: Molecular Dynamics, Multiscale Simulation of Avian Limb Development, Microscale Modeling of Cancellous Bone Damage and Environmental Biocomplexity- cover all interacting scales of Biocomplexity phenomena from molecular to environmental. New collaborations with groups working on Biological Networks and Modeling of Cytoskeleton will also greatly benefit from the Cluster. 25% of the CPU time of the Cluster will be accessible to other researchers in the Colleges of Science and Engineering. During academic year up to 5% of the computer time will be allocated for teaching purposes. The Cluster will also allow students participating in the Summer REU programs on Notre Dame campus to learn and apply high-end computational techniques as a part of their training. Interactive web pages will be developed with separate sections aimed at junior-high and high school students to provide educational materials on Biocomplexity which will utilize the Cluster.

The interdisciplinary study of Biocomplexity incorporates quantitative modeling into biology and related disciplines, and thus has broad impact on diverse fields such as Biology, Geology, Environmental Engineering, Life Sciences, Computer Science, and Mathematics. The Biocomplexity Cluster will be used to support interdisciplinary research projects and coursework, helping to train a new generation of students in the integration of interdisciplinary biological experimentation and modeling. Collaboration of ICSB with the newly established Indiana University Biocomplexity Institute at Bloomington and the Indiana University Medical School at Indianapolis, formalized as the Indiana Biocomplexity Consortium, will ensure broad impact through student exchange, development of new educational initiatives, and development of additional collaborative research projects. The Cluster will help the ICSB in achieving one of its major goals of developing new computational techniques and tools of broad utility to bioscientists and distributing these freely to researches within the scientific community.

This project will support the International Workshop Biocomplexity VI: Complex
Behavior in Unicellular Organisms, jointly organized by the Biocomplexity
Institute at Indiana University and the Interdisciplinary Center for the Study of
Biocomplexity at the University of Notre Dame. The collective behavior of
bacteria is as a problem in basic science and is significant in bioengineering, agriculture, medicine, naval architecture and geosciences.... Biofouling is a major problem in cases ranging from surgical implants to submarines, and biofilms are a major cause of antibiotic-resistant infections. The regulatory mechanisms for collective behaviors in bacteria differ from those in more advanced organisms and present an opportunity to compare different design solutions to similar biological problems related to embryonic development. This workshop will develop a more comprehensive view of our current understanding of these issues and include a panel to discuss and report on new directions and collaborations. It will bring together researchers in many disciplines who would not normally attend the same conference (including experimental and theoretical biology, biophysics, engineering, mathematics, and computer science). Approaches will range from single molecule interactions and genetics to systems biology and ecology. About fifty speakers will attend from the USA, Canada, Europe, Israel and Japan, with a total participation of about 100, including many non-specialists. The workshop will include tutorials for graduate students and junior scientists, especially those not currently in the field, but interested in learning about open problems, methodologies and opportunities. As part of the workshop's outreach effort, Dr. Eshel Ben-Jacob will present a public lecture for nonscientists and interested members of the community-at-large.

The proposed project will develop an integrated Wireless Phone Based Emergency Response System (WIPER) that is capable of real-time monitoring of normal social and geographical communication and activity patterns of millions of wireless phone users, recognizing unusual human agglomerations, potential emergencies and traffic jams. WIPER will select from these massive data streams high-resolution information in the physical vicinity of a communication or traffic anomaly, and dynamically inject it into an agent-based simulation system to classify and predict the unfolding of the emergency in real time. The agent-based simulation system will dynamically steer local data collection in the vicinity of the anomaly. Multiple distributed data collection, monitoring, analysis, simulation and decision support modules will be integrated using a Service Oriented Architecture (SOA) to generate traffic forecasts and emergency alerts for engineering, public safety and emergency response personnel.

Proposal Number: CBET-0742191
Principal Investigator: Kareem, Ahsan
Affiliation: University of Notre Dame
Proposal Title: VORTEX-Winds: A Virtual Organization for Reducing the Toll of EXtreme Winds on Society

Wind-related catastrophes inflict enormous devastation on the built environment and result in a staggering number of fatalities, which may continue to rise in the future given the increase in exposure as population migrates towards the coasts. To better manage the impact of extreme wind events, given the heavy reliance on empirical and experimental information in the design process, a new paradigm is required that utilizes shared resources and global collaborations. In order to address this critical issue, a Virtual Organization for Reducing the Toll of EXtreme Winds (VORTEX-Winds) is proposed that would enable such a paradigm shift by offering real-time shared access to geographically dispersed resources for more effective research and education in the area of wind effects on structures. The goals of this proposal are (i) to establish and sustain such a virtual community for wind hazard mitigation; (ii) to enhance this community?s analysis and design capabilities to address next generation challenges posed by wind; and (iii) to facilitate education and training of the future workforce in the field.

Through a collection of tools and services networked with a flexible architecture and interfaces to support research and education objectives in real-time, VORTEX-Winds promises to enhance the capability of its members and end users beyond their current resources through a synergistic, integrative approach to understanding and modeling wind-structure interactions. Thus, VORTEX-Winds will benefit those otherwise limited by their personal research tools, allowing them to address complex problems posed by wind in support of the wider stakeholder community.

Meanwhile, and perhaps more importantly, VORTEX-Winds will bring the analytical muscle currently lacking in the design industry?s next generation electronic information/data interchange platform, Building Information Modeling (BIM), to strengthen the competitive edge of its end users involved in the burgeoning infrastructure development around the world and ensure its safety and performance in extreme wind events. In addition, the EVO will offer an interactive knowledge base intended to aggregate and centralize the shared knowledge of the collaboratory, including a wind-wiki, damage database, help desk/FAQ, bulletin boards and curriculum tools to facilitate dissemination and education. The result will be a community as a whole better positioned to address the next frontiers in the field.

The PI and his graduate students are active OSS researchers, and experienced in e-Science portal and collaboratory design, database technology, search, retrieval and data mining.

Intellectual Merit: A self-sustaining community resource a data repository and infrastructure supporting researchers studying the important OSS phenomenon will be developed, deployed, and maintained. The proposed project will preserve, extend and share a unique one-of-a-kind data repository supporting scholarly research on the OSS phenomenon; additional users of the data include researchers in the fields of data mining, software engineering, management, information systems and social science.

Broader impact: Under represented groups will be recruited for participation on the project. The community resource will enable increased quantity and quality of research on OSS that could promote better decisions affecting US economic competitiveness, cyber-security, government policy, and the design of scientific cyberinfrastructure and critical industrial infrastructure. The community resource may support research beyond OSS, into areas such as organizational theory, social sciences, and commercial software engineering, and may provide a model for community resources in other research domains.

Summary: A large one-of-a-kind research data repository serving a large and growing research community, needs reliable equipment and graduate student support to preserve, organize, and expand its data and services. The research area is an open Source Software development that studies an important but not well-understood phenomenon will be well served by this unique Community Resource.

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

Cyber-Enabled Discovery and Innovation (CDI)

Proposal Number: 0941565
PI: Tracy Kijewski-Correa
Institution: University of Notre Dame
Title: CDI-Type II: Open Sourcing the Design of Civil Infrastructure (OSD-CI)

In this project, a virtual organization (VO) is proposed that would allowing all stakeholders engineers, public officials, researchers, students, and even the public at-large to engage as "Citizen Engineers" to rehabilitate our nations deteriorating civil infrastructure. To this end, the award will address four dimensions of collaboration: harnessing human effort, tapping collective knowledge, pooling communal software and leveraging distributed computational hardware. Linux and Wikipedia serve as evidence that loosely organized teams can create and maintain the complex technical and intellectual infrastructure upon which society increasingly depends. These projects have succeeded not by accepting participants indiscriminately, but by creating a meritocracy that rewards expertise regardless of its source.

OSD-CI is devised as a way that essential public-works projects could benefit similarly from the full expertise and latest advances available in the wider engineering community. The VO will use an archival Design Gallery, a Social Network, and a Tool Repository within an integrated cyberinfrastructure. The investigators expect that new types of discovery, education and engineering innovation will emerge to address the challenges facing civil infrastructure in an unprecedented fashion. Furthermore, the policies that result from this project are expected to define a new level of task complexity for problem-solving by crowds, thus providing a platform for new discoveries, insights and theories on the design and effectiveness of VOs that require extreme trustworthiness and openness.

By addressing challenges facing civil infrastructure with OSD-CI, there will be direct benefits to society reliant on this infrastructure. Furthermore, the social fabric of the OSD-CI Collaboratory provides a new paradigm for engaging the public at large in the research and design enterprise. It will offering new means of collaboration and networking among "Citizen Engineers." In addition, it will also aid education and mentoring of students worldwide, particularly those in developing areas lacking access to such opportunities locally. Eventually, OSD-CI is envisioned to become a virtual Town Hall where members of the public interface with decision makers, engineers, architects and planners to contribute to processes directly impacting them and their communities. Once the precedent is set, these open-source communal concepts could be extended to other fields as a basic framework and model for the effective use of VOs for addressing societal challenges.

This proposed project will design, develop, deploy, and operate a virtual Emergency Operations Center (vEOC) for (1) primary use as a research instrument, but with (2) secondary use for training and education. The vEOC, named Ensayo, will enable research on dynamic decision-making, individual and group problem solving, organizational learning, communication, coordination, and knowledge management in the context of roles and organizational structures to enable cross-institutional management of disasters. The vEOC will be web-based implemented using open source and open standards software and tools. Little substantive research has been conducted on large scale, emergent management structures. The size and complexity of these emergent structures affords a unique insight into studying the mechanisms (both successful and less successful) of operation, providing a valid substrate to formulate the components of the vEOC. Our initial research has yielded insights into the role that a vEOC could play in this, and other EOC contexts

The fundamental goal of Ensayo is to craft a research instrument that, although based on the elements of a local EOC, can be adapted to reflect a wide variety of EOC forms in order to support research, training and education. One of the collaborating institutions is minority serving, and located where the primary context for this work is important for the well-being of society ? hurricanes and emergency preparedness. Ensayo affords not only a research tool for academics, but also a resource for education, training and policy analysis for communities of practice who engage in any emergency operations event.

When disasters occur, they can severely impact the health and disrupt the continuity of communities. Emergency operations centers (EOCs) are temporary organizations that emerge to respond to disasters by bringing together dozens of private and public organizations to communicate, coordinate, and collaborate to ensure the continuity of the community. They have primary responsibility for public safety under the guidelines of the National Incident Management System (NIMS). Yet, EOCs are rarely engaged outside of a disaster situation, so there is little empirical data to provide insight into their processes and performance to support improvements. Observational research on such events is difficult; experimental research is even more difficult. The goal of this infrastructure enhancement project is to further develop an organizational simulation of an EOC, called Ensayo, that reflects a wide variety of EOC forms. The goal of Ensayo is not to model a disaster, but to model the organization that responds to a disaster. The simulation will be based on an initial prototype and developed with the collaboration of the the Miami-Dade Office of Emergency Management and partners in its EOC. Ensayo affords not only a research tool for academics, but also a resource for education, training and policy analysis for communities of practice who engage in an emergency operations event.

Ensayo II will be a reformulation and elaboration of the Ensayo infrastructure developed with prior NSF funding, based on experiences with the earlier project. The project has four major goals. First, Ensayo II will evolve the architecture and functionality of Ensayo. Experience with Ensayo has revealed the importance of crossing disciplinary boundaries (cognitive science, human-computer interaction, computer science, organizational science, systems engineering) in order to understand, model, and support the complexities of an emergency management decision-making structure. Second, the system will incorporate new collaboration and communication elements that are now found in EOCs. For example, Miami-Dade was one of the first to formally address and integrate into their structure a business recovery function. Third, the system will support informational and decision modeling and tracking. Entities in an EOC are generally guided by specific rules of communication and authority, both from within and without. Tracking (or simulating) decisions and information flow under various organizational stressors can provide unique predictive and explanatory insights into the social dynamics of EOC structures. Finally, the project will move from a prototype to an enhanced, operational research infrastructure that can be deployed as a core, open-source project. Through Ensayo II's improved infrastructure, researchers can investigate EOC structures in situ and probe the micro-mechanisms that underlie EOC choices impacting business and society.

An Emergency Operations Center (EOC) is a secure location in which upper level emergency managers gather together to prepare for, manage, and coordinate preparation and recovery activities in response to an emergency situation (e.g. hurricane, earthquake, epidemic or outbreak, tsunami). While in-person exercises are the gold standard for training, because of time and cost the frequency of such in-person training events is limited. The I-Corps team has developed a simulator that will enable emergency managers to train more effectively and more frequently in a virtual, distributed environment. The proposed technology will enable better training of emergency managers, potentially resulting in lives saved and reduction of property loss. Through advanced technological training, emergency managers, can train more often, for less cost.

When a disaster occurs, emergency personnel set up a management structure called an Incident Command System (ICS) to manage the incident. The personnel in the ICS have to gather information and coordinate among various organizations and across jurisdictions with local, state, and federal agencies. These are complex tasks that require training to ensure that all participants and their organizations are familiar with current plans, policies, agreements and procedures. Such training is typically performed by a range of in-person approaches, including discussion-based tabletop exercises and full-scale operations-based exercises simulating a specific incident with full participation of all responsible organizations. The proposed simulator,SimEOC, can simulate the emergency incident and the distributed web-based participation of all the participating organizations. A centralized web-server will support over 100 trainees in such a training exercise. At the end of the I-Corps immersion curriculum the existing research prototype (alpha version) could be used for a "live-code" proof-of-concept demonstration; optimistically the re-engineered enterprise quality version under current development (beta version) may be ready to preview as well.

Unmanned aerial vehicles (UAVs) are rapidly gaining in popularity and it is expected that many millions of these devices will be in operation within the next few years. UAVs are increasingly being considered for use in emergency response situations, where they can reduce first responders' exposure to unnecessary danger and enhance the effectiveness of the responders, for example by providing additional information such as unique viewing angles or fast deployment of specialized sensors. It is expected that most UAV operation will occur in cities, which will require the development of infrastructure and tools that enable safe and effective deployments of UAVs in urban settings. This project will support a planning process to identify the specific requirements for safe UAV operation for emergency response scenarios. Toward this end, the project team will collaborate with fire fighters to explore the challenges and benefits of UAV support for various rescue scenarios. Additionally, the project will use these collaborations and various activities and meetings to initiate fruitful discussions among the project team and potential collaborators and stakeholders in academia, industry, and city planning. It is expected that the planning activity will ultimately lead to the development of a proposal to fully implement the infrastructure and tools required for safe UAV for various application scenarios.

Over 80% of the US population reside in urban areas, which means that most UAV operation will occur in densely populated areas that are characterized by potentially dense and fluctuating traffic patterns, close proximity to humans and buildings, unreliable GPS, overhead flight paths, and fluctuating environmental conditions. Enabling independently controlled UAVs with diverse objectives, constraints, and capabilities to operate in such an environment is a challenging proposition. The long-term goal of this project is to develop cross-disciplinary solutions to urban UAV flight, integrating systems design, control theory, and software engineering research to specifically address technical aspects of urban UAV deployment for emergency response situations. The project team will complete a comprehensive needs assessment for the deployment of UAVs in urban emergency response scenarios. A main goal of this planning grant is to identify various stakeholders in the community involved in emergency response (e.g., fire, medical, disaster planning, etc.), their specific needs that can be addressed using UAVs, the opportunities provided by the UAVs, and the specific challenges of urban UAV emergency response support. An additional goal is to obtain deeper insights into the larger societal concerns with UAV operation, including ethics and policy challenges. The project team will organize a series of hands-on training sessions for various rescue operations, which will be used to highlight the potential benefits of UAVs, identify the concrete needs of emergency rescue teams, and elicit discussions among the various stakeholders that will ultimately lead to a deeper understanding of the opportunities and challenges of urban UAV deployments.