The Center For Research Computing’s Frameworks team has been working alongside Elliott Visconsi, Associate Professor of English and Concurrent Associate Professor of Law at Notre Dame to develop a Shakespeare application for the iPad. Shakespeare's The Tempest for iPad is the first featured text in this project.

The Adaptation Collaboratory Project is an effort to fill a significant gap in understanding about adaptation to climate change. Here, we are building a virtual organization for transformative research and outreach. Drawing from a variety of tools (e.g., cyberinfrastructure, data and knowledge management, simulations, scenario analysis, and visual analytics) the collaboratory’s goals include interdisciplinary integration and sound policy development regarding adaptation to climate change.

Cassandra is a Monte Carlo molecular modeling software that is designed in Fortran 90 following a modular philosophy with the ultimate goal of open source development. The code is being developed keeping in mind flexibility, high performance, ease of extensibility and ability to handle a large number of molecular systems ranging from a simple Lennard-Jones particles to large protein systems. It offers parallelization with openMP to take advantage of multicore processing capabilities of today's hardware.

The term land cover refers to the physical material at the surface of the earth, which may be natural or man-made. Land cover around the world is continually changing as a result of human activity and natural processes, potentially amplified by climate change. Monitoring these changes has become a priority of international importance. NASA’s observational satellites are collecting massive amounts of data, including derived variables such as vegetation indices. We are developing a computational framework for change detection in this context.

We have been working with Marya Lieberman in the Department of Chemistry and Biochemisty to create an educational animation explaining her research using DNA for nanofabrication. This animation, which describes the process of folding a single strand of viral DNA into desired shapes (referred to as DNA origami), incorporates Prof. Lieberman's real data with more abstract sections explaining unseen and less well understood parts of the process. The movie has been used in talks at scientific meetings and posted online. Music by Eric Henderson of Bumblefunk Music.

The Garki Project was a study conducted by the WHO and the Nigerian Government from 1969-1976 on the effects of various methods to control the spread of malaria in Sub-Saharan Africa. (Garki is the name of a district in Nigeria where the study was conducted.) The project’s data were collected on paper, transferred to magnetic tape, and eventually converted to SQL. The Garki Project Website is an effort to make the Garki Project’s now static database accessible and easily queried through a convenient Web interface. Moreover, work done on the Garki Project is now being used as a springboard for handling similar data from other, modern studies of mosquitoes and malaria.

The Green Cloud is an ongoing supercomputing project that aims to provide a stable cloud-computing platform that uses experimental techniques to remain as energy efficient as possible, helping the environment and lowering costs at the same time. Comprised of approximately 90 machines, the Green Cloud provides over 360 cores of processing power that can be used for a wide range of computing tasks, and employs an energy-saving technique called grid-heating to recycle the excess heat produced by the grid to heat the South Bend Green House. This innovative strategy drastically reduces the environmental and financial costs to maintain both the green house and the computing grid.

The Illustrative Information Interface (III) is a Web application that enables users to graphically and textually document perceived government repression. It accepts both historical and current information starting from the year 1900. Anyone with access to the Internet can use III to register his or her view of the scope and severity of government repression for a particular geographic area. The results of this information are immediately available, anonymously, for study.

In order to visualize the environmental simulation results as a more realistic data source, we propose to integrate them into a Geographic Information System (GIS) comprised of physical and socio-economic spatial data. The GIS will contain the road network, land cover and land use, building types, soil types, the Digital Elevation Model, pollution sources, and zonal data such as population, economic and health data. A GIS will provide more options to present and analyze the model results including the ability to downscale the simulation results to a more realistic resolution suitable for an urban environment. read more...

The MTC is a project patterned after the Garki Portal: a database of information related to malaria and its epidemiology combined with a Web portal front-end. Sponsored by the Bill & Melinda Gates Foundation, this project includes international collaborators who are gathering and analyzing data from Indonesia, Kenya, Tanzania, Zambia, the Solomon Islands, and Mali. The purpose of the MTC is to establish an evidence base that can help malaria control program managers make informed decisions about monitoring malaria transmission and implementing or adjusting malaria control interventions.

Regional and basin ecological processes are mediated by processes occurring at plot level. GIS-based spatially distributed models can be used as flexible tools to investigate the large-scale effects of changes in environmental factors. Such models also allow rigorous scaling up of existing field-based experiments and approaches studied within a plot level context. The programming within a GIS makes the model flexible in its application and, therefore, makes it easy to apply at a variety of scales.

OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. “sticky” atoms, point dipoles, and coarse-grained assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat interfaces, and nanoparticles) have all been simulated using force fields included with the code. OpenMD works on parallel computers using the Message Passing Interface (MPI), and comes with a number of analysis and utility programs that are easy to use and modify. An OpenMD simulation is specified using a very simple meta-data language that is easy to learn.

The Peace Accords Matrix project offers a good example of how a Web technology can bridge the gap between researchers and their data. Here, the Kroc Institute for International Peace Studies engaged the CRC's ICE team to rapidly build a Web server and database that would enable the storage and analysis of data related to peace accords throughout the world. Interactions with these data by the general public are made possible through a clickable map and a search dialog page. Data can be viewed online or downloaded as comma-delimited files.

Protomol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. The framework was developed by the LCLS group of Dr. Jesús Izaguirre at Notre Dame. It supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The use of fast electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), and Multigrid (MG) summation further enhances performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators.

The Varieties of Democracy project leverages the Plone content management system to collect and analyze democracy data from around the world. Hosted by the Kellogg Institute and the Department of Political Science at the University of Gothenburg, this project differs from the Peace Accords Matrix in that data are provided interactively through the website by knowledge-experts working abroad. The second iteration of the project (now under development) includes significant enhancements to administrative and data entry web pages, and enables several ways visualize data in chart-form.