Alaska Research Summer Challenge Interns Experience the Summer of a Lifetime

There are two certainties that come with summertime in Fairbanks: the days will be long and the UAF campus will be teeming with interns. This year, the Arctic Region Supercomputing Center hosted 16 undergraduate interns and five graduate interns, providing them with opportunity to increase their skill under the midnight sun. Twelve undergraduate interns in the Alaska Research Summer Challenge Research Experience for Undergraduates program (ARSC REU), sponsored by the National Science Foundation, faced new challenges and opportunities to strengthen their research and computer science skills. The ARSC REU interns, drawn from a wide range of backgrounds, were presented with high expectations and were rewarded with intensive research activity.

The projects completed by the ARSC REU interns covered a broad scope of disciplines, from remote imaging to molecular biology.

Remote Sensing and Glacial Databases
Huynh Nguyen, from Mississippi State University, and Luis Perez, from University of Texas at El Paso, worked with Research Associate Professor Matt Nolan and Peter Prokein to provide easier access to glacier databases in the National Snow and Ice Data Center (NSIDC). Nguyen created an information systems interface that will allow users to graphically search, query and visualize glacier data through the EarthSLOT web application. Nguyen used EarthSLOT to overlay two NSIDC glaciological databases with UAF airborne laser altimetry and NSIDC’s glacier photograph archive, making both searchable from a web-based front-end. Perez created an interactive online SQL database to retrieve information about glaciers through the EarthSLOT server, and incorporated glaciology and meteorology studies, as well as streaming server capabilities. In the process, Perez wrote three programs to acquire, check for duplicates and format the glacier database files for each glacier in the database. Perez then coded a front-end interface to allow users to select their query using a series of check boxes.

Accessibility for Alaska Native Languages
Zachary Marlow, from North Carolina State University, worked with Assistant Professor Gary Holton to develop a Web interface and database, using modern methods and tools to preserve and create access to the Alaska Native Language Center’s archives of scholarly works and Native language samples. By helping to preserve more than 20 Alaska Native languages and increase their accessibility, Marlow contributed to one of the most far-reaching projects undertaken during the course of the ARSC REU program. Marlow developed a web-based tool to allow access to digital archives of recordings of Alaska’s endangered indigenous languages. Anyone from around the world will soon have access to thousands of audio recordings of Alaska Native language speakers. The project included transferring archived data files from Windows format to an open MySQL database, and expanding the front-end interface functionality to enable search and display capability.

Upgrading Ionosphere Information Gathering
Larisa Stoltzfus of Grinnell College, Iowa, was mentored by Dr. Sergei Maurits and Dr. Anton Kulchitsky as she worked on correcting the UAF Polar Ionospheric Model to reconcile differences between modeled ionosphere distance data and data retrieved from ionosondes – radar transmitters that emit pulses and collect the returning signals to analyze the ionosphere. Stoltzfus analyzed data, collected every five minutes for 30 months from up to 20 ionosondes, to identify systematic error bias. Stoltzfus edited database scripts to identify the bias, and wrote scripts to perform numerical corrections on the model input data.

Frost Boil Modeling and Visualization
Theresa Turner, of the University of South Carolina Aiken, worked with Professor Debasmita Misra and Dr. Ron Daanen to adapt the WIT3D frost boil modeling program for multiprocessor compatibility using UNIX, Fortran, MPI and Open MPI. Turner streamlined the program to dramatically speed-up execution time by converting the code to read and write intermediate files as binary rather than ASCII. Cory Mohn of Northland College, Wisconsin, was challenged with creating the program to display the WIT3D output dataset three-dimensionally. Mohn used C++, OpenGL and VR Juggler to visualize the temperature, hydrological and vegetative data, and to provide a tool to allow vertical flux to indicate heave. He then developed a tool to navigate the visualization and manipulate multiple internal and external angles of the freezing and heaving scenarios. (See Challenges, page 18.)

Sea Ice Microstructure
Henry Kozachkov, from New York University, worked with UAF Professor Hajo Eicken and UAF master’s degree candidate Jeremy Miner to develop a tool to further the understanding of the microstructure of sea ice morphology, including air and brine inclusions. Kozachkov also participated in ice growth experiments and acquisition of raw x-ray tomography data. Using a variety of methods, Kozachkov processed the image data to extract useful information from “noisy” and dynamically-compressed images. The images were then segmented for three-dimensional visual reconstruction of the core samples.

Bioinformatics
Guifeng Guan, from Arizona State University, and Joel McEwen, of Texas Southern University, worked on configuring a molecular visualization tool to display a three-dimensional representation of the Protein Data Bank (PDB). Working with UAF President’s Professor Tom Marr and Dr. Roger Edberg, ARSC, the interns ported the Generic Genome Browser, open source software developed at ARSC, to a windows environment, and then configured the software to run without error.
Remote Imaging and Security
Christian Servin and Jesus Corral, both from The University of Texas at El Paso, worked with mentor Dr. Buck Sharpton and research associates Jay Cable and Dayne Broderson to develop a software and hardware system for motion detection using digital cameras and instant messaging protocols for immediate notification of anomalous intrusion and movement. The interns incorporated basic motion detection, image modification, data storage, and communication capabilities into their functional prototype, and provided proof of concept for statistical image analysis for identifying motion that exceeds a certain threshold. Possible future applications include security, analysis, and monitoring.

Mapping Terrain in 3D for Flight
Michael Bauer, of New Mexico Institute of Mining and Technology, worked with Dr. Sergei Maurits, ARSC, to use Geographical Information System (GIS) software to incorporate a USGS digital elevation model into interactive terrain visualization covering the state of Alaska. Data from Landsat satellites, obtained through the UAF Geographic Information Network Alaska (GINA) project, were overlaid onto the terrain model and integrated with a previously- created flight simulator program. Bauer created three-dimensional maps that convey location and elevation change, analyzed the flight simulation code to determine if the TerraVista software package format could be integrated with the flight simulator, and examined graphic displays for efficient use on a desktop machine.

Arctic Region Supercomputing Center
PO Box 756020, Fairbanks, AK 99775 | voice: 907-450.8600 | email:

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