From Proteins to Galaxies:NPACI’s Growing Outreach to Museums

he San Diego Natural History Museum lends exhibits of everything from seashells, leaves, and fossilized fish to beetles, butterflies, and bobcats. Three recent exhibits added to the museum’s lending rotation are 3-D models of undersea terrain and continental landforms. The computer-designed models were created in SDSC’s Design Visualization Lab. The models represent one of many exhibits provided by NPACI and SDSC researchers to museums, from visualizations of proteins to maps of bird habitats. "In addition to supporting the many worthy endeavors of educators and historians, these outreach efforts are helping to inspire the next generation of scientists and engineers while also increasing the public’s appreciation of science," said Fran Berman, director of NPACI and SDSC.

HANDS-ON GEOGRAPHY

Figure 1. Terrain Model This 3-D terrain map of part of North America, including the continental United States, is on display in the U.S. Library of Congress in Washington, D.C.

SDSC’s Design Visualization Lab fabricates a wide variety of solid models, which are used as unique forms of scientific visualization. The undersea terrain and continental landform models were made by a Laminated Object Manufacturing (LOM) machine from thousands of sheets of laser-cut paper bonded together. The models look and feel like wood.

The first of the geographical models to go into the lending rotation was a flat, cylindrical-projection map of the world, with vertical elevation exaggerated by a factor of 40. "With only a 12-mile spread between the lowest and highest points on an area 25,000 miles across, it’s necessary to exaggerate the data to show the land forms," said Mike Bailey, SDSC senior principal scientist and director of the lab. "Without the exaggeration, the map would look like a slightly bumpy piece of plywood."

Bailey picked a flat projection for ease of handling by students; the spherical model of the Earth would be about the size and weight of a bowling ball. "A flat map also allows students to directly compare mountain ranges across the world," said Bailey, who has contributed other terrain maps to the museum.

Figure 2. Galaxies in Collision Frames from the IMAX movie Cosmic Voyage, showing the collision and merger of two spiral galaxies.

The idea to contribute models sprang from a meeting of the master teachers of San Diego City Schools in 1999. After a presentation by Bailey, a teacher suggested that SDSC produce LOM models and give schools access to them via the specimen library program. A cooperative relationship between SDSC and the museums of San Diego’s Balboa Park quickly developed. "I would love it if more teachers requested models that would enhance the lessons they’re teaching," said Bailey.

A larger 3-D model from Bailey’s lab–a solid topographic map of the continental United States (Figure 1)–is on display in the U.S. Library of Congress in Washington D.C. "The model helps us depict and document new computer-assisted techniques of cartographic production," said James Flatness of the library’s Maps Division.

POPULARIZING PROTEINS

"The Art of Science" exhibit, which included images from the Protein Data Bank (PDB), was one of the more popular shows at The Gallery, a space dedicated to art exhibits at Rutgers University. "The exhibit looked at the beauty inherent in the three-dimensional structures of proteins," said Christine Zardecki, research assistant at the PDB and curator of the exhibit. "These structures have a very strong visual component."

Highlighted proteins included those available from PDB Structure Explorer pages, images of collagen made by Jordi Bella, assistant research scientist at Purdue University, and pictures from the PDB’s Molecule of the Month (Figure 3) series by David Goodsell, assistant professor of molecular biology at The Scripps Research Institute.

The PDB is operated by the Research Collaboratory for Structural Bioinformatics–a joint activity of Rutgers University, SDSC, and the National Institute for Standards and Technology. The PDB is supported by the National Science Foundation, the Department of Energy, the National Institute of General Medical Sciences, and the National Library of Medicine.

COSMIC VISTAS

A century’s telescope observations of a pair of colliding galaxies amounts to only a "freeze-frame" in a crash sequence that spans hundreds of millions of years. Simulations are key to understanding such events. For more than a decade, astrophysicists have been using SDSC’s supercomputers to model the forces and physical processes involved in galactic encounters and collisions.

In the mid-1990s, Lars Hernquist and Chris Mihos, both then at UC Santa Cruz, collaborated with SDSC and computer graphics director Donna Cox at the National Center for Supercomputing Applications (NCSA) to create a high-resolution video sequence of a galaxy encounter (Figure 2). It was the basis of the IMAX movie "Cosmic Voyage," which debuted at the Smithsonian National Air and Space Museum in 1996. One of the first IMAX films to use data-driven supercomputing and the first to feature extended scientific visualization sequences, "Cosmic Voyage" was nominated for an Academy Award. The simulation required 750 CPU hours on a Cray supercomputer at SDSC and generated 65 gigabytes of raw data. Cox and her graphics team at NCSA used software from Pixar Studios to render the visualization in IMAX image format (Figure 4).

Figure 3. Virus Art “The Art of Science” exhibit at Rutgers University displays images from the Protein Data Bank, including this illustration of a rhinovirus.

One of NPACI’s best-known museum collaborations is an all-dome video presentation, made with the help of SDSC and shown at the Hayden Planetarium of the American Museum of Natural History in New York. "Passport to the Universe," the planetarium’s premiere production, features a starship voyage through the heart of the Orion Nebula 1,500 light-years away. The strikingly beautiful computer graphics sequence maintains rigorous scientific accuracy, using data from NASA’s Hubble Space Telescope and the European Space Agency.

For nearly two years, SDSC researchers worked closely with the Hayden staff to create realistic views of diffuse astronomical objects. "We had to create unique enhancements to the renderer’s capabilities to handle astronomical data," said David Nadeau, the leader of SDSC’s technical team working with the planetarium. "The VISTA renderer and the tools we’ve developed for scene construction are applicable to many other problems in scientific visualization, and we believe other researchers and graphic artists will want to use them."

Figure 4. USS California Among the materials kept in the repository of The California Military History Museum Education Project is the story of the USS California. The battleship, commissioned in 1921 as the fifth vessel to bear the state’s name, was sunk in Hawaii’s Pearl Harbor on December 7, 1941.

"Our science education message for ‘Passport to the Universe’ led to our desire to recreate the nearest stellar nursery to our solar system," said Neil de Grasse Tyson, Frederick P. Rose, director of the Hayden Planetarium. "It all came together in the cyberspace of SDSC–without their participation we could have shown some pretty pictures, but they wouldn’t have had the impact of the full three-dimensional journey through the volume-rendered nebula."

In March, a new film created with Nadeau’s help and NPACI computing resources debuted at the Hayden. Journeying from the depths of Earth’s oceans and onward to planets outside our solar system, "The Search for Life: Are We Alone?" depicts how scientists are searching for signs of life beyond our world.

CALIFORNIA MILITARY HISTORY

Although World War II predates grade-school children and most of their parents, they can learn about it from the veterans via the Web. The California Military History Educational Project, an outreach effort by the California Military Museum in Sacramento, will be hosted on SDSC’s servers as part of the center’s Science and Technology Outreach program.

Figure 5. Finding Warblers with WhyWhere Statistical methods identify which environmental variables are the most accurate predictors of such species as the Cerulean Warbler.

"The idea is to have military history, with a California perspective, in a place where it can be accessed worldwide," said Ralph Ramirez, co-director of the project and deputy commander of the southern region for the California Center for Military History.

The project collects and stores oral histories of survivors, includes a "virtual field trip" on the Web, and provides online lesson plans, teacher resource kits, photo archives, data banks, special collections, and links to everything from California infantry soldiers to the USS California (Figure 4). Downloadable social studies lesson plans were developed in accordance with the California State Content and Performance Standards, and include supplementary materials, teacher rubrics and strategies, discussion questions, and examinations.

THE WORLD ACCORDING TO GARP

Figure 6. Fish Prediction The observed species occurences (black squares) of the tonguefish (inset) coincides with a map of the predicted distribution of the marine flatfish (red regions) by the WhyWhere application.

Museums traditionally have not coordinated their collections with other institutions or made the data available on the Internet, but NPACI researchers are in the forefront of a revolution. Science magazine featured the efforts of NPACI Earth Systems Science partners to put museum collections on line for the taxonomy and systematics communities as driving a "taxonomic revival." Leading the efforts to integrate the collections data from the world’s natural history museums with online tools are Leonard Krishtalka and David Vieglais at the University of Kansas Natural History Museum and Biodiversity Research Center, along with David Stockwell of SDSC, scientists in the Partnerships for Enhancing Expertise in Taxonomy (PEET) project, and the Kansas Natural History Museum.

Figure 7. Trogon Range This map shows the predicted distribution of the Eared Trogon (inset) using GARP. Red is high probability and green is low.

The Species Analyst software package developed by Vieglais queries and retrieves collection data from museums that have made their collections Internet-accessible and integrates those data for further analysis. The Species Analyst then forwards the geographic information about a given species to GARP (Genetic Algorithm for Rule-set Production), a program developed by Stockwell that runs on computers at SDSC. GARP maps the known geographic species occurrence data, combines it with environmental data about the general region, and predicts the geographic distribution of the species (Figures 5—7).

GARP has been incorporated into WhyWhere, a Web-based resource that provides quantitative answers to the question "Where is it found and why?" for any species, anywhere on the globe. An example of modern informatics infrastructure, WhyWhere supports researchers by giving them unprecedented access to environmental data, software for analysis and visualization, and high-end computing power, all integrated in an easy-to-use Web interface.

"WhyWhere demonstrates how advanced information infrastructure can help us reach out to a broader range of users and help them develop more reliable predictions of species distribution for regions of the terrestrial and marine environments that have been little studied," Stockwell said. –CF, MG

www.cmhep.org

biodi.sdsc.edu/ww_home.html

dvl.sdsc.edu

www.rcsb.org

www.amnh.org/rose/
haydenplanetarium.html