Visualizing Science: The OptIPuter Project

S C I E N T I F I C V I S U A L I Z A T I O N

For many areas of science and engineering, visualization has become more than aconvenient tool: it has become a necessity for interpreting the enormous amountsof data being produced by large-scale instrumentation, experiments andsimulations. One of the most creative—and useful—ways of presenting scientificdata is the large-scale tiled display. Ranging from tabletop versions to fullyimmersive 3D stereo virtual reality environments, these displays enable users toexplore features that may be hard or impossible to identify with conventional,personal computers.

Concluding the first session of the SciDAC 2007conference in Boston, SciDAC Program DirectorDr. Michael Strayer commented that one of themajor challenges facing the SciDAC multidiscipli-nary teams was “developing new visualization anddata management systems to support moving, stor-ing, analyzing, manipulating, and visualizing multi-petabyes of scientific data and objects.”

Scientific visualization indeed has become a crit-ical tool in understanding large datasets and thebehavior of complex systems. And a special formof scientific visualization—large-scale tiled dis-plays—is enabling scientists and engineers toexplore a wide range of applications, from struc-tural engineering of large buildings to medical stud-ies of extremely small cellular structures.

Tiled displays are not new. During the early1990s a number of planar tiled displays were builtand used for scientific studies. Several factors lim-ited their wide acceptance, however. They wereexpensive, large, and hence unsuitable for the typ-ical office environment. To address this situation,the California Institute for Telecommunicationsand Information Technology (Calit2) at the Uni-versity of California–San Diego (UCSD), and theElectronic Visualization Laboratory (EVL) at theUniversity of Illinois–Chicago (UIC) initiated theOptIPuter project.

The goal of the OptIPuter project is to developinnovative methods for scientists to explore verylarge remote data objects in an interactive and col-laborative fashion. It is an ambitious goal, and the

developers have enjoyed remarkable success.Without a doubt the highlight is the “OptIPor-tal”—a commodity-priced, easily replicable dis-play, with tens to hundreds of megapixels, whichcan be used by individual researchers or collabo-rative groups (figure 1).

“The OptIPortal is not a product,” emphasizesCalit2 research scientist Dr. Thomas DeFanti, UICdistinguished professor emeritus of computer sci-ence and co-principal investigator (co-PI) of theOptIPuter. (Larry Smarr of Calit2 is the PI, JasonLeigh of EVL is another co-PI, as are UCSD’s PhilPapadopoulos and Mark Ellisman). The OptIPuterwebsite provides system documentation andhardware specifications, enabling researchers tobuild their own OptIPortals. The hardware isbased on commodity PCs. The display tiles can bebuilt from LCD displays, such as those used fordesktop computers, plasma TVs, or video projec-tors. The software, based on EVL’s Scalable Adap-tive Graphics Environment (SAGE) specializedmiddleware, is easily downloadable and installed,along with other visualization libraries, byUCSD’s open source Rocks configuration tech-nology. The typical OptIPortal PC cluster nodeincludes two gigabit Ethernet network interfacecards (one for normal networking and controland the other for data transfer over the 10-gigabitOptIPuter private network), as well as nationaland international multi-gigabit networks, whichconnect to remote instruments, supercomputers,and data storage systems.

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A special form of scientificvisualization—large-scaletiled displays—is enablingscientists and engineersto explore a wide range ofapplications, fromstructural engineering oflarge buildings to medicalstudies of extremely smallcellular structures.

Visualizing Science: The OptIPuter Project

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Figure 1. Faculty and students conduct weekly research progress meetings in front of the 100-megapixel LambdaVision display at EVL/UIC. UsingEVL’s SAGE middleware, a variety of high-resolution information is juxtaposed on the walls to enable group discussion. Participants can be in the roomor communicating over distance mediated via high-definition video conferencing.

The goal of the OptIPuterproject is to developinnovative methods forscientists to explore verylarge remote data objectsin an interactive andcollaborative fashion.

OptIPortals are being deployed at academic institutionsaround the world:● Antartica McMurdo Station● Australia University of Melbourne● Canada Canadian Research Centre● China Computer Network Information Center of the

Chinese Academy of Sciences● Czech Republic Masaryk University● Japan Kyoto University; National Institute of Advanced

Industrial Science and Technology (AIST); Osaka University

● Korea Korea Institute of Science and Technology Information (KISTI); Gwangju Institute of Science andTechnology (GIST)

● Mexico Centro de Investigacion Cientifica y de Educacion Superior de Ensenada (CICESE)

● Russia Space Research Institute of the Russian Acad-emy of Sciences in Moscow; Science and Innovation Center in Chernogolovka, Russia

● The Netherlands University of Amsterdam; SARA● Switzerland University of Zurich

● Taiwan National Center for High-performance Computing (NCHC)

● United Kingdom Oxford University● United States Adler Planetarium; Massachusetts

Institute of Technology; NASA Goddard; Purdue University; Texas A&M University; U.S. Geological Survey(USGS) Earth Resources Observation and Science(EROS); UC–Davis; UC–Irvine/Calit2; UC–Santa Cruz;UCSD/Calit2; UCSD National Center for Microscopy andImaging Research; UCSD Scripps Institution of Oceanography; University of Hawaii; University of Illinois–Chicago/EVL; University of Illinois–Urbana-Champaign/National Center for Supercomputing Applications (NCSA); University of Michigan; University ofSouthern California; University of Washington

OptIPortals are also being used by several corporations,including:● Sharp Laboratories of America● Rincon● Nortel Networks

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The cost depends in part on the application. OptI-Portal applications fall into two broad categories:those that optimize for streaming video, strivingfor a balance between processor bandwidth andcommunications speed, and those that maximizepixel count per dollar. The former usually have LCDdisplays with 2.0–2.5 megapixels, each driven byone PC; the latter are generally built with two orfour 4-megapixel panels per PC.

User CommunitiesThis flexibility has resulted in the construction ofmany different OptIPortals. The OptIPuter teamhas developed a number of devices that range froma portable 15-tile, 2-megapixel OptIPortal called theOptIPortable (figure 2), which can be easily shippedto conferences, to a 70-tile, 286-megapixel displaywall (figure 3). Already, a wide community of sci-entific users pursuing diverse applications of theOptIPortal has been established (sidebar “OptIPor-tal Deployment Worldwide” p33). •Biomedicine The National Center forMicroscopy and Imaging Research (NCMIR),located at UCSD, is home to the coordinatingcenter of the Biomedical Informatics ResearchNetwork, which provides partner sites with infor-mation technology infrastructure. With funding

from Microsoft, NCMIR has created a Windows-based OptIPortal. The device was successfullydemonstrated in Microsoft’s booth at SC07—theinternational conference for high-performancecomputing, networking, storage, and analysis—as part of the NCMIR’s research collaborationswith colleagues at Oxford University.•Geosciences EVL has developed and is explor-ing the use of CoreWall, an integrated environ-ment for interpreting geoscientific data fromsediment and crystalline cores (figure 4, p36).The device, which relies on OptIPuter technolo-gies, is being used by the international Antarc-tic geological drilling program, a researchpartnership comprising the United States, Ger-many, Italy, and New Zealand. •Geoinformatics The U.S. Geological Survey(USGS) National Center for Earth ResourcesObservation and Science (EROS) deployed a 15-panel OptIPortal, which was demonstrated tomore than 200 researchers and federal officialsvisiting the USGS/EROS national center in 2007.USGS geophysicists have also worked with EVLand Calit2 staff to test the connectivity of theirOptIPortal to the National LambdaRail, a nation-wide infrastructure providing the U.S. researchcommunity with access to many different


Figure 2. Tellurion, a real-time planetary-scale data visualization being developed by EVL/UIC Ph.D. candidate Robert Kooima, is shown here on theCalit2 OptIPortable (the portable OptIPortal) at SC07. Tellurion uses NASA’s Blue Marble Next Generation and Shuttle Radar Topography Mission data.

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regional networks. Tests of the OptIPortal con-ducted with and without federal firewall con-straints demonstrated that it could be used intimes of emergencies, such as hurricanes, to dis-play and distribute large data volumes usingadvanced optical network connectivity. Theseresults were presented at the GeoinformaticsConference in 2007 in an invited presentationtitled “From CAVEs to OptIPortals.” •Marine Microbial Analysis As part of the Com-munity CyberInfrastructure for AdvancedMarine Microbial Ecology Research and Analy-sis (CAMERA) project, the Gordon and BettyMoore Foundation is funding Calit2 to assistthe placement of OptIPortals at several leadingmetagenomic laboratories nationwide, includ-ing UCSD, UC–Davis, the University of Wash-ington, Massachusetts Institute of Technology(MIT), and the J. Craig Venter Institute inRockville, Maryland. The OptIPortals are beingused for interactive study of microbial genomesand emerging applications, such as geneticallyengineered biofuel generation. At SC07, Dr.Ginger Armbrust, a researcher at the Universityof Washington, demonstrated how the OptI-Portal is enabling new insights in the study ofPuget Sound diatoms.

•Real-Time Observatories The ROADNet (Real-time Observatories, Applications and Datamanagement Network) project at UCSD,funded by the National Science Foundation(NSF), is intended to enhance capacity to moni-tor and respond to changes in the environmentby developing both the wireless networks andthe integrated, seamless, and transparent infor-mation management system to deliver seismic,oceanographic, hydrological, and physical datain real time. ROADNet receives this informa-tion from various sensors throughout SouthernCalifornia and then displays the images simul-taneously on OptIPortals. The technology wasdemonstrated at the American GeophysicalUnion conference in December 2007.•Space Visualization Little more than a yearago, the Adler Planetarium in Chicago openedits Space Visualization Laboratory, which fea-tures a variety of scientific visualization appli-cations and display technologies, including anOptIPortal developed in collaboration withEVL. Visitors are encouraged to participate inuser studies involving both application and pre-installation prototypes.•Technology Training NSF funds Florida Interna-tional University’s Global CyberBridges project

Figure 3. The 70-tile, 286-megapixel Highly Interactive Parallelized Display Space (HIPerSpace) OptIPortal, developed by the Calit2 VisGroup, displaysultra-high-resolution imagery from the Mars Exploration Rover Mission in different wavelengths, notably, McMurdo, Cape Verde, and Duck Bay.

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to use OptIPortals and SAGE in an internationalcollaboration to improve the technology train-ing for a new generation of scientists and toincrease the rate of discovery for all domains.Project participants come from the ChineseAcademy of Sciences, the City University ofHong Kong, and the University of Sao Paulo,Brazil.

StarCAVEOne of the most elaborate members of the OptI-Portal family is the StarCAVE (figure 5). An immer-sive virtual reality system, it uses tiled projectordisplays and OptIPuter technologies to surroundthe viewers 360 degrees with audio and life-sizeimages, enabling users to explore features that maybe hard or impossible to identify with conventional,non-immersive techniques. The concept of theCAVE, a recursive acronym for Cave Automatic Vir-tual Environment, dates back to 1991 when it wasconceived at EVL. When the CAVEs were firstdescribed, the idea of immersing oneself in ahuman cell or walking around the inside of a reac-tor seemed too much like science fiction. But afterthe initial showing to thousands of people at SIG-GRAPH’92 and SC92, scientists began to recognizethe possibilities of this innovative technology. AtArgonne National Laboratory, for example, the

CAVE was used for real-time simulation and analy-sis of pollution control systems for commercialboilers and incinerators.

The original CAVEs suffered from several limita-tions, however. Smooth animation was difficultbecause the graphics engines were primitive; thelighting was dim because the projectors were notvery bright; and the visual acuity was low, onlyabout 20/140, because the projectors were relativelylow resolution. The newest generation of the CAVEis brighter, bigger, and better than its ancestors. “TheStarCAVE is fast, bright, and crisp,” says Dr. DeFanti.“Using 34 HDTV 1080p JVC projectors and NvidiaQuadro 5600 cards, we have been able to increasevisual acuity in the StarCAVE to approximately20/40. Increasing the acuity to 20/20 would cost fivetimes as much in 2008.”

Developed at Calit2 by the team who developedthe hardware for the original CAVEs (Dr. DeFanti,Dan Sandin, and Gregory Dawe), the StarCAVEoperates at a combined resolution of more than 60million pixels (30 million per eye) distributed over15 rear-projected wall and two floor screens. It usesliquid crystal on silicon (LCOS) LCD projectors,offering smooth pixel edges and rich colors. More-over, the heavy shutter glasses of the old CAVEshave been replaced by lightweight, circular polar-ized “sunglasses.” Sonification is achieved by using


Figure 4. CoreWall is an integrated visualization tool for the study of lake and ocean sediment cores. It is a collaborative project among EVL/UIC,the U.S. National Lacustrine Core Repository (LacCore) at the University of Minnesota, the Integrated Ocean Drilling Program (IODP) through theJoint Oceanographic Institutions, the Lamont–Doherty Earth Observatory (LDEO) at Columbia University, and the ANDRILL Antarctic Drilling Program.

When the CAVEs were firstdescribed, the idea ofimmersing oneself in ahuman cell or walkingaround the inside of areactor seemed too muchlike science fiction, butafter the initial showing tothousands of people,scientists began torecognize the possibilitiesof this innovativetechnology.

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Figure 5. The Calit2 StarCAVE physical structure has five walls and a floor, with each wall consisting of three screens and the floor consisting oftwo screens. Shown here is the exterior of the StarCAVE with the entry wall almost closed.

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wave-field synthesis speakers, and the users caninteract with the data via an ART, Inc. wand/multi-camera wireless tracking system. Even the shape isnontraditional: the StarCAVE is a five-sided virtualreality room (plus floor), offering several advan-tages over the standard CAVE in the form of a cube,including minimization of glare and oblique views.

Arguably, the StarCAVE is expensive (about $1million). Nevertheless, the scientific benefits of thisnewest-generation CAVE are readily acknowledgedby avid researchers, who can get right inside theirsimulations in real time, gaining new insights intocomplex phenomena. The StarCAVE is being usedin a wide range of areas, from molecular biology toneuroscience. The following is a sampling of someapplications written for the StarCAVE in 2007 andearly 2008.

•Comparative Analysis With the establishmentof databases such as the Protein Data Bank(PDB), researchers can easily obtain access tomore than 50,000 structures (figure 6). Not soeasy, however, is analyzing those proteins, espe-cially if one wishes to compare numerous pro-tein structures at once. Several viewers and userinterfaces have been developed, but these typi-cally restrict the user to several proteins. Toaddress this problem, researchers at Calit2, incollaboration with researchers at EVL, devel-oped the Protein Viewer. This application con-nects the StarCAVE to the PDB data bank serverto download one of approximately 50,000 pro-tein structures and display it in 3D. PyMOL, afree molecular graphics package, is used to con-vert the PDB files to the Virtual Reality Model-ing Language format, which the StarCAVEvisualization software can read. The user canchoose between different visualization modes(cartoon, surface, or sticks), load multiple pro-teins, align proteins, or display the correspon-ding amino acid sequence. The high resolutionof the StarCAVE and its surround display capa-bility provides a view of a large number of pro-tein structures at once, which scientists like tofind similarities between proteins.•Neuroscience Researchers at UCSD are cur-rently working with neuroscientists to find outwhether the human brain works similarly forway-finding tasks in the StarCAVE and in the realworld. In this application, users are tracked asthey walk through a virtual replica of the Calit2building in the StarCAVE (figure 7). •Geospatial Visualization The open source soft-ware library ossimPlanet provides accurate, high-performance, double-precision 3D geospatialvisualization. Used with OpenCOVER, it allowsStarCAVE users to “fly” over the Earth withhighly detailed satellite images and 3D terrain.This application programming interface (API)already has been used in several applicationdomains, from the visualization of ocean cur-rents to genomics.•Social Science Opened in 2003 in Florence,Italy, ClusterCity featured two virtual realityenvironments in the Palazzo Vecchio: one repre-senting Florence in the Renaissance age and theother depicting Chicago in the gigabits age. Moti-vated by the success of this endeavor, UCSDresearchers recently constructed a visualizationof the Palazzo Vecchio itself. The applicationinvolves the visualization of a LIDAR scan of theHall of the 500, with about 26 million points as apoint cloud in the StarCAVE. A custom data dis-tribution and rendering algorithm achieves arendering rate of about 10 frames per second,giving a real feeling of “being there.”


Figure 6. StarCAVE displaying data from UCSD Protein Data Bank. RNA polymeraseenzyme data from the UCSD Protein Data Bank is displayed in the StarCAVE. The RNApolymerase is from yeast cells and is composed of a dozen different proteins.Together, they form a machine that surrounds DNA strands, unwinds them, and buildsan RNA strand based on the information held inside the DNA. Once the enzyme getsstarted, RNA polymerase marches confidently along the DNA copying RNA strandsthousands of nucleotides long. StarCAVE virtual-reality development is by Philip Weberand Jurgen Schulze of Calit2.

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From Walls to the DesktopFrom powerwalls to immersive virtual realityenvironments, the OptIPuter project has pro-vided researchers with a range of devices. Forinstance, the EVL team has designed and devel-oped a next-generation tabletop high-resolutiondisplay, called LambdaTable, and was recentlyfunded to develop an immersive autostereo ver-sion, called OmegaTable.

The LambdaTable is designed for interactivegroup-based data visualization (figure 8, p40). The24-megapixel digital table comprises six LCD 2560× 1600 displays driven by six computers. Sixinfrared cameras are mounted overhead to trackinput from many users simultaneously interact-ing with various interface devices, or pucks. Eachobject is identified by a unique pattern of embed-ded infrared LEDs. A real-time computer visionlibrary collects the camera video streams to deter-mine the orientation and position of each inputdevice, which is then passed to the applicationrunning on the LambdaTable display.

The Rain Table is one such application (figure 9,p40) and is being developed by EVL in collabora-tion with the Department of Geology at the Uni-versity of Minnesota and the Science Museum ofMinnesota to study rainfall. Using electronic puckinput devices, museum visitors indicate the loca-

tion of rainfall on two-dimensional topologicalmaps of locations on Earth. The visitors can thenobserve how the rain flows down mountains anddevelops channels of water that cut through slopes,merge, and flow into streams and oceans. The RainTable exhibit will help the public understand howrain in one place can cause flash floods in another.By extension, the museum participants can alsosee how the distribution of pollutants, such as lawnchemicals, can impact water supplies.

What’s on the Horizon?With successful demonstration of the OptIPutertechnologies in national-scale geoscience and bio-science projects, the OptIPuter team is ready toenhance the infrastructure and expand its usercommunities.

Currently, the effectiveness of the OptIPortalimplementations depends critically on the choiceof the graphics processing unit (GPU) and PC,matching the slots and power supply capacity.Ascertaining that the most up-to-date configura-tions are offered requires ongoing analysis. Onegoal, therefore, is to design “standard” OptIPortalspecifications, hardening both hardware and Rocksand SAGE core software specifications for ease ofuse by new user communities. Other plans includefurther integration with advanced communication


Figure 7. StarCAVE running the Calit2 building architectural model. The Calit2 StarCAVE enables participants to walk through a 3D architecturalmodel of the Calit2 building. The model was created by Ben Maggos of the UCSD Center for Research in Computing and the Arts and by DanielRohrlick of the UCSD Computer Science department and was ported to the StarCAVE by Jurgen Schulze of Calit2.

With successfuldemonstration of theOptIPuter technologies innational-scale geoscienceand bioscience projects,the OptIPuter team isready to enhance theinfrastructure and expandits user communities.

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protocols; integrated teleconferencing support withvarious high-definition video and audio streams;and additional system and application monitoring,analysis, and performance.

EVL is also continuing to enhance its visualiza-tion tools. A new tool, called Tellurion by itsauthor, EVL doctoral candidate Robert Kooima,was developed last year to enable the merging of

multi-resolution geographic and image data.Unlike traditional geographic rendering tech-niques, Tellurion’s data composition is generateddynamically and in real time (figure 10). “Manyterabytes of data exist describing the Earth, theMoon, and other planets. This continues toincrease exponentially as more powerful sensorsare put into service,” said Mr. Kooima. “While


Figure 8. LambdaTable visualizing a Purkinje cell. Collaborators sit at LambdaTable, a tiled LCD tabletop displaythat supports interactive group-based visualization of high-resolution data developed by EVL/UIC, examining avolume visualization of a Purkinje cell from a rat’s brain that was imaged using a multi-photon microscope at theNational Center for Microscopy and Imaging (NCMIR), UCSD. Each layer is a mosaic of smaller, high-resolutionimages that were stitched together, and then the layers were stacked to create a volumetric view of the neuron.

Figure 9. LambdaTable running the Rain Table museum exhibit. Rain Table is an interactive museum exhibitdeveloped for the LambdaTable by EVL/UIC graduate student Dmitri Svistula in collaboration with the Department ofGeology at the University of Minnesota and the Science Museum of Minnesota.

From powerwalls toimmersive virtual realityenvironments, theOptIPuter project hasprovided researchers witha range of devices.

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much of these data are related, little has been doneto bring widely disparate data together into acommon visualization. We’re working onGPU-centric solutions to this problem that allowsseparate, but related, planetary-scale datasets tobe flexibly composed in powerful ways.”

The researchers also hope to integrate betteraudio technologies into the StarCAVE. “Better audiowill provide an important dimension for scientiststo better understand complex physical and biolog-ical phenomena,” says Dr. DeFanti. ●

Contributors This article was written by the followingindividuals, with the assistance of Dr. Gail W. Pieper, seniorcoordinator of technical editing and writing in theMathematics and Computer Science Division at ArgonneNational Laboratory: Dr. Thomas A. DeFanti, Calit2 atUCSD, and EVL at UIC; Qian Liu, Mason Katz, Dr. PhilPapadopoulos, Joseph Keefe, Dr. Greg Hidley, Greg Dawe,Ian Kaufman, Bryan Glogowski, Dr. Kai-Uwe Doerr, Dr. Jurgen P. Schulze, Dr. Falko Kuester, Prof. Peter Otto,Dr. Ramesh Rao, and Dr. Larry Smarr, Calit2 at UCSD; Dr. Jason Leigh, Dr. Luc Renambot, Alan Verlo, Lance Long,Maxine Brown, Prof. Dan Sandin, Venkatram Vishwanath,and Robert Kooima, EVL at UIC; Dr. Javier Girado,Qualcomm, Inc.; and Dr. Byungil Jeong, Sun Microsystems

Acknowledgments UCSD receives major funding from theNational Science Foundation (NSF) for the OptIPuter,cooperative agreement OCI-0225642, Larry Smarr, principalinvestigator. UCSD also receives funding for OptIPortal andapplication development from the Gordon and Betty MooreFoundation for CAMERA, the Community Cyberinfrastructurefor Advanced Marine Microbial Ecology Research andAnalysis, and from the State of California for StarCAVE. UICreceives NSF support for OptIPuter via UCSD, as well as NSFaward CNS-0420477 for LambdaVision/LambdaTable andNSF award OCE-0602117 for CoreWall. UIC also receivesfunding for OptIPortal and application development from theScience Museum of Minnesota, the Adler Planetarium &Astronomy Museum and the Office of Naval Research onbehalf of the Technology Research, Education, andCommercialization Center (TRECC). Any opinions, findings,and conclusions or recommendations expressed in thispublication are those of the authors and do not necessarilyreflect the views of the funding agencies and companies

Further Reading

http://www.optiputer.nethttp://www.evl.uic.edu/cavernhttp://www.calit2.nethttp://www.scivee.tv/node/3648http://www.youtube.com/evltube


Figure 10. Tellurion shown on Varrier autostereo tiled display. Tellurion, a real-time planetary-scale data visualization being developed by EVL/UICdoctoral candidate Robert Kooima, is shown here on the Calit2 Varrier autostereoscopic tiled display. Tellurion uses NASA’s Blue Marble NextGeneration and Shuttle Radar Topography Mission data.

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Visualizing Science: The OptIPuter Project