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GA Technologies wins an NSF cooperative agreement in collaboration with UCSD to establish a SCS-40 supercomputer installed In pioneering efforts supercomputer center. at SDSC. in drug design, Paul Bash, et. al., using SDSC supercomputers, determine free energies Over 100 peer-reviewed of solvation for proteins and nucleic acids, and SDSC opens doors; Sid Karin is projects authorized for NSF, and SDSC relative free energies for binding, published in SDSC’s founding director. allocations. Science.

1985 1986 1987

SDSC’s fi rst SDSC, through SDSCnet, becomes SDSC establishes laboratory for graphics and supercomputer, the fi rst NSF center to have NSFnet animation. CRAY XMP-48, arrives. access. Electronic mail gateway established at SDSC; users exchange email with peers.

First calculations made on the SDSC CRAY on December 4, 1985 by Herbert Hamber, UC Irvine.

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First1987 Steps for the Rational Engineering1988 Designer Plants Atmospheric1989 Carbon Dioxide from Design of Drugs It’s the most abundant protein found in Fossil Fuels In a pioneering effort that allowed scientists nature, with a whimsical name reminiscent Beginning in the late 1950s, Charles Keeling to visualize the behavior of key biological of the company best known for its cookies. from UC San Diego’s Scripps Institution of molecules in the body, a team of scientists— But more important than its mere abundance, Oceanography (SIO) continuously collected data using supercomputing resources at SDSC—took RuBisCO is the key enzyme in the initiation of on the distribution of carbon dioxide around an important fi rst step in the relatively new photosynthesis, the by which green the globe. In 1989, Keeling—with SIO colleagues arena of rational drug design. In a paper plants make usable energy from sunlight. In Stephen Piper and Robert Bacastow, using SDSC published in the journal Science, the team— 1988, with the help of a new detector for x-ray resources—constructed a three-dimensional which included Paul Bash, Peter Kollman and crystallography and SDSC’s CRAY X-MP, a team model of the terrestrial carbon cycle Robert Langridge of UCSF and U. Chandra Singh of scientists led by Chapman et. al. reported, for that took advantage of the data collected by with the Scripps Clinic—reported that they had the fi rst time, the three-dimensional structure Keeling. The model was the fi rst to confi rm the determined the relative free energies of binding of RuBisCO, with a subsequent goal of building importance of fossil fuel combustion in loading for different chemical inhibitors at the same a new, improved RuBisCO to engineer designer the atmosphere with carbon dioxide, especially active molecular site. The result was signifi cant plants that would photosynthesize more over the northern hemisphere. since what makes one drug more powerful or effi ciently, creating more food for a hungry effective than another is that, at the molecular world. level, it binds more readily at the site at which it acts. CERFnet offi cially dedicated at SDSC; Vinton Governor George Cerf (no relation to the network) conducts Dave Nadeau and Deukemejian signs dedication. Holliday Horton legislation, introduced at SDSC create an by Assemblyman animation of accretion Dominic Cortese, disks – the fi ery giving SDSC $6 million to develop state-of-the- CRAY Y-MP8/864 su- and spinning art lab at SDSC. percomputer arrives at clouds in a primordial solar system – for a SDSC and made available planetarium show at S.D.’s Reuben H. Fleet NSFnet backbone becomes a production network. December 22. Space Center and Theatre.

1988 1989 1990

3-D structure Charles Keeling, et. al., with SDSC SDSC acquires 32-node iPSC/860 parallel of RuBisCo, the supercomputers, construct 3-D computer from DARPA, built by . key enzyme in model of the terrestrial carbon the initiation of cycle confi rming the importance photosynthesis and of fossil fuel combustion in loading the SDSC acquires 256- most abundant protein atmosphere with carbon dioxide. node NCUBE 2 parallel found in nature, is solved with aid of SDSC computer. supercomputers and published in Science.

KidLab, an after-school program for 10-12 year olds, established at SDSC.

UCSD/SDSC1991 Researchers Solve SDSC1992 Takes Big “STEP” with Catching1995 an Alleged Cyber-criminal Structure for the Body’s “Transistors” Innovative Program for Local On February 15, 1995, SDSC Senior Fellow Protein kinases have been likened to cellular Teachers Tsutomu Shimomura and Systems Analyst Andrew Gross collaborated with federal agents regulatory circuits in living organisms that With the beginning of the 1992 school year, to track down alleged computer criminal Kevin perform similar functions as transistors or chips SDSC launched its Supercomputer Teacher Mitnick. Shimomura and Gross applied their in a computer. In 1991, a team of researchers Enhancement Program (STEP) and presented knowledge of computer to help from SDSC and UCSD reported in a cover story its fi rst half-day-in-service to 25 educators agents apprehend Mitnick, then considered the in Science that they had solved its three- and parents from Grant Math Science Magnet “most-wanted computer criminal in the United dimensional structure; the solution—with the School. The program—a forerunner to SDSC’s States,” after an intruder broke into a network aid of the CRAY supercomputer at SDSC and award-winning TeacherTech program—was of computer systems at Shimomura’s home and a stereoscopic visualization system in SDSC’s designed to show teachers how scientists at SDSC. Mitnick, now a computer consultant Advanced Scientifi Visualization Lab (VizLab)— use to make discoveries, and it and author, was convicted of various computer- was considered one of the Grand Challenges introduced teachers to ways elementary school and communications-related crimes; he was of computational and biological science. students could use computers to learn about released from prison in January 2002. Researchers around the globe then began math and science. searching for specifi c kinase inhibitors that target specifi c diseases, including diabetes and tumor initiation and growth. UCSD/SDSC researchers solve the structure for protein kinase, likened to the body’s SDSC unveils “Grand transistor, and considered one Computer studies of Challenge Equations” of the Grand Challenges in exhibit. biological sciences; research corannulene, a bowl- makes cover of Science. shaped molecule that constitutes one-third of the molecular shell of the SDSC becomes fi rst site to send messages cross Bucky Ball, is subject of country through the NSFNET T-3 backbone; cover story of Chemical and Engineering News; at 45 Mb/s, it’s the fastest openly available research by Kim Baldridge and Jay Siegel from supercomputer arrives network for research and education. SDSC/UCSD. at SDSC.

1991 1992 1993

UC receives a 3-year, First workshop to discuss issues related to $15 million grant from the National Metacenter, a synthesis of the supercomputer arrives DEC to develop an intellectual and computational resources of the at SDSC; offi cially advanced information four NSF supercomputering centers — SDSC, installed during and data management Cornell Theory Center, NCSA, and PSC — was November press system to increase the productivity of held at SDSC. briefi ng. researchers studying global change – called Project . SDSC launches STEP (Supercomputer Teacher Enhancement Program) to develop education outreach programs for K-12 with local educators.

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Catching1998 a Speeding Enzyme SDSC1998 Releases Glue that Holds Computer1999 Reveal in the Act Data Together New Anti-HIV Strategy, Leading to With large-scale computer simulations run In 1998, the Storage Research Broker (SRB) AIDS Drug at SDSC, researchers showed how one of the 1.1 was released as the “” that Molecular dynamics simulations, conducted fastest enzymes–acetylcholinesterase (AChE), holds together data cache sites for NPACI, by a team led by UCSD chemist J. Andrew which controls communications among nerves the National Partnership for Advanced McCammon, provided new insights into and muscle cells–works. The speed of AChE had Computational Infrastructure. The SRB , attacking a third target against HIV—integrase— been puzzling, since its active site appeared to built on the work of Reagan Moore at SDSC, that helps the virus hijack the body’s cells. be accessible only by a partly blocked channel is still used by many U.S. and international The simulations, published in 1999 in the on the enzyme’s surface. Earlier work showed computational science research projects. It is Biophysical Journal, led to the development of that “breathing” motions in AChE open and considered a “middleware” in the sense that it Isentress, marketed by Merck as a new HIV drug close the channel to allow acetylcholine is built on top of other major software packages approved for patient use by the FDA. Hailed as (ACh) to enter the active site. The new work (various storage systems, real-time data sources, the most important new AIDS drug in a decade, showed that the breathing motions allowed etc.) and it has callable functions that the drug was the fi rst AIDS medicine to block ACh to bind almost as fast as if the channel can be used by higher-level software. SDSC’s integrase, considered crucial in the process HIV were always open. A A team of researchers, Chaitan Baru, Michael Wan, Arcot Rajasker and uses to replicate. including J. Andrew McCammon (UC San Diego) Wayne Schroeder were members of the original combined computational models and theoretical team that developed SRB. calculations to obtain their results, published in the August 4 Proceedings of the National Academy of Sciences. Chris Mihos and Lars Hernquist of UC Santa Cruz collaborate with computer artists at NCSA, using computational resources at SDSC CRAY C90, to create high-resolution images of a galaxy encounter for IMAX cosmic voyage, CRAY T3E supercomputer installed which debuts at the Smithsonian National Air at SDSC. and Space Museum in D.C. A data transfer speed record of 630 Mb/s is SDSC receives $8.4M contract from DARPA to achieved across the 100-mile CASA Gigabit SDSC establishes the develop Distributed Object Computation Testbed Testbed link between SDSC and Caltech, telemanufacturing (DOCT) for handling complex documents on accelerating solution of the reaction of atomic facility to rapidly geographically distributed data archives and hydrogen with molecular heavy hydrogen prototype 3D models computing platforms; to focus on the needs of (deuterium) by a factor of 3.3. from digital geometry data. the US Patent and Trademark Offi ce.

1994 1995 1996

NIH approves $3.286M to For the fi rst time, SDSC A model of the nicotinic acetylcholine SDSC to fund the National harnesses the power receptor is developed by Igor Tsigelny, Naoya Biomedical Computation Resource (NBCR). of a new very high- Sugiyama and Palmer Taylor at UCSD/SDSC, speed network (vBNS) in collaboration with Steven Sine at the Mayo Thinking Machines CM-2 by distributing portions Foundation; enzyme is a target for addictive arrives at SDSC to support of a computation across high-performance activity from nicotine. UCSD education and research. computers located on the east and west coasts. The cover of Chemical Tsutomu Shimomura, SDSC Senior Fellow, and Engineering News collaborates with federal agents to track down features an image of alleged “notorious cybercriminal” Kevin Mitnick, cyclohexatriene molecule; then considered the “most-wanted computer research results from criminal in the .” computational and experimental collaboration of Kim Baldridge at SDSC and Jay Siegel, at UCSD.

World’s1999 Largest Repository of Protein Transporting2000 Theater-goers SDSC2000 Technologies Provide Huge Image Structures Housed at UCSD/SDSC at Hayden Planetarium to the Archive to Study Human Embryology On July 1, 1999 responsibility for the Protein Orion Nebula SDSC-developed storage and visualization Data Bank (PDB)–the world’s largest archive Astronomically accurate visualizations made technologies were integrated into a National for biomedical structures–formally shifted possible for the fi rst time by SDSC researchers Library of Medicine project to create one of to the Research for Structural and the IBM Blue Horizon supercomputer at the largest-ever medical image . The Bioinformatics (RCSB) with a new PDB website SDSC transported space theater visitors to project, called “Human Embryology Digital and ftp archive. Today, the program is managed the Orion Nebula—the fi rst destination of the Library and Collaboratory Support Tools,” was jointly by two partner sites: Rutgers University, virtual starship departing from the reopened designed to demonstrate how leading-edge under the direction of Helen Berman; and Hayden Planetarium at the American Museum of information technologies in computation, SDSC and the Skaggs School of Pharmacy and Natural History in New York. The visualizations visualization, collaboration, and networking Pharmaceutical Sciences at UCSD. The PDB were made possible by SDSC’s Galactic MPIRE can expand the capabilities of medical science houses about 100,000 biological structures, volume-rendering software package, under the in developmental studies, clinical work, including proteins associated with the common technical leadership of SDSC’s Dave Nadeau. and teaching. The allowed project cold, avian fl u, HIV, West Nile virus, Alzheimer’s participants to study data sets of sizes up to a disease, and a wide variety of cancers. terabyte, in multi-gigabyte images, using the IBM HPSS archival storage system at SDSC, the Storage Resource Broker, and the MPIRE 3-D system to support the 3-D rendering of data. The Research The world’s largest and Collaboratory for SDSC named leading-edge site for the National most powerful transmission Structural Bioinformatics Partnership for Advanced Computational electron microscope is (RCSB), under the Infrastructure (NPACI), launched in October. operated from UC San Diego management of Helen and the National Center Berman at Rutgers CAIDA established for Microscopy and Image University, and Phil with a NSF seed grant Research (NCMIR) in a Bourne at UCDS/ to promote a more successful demonstration of SDSC, assumes primary robost, scalable trans-Pacifi c telemicroscopy responsibility for the Protein Data Bank — the infrastructure; principal by American and Japanese world’s largest archive for biomedical structures investigator, kc Claffy. researchers. used in pharmacological and medical research.

1997 1998 1999

SDSC publishes “Women in The Storage Research Broker (SRB) 1.1 is The HPC Systems group completes the fi rst Science,” featuring bios of released as “middleware” to hold together data installation of a user fi le system that is greater women who had a career cache sites from NPACI, led by SDSC. The SRB than one terabyte in capacity. in, or made signifi cant software is built on work led by SDSC’s Reagan contributions, to a Moore; Chaitan Baru, Michael Wan, Arcot Molecular dynamics scientifi c discipline. Rajasekar and Wayne Schroeder are members of simulations, led by J. the original team that developed SRB. Andrew McCammon at UCSD, show With large-scale computer simulations run at how to attack a third enzyme target integrase, SDSC, researchers led by J. Andrew McCammon a crucial enzyme used by HIV to replicate; at UCSD show how one of the fastest enzymes research led to the development of Isentress, an in the world, acetylcholinesterase, does its work; anti-AIDS drug marketed by Merck. results are published in the Proceedings of the National Academy of Sciences.

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On2001 the “Rocks”– Cluster Computing TeacherTech2001 Launched, Bringing SDSC2002 Experts Help Reveal Impact of Made Simple to the Classroom Climate Change on Mexico Under the leadership of Phillip Papadopoulos at SDSC organized the fi rst San Diego TeacherTech In a study published in Nature, a team of SDSC, the National Partnership for Advanced during the summer of 2001, a program designed researchers from SDSC, the University of Kansas, Computational Infrastructure (NPACI) designed to help educators bring new technology tools and the Universidad Nacional Autonoma de and released an enhanced version of the NPACI and technology-enabled science concepts into Mexico (UNAM) reported they had analyzed Rocks Cluster Toolkit, a set of open-source K-12 curricula. Within fi ve years, the program the potential impacts of climate change on enhancements for managing -based attracted more than 1,200 teachers from more the ecosystems of Mexico–the fi rst such computer clusters. Over time, Rocks—simple, than 150 area schools to its workshops; it was analysis for entire country–including 1,870 self-contained, scalable and upgradable—slowly estimated that these educators reached as many species of mammals, birds, and butterfl ies. became the de facto software package for as 200,000 students from San Diego County and The interdisciplinary study was made possible implementing clusters. By the end of 2001, Baja, Mexico. In 2006, SDSC TeacherTECH was with the help of a powerful software program, NPACI Rocks was used to establish clusters presented with a Partner of the Year Award by the Genetic for Rule-Set Prediction at the Pacifi c Northwest National Laboratory, the San Diego Science Alliance. (GARP), created by SDSC’s David Stockwell. Northwestern University, the University of Texas, and Caltech. Animated visualizations made possible for the fi rst time by SDSC’s Galactic MPIRE volume-ren- Using dering software and Blue Horizon are displayed sophisticated in the all new Hayden Planetarium of the Ameri- “backscatter can Natural History Museum on New Year’s Eve. analysis”, CAIDA researchers track IBM’s Blue Horizon is delivered to SDSC as the the progress of a worm dubbed Code-Red Worm, most powerful which infected hundreds of thousands of Web computer servers around the world. available to the US academic SDSC organzies the fi rst San Diego “The Search for Life: Are We Alone?” — a new community – TEACHERTECH, designed to allow San Diego space show at the Hayden Planetarium in New capable of 1 K-12 teachers to explore and examine different York — premiers to rave reviews. SDSC plays trillion FLOPS. multimedia and web applications for use in the a key role in creating a realistic animation classroom. showing the birth of our solar system

2000 2001 2002

A map showing possible paths an email message NSF establishes The fi rst analysis of the might take in the Internet, created by the skitter TeraGrid to support potential impacts of tool developed at CAIDA at SDSC, makes the world-class climate change for an cover of Nature. scientifi c discovery entire country, Mexico, and education is reported in a paper SDSC-developed storage and visualization through a grid-based cyberinfrastructure; SDSC published in Nature by technologies — integrated into a National is one of the founding sites. a team that included Library of Medicine project — create one of the researches from SDSC. largest-ever medical image databases. Fran Berman becomes director of SDSC. NSF awards $2.3 million, three-year grant to UCSD to create, demonstrate, and evaluate a non-commercial prototype, high-performance A team led by Vincent Crespi at Penn State used wide-area wireless network for research and computer simulations and resources at SDSC to education (HPWREN)—a multi-institutional discover carbon fi bers with mechanical strength collaboration led by Hans-Werner Braun at comparable to a diamond — strong and stiff SDSC and Frank Vernon at SIO. carbon tubes called nanotubes.

In2004 the Beginning… Envisioning2004 the “Big One” for Predicting2006 “Solar Storms” Michael Norman, professor of physics at the Southern California At times, “solar storms” ejected from the sun’s Center for Astrophysics and Space Sciences A collaboration of 33 earthquake scientists, corona–it’s ghostly outer atmosphere–can (CASS) at UC San Diego, together with computer scientists, and others from eight eject plasma in the direction of the Earth, colleagues at CASS and SDSC, ran the world’s institutions produced the largest and most resulting in potentially serious disruptions largest and most complex scientifi c detailed simulation yet of just what might in satellite operations, communications, and of the evolution of the universe ever performed. happen during a major earthquake–magnitude even electrical power grids. Since society is Using SDSC’s IBM Blue Horizon supercomputer, 7.7–on the southern San Andreas Fault. The heavily dependent on these infrastructures, the team tracked the formation of enormous simulation, known as TeraShake, used the new predicting “solar storms” are of tremendous structures of galaxies and gas clouds during 10 terafl ops IBMDataStar supercomputer importance. The March 29, 2006 solar eclipse the millions and billions of years following the and large-scale data resources of SDSC. The gave scientists from the Solar Physics Group Big Bang. Norman ran his “Enzo” cosmology simulation provided more detail into how at SAIC (Science Applications International program for more than 100 hours on all 128 intensely the earth would shake during such Corporation) an opportunity to check their computing nodes of the Blue Horizon. an event, and what impact it would have predictions of the state of the solar corona on structures, particularly in the populated based on a computational model using observed sediment-fi lled basins of Southern California photospheric magnetic fi eld data. Using and northern Mexico. dedicated time on SDSC’s IBM supercomputer DataStar and NASA’s Columbia system, this work represented the most true-to-life computer simulation ever made of the solar corona. Mike Norman, and colleagues at Center for Data experts at Astrophysics and Space Sciences at UCSD, run SDSC collaborate PRAGMA the world’s largest and most complex scientifi c with American (Pacifi c Rim simulation of the evolution of the universe ever Red Cross to help Applications and performed. locate missing loved Grid Middleware ones in the wake Assembly), SDSC’s High of Hurricane Katrina; results in “Safe and Well” launched during a workshop at SDSC and Performance website. funded by NSF, shows how relationships and Storage System expertise developed to tackle computational (HPSS) reaches the CENIC announces that the fi rst production 10 research could also help thousands of SARS milestone of one Gigabit campus connection in the U.S. patients in . petabyte of stored data. has been installed from UCSD.

2003 2004 2005

The TeraGrid enters Scientists led by UCSD’s J. Andrew McCammon SDSC receives $2.2M award from NIH to provide production with two use molecular simulations and SDSC resources Next Generation Biology Workbench, building on clusters installed at to identify a potential mechanism underlying the work of the “Workshop” concept developed SDSC: IBM/Intel IA- the drug resistance of the worst mutant HIV by Shankar Subramaniam at UCSD/SDSC. 64 TeraGrid Phase 1 strain; in same work, the researchers identify a Cluster and IBM/Intel separate region of protease enzyme that might Astrophysicist IA-64 TeraGrid Phase 2 Cluster. serve as new drug target. Richard Klein from UC Berkeley SDSC is the fi rst and others use academic institution in simulations run at the world to install the SDSC to explode one of two competing theories new IBM eServer Blue about how stars form inside immense clouds of Gene Solution computing interstellar gas; results published in Nature. system. SDSC launches DataCentral, the fi rst program of its kind to support large community data collections and databases.

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Predicting2006 Protein Structure in HPWREN2006 Comes to the Aid of Zeroing2007 in on the Cause of Record Times Local Fire Fighters Alzheimer’s and Parkinson’s Disease Researchers from SDSC, contributing their Firefi ghters facing fast-spreading Using the massive computer-simulation power massive computational capabilities to a wildfi res, especially in remote areas where of SDSC, researchers at UC San Diego homed in collaboration with colleagues at the University communications and other resources are scarce, on the causes of Alzheimer’s disease, Parkinson’s of Washington and IBM, helped achieve the added “cyberinfrastructure” to their fi ghtfi ghting disease, and other neurological disorders. A largest-ever protein structure prediction–and arsenals during the 2006 “Horse Fire” in cover story in the March issue of the Federation completed the complex simulation in less than California’s Cleveland National Forest. Experts of European Biochemical Societies Journal three hours, a task that previously took weeks. from the High Performance Wireless Research (FEBS) offered, for the fi rst time, a model for The ground-breaking demonstration used UW Educational Network (HPWREN)—a resource the complex process of aggregation of a protein Professor David Baker’s Rosetta Code and ran supported by the NSF and staffed by researchers known as alpha-synuclein, which in turn, leads on more than 40,000 central processing units at SDSC, Scripps Institution of Oceanography, to harmful ring-like or pore-like structures in of IBM’s Blue Gene Watson supercomputer, and San Diego State—responded to the urgent human membranes—the kind of damage found using the experience gained on the IBM’s Blue request of state fi refi ghters for quick and in Parkinson’s and Alzheimer’s patients. The Gene system at SDSC. Ross Walker, a SAC reliable wireless communications among researchers also found that the destructive computational scientist at SDSC, managed the widespread teams. Within a day, HPWREN properties of alpha-synuclein can be blocked Baker’s group access to SDSC machines, helping experts were on the scene, establishing high- by beta-synuclein—a fi nding that could lead to them to optimize their code. speed wireless data links needed to contain the treatments for many debilitating diseases. fl ames. UCSD/SDSC NARA and SDSC, with concurrence from NSF, researchers zero sign a landmark MOU that provides an avenue in on causes The source of spider silk’s strength, as strong as for preserving valuable digital data collections; of Parkinson’s steel, is simulated by MIT scientists in collabora- fi rst time NARA establishes an affi liated disease, tion with applications scientist Ross Walker at relationship for preserving digital data with an Alzheimer’s SDSC, on SDSC’s IBM Blue Gene/L supercom- academic institution. disease, and other puter. neurological Researchers at disorders with a computer model featured on A team led by SDSC — working cover of the Federation of European Biochemical Laura Carrington at with colleagues at Societies Journal (FEBS). SDSC successfully the University of completes a record- Washington — achieve SDSC releases version 0.5 of iRODS, the open- setting, petascale- the largest-ever source Integrated Rule-Oriented Data System, level simulation of protein structure prediction and complete the which represents a new approach to digital data the earth’s inner simulation in less than three hours. management. structure; a fi nalist for .

2006 2007 2008

Firefi ghters facing A team of researchers from NCAR, SDSC, fast-spreading LLNL and IBM Watson, led by Allan Snavely at wildfi res urgently SDSC, set U.S. records for size, performance, request cyberinfra- and fi delity of computer weather simulations, structure resources modeling the kind of “virtual weather” that from HPWREN to society depends on for accurate weather help combat the forecasts; a fi nalist for Gordon Bell Prize. SDSC dedicates a new, energy-effi cient building “Horse Fire” in Cleveland National Forest. extension as a key resource for UC San Diego and beyond. Science is coming to the YouTube generation The most true-to-life computer simulation with the advent of “SciVee,” a collaboration ever made of our sun’s corona — created by between the NSF and SDSC, under the direction CAIDA researchers Dmitri Krioukov and kc Claffy, researchers at Science Applications International of Phil Bourne, UCSD/SDSC. along with Marián Boguñá (Universitat de Corp., with the help of SDSC resources — Barcelona), reveal in Nature Physics a previously successfully predicted its actual appearance unknown mathematical model called “hidden during the total solar eclipse of March 29. metric space” that may explain the “small world phenomenon,” offering a potentially more effi cient way to pass messages on the Internet.

Setting2007 Records for “Virtual Removing2008 Bottlenecks from Modeling2008 Earth’s Enigmatic Core Weather” Prediction the Internet To learn more about the inner sanctum of the A team of researchers from SDSC, the National SDSC/CAIDA researchers Dmitri Krioukov and earth’s core, seismologists take advantage of one Center for Atmospheric Research (NCAR), Kimberly Claffy, along with Marián Boguñá of nature’s most destructive forces: earthquakes. Lawrence Livermore National Laboratory, and (Universitat de Barcelona), reveal in Nature Somewhat like the way a CAT scan images the the IBM Watson Research Center set U.S. Physics a previously unknown mathematical brain, seismologists track seismic wave patterns records for size, performance, and fi delity of model called “hidden metric space” that may from earthquakes to model the structure of computer weather simulations, modeling the explain the “small world phenomenon” — the earth’s core. One of the great challenges is kind of “virtual weather” that society depends discovered in the by sociologist Stanley to capture the propagation of high-frequency on for accurate weather forecasts. The research, Milgram—and its relationship to natural and waves, with periods of 1 to 2 seconds, as they led by Allan Snavely at SDSC, was a fi nalist for manmade networks. The novel concept suggests travel across the globe. In 2008, a team of the Gordon Bell Prize. a new approach for removing bottlenecks within researchers from SDSC employed a spectral- the Internet that threaten the smooth passage element application called SPECFEM3D_GLOBE of digital information around the globe. to complete record-setting, petascale-level simulations of the earth’s core at frequencies over just over a second. Results of these simulations were announced at SC08, where the research led by Laura Carrington of SDSC was a fi nalist for the Gordon Bell Prize. The CIPRES portal, used to help researchers track evolutionary relations among species, becomes Trestles, an HPC the most heavily used portal in the TeraGrid, system designed to SDSC awarded accounting for 20% of active TeraGrid users offer modest-scale 5-year, $20 million during the fi rst quarter of 2010. and gateway users grant from NSF rapid job turnaround to build Gordon, Researchers at SDSC, to increase researcher a powerful SDSU and UCSD productivity, is supercomputer create the largest- launched under a $2.8 million NSF grant. featuring “fl ash memory” and “supernodes” to ever simulation solve critical data-intensive science problems. of a Magnitude 8 The Center for Large-scale Data Systems earthquake, primarily Research (CLDS), bringing together industry and SDSC unveils Dash, a “fl ash-memory-based” along the southern university research to investigate “” supercomputer to accelerate solutions for data- section of the San challenges, is launched under the direction of intensive science problems. Andreas fault. SDSC researcher Chaitan Baru.

2009 2010 2011

SDSC offi cially launches theTriton Resource, SDSC launches Researchers from an integrated data-intensive computing system a volunteer UC Irvine, led by primarily designed to support UCSD and UC. internship Rommie Amaro and program for using SDSC expertise SDSC completes high school students – Research Experience and resources, fi nd a comprehensive for High School Students (REHS) – to help a new approach to upgrade to its them gain experience in a particular area of create customized tape-based computational research. therapies for virulent fl u strains that resist archival storage current antiviral drugs. The fi ndings were capacity, Mike Norman named SDSC director. published in Nature Communications. increasing its total to 36 petabytes, the largest digital storage capacity of any academic center in the world.

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Providing2009 a Portal to Build the Using2011 Simulations to Create Customized Internet2012 Censorship Revealed Tree of Life Therapies for Virulent Flu Strains Through a Maze of Malware To help scientists build the Tree of Life—to The search for effective fl u drugs has always In January 2011, Egypt—with 23 million Inter- infer the evolutionary history of Earth’s myriad been hampered by the infl uenza virus itself, net users—vanished from cyberspace after its species starting from biomolecular sequence which mutates from strain to strain, making it government ordered an Internet blackout amidst data—the NSF funded a project called CIPRES diffi cult to target with a specifi c pharmaceutical anti-government protests. The following month, (CyberInfrastructure for Phylogenetic RESearch). approach. Researchers from UC Irvine, with the Libyan government, also under siege, imposed As part of this project, SDSC developed the assistance of SDSC expertise and computer an Internet “curfew” before completely cutting CIPRES portal—a browser interface to the most resources, found a new approach to create access for almost four days. To help explain how widely used phylogenetic codes—along with customized therapies for virulent fl u strains these governments disrupted the Internet, a team faster versions of these codes. In December that resist current antiviral drugs. The fi ndings, of scientists led by kc Claffy, director and founder 2009 the portal was migrated to the TeraGrid, published in Nature Communications, offered an of CAIDA at SDSC, conducted an analysis based the nation’s largest open-access network of avenue to build new drugs that exploit so-called largely on the drop in a specifi c subset of observ- high-performance computers. Within the fi rst fl u protein ‘pockets.’ Using powerful computer able Internet traffi c that is a residual product of quarter of 2010, the portal had 500 users, the simulations on SDSC’s Trestles system, UCI’s malware. Their analysis, funded by the NSF and most of any TeraGrid portal and 20 percent of Rommie Amaro and Robin Bush with SDSC’s Department of Homeland Security—and including all active TeraGrid users. Each month since Ross Walker created a method to predict how scientists from Italy and The Netherlands—was then, more than 100 new users have accessed pocket structures on the surface of infl uenza the fi rst published research to demonstrate how TeraGrid resources through the portal, attesting proteins promoting viral replication could be malware-generated traffi c pollution could be to the broad impact of this enabling interface. identifi ed as these proteins evolve, allowing for used to analyze Internet censorship and other possible pharmaceutical exploitation. macroscopic network outages. A study led by SDSC’s James Short predicts that by 2015, the sum of media delivered to consumers on mobile devices and to their homes would take 15+ hours a day to consume. That’s equal to nine DVDs worth of data per person per day. Researchers from SDSC, the The NSF awards SDSC a $12 million grant to U.S. Geological deploy Comet, a new petascale supercomputer Survey, and the To help explain how governments disrupt the designed to transform advanced scientifi c com- San Diego Zoo’s Internet, a team of scientists led kc Claffy, puting by expanding Institute for director and founder of CAIDA at SDSC, access and capacity Conservation Research develop methodology conducts the fi rst published research showing among traditional that for the fi rst time combines 3D and how malware-generated traffi c pollution can be as well as non- advanced range estimator technologies, used to analyze Internet censorship and other traditional research providing detailed data on the movements of network outages. domains. terrestrial, aquatic, and avian wildlife species.

2012 2013 2014

The Predictive Analytics Center of Excellence WIFIRE, designed A published global genome (PACE), is funded by SDSC to leverage the to build a study using SDSC’s Center’s data-intensive expertise and resources cyberinfrastructure data-intensive Gordon to provide the critical skills to design, build, to perform real- supercomputer have verify, and test predictive data models. time data-driven researchers rethinking how assessments of avian lineages diverged Arman Bilge, a wildfi res, is funded under a three-year NSF after the extinction of the 10th grader at grant to SDSC, Calit2/Qualcomm Institute, dinosaurs. The four-year the Lexington and the Jacobs School of Engineering’s MAE project, called Avian Genome Consortium, is High School in department. Also participating is the University published in the journal Science in late 2014. Massachusetts, used of Maryland’s Department of Fire Protection the CIPRES science Engineering. gateway, developed by SDSC researchers, to create a map and timeline that identifi ed when HIV arrived in Americas, and where and when it spread across North and South America.

U.S.2013 Media Intake to Rise to 15.5 Genomic2014 Analysis of 115 Rethinking2014 How Our Feathered Hours per Day, per Person, by 2015 Year-old Woman Friends Evolved A study led by a researcher at SDSC predicted Researchers investigating the genome of a A published global genome study that used that by 2015, the sum of media asked for and healthy supercentenarian discovered many SDSC’s data-intensive Gordon supercomputer delivered to consumers on mobile devices and somatic mutations that arose during the had researchers rethinking how avian lineages to their homes would take more than 15 hours woman’s lifetime. However, very few mutations diverged after the extinction of the dinosaurs. a day to see or hear. That volume is equal to 6.9 mapped to regions in genes that code for The four-year project, called Avian Genome million-million gigabytes of information, or a proteins, whereas the overwhelming majority Consortium and published in the journal daily consumption of nine DVDs worth of data were in genomic regions predicted to have Science in late 2014, resulted in a new family per person per day. “One can actually have more neither adverse nor favorable impact on genetic “tree” for nearly all of the 10,000 species of than 24 hours in a media day,” explained James fi tness. Led by Erik Sistermans and Henne birds alive today by comparing the entire DNA E. Short, the author of the latest “How Much Holstege from the VU University Medical codes (genomes) of 48 species as varied as Information?” report, produced by the Institute Center in Amsterdam, the team—including parrot, penguin, downy woodpecker, and Anna’s for Communications Technology Management SDSC researchers Wayne Pfeiffer and Mark hummingbird. The massive undertaking, started (CTM) at the University of Southern California’s Miller—published its fi ndings in the journal in 2011, involved more than 200 researchers Marshall School of Business. “As we increase our Genome Research. The work involved numerous at 80 institutions in 20 countries, with related level of multi-tasking, we have to expect that computations, some of which were done on the studies involving scientists at more than 140 total hours will grow even as the total number Triton cluster at SDSC. At the time of her death institutions worldwide. of physical hours a viewer can consume media at the age of 115, the subject woman was the will remain roughly constant.” second oldest person in the world and showed no signs of vascular disease or dementia. About this Brochure

On November 14, 1985, the San Diego Supercomputer Center opened its doors on the northwestern corner of the UC San Diego campus and showed off its first supercomputer, a CRAY X-MP/48 — clocking at what one newspaper article called a “mind-boggling” billion calculations per second… a gigaflop. Actually, the peak performance was closer to 800 million calculations per second, but still pretty fast then. Some 100 researchers — all from traditional disciplines such as astrophysics, biochemistry, geology, and oceanography — applied for time on the new supercomputer, which promised to usher in a new era of scientific discovery.

Since that day, scientific and technological advances made possible, and/or created by SDSC staff and resources like the original CRAY, have made a major mark in academia, industry, and society-at-large – “turning data to discovery,” a phrase that has become associated with SDSC. The Center has brought together researchers at UC San Diego and across the nation and world, in partnerships and collaborations that now are the hallmark of today’s scientific enterprise. SDSC also has proven to be a good neighbor, providing its expertise and considerable resources to local educators and students, firefighters and other “first-responders,” families of military serving overseas, and others in time of need.

To help commemorate SDSC’s 30th anniversary, SDSC has pulled together a timeline of the most significant events in the Center’s history. This timeline, now located outside SDSC’s in the building’s East Wing addition, serves as a physical reminder of the historical milestones that have made SDSC a local, state, and national resource for high-performance and data-intensive computing, and a leader in research and development of the nation’s vast cyberinfrastructure.

As an added element to this celebration, this brochure spotlights 30 significant moments and/or advances in science, technology, and outreach made possible by the Center and its staff. The “Top 30” list, published in this document, represents but a small sampling of the hundreds of major accomplishments over SDSC’s history; clearly, many other achievements also deserve recognition. We are confident this list will be discussed and debated, and ultimately revised and updated when the next such list is developed!

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