Cyberinfrastructure

1. Cyberinfrastructure SDSC Summer Institute 2004 Dr. Fran Berman Director, San Diego Supercomputer Center and NPACI Professor and High Performance Computing Endowed Chair, UCSD

2. Welcome to SDSC! • What is Cyberinfrastructure • SDSC and Cyberinfrastructure

3. Cyberinfrastructure • Cyberinfrastructureis the organized aggregate of technologies enabling access and coordination of information technology resources to facilitate science, engineering, and societal goals. • Data • Computation • Communication • Visualization • Scientific Instruments • Expertise, etc. National Science Foundation’s Cyberinfrastructure NSF Blue Ribbon Panel (Atkins) Report provided a compelling and comprehensive vision of an integrated Cyberinfrastructure

4. Grid Cyberinfrastructure: Formalizing Science and Technology Integration Shared Input data Tasks Raw Output Post-processing Final Output MCell as computerscientistssee it Models providedata forsimulation MCell as biologists see it Simulation executed on available resources: supercomputers tolab clusters. Feedback Improves modelaccuracy TomographicReconstruction MCell codedeveloped to target widevariety of technologies Electron Microscope Biologicalmodeling from physical samples

5. Data from sensors Data – Key driver for Cyberinfrastructure • Data comes from everywhere • Scientific instruments • Experiments • Sensors and sensornets • New devices (personal digital devices, computer-enabled clothing, cars, …) • And is used by everyone • Scientists • Consumers • Educators • General public • Software environment must support unprecedented diversity, globalization, integration, scale, and use Data from instruments Data from simulations Data from analysis

6. Data Integration in the Biosciences Data Integration in the Geosciences Anatomy Software to access data Software to federate data Disciplinary Databases Users Physiology Organisms Cell Biology Organs Proteomics Cells Organelles Genomics Biopolymers Medicinal Chemistry Atoms Data Integration from a Science Perspective Where can we most safely build a nuclear waste dump? Where should we drill for oil? What is the distribution and U/ Pb zircon ages of A-type plutons in VA? How does it relate to host rock structures? Data Integration Complex “multiple-worlds” mediation Geo-Physical Geo-Chronologic Geo-Chemical Foliation Map Geologic Map

7. How do we combine data, knowledgeand information management with simulation and modeling? Applications: Medical informatics, Biosciences, Ecoinformatics,… Data Visualization How do we represent data, information and knowledge to the user? Data Mining, Simulation Modeling, Analysis, Data Fusion How do we detect trends and relationships in data? INTEGRATION Knowledge-Based Integration Advanced Query Processing How do we obtain usableinformation from data? HPC platforms for modeling,simulation, analysis How do we collect, accessand organize data? Grid Storage Filesystems, Database Systems How do we configure computer architectures to optimally support data-oriented computing? High speed networking Networked Storage (SAN) Storage hardware instruments sensornets INTEROPERABILITY Data Integration from a Technology Perspective

8. TeraGrid: nationalGrid infrastructure NEES: Earthquake Engineering infrastructure BIRN: Biomedical Informatics Research Network GEON: GeosciencesGrid infrastructure Cyberinfrastructure is a work-in-progress • Building Cyberinfrastructure makes research questions out of previously solved problems • Installation • Configuration • Accounting • And brings added complexity to existing problems • Performance analysis • Debugging • Scheduling • Security • Fault tolerance, etc. Cyberinfrastructure’s “first responders”

9. You are a pioneer • Cyberinfrastructure can extend the reach of your project, research lab, discipline. • Using, developing and refining Cyberinfrastructure will help enable a new generation of discoveries, advances, and knowledge. high-end integration campus, research lab Sensors, personal devices, small-scale, home coordination

10. SDSC in a nutshell ProductionSystems User Servicesand Development SDSC • Employs nearly 400 researchers, staff and students • National facility and UCSD Organized Research Unit • Home of many associated activities including • National Partnership for Advanced Computational Infrastructure • ETF • NLANR (with PSC, NCSA, etc.) • NLADR (with NCSA, etc.) • Alliance for Cell Signaling • Biomedical Informatics Research Network (BIRN) Coordinating Center • High Performance Wireless Research and Education Network (HPWREN) • Geosciences Network (GEON) • NEES IT, etc. TechnologyResearch and Development ScienceResearchand Development Data andKnowledge Systems

11. Next-generation Storage SDSC Technologies enable Science and Engineering SDSC Storage systems set land-speed records on data transfer. Cross country and from disk to tape. Advanced storage capacity critical for preserving and handling large-scale data collections. Networking • The “Slammer” worm took over 75,000 computers in 10 minutes worldwide, interrupting a Canadian election and disrupting internet trading on the South Korean stock exchange. DATAStar Education Applications Training Operations Services Software SDSC, national, an international partners building production Grid infrastructures enabling global-scale computing SDSC’s next-generation supercomputer will execute at 10 trillion calculations per second and is among the 25 fastest machines In the world enabling new computational science discoveries Grid Technologies

12. A Partial List of Databases and Data Collections currently housed at SDSC • 2Micron All Sky Survey (astronomy data) • Digital Palomar Observatory Sky Survey Collection(astronomy data) • Sloan Digital Sky Survey Collection (astronomy data) • Interpro Mirror (protein data) • HPWREN Wireless Network Network Analysis Data • HPWREN Sensor Network Data • Security logs and archives (security information) • Nobel Foundation Mirror(information) • EarthRef Digital Archive (Earth Science information) • GERM (earth reservoir information) • PMAG (paleomagnetic information) • GEOROC (petrological and geochemical data for igneous rocks) • Kd’s DB (rocks and minerals) • Braindata (Rutgers neuroscience collection) • LTER (hyperspectral images) • SIO-Explorer (oceanographic voyages) • Scripps (oceanographic research data) • Transana (classroom video) • WebBase (web crawls) • Alexandria Digital Library(photographs) • Backskatter Data (from UCSD network telescope) • Digital Earth Data Library (earth sciences related datasets) • PETDB (petrological and chemical data) • Seamount Catalogue (bathymetric seamount maps) • IPBIR (primate information) • Hayden Planetarium Collection (astronomical data) • TeraGrid Data (science and engineering collections) • Digital Embryo (human embryology) • National Archives (persistent archive) • San Diego Conservation Resources Network (sensitive species map server) • Bionome (Biology network of modeling efforts) • KNB (Knowledge networks for biocomplexity) • LDAS (land data assimilation system) • SEEK (ecology data) • ROADNET(sensor data) • NPACI Data Grid (scientific simulation output) • Salk (biology data archive) • CUAHSI (community hydrological collection) • Backbone Packet Header Traces (OC48, OC12) • Protein Data Bank(protein data) • National Virtual Observatory (astronomical data) • UCSD Libraries Image Collegion (ArtStore) • National Science Digital Library (education collection) • SCEC (earthquake data) • BIRN (neuroscience data) • Encyclopedia of Life (genomic data) • Protein Kinase Resource (protein data) • TreeBase (phylogeny and ontology information) • Transport Classification Database (protein information) • PlantsP (plant kinase information) • PlantsT (plant transporter information) • PlantsUBQ (plant protein information) • CKAAPS (protein evolutionary information) • AfCS Molecule Pages (protein information) • SLACC-JCSG (structural genomics data) • APOPTOSIS DB (proteins related to cell death data) • NAVDAT (geochemistry data) • QRC (NSF data on Supercomputer Centers and PACI) • Network Topology Data (Skitter project) • Biology Workbench Databases (mirrors and “originals” of over 80 biology databases) • San Diego and Tijuana Watersheds(water resources mapping)

13. Nancy Jensen, Event Planning Nancy can help withany problem you haveand is greatly appreciatedas SDSC’s guardian angel. Steve CutchinVisualization Services Steve works extensivelywith data visualization and is currently working with Butterfly.net on a“gaming grid” Reagan Moore,Director ofKnowledge Systemsand SRB Lab Reagan is the “father of data-intensive computing” and one of the originators of SRB Vijay SamalamSDSC ExecutiveDirector Vijay makes sureeverything is working smoothly, leads SDSC Networking, and is interested in Quantum Computing Anke Kamrath,Division Director,User Services Anke also heads upthe IT services groupfor NEES Nancy Wilkins-DiehrUser Services Nancy works extensivelywith the SDSC and TeraGridcomputationalscience communities helpingthem get the best use ofhigh-end technologies Faces of SDSC

14. While you’re in San Diego … • Go to the beach • Hike in Torrey Pines State park (right near here) • Eat fish tacos (they’re better than they sound) • Talk to SDSC staff about your work • Enjoy yourself!