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Computational Science and theSchool of Informatics at
Indiana University
IU/HBCU STEM InitiativeIUPUI
April 11 2007Geoffrey Fox
Computer Science, Informatics, PhysicsPervasive Technology Laboratories
Indiana University Bloomington IN 47401
[email protected]://www.infomall.org
What is Computational Science?What is Computational Science? InformaticsInformatics is the integration of the art, is the integration of the art,
science, and the human dimensions of science, and the human dimensions of information technologyinformation technology to provide solutions to to provide solutions to discipline-specific problemsdiscipline-specific problems
Informatics is a response to the Informatics is a response to the data/information/knowledge gaps (data/information/knowledge gaps (data delugedata deluge) ) caused by “billions and billions of bits”caused by “billions and billions of bits”• GridsGrids are technology supporting this in distributed are technology supporting this in distributed
researchresearch Computational ScienceComputational Science could be the same as could be the same as
this or focus on the large scale simulation partthis or focus on the large scale simulation part MulticoreMulticore chips will revitalize simulation! chips will revitalize simulation!
Bioinformatics Data DelugeBioinformatics Data DelugeChallenge and OpportunityChallenge and Opportunity1985 2000
1 experiment
1 gene
10 data
1 experiment
10,000 genes
10,000,000 data
e-moreorlessanything and the Grid ‘e-Science is about global collaboration in key areas of science,
and the next generation of infrastructure that will enable it.’ from its inventor John Taylor Director General of Research Councils UK, Office of Science and Technology
e-Science is about developing tools and technologies that allow scientists to do ‘faster, better or different’ research
Similarly e-Business captures an emerging view of corporations as dynamic virtual organizations linking employees, customers and stakeholders across the world. • The growing use of outsourcing is one example
The Grid provides the information technology e-infrastructure for e-moreorlessanything.
A deluge of data of unprecedented and inevitable size must be managed and understood.
People, computers, data and instruments must be linked. On demand assignment of experts, computers, networks and
storage resources must be supported
Why Grids/ Cyberinfrastructure Useful Supports distributed science – data, people, computers Exploits Internet technology (Web2.0) adding management,
security, supercomputers etc. It has two aspects: parallel – low latency (microseconds)
between nodes and distributed – highish latency (microseconds) between nodes
Parallel needed to get high performance on individual 3D simulations, data analysis etc.; must decompose problem
Distributed aspect integrates already distinct components Cyberinfrastructure is in general a distributed collection of
parallel systems Grids are made of services that are “just” programs or data
sources packaged for distributed access Web 2.0 can be used “instead of” Grids
TeraGrid: Integrating NSF Cyberinfrastructure
TeraGrid is a facility that integrates computational, information, and analysis resources at the San Diego Supercomputer Center, the Texas Advanced Computing Center, the University of Chicago / Argonne National Laboratory, the National Center for Supercomputing Applications, Purdue University, Indiana University, Oak Ridge National Laboratory, the Pittsburgh Supercomputing Center, and the National Center for Atmospheric Research.Today 100 Teraflop; tomorrow a petaflop; Indiana 20 teraflop today and doubling
SDSCTACC
UC/ANL
NCSA
ORNL
PU
IU
PSCNCAR
Caltech
USC-ISI
UtahIowa
Cornell
Buffalo
UNC-RENCI
Wisc
APEC Cooperation for Earthquake Simulation ACES is a seven year-long collaboration among scientists
interested in earthquake and tsunami predication• iSERVO is Infrastructure to support
work of ACES
• SERVOGrid is (completed) US Grid that is a prototype of iSERVO
• http://www.quakes.uq.edu.au/ACES/
Chartered under APEC – the Asia Pacific Economic Cooperation of 21 economies
Database Database
Analysis and VisualizationPortal
RepositoriesFederated Databases
Data Filter
Services
Field Trip DataStreaming Data
Sensors
?DiscoveryServices
SERVOGrid
ResearchSimulations
Research Education
CustomizationServices
From Research
to Education
EducationGrid ComputerFarmGrid of Grids: Research Grid and Education Grid
GISGrid
Sensor GridDatabase Grid
Compute Grid
SERVOGrid and Cyberinfrastructure Grids are the technology based on Web services that implement
Cyberinfrastructure i.e. support eScience or science as a team sport
• Internet scale managed services that link computers data repositories sensors instruments and people
There is a portal and services in SERVOGrid for• Applications such as GeoFEST, RDAHMM, Pattern
Informatics, Virtual California (VC), Simplex, mesh generating programs …..
• Job management and monitoring web services for running the above codes.
• File management web services for moving files between various machines.
• Geographical Information System services • Quaketables earthquake specific database• Sensors as well as databases• Context (dynamic metadata) and UDDI system long term
metadata services• Services support streaming real-time data
LEAD Gateway PortalNSF Large ITR and Teragrid Gateway - Adaptive Response to Mesoscale weather events - Supports Data exploration,Grid Workflow
Grid Workflow Datamining in Earth Science Work with Scripps Institute Grid services controlled by workflow process real time
data from ~70 GPS Sensors in Southern California
Streaming DataSupport
TransformationsData Checking
Hidden MarkovDatamining (JPL)
Display (GIS)
NASA GPS
Earthquake
Some Organizations I work with• MSI CI2 Minority-Serving Institutions (MSI) Cyberinfrastructure Institute
led by the• Alliance for Equity in Higher Education. Working with the Alliance will
have systemic impact on at least 335 Minority Serving Institutions covered by the
• AIHEC American Indian Higher Education Consortium)• HACU Hispanic Association of Colleges and Universities• NAFEO National Association for Equal Opportunity in Higher Education• MSI-CIEC Minority-Serving Institution Cyberinfrastructure (CI)
Empowerment Coalition led by• UHD University of Houston Downtown as a major Hispanic Serving
Institution• I am Senior Research Associate in the Center for Computational Science
and Advanced Distributed Simulation at UHD and Visiting Scholar for Cyberinfrastructure Development at the Alliance for Equity in Higher Education
Basic Ideas• Cyberinfrastructure is critical to all involved in
Research and Education• Cyberinfrastructure is intrinsically democratic
supporting broad participation• MSI’s should lead MSI integration with
Cyberinfrastructure• One should guide the projects with experts• One should aim at scalable (systemic) approaches• Goal is peer collaborations involving all institutions of
higher education
2/22/2001 JSUFall97Master http://www.npac.syr.edu [email protected]
1
Programming for the WebProgramming for the WebGeneral IntroductionGeneral Introduction
Course at Jackson State University Spring98 Course at Jackson State University Spring98 and Fall 97and Fall 97
http://www.npac.syr.edu/users/gcf/jsufall97introNancy McCracken
Geoffrey Fox, Tom Scavo
Syracuse University NPAC
111 College PlaceSyracuse NY 13244 4100
3154432163
JSUSyracuse
Teaching Jackson State Fall 97 to Spring 2005
Example: Setting up a Polar CI/Grid• NSF CI-Team project with HBCU ECSU in North Carolina and
Kansas University will design and set up a Polar Grid – CI Enable MSIs (ECSU Haskell) and a community (Polar Science)
• The North and South poles are melting with potential huge environmental impact– We have changed the 100,000 year Glacier cycle into a ~50 year cycle;
the field has increased dramatically in importance and interest• Polar Grid is a network of computers, sensors (on robots and
satellites), data and people aimed at understanding science of ice-sheets and impact of global warming
• We are planning Polar Grid relevant CI Education Infrastructure and initial projects with Undergraduate students (ECSU) and Graduate students (Kansas)– Polar weather stations as Grid resources– Use distance education to cover all CReSIS sites
CReSIS PolarGrid• Important CReSIS-specific Cyberinfrastructure components include
– Managed data from sensors and satellites – Data analysis such as SAR processing – possibly with parallel
algorithms– Electromagnetic simulations (currently commercial codes) to design
instrument antennas– 3D simulations of ice-sheets (glaciers) with non-uniform meshes– GIS Geographical Information Systems
• Also need capabilities present in many Grids– Portal i.e. Science Gateway– Submitting multiple sequential or parallel jobs
• TeraGrid etc. (the National Cyberinfrastructure) is having Cyberinfrastructure days at various places around country to popularize and identify how institutions can participate– ECSU will be later this year
Indiana University Cheminformatics Center Summary
Indiana University is focusing on two major areas:• Creating a comprehensive, easily accessible infrastructure for
chemoinformatics tools and data sources, linked with PubChem and made available as web services, and partnering with screening centers and other users to demonstrate how this infrastructure can be usefully applied– Infrastructure can include any tools, not just ours (commercial/open source,
chemoinformatics, bioinformatics, and so on)
– New, custom applications can be built quickly using existing services in a similar way to Google Maps and other “web 2.0” resources
• Being a central hub of chemoinformatics education, including offering distance courses on chemoinformatics theory and techniques, practical workshops on using chemoinformatics resources, and freely available web-based educational resources– We currently offer a Ph.D, M.S. and graduate certificate (distance) in chemical
informatics
– Distance education program allows you to “pick and choose” courses to meet educational needs: certificate is awarded on completion of four courses
CICC Combines Grid Computing with Chemical Informatics
CICCCICC CICCCICCChemical Informatics and Cyberinfrastucture Collaboratory
Funded by the National Institutes of Healthwww.chembiogrid.org
Indiana University Department of Chemistry, School of Informatics, and Pervasive Technology Laboratories
Science and Cyberinfrastructure
.
Large Scale Computing Challenges
Chemical Informatics is non-traditional area of high performance computing, but many new, challenging problems may be investigated.
CICC is an NIH funded project to support chemical informatics needs of High Throughput Cancer Screening Centers. The NIH is creating a data deluge of publicly available data on potential new drugs.
CICC supports the NIH mission by combining state of the art chemical informatics techniques with
• World class high performance computing• National-scale computing resources (TeraGrid)• Internet-standard web services • International activities for service orchestration• Open distributed computing infrastructure for scientists world wide
NIHPubMed
DataBase
OSCARText
Analysis
POVRayParallel
Rendering
Initial 3DStructure
Calculation
ToxicityFiltering
ClusterGrouping
Docking
MolecularMechanics
Calculations
Quantum Mechanics
Calculations
IU’sVaruna
DataBase
NIHPubChemDataBase
Chemical informatics text analysis programs can process 100,000’s of abstracts of online journalarticles to extract chemical signatures of potential drugs.
OSCAR-mined molecular signatures can be clustered, filtered for toxicity, and docked onto larger proteins. These are classic “pleasingly parallel” tasks. Top-ranking docked molecules can be further examined for drug potential.
Big Red (and the TeraGrid) will also enable us to perform time consuming, multi-stepped Quantum Chemistry calculations on all of PubMed. Results go back to public databases that are freely accessible by the scientific community.
CICC Web Service Infrastructure
Portal ServicesRSS FeedsUser ProfilesCollaboration as in Sakai
Grid ServicesService RegistryJob Submission and Management
Local ClustersIU Big RedTeraGrid, Open Science Grid
Varuna.netQuantum Chemistry
Statistics Services Database Services
Core functionality Computation functionality 3D structures byFingerprints Regression CIDSimilarity Classification SMARTSDescriptors Clustering 3D Similarity2D diagrams Sampling distributionsFile format conversion
Docking scores/poses byApplications Applications CID
Docking Predictive models SMARTSFiltering Feature selection Protein
2D plots Docking scoresToxicity predictions
Anti-cancer activity predictionsCID, SMARTS
Cheminformatics Services
DruglikenessArbitrary R code (PkCell)
Mutagenecity predictionsPubChem related data by
Pharmacokinetic parametersOSCAR Document AnalysisInChI Generation/SearchComputational Chemistry (Gamess, Jaguar etc.)
Varuna environment for molecular modeling (Baik, IU)
QMDatabase
ResearcherResearcher
Simulation ServiceFORTRAN Code,
Scripts
Chemical Concepts
Experiments
QM/MMDatabasePubChem, PDB,
NCI, etc.
ChemBioGridChemBioGrid
ReactionDB
DB ServiceQueries, Clustering,
Curation, etc.
Papersetc.
Condor
TeraGridSupercomputers
“Flocks”