Opportunities for Collaboration with IBM

1. Opportunities forCollaboration withIBM

2. Outline • Goals • Areas of opportunity • CIS undergraduate / graduate educational programs • Lundquist College of Business • Resource development • Research areas • Computational science • TAU parallel performance system • BBMI / UO Neuroinformatics Center • Integrative Science Complex

3. Goals for IBM Collaboration • Establish and foster a relationship with IBM Beaverton • Human opportunities • Enhance educational programs in CIS and UO • Create and strengthen institutional partnerships • Provide new internship opportunities to CIS students • Improve funding support through fellowships • Partner on broader education and diversity initiatives • Research and development opportunities • Explore strategic development and research alliances • Link UO research activities with IBM efforts • Work on joint projects and write joint proposals

4. CIS Undergraduate Program • Major requirements consist of • CIS core courses • Completion of a traditional CIS or interdisciplinary track • CIS core courses • Lower division  Fundamental • CIS 210-12, Intro to CS  CIS 313, Data structures • Math 231-33, Discrete Math  CIS 314, Computer organization • Upper division  CIS 315, Intro to algorithms • CIS 415, Operating systems  Writing (either) • CIS 422, Software methodology  WR 320, Scientific / Technical • CIS 425, Programming languages  WR 321, Business communication

5. CIS Undergraduate Tracks • Traditional • Foundations • Software Development • Computer Networks • Database and Informatics • Interdisciplinary • Bioinformatics • Computational Biology • Computational Arts: Multimedia • Business Information Technology

6. CIS Minor, CIT Minor, and MACS Major • Mathematics and Computer Science (MACS) major • Joint major with Math department • Explore computer science with foundation in mathematics • Develop team players for information-base occupations • CIS Minor • Introduces theories and techniques of computer science • Develop skills applicable to major discipline • Computer Information Technology (CIS) Minor • Train students to work with evolving technologies • Business databases, computer networks, web applications, software systems

7. CIS and Lundquist College of Business • Business Information Technology track in the CIS major • Approved by College of Arts and Science for Fall ‘06 • CIS major (slightly modified) plus minor in business • Will have capstone projects for the students in this track • CIT minor • Work with Faculty in Decision Sciences to update and revamp • Add more classes that business students can take in CIS • Computer Ethics (already OKed) plus two additional • Certificate program in Business Information Technology • Offered by CIS • CIT minor + three additional 400 level classes

8. CIS and Business Interactions • Leadership in Action practicum (Spring ‘06) • Experimental teams (2 business majors + 2 CIS majors) • Teams go out to do a project for local non-profit (Mt. Pisgah) • Technology Entrepreneursip Program • Technology transfer program with UO departments and PNNL • Prof. Jun Li's mSSL secure authentication protocol selected • Symantec • Favorable response to CIT/CIS business interdisiplinary student • Has hired several students from UO/CIS • Portland IT Association funds for IT scholarships • Outstanding CIT minors • First awards Fall ‘06

9. Human Collaboration Ideas • Career mentoring • Career Mentorship Colloquium (Winter ‘07) • IBM guest speakers • Internship program • Create co-op / work-study program • 6 month (fall/spring + summer) IBM intern • 6 month (fall+winter / winter+spring) academic program • Summer research internships • IBM fellowships • Extreme Blue • Research fellowships (T.J. Watson, Almaden, …) • IBM post-docs

10. Resource Initiatives • Improve educational and research resources • UO wide • CIS specific • Enhance CIS tracks • Establish bridges from CIS curriculum to research • Enhance interdisciplinary activities within UO • Add value to existing initiatives • Create opportunities for establishment of new projects

11. Digital Collaborative Work-Learn-Play Space • Collaboration with AAA Fab Lab • Modular, reconfigurable high-tech spaces • State of the art digital hardware, software, tools, and toys • Support • Interdisciplinary cross-campus innovation • Experimental classes • Special lectures and events • Hands-on experimentation with newest gadgets and gizmos • High-tech social events • 3D movies, graphics film fest • Digital relaxation and conversation • Phase I conceptualizaiton and planning

12. CIS Scientific Innovation Center • Support interdisciplinary computer science • Informatics • Computational science • Resource development • Phase 1 (complete) • NSF MRI grant ($1M) • ICONIC Grid • Phase II (underway) • Visualization Lab ($100K) • 3x4 tiles 24” LCD display • rear projection, stereo display • Phase III (with sponsors)

13. UO ICONIC Grid

14. World Community Grid • Invitation to be a partner in the WCG • CIS and UO excited to join • Involvement ideas • Introduce to CIS students in undergraduate/graduate courses • Feature participation on CIS webpage • Allocation of dedicated servers • Contribution of application ideas • Help promote broader UO involvement • NIC involvement • Participation in human brain science projects • Integration with ICONIC Grid

15. Math Biology Computer Science Geoscience Neuroscience Psychology Paleontology Computational Science • Integration of computerscience in traditionalscientific disciplines • Increasingly acceptedmodel of scientific research • Application of high-performancecomputation, algorithms, networking,database, and visualization • Parallel and grid computing • Integrated problem-solving environments • Computer science research at the core • Support for interdisciplinary science

16. Computational Science Projects at UO • Geological science • Model coupling for hydrology • Bioinformatics • Zebrafish Information Network (ZFIN) • Evolution of gene families • Oregon Bioinformatics Toolkit • Neuroinformatics • Paleontology • Dinosaur skeleton and motion modeling • Artificial intelligence and data mining • Semantic web, data ontologies, and information integration • Oregon Computational Science Institute

17. HPC Research Project Areas at UO • Parallel modeling and simulation • Computationalsciences • Bioinformatics • Scientific problem solving environments • Grid computing • Parallel performance evaluation and tools • Parallel language systems • Tools for parallel system and software interaction • Source code analysis • Parallel component software • Data mining

18. HPC Research Affiliations at UO • Strong associations with DOE national laboratories • Los Alamos National Lab, Lawrence Livermore National Lab, Sandia National Lab, Argonne National Lab, Pacific Northwest National Lab • DOE funding • Office of Science, Advance Scientific Computing Research • Accelerated Strategic Computing (ASC/NNSA) • NSF funding • Academic Research Infrastructure • Major Research Instrumentation

19. TAU Performance System • Tuning and Analysis Utilities (14+ year project effort) • Performance system framework for HPC systems • Integrated, scalable, flexible, and parallel • Open source toolkit for performance problem solving • Instrumentation, measurement, analysis, and visualization • All computing platforms, processor architectures, OSs • IBM, HP, Sun, Linux, SGI, Cray, Apple, Windows, … • Many programming languages and compilers • C, C++, Fortran 90/95, UPC, HPF, Java, OpenMP, Python • IBM, Intel, PGI, GNU, Sun, Microsoft, SGI, Cray, HP, … • Partners: LLNL, ANL, Research Center Jülich, LANL

20. TAU Projects • TAU performance system • ParaProf: parallel profile analysis and visualization • PerfDMF: performance data management • PerfExplorer: performance data mining • KTAU: Linux kernel performance monitoring • Integration with the Eclipse Platform • Open Trace Format (OTF) for scalable parallel tracing • Performance analysis of large-scale applications • CCSM / ESMF / WRF climate/earth/weather simulation • National laboratory applications • DOE SciDAC and DoD PET (Programming Environments and Tools)

21. TAU Eclipse Integration • Eclipse GUI integration of existing TAU tools • New Eclipse plug-in for code instrumentation • Integration with CDT and FDT • Java, C/C++, and Fortran projects • Can be instrumented and run from within eclipse • Each project can be given multiple build configurations corresponding to available TAU makefiles • All TAU configuration options are available • Paraprof tool can be launched automatically

22. TAU Eclipse Integration TAU experimentation TAU configuration

23. TAU Eclipse Future Work • Development of the TAU Eclipse plugins ongoing • Java and the CDT/FDT • Planned features include: • Full integration with the Eclipse Parallel Tools Project (PTP) • Database storage of project performance data • Refinement of the plugin settings interface • easier selection of TAU runtime and compiletime options • Accessibility of TAU configuration and commandline tools • via the Eclipse UI

24. ZeptoOS and TAU • DOE OS/RTS for Extreme Scale Scientific Computation • OS research for petascale systems • ZeptoOS project • scalable, adaptive components for petascale architectures • Argonne National Laboratory and University of Oregon • University of Oregon • Kernel-level performance monitoring • OS component performance assessment and tuning • KTAU (Kernel Tuning and Analysis Utilities) • integration of TAU infrastructure in Linux kernel • port to 32-bit and 64-bit Linux platforms • include in ZeptoOS and port to IBM BG/L (I/O node)

25. Linux Kernel Profiling using TAU – Goals • Fine-grained kernel-level performance measurement • Parallel applications • Support both profiling and tracing • Both process-centric and system-wide view • Merge user-space performance with kernel-space • User-space: (TAU) profile/trace • Kernel-space: (KTAU) profile/trace • Detailed program-OS interaction data • Including interrupts (IRQ) • Analysis and visualization compatible with TAU

26. KTAU Architecture

27. KTAU Future Work • Dynamic measurement control • Enable/disable events w/o recompilation or reboot • Add new performance data sources • Look into hardware counters • Improve user-space integration • Full callpaths and phase-based profiling • Merged user/kernel traces • Integration with monitoring technology • SuperMon, MRNet, TAUg • New porting efforts • IA-64, PPC-64 and AMD Opteron • System characterization studies

28. IBM Involvement • TAU runs on all IBM platforms and processors • pSeries, xSeries, BG/L (64K system at LLNL) • All national laboratory IBM systems run TAU • Porting to Cell processor • IBM Petascale Tools Workshop (‘05 and ‘06) • IBM T.J. Watson Research Center (David Klepacki) • Student participation (K. Huck, A. Nataraj) • IBM HPCS project • TAU integration in Eclipse Parallel Tools Platform (PTP) • Open Software Development Lab (OSDL) • University of Oregon membership

29. TAU Support Acknowledgements • Department of Energy (DOE) • Office of Science • MICS, Argonne National Lab • ASC/NNSA • University of Utah ASC/NNSA Level 1 • ASC/NNSA, Lawrence Livermore National Lab • Department of Defense (DoD) • HPC Modernization Office (HPCMO) • Programming Environment and Training (PET) • NSF Software and Tools for High-End Computing • Research Centre Juelich • Los Alamos National Laboratory • ParaTools, Inc.

30. Neuroinformatics Center (NIC) • UO Brain, Biology, and Machine Initiative (BBMI) • Interdisciplinary research in cognitive neuroscience, biology, physics, and computer science • Human neuroscience focus • Computational science applied to human neuroscience • Tools to help understand dynamic brain function • Tools to help diagnosis brain-related disorders • HPC simulation, large-scale data analysis, visualization • Integration of neuroimaging methods and technology • Interaction with Electrical Geodesics, Inc. • Technology transfer to Cerebral Data Systems

31. NIC Projects • Advanced statistical signal analysis (PCA, ICA) • HiPerSAT • high-performance signal analysis toolkit • parallelize ICA, wavelet, and other algorithms • APECS • automated protocol for EEG component separation • Computational human head / brain modeling • Conductivity modeling and source localization modeling • Image segmentation and brain structure extraction • Distributed and grid computing • GEMINI • Mc (Matlab concurrent)

32. Electrical Geodesics Inc. (EGI) • EGI Geodesics Sensor Net • Dense-array sensor technology • 64/128/256 channels • 256-channel geodesics sensor net • AgCl plastic electrodes • Carbon fiber leads • Net Station • Advanced EEG/ERP data analysis • Stereotactic EEG sensor registration • Research and medical services • Epilepsy diagnosis, pre-surgical planning

33. Dipole Sources in the Cortex • Scalp EEG is generated in the cortex • Interested in dipole location, orientation, and magnitude • Cortical sheet gives possible dipole locations • Orientation is normal to cortical surface • Need to capture convoluted geometry in 3D mesh • From segmented MRI/CT • Linear superposition

34. Building Computational Brain Models • MRI segmentation of brain tissues • Conductivity model • Measure head tissue conductivity • Electrical impedance tomography • small currents are injectedbetween electrode pair • resulting potential measuredat remaining electrodes • Finite element forward solution • Source inverse modeling • Explicit and implicit methods • Bayesian methodology

35. GEMINI • “Grid-based Environmentsand Methods for IntegratedNeuroimaging” • Dynamic neuroimagingalgorithms and visualization • Grid-based integration(processing and data sharing) • High-end tool integrationand environments • Neuroinformatics dataontologies

36. Technology Transfer in Human Neuroscience • UO’s BBMI is conducting pioneering research and development in human neuroscience, genetics and proteomics, and computational science for future neurological medicine and health care • Greater precision and speed in brain imaging has high research and medical relevance • Integrated medical imaging (EEG/MEG, MRI, radiology) • Automatic image assessment (detection and diagnosis) • Neurological evaluation and surgical planning • Linking of genetics factors with complex cognitive traits (personality, learning, attention) has potential for therapies and pharmaceutical clinical drug development

37. Leveraging Internet, HPC, and Grid Computing • Telemedicine imaging and neurology • Distributed EEG and MRI measurement and analysis • Neurological medical services • Shared brain data repositories • Remote and rural imaging capabilities • Need to enhance HPC and grid infrastructure in Oregon • Build on emerging web services and grid technology • Establish HPC resources with high-bandwidth networks • Create institutional and industry partnerships • UO is working closely with EGI to develop high-end EEG analysis services framework • Pilot neuroimaging services model on ICONIC Grid

38. Assistive Technology and Brain Injury Research • Technology for people with cognitive impairments • Navigation • Email • Trimet • Multi-disciplinary research • Prof. Steve Fickas, CIS • Wearable Computing Lab • Prof. McKay Sohlberg, Education • NSF grants • CogLink, Inc. • Startup company • http://www.go-outside.org/

39. Genomics and Bioinformatics • Research in comparative genomics analyzes similarities and differencesbetween orthologous genes • ortholog = “same word” • Zebrafish, salmon, and otherteleost fish often have twoorthologs of a single human gene • UO project: software to scanhuman chromosomes, identifyco-orthologs in zebrafish • Studying co-orthologs improvesour ability to understand functionsof genes, potential medical applications JohnConery(CIS) JohnPostlethwait(Neuroscience) Salmon calcitonin is up to 50 times more effective than human calcitoninin treating osteoporosis

40. Computational Paleontology • Dinosaur 3D modeling • DinoMorph modeling engine • Paleontology-based • Reconstructs true dimensions, poses,flexibility, and movements • Dinosaur species • Other domestic, wild, and fancifulanimals • Kaibridge, Inc. • Startup company • Dinosaur interactive museum exhibits • Dinosaur educational software • BBC online mystery game Photo by Rick Edwards, AMNH, 2006

41. UO Integrative Science • Discoveries of the 21th century will arise from integrative science • Evolution in how science is done • UO CAS is positioned at the forefront • Tradition of interdisciplinary and interdepartmental research • Institutes and centers report to UO Vice President for Research • Only Oregon member of Association of American Universities • Carnegie Foundation rates UO as having high research activity • Highlights • Institute of Molecular Biology  Institute of Theoretical Science • Materials Science Institute  Institute of Neuroscience • Oregon Center for Optics  Institute of Cognitive & Decision Science • Zebrafish Information Network  Brain, Biology, and Machine Initiative • Lewis Center for Neuroimaging / NIC  ONAMI

42. UO Integrative Science • UO Integrative Science Complex (ISC) • Catalyst for innovation • Bring leading researchers from diverse disciplines together • Biology  Neuroimaging • Geological Science  Cognitive Neuroscience • Materials Science  Computer Science • Green Nanoscience  Optics • Genomics  Molecular Biology • Two phase plan • Phase I: “From Nano to Neuro” • Fall 2007, $16M • Phase II • Estimated completion 2010-11, $50M

43. UO Integrated Science Complex - Phase I • Signature research center (Lokey Laboratory) • Oregon Nanoscience and Microtechnologies Institute (ONAMI) • High-tech extension service for ONAMI • “Best in class” facility for nanoscale research • Gold standard for minimal vibration • Encased in bedrock 19 feet below ground • Open to all Oregon institutions • Space for corporations to lease • Proprietary or collaborative research • Lorry Lokey • Chairman and CEO, Business Wire

44. UO Integrated Science Complex - Phase II • New ISC building • Uniting Streisinger, Huestis, and Deschutes Halls • New faculty research facilities • New classroom space • Facilitate interaction andintegrations across scientificdisciplines • Above-ground entrance to theLokey Laboratories • Focus on biological sciences Phase II Phase I