SURA Cyberinfrastructure Workshop:

Life Sciences and the Grid

Virginia Commonwealth University * Richmond, Virginia
January 9-11, 2006

   

About the Workshop

Background:

Research in the life sciences, mathematics and computing is at an important nexus driven by the generation of large volumes of rapidly expanding data and the capabilities of technology to share distributed data and resources. The core of this nexus affords researchers the opportunity to address large and complex problems, even model entire organisms. Grid technology, high-performance computing or “cyberinfrastructure” provides the ability to process, analyze, store, and share data on unprecedented scales. Synergy between these research disciplines enables “big” science through “team” science. This workshop endeavors to contribute to this synergy.

Audience:

The workshop aimed to benefit those involved in many areas of study including genomics, proteomics, transcriptomics, sequence analysis, neuroinformatics, image reconstruction and analysis, drug discovery, evolution and phylogeny, computational biology, networks and systems biology, molecular chemistry, structural bioinformatics, bio-ontologies, biological data modeling and integration, translational research, agriculture, zoology and more.

Attendees were NOT required to have prior knowledge or experience involving computer science, research computing or the grid.

The workshop addressed several topics of interest:

Click here for a downloadable Life Sciences and the Grid flyer.

Click here for a downloadable List of Attendees at the workshop.


Agenda

MONDAY, JANUARY 9, 2006

Location: Crowne Plaza Hotel - Grand Ballroom (click for map of hotel)

4:30-6:30 PM
Registration Open

5:30-7:00 PM
Reception

Welcome
Dr. Eugene P. Trani, President, Virginia Commonwealth University
Dr. Jerry P. Draayer, President & CEO, SURA

Keynote Address
"Building a Cyberinfrastructure for the Life Sciences"
Dr. John Wooley, Associate Vice Chancellor of Research, University of California, San Diego

Dr. Wooley is Associate Vice Chancellor for Research at the University of California San Diego, an adjunct Professor in Pharmacology, and in Chemistry and Biochemistry, and a Strategic Advisor and Senior Fellow of the San Diego Supercomputer Center. He received his Ph.D. degree in 1975 at The University of Chicago, working with Al Crewe and Robert Uretz in biological physics. Dr. Wooley created the first programs within the US federal government for funding research in bioinformatics and in computational biology, and has been involved in strengthening the interface between computing and biology for more than a decade. FULL BIO


TUESDAY, JANUARY 10, 2006

Location: Eugene P. and Lois E. Trani Center for Life Sciences
(click above for for map of Center and West Cary Street Parking Deck)
Virginia Commonwealth University

8:30-9:30 AM
Featured Speaker
"Virtual Organizations: Building Interdisciplinary Collaborations"
Daniel Reed, Ph.D., Director, The Renaissance Computing Institute (RENCI)

Dr. Reed is the Chancellor's Eminent Professor at the University of North Carolina at Chapel Hill, as well as the Director of the Renaissance Computing Institute (RENCI), a venture supported by the State of North Carolina as well as the University of North Carolina at Chapel Hill, Duke University and North Carolina State University. RENCI is exploring the interactions of computing technology with the science, arts and humanities. Reed also serves as the Vice-Chancellor for Information Technology and Chief Information Officer for the University of North Carolina at Chapel Hill. He recently led the computational science activity of the President's IT Advisory Committee, which produced a report on the relationship between computational science and economic competitiveness. FULL BIO ABSTRACT

Life Sciences Grid Initiatives

9:30-10:15 AM
"Vision and Infrastructure Behind the Cancer Biomedical Informatics Grid"
Peter Covitz, Ph.D., Director, Core Infrastructure, National Cancer Institute Center for Bioinformatics
BIO

10:30-11:15 AM
"The Global Bio Grid"
Andrew Grimshaw, Ph.D., Professor, Department of Computer Science, School of Engineering and Applied Science, and Director, Virginia Center for Grid Research, University of Virginia
BIO

11:15-11:30 AM
Question & Answers
Announcements
Mary Fran Yafchak, IT Program Coordinator, SURA

11:30 AM-12:15 PM
Virtual Tour: Center for the Study of Biological Complexity, Virginia Commonwealth University
Host: Gregory A. Buck, Ph.D., Director, Center for the Study of Biological Complexity,
Virginia Commonwealth University

12:15-1:45 PM
Lunch & "Ask a Grid Expert" Panel
Host: Francis L. Macrina, Ph.D., Vice President for Research, Virginia Commonwealth University
Dan Hushon, Chief Technologist, Sun Grid, Sun Microsystems
BIO
Elliot Lefkowitz, Ph.D., Associate Professor, University of Alabama at Birmingham
John Wooley, Ph.D., Associate Vice Chancellor of Research, University of California, San Diego
Daniel Reed, Ph.D. , Vice-Chancellor for Information Technology and CIO, University of North Carolina
Martín F. Maldonado, Ph.D., Senior Technical Architect, Grid & Virtualization, IBM Corporation
BIO

Parade of Life Sciences Research & Applications

1:45-2:30 PM
"Viral Evolution and Pathogenesis: The use of HPC/GRID Technologies to make intelligent biological inferences"
Elliot J. Lefkowitz, Ph.D., Associate Professor, Department of Microbiology and Director of the UAB Molecular and Genetic Bioinformatics Facility, University of Alabama at Birmingham
BIO ABSTRACT

2:30-3:15 PM
"AnimatLab: A Toolkit for Analysis and Simulation of the Neural Control of Behavior"
Ying Zhu, Ph.D., Assistant Professor, Department of Computer Science, Georgia State University
BIO ABSTRACT

3:30-4:15 PM
"Virtual Parasite Project - A Model for In Silico Laboratories in High Performance Computing Environments"
Tarynn M. Witten, Ph.D., MSW, FGSA, Director of Research and Development, Center for the Study of Biological Complexity, Virginia Commonwealth University

4:15-5:00 PM
"Cross Genome Comparison of Cell Death Regulation"
Lei Zhou, Ph.D., Assistant Professor, Department of Molecular Genetics and Microbiology
Member, UF Shands Cancer Center, College of Medicine, University of Florida
BIO ABSTRACT

5:00-5:30 PM
Discussion, Questions & Answers
Moderator: Daniel Reed, Ph.D.

6:00-7:30 PM
Location: Crowne Plaza Hotel - Grand Ballroom
Reception - Wine & Cheese


WEDNESDAY, JANUARY 11, 2006

Location: Eugene P. and Lois E. Trani Center for Life Sciences
(click above for map of Center and West Cary Street Parking Deck)
Virginia Commonwealth University

Towards Implementation

8:00-8:30 AM
"Instantiating MathBioGrid: A Mathematical Biologist's Perspective"
Tarynn M. Witten, Ph.D., MSW, FGSA, Director of Research and Development, Center for the Study of Biological Complexity, Virginia Commonwealth University
BIO ABSTRACT

8:30-9:00 AM
"Survey of Research and Funding Opportunities in Biomedical Computing"
Michael T. Marron, Ph.D., Director, Biomedical Technology, NIH, National Center for Research Resources (NCRR); NIH, Biomedical Informatics Research Network (BIRN)
BIO

9:30-10:00 AM
"Think Outside the PACS: Enterprise Grid Solutions for Medical Imaging"
Richard S. Bakalar, M.D., Chief Medical Officer, IBM Healthcare and Life Sciences
BIO ABSTRACT

10:15-10:45 AM
"Managing Gene Annotation Information: The search is over, one problem ends and another begins"
William Farmerie, Ph.D., Scientific Director, Interdisciplinary Center for Biotechnology Research (ICBR) Genome Sequencing Services Laboratory, University of Florida

BIO ABSTRACT

10:45 AM-11:45 PM
Panel: "Information Management and Computation Scheduling for Life Science Applications"
Charles Koelbel, Ph.D., Research Scientist, Department of Computer Science, Rice University
Sanjay Ranka, Ph.D., Professor, Department of Computer Science, University of Florida
BIO

11:45 AM-12:00 PM
Discussion, Questions & Answers
Moderator:
Tarynn M. Witten, Ph.D., MSW, FGSA

1:00-1:30 PM
"Cooperative Resource Management: Policies and Practices for Playing in the Sandbox"
Laura F. McGinnis,
Project Coordinator, Data & Information Resource Services, Pittsburgh Supercomputing Center
BIO ABSTRACT

1:30-2:30 PM
Panel: Industry Development
"Grids and Industry Objectives - How compatible are they?"
ABSTRACT
Moderator: Maciek Sasinowski, Ph.D., CEO, INCOGEN, Inc.
BIO
Susie Stephens, Ph.D., Principal Product Manager, Life Sciences, Oracle, Corp.
BIO
Loralyn Mears, Ph.D., Vice President for Genomics Alliances, Gene Logic, Inc.
BIO

Government

2:45-3:30 PM
The Military Health System: Managing Data to Improve Care (Note: This file is 22.3 Mgb)
Mr. Carl Hendricks, CIO, Military Health System, Department of Defense
BIO

3:30-4:00 PM
Discussion, Questions & Answers
Moderators:
Tarynn M. Witten, Ph.D., MSW, FGSA, Director of Research and Development, Center for the Study of Biological Complexity, Virginia Commonwealth University

4:00 PM
Adjourn


Presentation Abstracts and Speaker Bios

Dr. John Wooley, Associate Vice Chancellor of Research, University of California, San Diego
FULL BIO
Dr. Wooley is Associate Vice Chancellor for Research at the University of California San Diego, an adjunct Professor in Pharmacology, and in Chemistry and Biochemistry, and a Strategic Advisor and Senior Fellow of the San Diego Supercomputer Center. He received his Ph.D. degree in 1975 at The University of Chicago, working with Al Crewe and Robert Uretz in biological physics. Dr. Wooley created the first programs within the US federal government for funding research in bioinformatics and in computational biology, and has been involved in strengthening the interface between computing and biology for more than a decade. For the new UCSD California Institute for Telecommunication and Information Technology, Dr. Wooley directs the biology and biomedical layer or applications component, termed Digitally-enabled Genomic Medicine (DeGeM), a step in delivering personalized medicine in a wireless clinical setting. His current research involves bioinformatics and structural genomics, while his principle administrative objectives at UCSD are to stimulate new research initiatives for large scale, multidisciplinary challenges. He also collaborates in developing scientific applications of information technology and high performance computing; creating industry-university collaborations; expanding applied life science opportunities, notably around drug discovery; establishing a biotechnology and pharmacology science park on UCSD's health sciences campus zone.

Daniel Reed, Ph.D., Director, The Renaissance Computing Institute (RENCI)
FULL BIO
Professor Daniel A. Reed is Vice-Chancellor for Information Technology and Chief Information Officer for the University of North Carolina at Chapel Hill. He is also Director of the Renaissance Computing Institute (RENCI), an interdisciplinary center spanning the University of North Carolina at Chapel Hill, Duke University and North Carolina State University. RENCI is exploring the interactions of computing technology with the sciences, arts and humanities. A "Renaissance team" approach is bringing scientists, engineers, artists and institute staff together to explore interdisciplinary approaches to scholarship, discovery and education. The institute is also partnering with business leaders to enhance the competitiveness of North Carolina industries. He holds the Chancellor’s Eminent Professorship at the University of North Carolina at Chapel Hill, where he conducts interdisciplinary research in high-performance computing.
Dr. Reed was previously Director of the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign, where he also led National Computational Science Alliance, a consortium of roughly fifty academic institutions and national laboratories that is developing next-generation software infrastructure of scientific computing. He was also one of the principal investigators and the chief architect for the NSF TeraGrid. Professor Reed is also the former head of the Department of Computer Science at the University of Illinois, where he spearheaded more than $100 million in construction to create a new information technology quadrangle on the Illinois campus.
Dr. Reed is a member of President George W. Bush's Information Technology Advisory Committee, charged with providing advice on information technology issues and challenges to the president, a member of the Biomedical Informatics Expert Panel for the National Institute of Health's National Center for Research Resources and serves on the board of directors of the Computing Research Association, which represents the interests of the major academic departments and industrial research laboratories.

ABSTRACT
Legend says that Archimedes remarked, on the discovery of the lever, "Give me a place to stand, and I can move the world." Today, computing pervades all aspects of science and engineering. "Science" and "computational science" have become largely synonymous, and computing is the intellectual lever that opens the pathway to discovery.

Moreover, one aspect of computing distinguishes it from other scientific instruments - its universality as an intellectual amplifier. This talk will describe emerging opportunities in biomedicine where interdisciplinary applications of computing can have profound impact on discovery and creative expression. Key to enabling such activities is the creation of nimble and adaptive virtual organizations that can tap the best ideas and talent, regardless of geographic distribution. In turn, these virtual organizations require distributed infrastructure and capabilities that can function as an integrated whole. The resulting cyberinfrastructure promises to transform the day-to-day practice of science.

Peter Covitz, Ph.D., Director, Core Infrastructure, National Cancer Institute Center for Bioinformatics
BIO
Peter Covitz is currently Director of Bioinformatics Core Infrastructure at the NCI Center for Bioinformatics in Rockville, Maryland. Prior to joining the NCI, Dr. Covitz was Vice President of Professional Services at InforMax, Inc. where he ran the bioinformatics service and support division of the company. Earlier in his career Dr. Covitz worked as a research scientist and manager at Incyte Pharmaceuticals and Molecular Applications Group. Dr. Covitz did his graduate work on transcriptional regulation at Columbia University, and post-doctoral training in genomics and bioinformatics at Stanford University.

Andrew Grimshaw, Ph.D., Professor, Department of Computer Science, School of Engineering and Applied Science, and Director, Virginia Center for Grid Research, University of Virginia
BIO
Andrew S. Grimshaw is Professor of Computer Science at the University of Virginia and founder and former CTO of Avaki Corporation. Dr. Grimshaw received his M.S. and Ph.D. from the University of Illinois at Urbana-Champaign in 1986 and 1988 respectively. His research interests include grid computing, high-performance parallel computing, heterogeneous parallel computing, operating systems, and the use of grid computing in the life sciences. He is the chief designer and architect of Mentat and Legion. Legion is one of the earliest and largest grid computing projects in the world, and was the genesis for Avaki - the realization of production grids in a commercial setting. Dr. Grimshaw has published extensively on both parallel computing and grid computing and regularly speaks on grid computing around the world. He has served on the NPACI Executive Committee, the DoD MSRC PET (Programming Environments and Training) Executive Committee, the CESDIS Science Council, the NRC Review Panel for Information Technology, Board on Assessment of NIST Programs, and others. Dr. Grimshaw is currently a member of the Global Grid Forum Steering Committee and the Architecture Area Director in the GGF.

Lunch & "Ask a Grid Expert" Panel
Host: Francis L. Macrina, Ph.D., Vice President for Research, Virginia Commonwealth University
Dan Hushon, Chief Technologist, Sun Grid, Sun Microsystems
BIO
Dan Hushon is one of the Chief Technologists for the Utility Services business unit. He leads the technical architecture, cross-Sun alignment, and execution of Sun's utility computing strategy as it applies to application development and deployment. The manifestation of this model is Sun Grid, a pay as you go, multi-tenant isolated network of computing resources linked by a network operating system. Dan's specific expertise lies in the areas of adaptive enterprise architectures, distributed and distributable service oriented architectures (SOAs), and utility computing. Prior to his position as Chief Technologist, Dan was the Chief Technologist for US Client Solutions, Sun's field sales organization.

Since joining Sun in 1996, Dan has been involved in a variety of Enterprise Technology Insertion projects in the telecommunications, defense, financial and manufacturing vertical markets. These projects have leveraged distributed service based architectures to integrate legacy systems, while creating a loosely coupled environment to facilitate service re-use and provide architecture resiliency to constantly changing demand/load as well as service composition. Dan's consulting experience ranges a broad set of Sun technologies that include the Java Enterprise System, Java 2 MicroEdition (J2ME), Jini Connection Technology, Jxta, JavaCard, Edge, N1 and Blade services and deploying these technologies to a variety of enterprise infrastructure targets. The specific target markets have included wireless application and Internet Service Providers (WASP/WISP), Virtual Network Service Providers (VNSP), as well as broadband, digital television and traditional enterprise customers. To this end, Dan has engaged with several DoD program offices including US Navy SPAWAR, US Army MTMC and TACOM/NAC, US TRANSCOM GTN21, DARPA, through engagements with top Government System Integrators; as well as a number of commercial entities including Ford Motor Company, Telefonica Moviles, Sprint PCS, Vodafone, AT&T Wireless and others in the application of Sun's advanced technologies to solve critical business challenges with respect to dynamic, deterministic service based networks.

Prior to Sun, Dan spent more than 5 years growing a DoD/commercial products effort (focused on MPP Signal Processing) for a mid-sized government consulting firm. With more than 16 years of software development expertise in the areas of Object Oriented Analysis & Design, embedded system/ real-time software development, and massively parallel processing. An alumnus of Carnegie Mellon University where he worked in Computational Bio-Physics, and the Capability Maturity Model (CMM) which was under development at the SEI; Dan continues to be involved with measurable development and architectural methodologies.

Dan has extensive experience in distributed object technology including RPC/OORPC,CORBA, RMI, Java 2 Enterprise Edition, Jini, Jxta/P2P, as well as around Web Services and the J2ME platforms, and helping Sun customers with the successful deployment of these technologies through the application CMM/Six Sigma techniques.

Martín F. Maldonado, Ph.D., Senior Technical Architect, Grid & Virtualization, IBM Corporation
BIO
Dr. Martin F. Maldonado is an IBM Certified Specialist in Grid Computing Technical Sales in the Grid Computing Americas Team, with a focus on Higher Education and Research. He advises customers on the use of grid technology and architecture. In addition to Grid Computing, he has technical consulting experience in e-business application design, development and implementation, which includes system integration. Martin has a background in manufacturing, distribution, transportation, US shipbuilding, Defense and education industries. Previously, Martin was a member of the team developing WebSphere Commerce Suite and Catalog Architect, where he worked with suppliers in the US shipbuilding industries to build electronic product catalogs supporting their e-business initiatives with shipyards. He received an IBM Invention Achievement Award First Plateau for patent submissions and technical disclosures in such areas as electronic data interchange (EDI) and data modeling. Also, he is IBM Certified for e-business -Solution Designer, IBM Certified Solution Developer - XML and related technologies and Certified Computing Professional (CCP) from the Institute for Certification of Computing Professional. Martin received a Ph.D. in Information and Computer Science from the Georgia Institute of Technology.

Elliot J. Lefkowitz, Ph.D., Associate Professor, Department of Microbiology and Director of the UAB Molecular and Genetic Bioinformatics Facility, University of Alabama at Birmingham
BIO
Elliot Lefkowitz, Associate Professor, Department of Microbiology and Director of the UAB Molecular and Genetic Bioinformatics Facility, received his B.S. degree in Microbiology at the University of Maryland-College Park in 1977. He received his PhD in Microbiology from the University of Texas Medical Branch-Galveston in 1983 where he studied the regulation of interferon-gamma activity. He continued his training as a postdoctoral fellow at the University of Wisconsin-Madison where he participated in research projects involving the cloning of interferon-inducible genes and the molecular biology and evolution of vaccinia and vesicular stomatitis viruses. Dr. Lefkowitz came to UAB in 1987 and in 1991 became director of the UAB AIDS Center Biological Computing Resource Facility that is now part of the institution-wide Molecular and Genetic Bioinformatics Facility. His current work includes research on microbial genomics and evolution, and the development of bioinformatics resources (databases, analytical tools, and web-based interfaces) to support these interests.

ABSTRACT
Poxviruses, including variola virus the causative agent of smallpox, are highly successful pathogens known to infect a variety of hosts.
Studies of orthologous genes have established the basic evolutionary relationships of members within the Poxviridae family. It is not clear however, how variations between family members arose in the past - an important issue in understanding how these viruses may vary in the future, possibly producing new or re-emergent pathogens. As the first step in performing a comprehensive comparative analysis of poxvirus species, and to support the consistent annotation of poxvirus genomic sequences, we developed the Poxvirus Genome Annotation System (PGAS). This tool combines various measures intrinsic to the poxvirus genomic sequence as well as extrinsic measures derived from comparative analyses to provide an assessment of the overall coding potential of every putative poxvirus gene. This then allowed us to more accurately predict the complete genetic complement of all poxvirus genomes.

PGAS utilizes several newly developed analytical applications that are based on HPC (High performance Computing), and in the future, GRID technologies, to make the various analyses computationally feasible. The genome annotations resulting from the use of PGAS were used as the basis for a comprehensive assessment of poxvirus pathogenecity and evolution. The results of this analysis supports a theory of reductive evolution in which a reduction in size of the core gene set of a putative ancestral virus played a critical role in virus speciation, host range, and pathogenecity. Novel genes originating from duplication and modification, as well as genes captured from the host cell, further determine the biology of each particular species. In addition, based on a study of poxvirus promoters, we have determined that most of the highly conserved housekeeping genes in the conserved central region of each genome have highly conserved-if not identical-promoters. However genes outside the conserved central region not only vary in their primary amino acid sequence, but also show significant variation in the core regions of their predicted promoters. This finding suggests that the expression levels of these genes might vary from one virus to another and that each virus will likely display a unique gene expression profile.

Finally, in collaborations with several other groups, we have used these techniques in a comparative study of the genomic sequences of several Monkeypox virus isolates, including an isolate obtained during the outbreak that occurred in the Midwest United States in the spring of 2003. These studies showed that the U.S. isolate was similar in sequence and pathogenecity to West African Monkeypox isolates. In addition, the reduced pathogenecity of these isolates in comparison to Central African isolates, putatively maps to a Monkeypox gene involved in inhibition of the host's immune defenses.
These results represent just a few examples of ongoing and future work that is designed to enhance our understanding of microbial pathogenesis and evolution. These efforts are increasingly dependent on large datasets and our ability to rapidly analyze those datasets.
And it is through the availability of HPC and GRID technologies that these analyses become feasible.

Ying Zhu, Ph.D., Assistant Professor, Department of Computer Science, Georgia State University
BIO
Ying Zhu is an assistant professor in the Department of Computer Science at Georgia State University (GSU). He received his PhD in Computer Science from George Mason University in 2000. Before joining Georgia State University in 2003, he was a senior software developer at Computer Associates International (Dallas, TX). Dr. Zhu's main research interest is in 3D computer graphics, visualization, and their applications in biology. At GSU, he is collaborating with biologists in several bioinformatics projects, ranging from computational neuroscience simulation, visualization, to collaborative molecular modeling. Dr. Zhu is a member of ACM and SIGGRAPH.

ABSTRACT
A central goal of neuroscience is to understand how the nervous system is organized to control behavior. This control must be dynamic and depend on a constant dialog between sensory feedback and motor commands. Despite the importance of this dynamic relationship between nervous function and behavior, it is poorly understood because of technical limitations in our ability to record neural activity in freely behaving animals. This is true for crayfish escape behavior, where some 300 identified central neurons and many more primary afferents have been identified and described, and their patterns of synaptic connection have been mapped into apparently functional neural circuits. However, the ability of these crayfish circuits, and sensory-motor circuits in all other animals, to account for freely moving behavior remains untested, and the requirements for dynamic control of behavior remain unexplored.
AnimatLab is a 3D computer graphics environment for neurobiologists to visualize and test computational models of neurons, neural circuits, and their control of a model animal’s behavior in a physics-based virtual world in real time. Through real-time computer graphics simulation, AnimatLab can help formalize and test hypotheses about functional relationships between components of a nervous system. We are using AnimatLab to create a model of the crayfish and its neural circuits for escape that is based on experimental analyses of the escape circuitry, the structure and properties of the exoskeleton and its musculature, and the kinematics of escape behavior. The behavior of the model crayfish will be governed by the interactions of model neurons in networks that link sensory inputs to motor outputs. The motor outputs will be translated into muscle forces, which, together with external gravitational, friction and inertial forces, will drive the physics-based real-time animation of a 3D crayfish model. The completed system will be a behavior-driven, physics-based virtual crayfish that will be tested to identify those aspects of the neural and body structure and function that govern the triggering, execution, and dynamic control of escape behavior. We are also improving AnimatLab to make it more versatile and transparent, and useful for researchers to study and teachers to illustrate the dynamic control of behavior in a variety of organisms. The next generation AnimatLab will take advantage of the Grid infrastructure at Georgia State University to improve the performance of its simulation.

Lei Zhou, Ph.D., Assistant Professor, Department of Molecular Genetics and Microbiology
Member, UF Shands Cancer Center, College of Medicine, University of Florida
BIO
Dr. Lei Zhou received his medical degree (1991) from Beijing Medical University in China and his Ph.D. (1997) from University of Massachusetts at Amherst. He then moved to MIT for postdoctoral training, working on genetic regulation of programmed cell death (apoptosis). At MIT he developed a set of computer programs that helped to uncover the conservation of cell death regulatory genes in the genetic model organism Drosophila melanogaster. He joined the faculty at University of Florida College of Medicine in 2001. Research work conducted in his group focuses on the understanding of the molecular mechanisms that mediate irradiation induced cell death. High performance computer (Grid) was utilized for large scale cross genome comparison studies, which helped to elucidate the conservation and regulation of pro-apoptotic genes.

ABSTRACT
Programmed cell death (PCD) is an essential biological process whereby a damaged or obsolete cell undergoes suicide through a morphological ritual termed "apoptosis". Proper regulation of apoptosis is important for animal development as well as tissue homeostasis. The execution of apoptosis is carried out by a special kind of protease called Caspases (Cysteine aspartic acid-specific proteases), which are present in all cells but remain dormant in live ones. The activation of caspases leads to the destruction of the cell and it is under the control of multiple regulatory pathways.
Cross genome comparison of these pathways revealed interesting facts that shed light for our comprehensive understanding of this system.

Tarynn M. Witten, Ph.D., MSW, FGSA, Director of Research and Development, Center for the Study of Biological Complexity, Virginia Commonwealth University
BIO
Dr. Tarynn M. Witten is a Fellow of the Gerontological Society of America and holder of the Inaugural Nathan W. and Margaret Shock New Investigator Research Award for her work on the use of supercomputing algorithms to study the effects of sample size estimation on mortality patterns in different animal species. She holds simultaneous appointments of Associate Professor of Biological Complexity at the Center for the Study of Biological Complexity, Associate Professor of Emergency Medicine, and Adjunct Associate Professor of Gerontology and Social Work, and is on the Research faculty of the Department of Biostatistics at Virginia Commonwealth University-Medical College of Virginia Campus. Additionally, she serves as Senior Fellow and Director of Research and Development, and Director of the Center for Advanced Scientific Computation at the Center for the Study of Biological Complexity, Virginia Commonwealth University. She was recently awarded Apple Computer Corporation’s 2005 Distinguished Educator of the Year Award for her use of high performance computing in teaching. She is listed in Who's Who In International Science - 1989/90, Who's Who In Computing - 1989/90, Who's Who In Health & Medicine-1990/91, Who's Who Worldwide - 1990/93/94, Who's Who In Science And Engineering - 1992/93/94, Who's Who In The South And Southwest - 1992/94/97, Who's Who In American Education - 1993/94, International Who's Who of Information Technology 1996/1997, Who’s Who In the World 2000, International Who’s Who of Professionals 2000, and as one of the Top 2000 Women Scientists in the World 2001.

Dr. Witten has presented over 200 international scientific talks on aging-related issues, mathematical modeling and simulation, and the role of high performance computation in medicine and has written over 100 papers on mathematical modeling and computer simulation of aging processes, high performance computing in medicine, and mathematical models of biomedical processes. She is the ongoing author of the Encyclopedia of Computer Science entry on Computational Biology and Medicine and has worked for such companies as ETA Systems, Control Data Corporation and served as a consultant for Amgen, Eli Lilly, Merck, Smith Kline French, Amdahl, Cray Computing, MassPar, Thinking Machines, and numerous other corporate high performance computing-related companies. She was the former Director of Applications Research and Development and Associate Director of the University of Texas System Center for High Performance Computing where she founded the GenTools Project™ (the first public domain, multi-platform, transparent computing, genomic analysis environment), initiated collaborative efforts with Los Alamos for the first internet based automated download of GenBank, served as one of the original NSF/NIH Supercomputer Center reviewers, and currently serves as a grant reviewer for both NIH and the MRC (England). She has also served as a consultant to the NSF/DOE Collaboratories Project. Since the 1990’s, she has organized numerous sessions at the various Supercomputing World conferences as well as Supercomputing 1991. In 1994 she organized and chaired the First World Congress on Computational Medicine, Public Health, and Biotechnology at which the Affymetrix Chip group had its first meeting. Her work has appeared in Supercomputing World, Unix Today, Computer Graphics, SunWorld, and numerous other computer trade magazines. She was an active member of MacSciTech. She was one of the first supercomputing futurists to talk about grid computing for the development of ultra-large scale simulation models of the human. She coined the term “bionanoids” as a descriptor of nano-scale biocompatible robots, and is currently the conceptual designer and project leader of the first “in silico experimental laboratory,” the Virtual Parasite Project at the VCU.

In her spare time, Dr. Witten is a composer and conductor. She has recently released her first CD entitled Vox Spiritualis and has composed a commissioned oboe sonata entitled “Oboe Sonata in π/e” for the former first oboist of the Austin Symphony Orchestra. Some of her other pieces include “Bugged 1.0: A Piece for Insect Robots” and “Flight of the Relativistic Bumblebee.” She has also served as an invited poet at the Austin International Poetry Festival.

ABSTRACT
Infectious diseases, in spite of antibiotic and other treatments, remain one of the biggest medical problems to date. The overall problem of understanding host-parasite dynamics is extremely important, as it is intrinsic to the study of infection at all organismal scales. Many examples of such host-parasite systems exist, with debilitating and/or fatal consequences for humans all over the planet; malaria, schistosomiasis, and Chagas’ Disease, for example. Epidemiologically, it is estimated that around 2 billion people are estimated to harbor STH and schistosomiasis worms. Morbidity estimates are that 300 million individuals are severely ill with worms, of which 50% are school-age children. Mortality estimates, for Africa alone, find that the death toll due to schistosomiasis may be as high as 200,000 per year. Despite recent advances in the control of Chagas Disease, millions of Latin Americans and numerous US citizens remain at risk for infection with the T. cruzi parasite, the causal agent in Chagas Disease. In terms of disability adjusted life years, Chagas Disease is globally ranked behind only malaria and schistosomiasis as the most serious parasitic diseases worldwide. Twelve species of triatomines are known to occur in the United States, the most important being Triatoma sanguisuga in the eastern United States, Triatoma gerstaeckeri in the region of Texas and New Mexico, and Triatoma rubida and Triatoma protracta in Arizona and California. Because of its complex life cycle, T. cruzi provides one of the most fascinating and complex, yet sophisticated initial model systems for investigation. American trypanosomiasis, or Chagas disease, is a protozoan zoonotic disease caused by the haemoflagellate Trypanosoma cruzi, and is transmitted to humans either by bloodsucking triatomine vectors, blood transfusion or congenital transmission. This parasite infects over 150 species from 24 families of domestic and wild mammals, as well as humans. In the vertebrate host, T. cruzi infects many different cells, but in the human host, the disease is conspicuously limited to the myocardium and to gut nerve fibers. Chagas disease is present in 18 countries on the American continent in two different ecological zones. Countrywide cross-sectional surveys in the 1980s found an overall prevalence of 17 million cases, with 4.8–5.4 million people exhibiting clinical symptoms, an annual incidence of 700,000-800,000 new cases and 45,000 deaths due to the cardiac form of the disease. Other studies indicate an infection prevalence of 13 million, with 3.0–3.3 million symptomatic cases and an annual incidence of 200,000 cases in 15 countries, with estimates of death around 50,000 people. Despite nearly 100 years of research on the T. cruzi parasite, we still understand very little about its dynamics.

Michael T. Marron, Ph.D., Director, Biomedical Technology, NIH, National Center for Research Resources (NCRR); NIH, Biomedical Informatics Research Network (BIRN)
BIO
Dr. Marron is Director of the Division of Biomedical Technology in the National Center for Research Resources at the National Institutes of Health with responsibility for supporting research, development, and access to sophisticated technologies at resource centers nationwide and grants for acquisition of state-of-the-art instrumentation. Areas of emphasis include high performance computing, molecular and cellular structural biology technologies, noninvasive imaging and spectroscopy, and mathematical modeling and computer simulations.

Richard S. Bakalar, M.D., Chief Medical Officer, IBM Healthcare and Life Sciences
BIO
Richard Bakalar joined IBM Healthcare and Life Sciences team after 26 years service in the US Navy Medical Corps. He has extensive experience in clinical medicine, diagnostic imaging, military medical flight operations, and applied information technology. He is board certified in both Internal and Nuclear Medicine. Dr. Bakalar served as the Executive Assistant to Navy Surgeon General for Global Telemedicine initiatives. He established the Naval Telemedicine Business Office to coordinate Navy wide Telehealth activities to design, budget, field and manage a Global Digital Teleradiology PACS network for 30 Navy ships, 23 shore-based medical facilities and three medical centers. Dr. Bakalar is a subject matter expert to the National Research Council and has been a panelist, which conducts annual independent assessments of NIST (Information Technology Laboratory -Division Software Diagnostics and Conformance Testing). He is the President-elect of the American Telemedicine Association and has chaired its committee on Standards and Guidelines. Dr. Bakalar has medical imaging experience in digital Radiology, Cardiology, Pathology and Retinal Imaging.
Dr. Bakalar is the Chief Medical Officer in the Information Based Medicine Emerging Business Opportunities Unit of IBM's Healthcare and Life Sciences Industry Team. He is the senior clinical advisor to the US and Canadian Business Consulting Services Healthcare teams which have hosted informational workshops and seminars. He has consulted in enterprise diagnostic imaging strategic planning engagements in British Columbia, New Brunswick, Alberta and Ontario. As a medical leader in the clinical transformation process, Dr. Bakalar has facilitated regional health authority clinical focus groups to elicit clinical imperatives and best practices. These key business drivers establish the functional basis and medical business case for an enterprise Diagnostics ON DEMAND collaborative framework compliant with local, regional and national healthcare policies and regulations.
Dr. Bakalar graduated from Rice University in 1977 with an emphasis in Biology, Psychology and Computer Science. He graduated from the USUHS (DoD), in Bethesda, MD in 1982 (M.D)

ABSTRACT
The business objective to share DICOM-compliant medical imaging studies across multiple medical facilities inside and outside of hospital firewalls is significant technical challenge. Fortunately there are proven software (middleware) breakthrough innovations in Grid Computing to address this real-world technical challenge today. For example, new DICOM-aware grid storage system solutions enable Radiologists, clinicians and life science researchers from disparate locations to dynamically and reliably share Radiology or other medical imaging studies with existing hybrid hardware storage archives and multiple DICOM-compliant PACS viewing applications. Performance and network security is enhanced with predefined best practices configuration business rules. Grid storage systems permit authorized end users to securely request (DICOM Query and Retrieve) studies from an expanded virtual storage archive across traditional enterprise boundaries without having to change their preferred DICOM-compliant PACS viewer.

In addition to expanded secure user access to patient studies, these grid storage systems permit improved and more efficient system administration, improved study availability without inconvenient scheduled maintenance downtimes and enhanced network reliability. Built-in software tools consolidate, simplify and automate storage system administration from a single web enabled desktop dashboard. Automated routine maintenance and system administration functions include workload leveling, data streaming and Smart caching for improved network performance, auto-routing of data to the appropriate hardware storage class device to optimize data access and equipment component costs, routine decentralized multi-copy data back-up configurations, scheduled data migration from obsolete hardware, and dependable disaster recovery.

In summary these new Grid Storage Systems offer affordable and improved user access to patient imaging studies over an expanded enterprise virtual network; enhanced technical security and system administration; and reduced aggregate total cost of ownership of an expanded enterprise PACS archive infrastructure.

For more detailed information: IBM Grid Medical Archive Solution, http://www-1.ibm.com/businesscenter/smb/us/en/xslpage/xmlid/33017,
http://www-03.ibm.com/industries/healthcare/doc/content/solution/1384520305.html

William Farmerie, Ph.D., Scientific Director, Interdisciplinary Center for Biotechnology Research (ICBR) Genome Sequencing Services Laboratory, University of Florida
BIO
Dr. William Farmerie is the Scientific Director of the Molecular Services Group of the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida. The ICBR is a campus-wide research-support organization developing and operating centralized core facilities for large-scale DNA sequencing, gene transcription analysis, and computational manipulation of gene sequence and gene expression information.

ABSTRACT
Over the last 20 years the cost-efficiency of production-oriented DNA sequencing follows a near exponential increase. The recent introduction of the 454 Life Sciences ( Branford, CT) GS-20 DNA sequencing instrument exemplifies the trend toward faster and more cost efficient, genome-scale DNA sequencing. The GS-20 promises a hundred-fold increase in DNA sequence production at less than one tenth the cost of conventional dideoxy terminator-based methods. New DNA sequencing technologies currently in development promise even greater productivity gains. As DNA sequencing cost declines, gene-based investigation becomes accessible to a greater number of scientific applications. Large-scale DNA sequencing is only the first step on the path of gene-based investigation. Nucleotide sequences must be annotated as much as possible to identify genes and assign possible biological roles or functions, The annotation process typically begins with homology-based searches using applications like BLAST or HMMER of public databases such as SwissProt or GenBank. Scaleable computer clusters and grids provide the power to perform homology searches in a reasonable time scale. The amount of annotation information generated by even a moderate DNA sequencing project poses numerous challenges. Centralized databanks and information management is a logical extension of core lab function. We developed several web-based tools helping scientists and their collaborators with this data management challenge.

Sanjay Ranka, Ph.D., Professor, Department of Computer Science, University of Florida
BIO
Sanjay Ranka is a Professor in the Department of Computer Science. He is a world-renowned technologist in the areas of large-scale software systems, high performance networking, interactive marketing, CRM, data mining and optimization. Most recently he was the Chief Technology Officer at Paramark where he developed real-time optimization software for optimizing marketing campaigns. Sanjay has also held positions as a tenured faculty positions at Syracuse University and as a researcher/visitor at IBM T.J. Watson Research Labs and Hitachi America Limited.
Sanjay earned his Ph.D. (Computer Science) from the University of Minnesota in 1988 and a B. Tech. in Computer Science from IIT, Kanpur, India in 1985. He has coauthored two books: Elements of Neural Networks (MIT Press) and Hypercube Algorithms (Springer Verlag), 40+ journal articles and 100+ conference and workshop papers. He serves on the editorial board of the Journal of Parallel and Distributed Computing and was a past member of the Parallel Compiler Runtime Consortium and the Message Passing Initiative Standards Committee. He was one of the main architects of the Syracuse Fortran 90D/HPF compiler. He is a fellow of the IEEE, advisory board member of IEEE Technical Committee on Parallel Processing and a member of IFIP Committee on System Modeling and Optimization.

Laura F. McGinnis, Project Coordinator, Data & Information Resource Services, Pittsburgh Supercomputing Center
BIO
Laura McGinnis is a project coordinator at the Pittsburgh Supercomputing Center. Her primary area of focus is leading teams of developers addressing system and site administration challenges in high-performance computing. She has been with PSC for 9 years, and involved in grid computing since 1999. She holds a Bachelor of Science in Computer Science from the University of Pittsburgh and a Master of Science in Industrial Administration from the Tepper School of Business at Carnegie Mellon University.

ABSTRACT
Many grid resource providers are finding that building the systems and keeping them running are often the easier part of providing a production-quality grid computing experience. Surprisingly, the bottlenecks are often in softer areas like accounting and project management. Working under the premise that "forewarned is forearmed", this presentation highlights areas that put grid initiatives at risk and offers suggestions which could mitigate some of these risks as grid computing evolves. In particular, we will examine some of the policies and practices developed while making the SABER grid available to researchers for energy applications in southwestern Pennsylvania and West Virginia.

Panel: Industry Development
"Grids and Industry Objectives - How compatible are they?"

ABSTRACT
Recent advances in genomics and proteomics have greatly increased our understanding of the molecular basis for functions of organisms. However, the characterization of single genes or proteins has provided only limited insight and benefits toward early diagnoses, improved subtyping and prognoses, and treatment of diseases. To understand the intricate web of interactions that makes up the biological functioning of life, we must try to decipher how a gene or protein fits into this dynamic environment with thousands of other genes and proteins. A comprehensive understanding of biological phenomena can only be pursued through the melding of information and insights from technologies that characterize genes and proteins at the level of sequence, transcription, regulation, structure, function, kinetics, and localization. This integration of knowledge requires a departure from conventional approaches toward life science research and is only possible by combining state-of-the-art technologies and enabling knowledge exchange from traditionally divergent fields such as molecular biology, clinical research, computational science, physics, statistics, and hardware engineering. To this end, grid technology infrastructure provides the ability to store, share, and analyze data on unprecedented scales. However, significant challenges remain, such as the semantic integration of the available information as well as concerns about data sharing and intellectual property. These challenges combined with perhaps unrealistic expectations may be impeding the adoption and enthusiasm of industry researchers toward grid-enabled technologies. During the panel, we will address industry perspectives toward grid computing and discuss grid-enabling applications and their challenges.

Maciek Sasinowski, Ph.D., CEO, INCOGEN, Inc.
BIO
Maciek Sasinowski earned a Ph.D. in computational plasma physics from The College of William and Mary. Prior to his work in bioinformatics, he developed the delta-f Monte Carlo algorithm used to predict the behavior of thermonuclear fusion plasmas. The algorithm constitutes a 10,000-fold improvement in computational speed over traditional Monte Carlo algorithms used in the field.
In 1996, Dr. Sasinowski was appointed to establish the Bioinformatics Center at the Clemson University Genomics Institute. There, he attracted a staff of twenty scientists and technicians and directed the bioinformatics infrastructure to support the research and production work of 85 scientists.
In 1998, Dr. Sasinowski founded INCOGEN. He was one of the founding members of the Integrated Informatics Infrastructure Consortium (I3C) and continues to play leading roles in community efforts such as the National Cancer Institute Cancer Biomedical Informatics Grid (caBIG). In 2001, Dr. Sasinowski was chosen by the Genome Technology magazine as one of the 15 most influential people in the field of genomics under the age of 30. More recently, he was voted among the top three most influential people in genomics tool development in an Internet survey conducted by GenomeWeb. Dr. Sasinowski is a member of the Governor's Technology Transition Policy Committee and serves as the Chair of the Board of Directors of the Virginia Biotechnology Association (VABio).

Susie Stephens, Ph.D., Principal Product Manager, Life Sciences, Oracle, Corp.
BIO
Dr. Susie Stephens joined Oracle in 2002 to lead the development of the Database, Application Server and Collaboration Suite, to further enhance their capabilities as a powerful infrastructure platform and analytical engine for drug discovery. In 1998, following a molecular biology post-doc and physiology Ph.D., she joined Sun Microsystems as a Pre-Sales Systems Engineer aligned to the pharmaceutical industry. In 2000, she was promoted to the global position of Life Sciences Market Segment Manager at Sun, where she played a key role in establishing Sun's presence in the life sciences industry. Her technical roles at Oracle and Sun Microsystems, combined with her life sciences background, enable Dr. Stephens to have a valuable perspective on the application of IT to drug discovery.

Loralyn Mears, Ph.D., Vice President for Genomics Alliances, Gene Logic, Inc.
BIO
Dr. Mears is an experienced technical market and business development specialist formally trained as a molecular biologist, with nearly ten years of experience in the industry. As Gene Logic’s Vice President of Genomics Alliances, she is responsible for managing key relationships important to the growth of the Genomics business unit. She is tasked with establishing new alliances to broaden selling and marketing efforts through indirect channels and will be looking to in-license new and innovative technologies, solutions and products to augment the existing Genomics offerings. Dr. Mears comes to Gene Logic after successfully establishing and managing Sun Microsystems’ life sciences program. She had a major influence in defining Sun as a premiere platform partner of discovery solutions. In the past, she served as a scientific applications consultant at NetGenics and helped them grow from a start-up until they were later acquired by LION Biosciences.
Dr. Mears earned her Ph.D. in molecular biology from Case-Western Reserve University & Queens’ University, Canada. Her academic career has provided a combination of scientific research and use of experimental technologies that make her an authority in this field. Her research and articles have been published in academic, scientific and media publications and she has given numerous presentations and interviews worldwide.

Mr. Carl Hendricks, CIO, Military Health System, Department of Defense
BIO
Mr. Carl E. Hendricks began serving in August 2005 as the Chief Information Officer for the Military Health System (MHS) and Director of the Information Management, Technology and Reengineering Directorate for the TRICARE Management Activity (TMA). He is the principal advisor to Department of Defense medical leaders on all matters related to information management, information technology (IT), information protection, enterprise architecture, IT capital investment and IT strategic planning. He works closely with Army, Navy and Air Force deputy surgeons general, and the executive director of TMA to ensure MHS health IT programs are well managed, comply with applicable statutes and policies, and align with the objectives of the MHS.

Mr. Hendricks is a former Colonel in the Army Medical Service Corps, who served in a variety of positions spanning 26 years of military service, with a concentration of experience in medical information technology and acquisition management. Most recently, he was the Chief Information Officer for the Arizona Telemedicine Program, and at the same time, through an Intergovernmental Personal Assignment, he was a Special Assistant to the Director of the Telemedicine and Advanced Technology Research Center, a division of the Medical Research and Materiel Command at Fort Detrick, MD. In his last assignment prior to retiring from the Army, he was appointed by the Assistant Secretary of Defense for Health Affairs to serve as the Program Executive Officer, Joint Medical Information Systems Office, in August 2000. Prior to that assignment, he served as the Chief Information Officer for the Office of the Army Surgeon General and the Assistant Chief of Staff for Information Management, U. S. Army Medical Command. Mr. Hendricks has returned to public service in the Department of Defense, having been appointed to the Senior Executive Service.

Mr. Hendricks graduated with a Bachelor’s Degree in Public Administration from the University of Arizona in 1975. In 1989 he received his first Master’s Degree from Boston University, with a focus on Business Administration. He earned his second Master’s Degree in Biomedical Engineering from Worcester Polytechnic Institute in 1992. In addition, he was awarded full certification by the Army in the functional specialty of Program Management through the Defense Acquisition University.

Mr. Hendricks is a member of the Order of Military Medical Merit, the Project Management Institute, the Association for the Advancement of Medical Instrumentation, and the Institute of Electrical and Electronic Engineers.

Mr. Carl E. Hendricks began serving in August 2005 as the Chief Information Officer for the Military Health System (MHS) and Director of the Information Management, Technology and Reengineering Directorate for the TRICARE Management Activity (TMA). He is the principal advisor to Department of Defense medical leaders on all matters related to information management, information technology (IT), information protection, enterprise architecture, IT capital investment and IT strategic planning. He works closely with Army, Navy and Air Force deputy surgeons general, and the executive director of TMA to ensure MHS health IT programs are well managed, comply with applicable statutes and policies, and align with the objectives of the MHS.

Mr. Hendricks is a former Colonel in the Army Medical Service Corps, who served in a variety of positions spanning 26 years of military service, with a concentration of experience in medical information technology and acquisition management. Most recently, he was the Chief Information Officer for the Arizona Telemedicine Program, and at the same time, through an Intergovernmental Personal Assignment, he was a Special Assistant to the Director of the Telemedicine and Advanced Technology Research Center, a division of the Medical Research and Materiel Command at Fort Detrick, MD. In his last assignment prior to retiring from the Army, he was appointed by the Assistant Secretary of Defense for Health Affairs to serve as the Program Executive Officer, Joint Medical Information Systems Office, in August 2000. Prior to that assignment, he served as the Chief Information Officer for the Office of the Army Surgeon General and the Assistant Chief of Staff for Information Management, U. S. Army Medical Command. Mr. Hendricks has returned to public service in the Department of Defense, having been appointed to the Senior Executive Service.

Mr. Hendricks graduated with a Bachelor’s Degree in Public Administration from the University of Arizona in 1975. In 1989 he received his first Master’s Degree from Boston University, with a focus on Business Administration. He earned his second Master’s Degree in Biomedical Engineering from Worcester Polytechnic Institute in 1992. In addition, he was awarded full certification by the Army in the functional specialty of Program Management through the Defense Acquisition University.

Mr. Hendricks is a member of the Order of Military Medical Merit, the Project Management Institute, the Association for the Advancement of Medical Instrumentation, and the Institute of Electrical and Electronic Engineers.


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