Technical Programs

Monday, August 13, 2007


8:30AM-9:30AM, Registration (SC Engineering Building)
9:30AM-9:40AM (Room 1505 SC, Engineering Building's Large Auditorium): Conference Opening Opening: by Dr. Jun Ni, Program Chair of IMSCCS|07
Theme: Cyberinfrastructure-enabled "Dynamic Computing" for Multi-disciplinary Research
9:40AM-9:45AM (Room 1505 SC, Engineering Building's Large Auditorium): Welcome Message by Dr. Sally Mason, President of the University of Iowa
9:45AM-10:45AM: Invited Keynote Talks:
Title: –  Future Cyberinfrastructure available today and used by over 24,000 users
( (presentation)

Speaker: Dr. Gerhard Klimeck, Professor and Technical Director, NSF - Network for Computational Nanotechnology (NCN), Purdue University, W. Lafayette, IN

Abstract. The National Science Foundation envisions future cyberinfrastructures to be built on the four pillars of virtual organizations, high performance computing, visualization and data. embodies such a cyberinfrastructure today that serves over 24,000 users worldwide on an annual basis.  Over 5,500 of these users have run over 217,000 simulations, including HPC-based runs and visualized date interactively. nanoHUB is used by all top 50 engineering schools.  Over 50 applications are available online ranging from toy models to sophisticated simulation engines. The nanoHUB provides the resources for modeling, simulating and computing without any software installation to users with access to a web browser.  All nanoHUB services are freely open to the public. The nanoHUB represents a community–based, service–oriented, science architecture that leads the way for new cyberinfrastructure-enabled science. We have identified 81 citations in the literature by non-nanoHUB affiliated scientists and engineers.

This presentation will provide a nanoHUB overview and demonstrate how effective, user-friendly cyberinfrastructure can bridge education and research seamlessly for computational experts, experimentalists, educators, and students.  The development and deployment of the nanoelectronic Modeling Tool (NEMO 3-D) in the nanoHUB with its capability to perform multi-million atom electronic structure calculations on high-end HPC platforms as well as rapid second-fast executions in an educational module will be highlighted.  The presentation will conclude with a vision for future expansions into other HUBs for other fields.

Biosketch: Gerhard Klimeck is the Technical Director of the Network for Computational Nanotechnology at Purdue University and a Professor of Electrical and Computer Engineering since Dec. 2003. He was the Technical Group Supervisor of the High Performance Computing Group and a Principal Scientist at the NASA Jet Propulsion Laboratory. His research interest is in the modeling of nanoelectronic devices, parallel cluster computing, and genetic algorithms. Gerhard developed the Nanoelectronic Modeling tool (NEMO 3-D) for multimillion atom simulations. Previously he was a member of technical staff at the Central Research Lab of Texas Instruments where he served as manager and principal architect of the Nanoelectronic Modeling (NEMO 1-D) program. Dr. Klimeck received his Ph.D. in 1994 from Purdue University and his German electrical engineering degree in 1990 from Ruhr-University Bochum. Dr. Klimeck's work is documented in over 170 peer-reviewed publications and over 270 conference presentations. He is a senior member of IEEE and member of APS, HKN and TBP.

10: 45AM-11:00AM: Coffee Break

11:00AM-12:00PM (Room 1505 SC, Engineering Building's Large Auditorium): Invited Keynote Talk:

Biomedical Informatics: Overview and Collaborative Opportunities

Speaker: Dr. Brian D. Athey, Associate Professor of Biomedical Informatics, and PI, NIH- National Center for Integrative Biomedical Informatics (NCIBI), one of seven National Centers for Biomedical Computing (NCBC).


Biosketch: Dr. Brian Athey received his Ph.D. in Cellular and Molecular Biology (Biophysics concentration) from the University of Michigan (1990), with a research focus in macromolecular structural biology. Dr. Athey is currently an Associate Professor of Biomedical Informatics in the University of Michigan Medical School Department of Psychiatry; Brian is also an Associate Professor of Bioinformatics and Computational Biology in the UM Bioinformatics Program and he is an active course master in the Program. In addition, he is Director of the Michigan Center for Biological Information (MCBI), the Bioinformatics Computing and Digital Library Hub of the Michigan Life Science Corridor (MLSC) Infrastructure Initiative, administratively housed in the University of Michigan Office of the Vice President for Research ( Brian was recently named Associate Director of the University of Michigan Center for Computational Medicine and Biology (, where his is responsible for the computing and data infrastructure build out for the Center and the Medical School.

During his Ph.D. thesis research in the 1980s, Brian proposed the double helical crossed-linker model for the structure of chromatin, at that time controversial, but now thought to be the correct model for this critical macromolecular complex, and featured in many textbooks. In the mid 1990s, Brian served as the Director of Biological Imaging Programs at the Environmental Research Institute of Michigan (ERIM) (now part of General Dynamics). Dr. Athey is also a founding member of the Michigan Nanotechnology Institute for Medicine and Biology ( He was also a longtime collaborator and friend for the world famous and late Professor Emmett Leith, the inventor of off-axis holography. He and Leith invented and demonstrated an incoherent white light holographic microscope in 2001 with their student Kurt Mills and collaborator David Dilworth.

Brian is best known for his work with the National Library of Medicine (NLM) Visible Human Project where he has been a leader in establishing a nationwide Internet2 end-to-end test bed demonstration project with NIH/NLM sponsorship in collaboration with Pittsburgh Supercomputing Center, Stanford University, and the Uniformed Services University of the Health Sciences (USUHS) ( This project naturally lead to the establishment of the very successful DARPA Virtual Soldier Project (, a nationwide consortium which he runs that builds from the visible human project to extend from basic human anatomy to physiological modeling, functional simulation and prediction after a traumatic injury.

Brian is the Principal Investigator of the recently established (Fall, 2005) National Center for Integrative Biomedical Informatics (, only one of seven NIH National Centers for Biomedical Computing (NCBC), a center piece of the NIH Roadmap initiative. The mission of the National Center for Integrative Biomedical Informatics (NCIBI) is to facilitate scientific exploration of complex disease processes on a much larger scale than is currently feasible by developing interactively integrated analytical and modeling technologies to acquire or create context-appropriate molecular biology information from emerging experimental data, international genomic databases and the published literature.

Dr. Athey has published over 45 papers and book chapters in the scientific literature and has given well over 100 talks nationally, including several keynotes and plenary talks. Brian has been a Peace Fellow of the Federation of American Scientists (FAS) since 2000, and is active in international educational and treaty efforts to prevent biological warfare and terrorism. He is also active with the FAS Learning Federation ( Dr. Athey is a founder and board of Advisor member of Scientist and Engineers for America (

12:00PM-1:30PM Lunch (Chinese lunch box provided)
1:30PM-2:20PM (Room 1505 SC, Engineering Building's Large Auditorium):

Parallel I/O and Storage Considerations for Performance of Scalable HPC Applications

Speaker: Stan Posey, Director, Applications and Industry Development, Panasas Inc, Fremont, CA, USA

Abstract: As expectations grow for Linux clusters to meet levels of capability for even challenge-scale HPC applications, the reality of overall scalability in practice is limited by I/O that will not scale on conventional file system implementations. As such, a new class of object-based parallel file systems and storage technology has developed that is designed to extend overall scalability of conventional clusters. These commodity storage systems can offer a large single resource of shared storage that provides parallel data access directly between cluster compute nodes and the storage system. In this way, a simulation has direct access to a storage system for both parallel computational I/O, and for subsequent post-processing and visualization of the results without the need for non-productive large file transfers. This approach eliminates the typical bottleneck of a head node collecting serial I/O streams from individual partitions, and also eliminates the need and expense of NFS servers. This technical presentation will examine the industry motivation for such parallel file systems and storage, and describe the features and benefits of a Panasas implementation, through examples of various HPC workflow requirements, for a variety of production-level applications.

Biosketch: Stan Posey currently manages the Panasas strategy of HPC Applications and Industry Development for a variety of target vertical markets. Mr. Posey is responsible for company guidance and consultation on Panasas advancement of HPC technology and solutions, with emphasis on applications in computational mechanics and sciences. Prior to joining Panasas in 2007, Mr. Posey has contributed for more than 20 years in various roles of HPC applications development including applications engineering and market development roles at SGI, research and engineering positions with the US Department of Energy, Oak Ridge National Laboratory, consulting and ISV software vendor CD-adapco Group, and systems vendor Control Data Corporation. Mr. Posey has co-authored several papers for HPC research journals and technical conferences, and his education includes a M.Sc. in Mechanical Engineering from the University of Tennessee, Knoxville, TN, USA.

2:20PM-2:40PM (Room 1505 SC):
Improving Introductory Calculus Education with 3-D Visualization and Virtual Touch (Haptics)
Jason Boggess and Chris Harding, Iowa State University, USA
3:00PM-3:10PM (Coffee Break)
Nonlinear Dynamics of Trafic Jams
Tong Li, University of Iowa, USA
Cluster Abstraction: towards Uniform Resource Description and Access in Multicluster Grid
Maoyuan Xie, Zhifeng Yun, Zhou Lei and Gabrielle Allen
Louisiana State University, USA
An Innovative Simulation Approach for Water Mediated Attraction Based on Grid Computing
Zhifeng Yun, Maoyuan Xie and Zhou Lei
Louisiana State University, USA
Collaborating Mechanical Design Phases Across A Grid
Maoyuan Xie, Zhifeng Yun and Zhou Lei
Louisiana State University, USA
SkipMard: A Multi-attribute Peer-to-Peer Resource Discovery Approach
Tao He, Jun Ni, Alberto M Segre, Shaowen Wang, Boyd M Knosp, University of Iowa, USA
TOPSAW Sawing Optimization Analysis Using Grid Computing
Ashwin Bommathanahalli, Maoyuan Xie, Zhifeng Yun, Sun Joseph Chang, Zhou Lei and Gabrielle Allen
Louisiana State University, USA
Octree-Path-Chain Data Structure in Knowledge-based ICAS for Nose Surgery in Otolaryngology
Ying Chen, Jun Ni, Jiadong Wang, and Lu Zhang
School of Medicine, Shanghai Jiao Tong University, China
Testing Approach of Component Security Based on Dynamic Monitoring
Jinfu Chen, Yansheng Lu, Xiaodong Xie, and Wei Zhang
Huazhong University of Science and Technology, China
6:00PM- Dinner (Vito's Italian Restaurant, Iowa City)

Tuesday, August 14, 2007

Symposium of Computational Biology and Bioinformatics 2007 (SCBB07) (Room 1505 SC)

8:30AM-8:40AM (Room 1505 SC, Engineering Building's Large Auditorium):
Open and Introduction to UI-CBCB
Professor Tom Casavant
, Roy J. Carver, Jr. Chair in Bioinformatics and Computational Biology, Director: UI Center for Bioinformatics and Computational Biology (CBCB) at the Univ. of Iowa (
8:40AM-9:10AM (Room 1505 SC, Engineering Building's Large Auditorium):
Invited Talk. Rigorous Mapping of Orthologous Bidirectional Promoters in Vertebrates

Speaker: Dr. Mary Qu Yang, National Genomics Research Institute, National Institutes of Health, U.S. Department of Health and Human Services and Oak Ridge, DOE, USA.

Abstract: Orthology between gene pairs allows the identification of ancestral patterns of gene regulation. We have mapped the ortholgous gene pairs flanking bidirectional promoters, which regulate expression of protein coding genes. We then examine the evolutionary history of bidirectional promoters across multiple phyla. Using knowledge of the genes regulated by bidirectional promoters across long evolutionary distances, such as human to fish, we are able to predict when gene annotations are missing or where assembly problems exist in the genomic sequences of higher vertebrates. We use these orthology assignments to examine the evidence for selective pressure which maintains the bidirectional gene pairing versus a tail to tail arrangement of genes. Furthermore, we apply a discriminatory method, known as ESPERR, to test our ability to discriminate among two classes of promoters, bidirectional promoters and monodirectional promoters. The results of these analyses will lead to improved annotations of regulatory regions in vertebrate genomes and contribute toward the goal of de novo classification of promoters using sequence-based genomic features. This work was collaborating with Dr. James Taylor of NYU Courant Institute of Mathematical Sciences and Dr. Laura L. Elnitski, Head of Genomic Functional Analysis, National Genomics Research Institute (NHGRI), NIH.

Biosketch: Mary Qu Yang received her interdisciplinary Ph.D. degree in Biophysics and Computer Engineering with specialization in Computational Science and Engineering from Purdue University and holds Master of Electrical and Computer Engineering Degree in Computer Engineering, and Master of Science Degree in Biophysics, also both from Purdue. She was the recipient of an Outstanding Bilsland Dissertation Fellowship, the recipient of a NIH Post Doctoral Fellowship for National Human Genome Research and also the recipient of a NIH - Oak Ridge, DOE research specialist fellowship. She was trained as combined computational and experimental scientist with more than 15 years of teaching, research and engineering practice experience in the fields of software engineering and biomedicine. Dr. Yang has received a number of outstanding achievement awards, best paper awards and plenary keynote speaker invitations, and has been an editor of a number of journals and proceeding books. He is currently on the editorial boards of Journal of Supercomputing, International Journal of Bioinformatics Research and Applications, Journal of Computational Intelligence in Bioinformatics and International Journal of Data Mining and Bioinformatics. She has published more than 40 peer-reviewed papers and several book chapters.

Technical Paper Session I (Chair Dr. Guoqing Lu)
9:10AM-9:30AM: Ontology-Driven Hypothetic Assertion (OHA) for Drug Interaction Prediction
Takeshi Arikuma, Sumi Yoshikawa, Kentaro Watanabe, Kazumi Matsumura and Akihiko Konagaya
Institute of Technology, and Riken Genomic Sciences Center, Japan
9:30AM-9:50AM: MLIP: A Multiprocessor Linkage Analysis System
Manika Govil, Alberto M. Segre and Veronica J. Vieland
University of Pittsburgh; University of Iowa; Columbus Children's Research Institute & The Ohio State University, USA
9:50AM-10:10AM: Multiplicity Adjustment for Intersection-union Test: Detecting Overlapping Genes from Multiple Microarray Gene Lists
Xutao Deng, Jun Xu, and Charles Wang
Transcriptional Genomics Core, Cedars-Sinai Medical Center; UCLA, David Geffen School of Medicine; Burns Allen Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
10:10AM-10:20AM, Coffee Break
10:40AM-11:00AM: Protein Structural Class Prediction by Combining Conditional Probability with Information Content
Fei Gu and Hang Chen
Zhejiang University, China
11:00AM-11:20AM: Asymmetric Bagging and Feature Selection for Activities Prediction of Drug Molecules
Guo-Zheng Li; Hao-Hua Meng, Mary Qu Yang, Jack Y. Yang
Shanghai University, Shanghai 200072, China
National Human Genome Research Institute, National Institutes of Health (NIH), USA
Harvard Medical School, Harvard University, USA
11:20AM-11:40AM: Rigorous mapping of orthologous bidirectional promoters in vertebrates
Mary Q. Yang, James Taylor, Laura Elnitski
National Human Genome Research Institute, NIH, USA
11:40AM-12:00PM: Evolutionary Conservation of DNA-contact Residues in DNA-binding Domains
Yao-Lin Chang, Huai-Kuang Tsai, Kao Cheng-Yan and Jinn-Moon Yang
National Taiwan University; Academia Sinica, National Chiao Tung University, Taiwan
12:00PM-1:30PM Lunch (Pizza provided)
1:30PM-2:10AM (Room 1505 SC, Engineering Building's Large Auditorium):

Invited Talk: Developing Synergistic Bioinformatics and Machine Learning Approaches to Predict Potential Malignancies

Speaker: Dr. Jack Y. Yang, Harvard Medical School, Harvard University, Massachusetts, USA.

Abstract: This lecture will present a novel parallel paradigm on cancer with an intelligent medical decision system. We have combined a number of ensemble methods that including Boosting, Bagging and Consensus Networking, and have designed a novel classification scheme that advantageously combines several machine learning algorithms, namely the variants of Self-Organizing Feature Map (SOFM) algorithm, and the Maximum Contrast Trees (RMCT). New algorithms such as Boosting and Bagging have been advantageously combined. When all of the above are combined into one integrated intelligent medical decision system, the power of predicting tumor malignancy has been significantly enhanced and the parallel paradigm on cancer has been further validated. This work was collaborating with Dr. Mary Qu Yang of National Genomics Research Institute, NIH and Oak Ridge, DOE.
Technical Paper Session II (Chair Dr. Guoqing Lu)
2:10PM-2:30PM: A Weighted k-Nearest Neighbor Method for Gene Ontology Based Protein Function Prediction
Saket Kharsikar, Dale Mugler, Daniel Sheffer, Francisco Moore and Zhong-Hui Duan, University of Akron, USA
2:30PM-2:50PM: ArrayWiki: Liberating Microarray Data from Non-collaborative Public Repositories
Todd Stokes, J. T, Torrance, Nolwenn Le Goasduff, Henry Li and May D. Wang
Georgia Institute of Technology, USA
2:50PM-3:10PM: Multi-dimensional Cluster Misclassification Test for Pathway Differential Analysis of Diabetes
Lily Liang, Vinay Mandal, Yi Lu and Deepak Kumar,
University of the District of Columbia; Wayne State University; Prairie View A&M University, USA
3:10PM-3:20PM, Coffee Break
3:20PM-3:40PM: A High-Performance Computational Framework for Bionetwork Analysis
George Chin Jr., Daniel G. Chavarria, Grant C. Nakamura and Heidi J. Sofia
Pacific Northwest National Lab, DOE, USA
4:20PM-4:40PM: Influenza A Virus Informatics: Genotype-Centered Database and Genotype Annotation
Guoqing Lu, Kashi Buyyani, Naresh Goty, Ruben Donis, and Zhengxin Chen
University of Nebraska at Omaha, USA

Wednesday, August 15, 2007

Technical Session III (Tutorials)

9:30AM-11:50AM (Room 2217, SC)
Tutorial: Computational Domains for Explorations in Nanoscience and Technology (presentation materials)

Dr. Jun Ni and Dr. Shaoping Xiao, College of Engineering, University of Iowa, USA; Dr. Deepak Srivastava, Scientist, Dr. Meyya Meyyappan, Director, NASA Ames Research Center
Abstract: In this tutorial, we will give a description about the current progress in the development of nanotechnology, especially computational nanotechnology. First, we will introduce various numerical methods commonly used in nanotechnology as well as the forefront area of computational nanotechnology. Those methods include molecular dynamics, nanoscale continuum methods, multiscale modeling/simulation and its enhancement with high performance computing techniques. We will also describe the application of computational nanotechnology in designing novel nanoscale materials and devices.