Boost for Bioinformatics and Computational Biology

Transcription

1 BULLETIN Boost for Bioinformatics and Computational Biology SPRING 05 New consortium forms as part of Microsoft agreement I A new consortium n March, University President Bob Bruininks announced the establishment of the Consortium for Bioinfor- headquartered in the Digital matics and Computational Biology Technology Center (DTC) (CBCB). Funded by $5 million from a settlement with Microsoft Corp. and will help bolster research in matching University funds, the CBCB bioinformatics the application will coordinate and strengthen existing activities in bioinformatics and of information technology to computational biology at the University. Biomedical areas are making major biological issues throughout advances, and they promise breakthrough contributions to health, safety, and the University. prosperity, says Bruininks. While the University has excellent researchers and equipment in relevant fields, we do not have as many as will be needed, and they are insufficiently coordinated. The CBCB will compensate for this and enable us to carry out the research that is required. The consortium will add five new faculty members with expertise in the field, including a senior researcher who will serve as CBCB director, and will bring together the related resources of nine colleges on the Twin Cities campus and of the University of Minnesota, Duluth. The colleges include the: Institute of Technology Medical School College of Biological Sciences (Left to right) Peter Fox (Microsoft), Richard College of Agricultural, Food, and Hagstrom (class action counsel), Institute of Environmental Sciences Technology Dean Steven Crouch, University of Minnesota Regent David Metzen, and University School of Pharmacy President Bob Bruininks stand next to the ceremonial checks from Microsoft. The funding will School of Veterinary Medicine School of Dentistry support the establishment of the Consortium for Bioinformatics and Computational Biology. School of Public Health College of Natural Resources The DTC has maintained a focus on bioinformatics and computational biology since its start, says Andrew Odlyzko, DTC director, ADC Professor, and assistant vice president for research. The new consortium will allow us to build on and expand our current efforts. In 2002, the DTC received a grant from the National Science Foundation and the National Institutes of Health to launch the Bioinformatics Summer Institute (BSI) through The BSI introduces undergraduate students from throughout the country to the fields of bioinformatics and computational biology and offers them opportunities to conduct hands-on research (see page 6). The University has received $2.5 million in cash and $2.5 million in product vouchers. Microsoft agreed to the payment as part of an April 2004 settlement agreement resulting from an antitrust class action lawsuit that the state of Minnesota brought against Microsoft. Funding also will support two research associates and two systems administrators for five years. The CBCB will allow the University of Minnesota to achieve a prominent position in an exciting and enormously important new discipline, says Steven Crouch, Institute of Technology dean. We intend to make the most of this opportunity. Odlyzko agrees. We have made great strides in this interdisciplinary area of research, and with the consortium, we can make even greater advancements.

2 Diverse Pursuits DTC open house featured updates on DTC research initiatives The small robot uses its arms to propel itself and moves quickly on command across the floor in a modest demonstration of its abilities for the industry representatives who attended the 2004 Digital Technology Center (DTC) Industrial Affiliates Open House in October. A team of DTC-affiliated faculty developed the CRAWLER Scout, and its quick trips around the DTC reception area are an only an elementary example of its abilities. Researchers designed the Scout to assist in search and rescue operations and other emergencies. As a result, it can manipulate and negotiate over heavy rubble and difficult terrain. The Scout was only one highlight of the second DTC Open House, which featured updates on key areas of research at the DTC and a series of presentations and demonstrations (see related story) for more than 70 attendees. The DTC helps build a bridge for University and industry collaborations, said Andrew Odlyzko, DTC director, ADC Professor in the School of Mathematics, and assistant vice president for research, in his opening comments. This open house allows us to share information about our research and outreach initiatives. DTC faculty, industry partners, students, and staff have made significant progress in increasing collaborations, in launching new research projects, in attracting additional research funding from diverse sources, in enhancing existing facilities and labs, and in involving students and the University community. In , for example, research expenditures reached $6.5 million, and the work of DTC faculty has resulted in numerous applications for patents or patents. At the DTC, we ve developed a critical mass of technical expertise, said Odlyzko. The DTC offers the infrastructure that supports collaborations and leverages funding from different sources that help multiply the impact of the work. Jim Licari, DTC assistant director for industrial liaison, discusses DTC partnership programs and opportunities with two DTC open house participants. Advances in intelligent storage Two years ago, the DTC formed its first consortium, the DTC Intelligent Storage Consortium (DISC). Consortiums provide a structured way for industry and faculty members to advance research and application in areas where DTC strengths and industry interests intersect. We are really looking at complex solutions from technical to business aspects of storage technology development, David Du, DISC director and computer science and engineering professor, explained at the open house. DISC currently has five consortium members and has hosted three workshops on intelligent storage development for industry. DISC research explores the technology of intelligent storage systems including object-based storage devices with an emphasis on application of storage technology, said Du. The consortium helps DISC researchers understand more about issues related to the storage industry, as well as encourage conversations with the community at large. We learn much about what s key to development by talking and working with consortium members, said Du. In addition to DTC faculty presentations, the DTC Industrial Affiliates Open House included poster presentations that highlighted many of the research projects being conducted at the DTC. Computational power The Supercomputer Institute for Digital Simulation and Advanced Computation makes available a dazzling array of computational resources to researchers. Our facilities support diverse applications in physical and materials sciences, social sciences, biology, mathematics, and computer science, said Donald Truhlar, institute director and chemistry professor, in his presentation. Part of the DTC, the Supercomputer Institute is located on the fifth floor and basement of Walter Library and in three distributed laboratories, two on the Minneapolis campus and 2 DTC Bulletin

3 A broad view The DTC Industrial Affiliates Open House also featured the following demonstrations and poster presentations. one on the St. Paul campus. Institute resources often play a key role in the research projects of DTC faculty. Rugged robots Maria Gini, DTC faculty member and computer science and engineering professor, discussed the evolution of robotics research at the University. Work initially began to develop a team of heterogeneous robots and the software for autonomous control of those robots. The Scout robot evolved from the research, as did an opportunity for a unique collaboration. In 2004, the University of Minnesota team joined forces with the University of South Florida, also known for its use of robotics in search and rescue operations. They received designation as a Safety, Security, and Rescue Research Center (SSR-RC) by the National Science Foundation. The designation also includes the involvement of industry as key partners in the collaboration. Expanding connections The number of companies that are involved with the DTC and its research continues to grow, reported Jim Licari, assistant director for industrial liaison. Our Partnership Program offers companies options for participation, said Licari. We wanted to make it a win-win situation for companies with different needs. The Affiliates Program offers companies participation in the DTC Advisory Team, an annual meeting to review research, updates, exclusive access with reduced fees to the DTC Usability Laboratory, and free or reduced registration fees to Supercomputing Institute workshops and symposiums. There are currently 12 companies in the Affiliates Program. In addition, consortium membership is also available. Consortiums involve members at a deeper level in the research and application of a specific area of technology. The DTC currently has two consortiums DISC and the Digital Design Consortium (see story on page 5). In the future, the DTC plans to expand the number of consortiums to four or five, says Licari. Companies also can work one-on-one in proprietary relationships with DTC faculty as part of the Research Program. We are looking at substantial interaction with industry, Licari told participants. We have some 30 to 40 companies working with us now. The DTC helps open the door to the University for companies. Communication plays an important part in developing new relationships and sustaining current ones, said Odlyzko. We are open to all types of discussion because they help us build those bridges with industry. Artificial Intelligence, Distributed Robotics, and Vision Distributed Robotics Research Group Maria Gini, Nikos Papanikolopoulos, Stergios Roumeliotis, Richard Voyles Bioinformatics and Computational Biology Yiannis Kaznessis Research Group Molecular Dynamics Simulations of Antimicrobial Peptides in Membrane Environments: The Search for Novel Therapeutic Agents, Himanshu Khandelia Using Stocastic Methods to Design Gene Networks, Howard Salis Jiali Gao Research Group Effects of Enzyme Dynamics on Haloalkane Dehalogenase Catalyzed Reaction Combined QM/MM Study, Kwangho Nam A Combined QM/MM Study of the Catalytic Pathway of Human Cathepsin K: The Hydrolysis of Peptide in Enzyme and Solution, Shuhua Ma Databases and Data Mining George Karypis Research Group Efficient Pattern Discovery Algorithms for Diverse Datasets Using Data Mining to Unravel the Puzzle of Life Digital Design Consortium Digital Design Consortium Affiliated Research Groups Color Simulations Virtual Reality Window Laboratory for Computational Science and Engineering Paul Woodward Research Group Demonstration of the LCSE s PowerWall Networking and Intelligent Storage David Du Research Group Infrastructure for Data Mining Computing QoS Provisioning for OSD-Based System Supercomputing Institute for Digital Simulation and Advanced Computation University of Minnesota Faculty-Directed Research Projects Usability Laboratory Usability Services Staff, Office of Information Technology Demonstration of Usability Laboratory Wireless Communication and Signal Processing Georgios Giannakis Research Group MIMO and Cross-Layer Designs for Fourth-Generation Wireless Innovations in Multiple Access and Wireless Sensor Networks Tom Luo Research Group Energy Efficient Decentralized Estimation in Wireless Sensor Networks Quasi-Maximum-Likelihood Detection in Wireless Communications SPRING 05 3

4 FROM THE DIRECTOR Good News External review notes DTC progress Andrew Odlyzko is the DTC director, an ADC Professor in the School of Mathematics, and Assistant Vice President for Research. He can be reached at T he Digital Technology Center (DTC) began as one of several interdisciplinary initiatives to build on University expertise and strengthen Minnesota industry. As a way to track impact, the University coordinated an external review of each initiative. This past summer, an external review committee with members from Argonne National Laboratory, Rutgers University, and Microsoft visited the DTC. They interviewed 25 industry representatives, faculty, administrators, and staff about DTC objectives, initiatives, successes, and challenges. The review committee was impressed with DTC progress since its start, including hiring new faculty, involving University faculty, and developing working relationships with the Supercomputing Institute for Digital Simulation and Advanced Computation and the Laboratory for Computer Science and Engineering (LCSE). Committee members also cited the growth in collaboration with industry, including the establishment of two consortiums and other joint research projects. In their report, members noted that every industry person we spoke to was pleased with the progress and optimistic about the future. They also found a supportive group of faculty members. The faculty is strongly energized by the DTC facilities and research environment, members wrote in their report. DTC seed funding of research projects is also proving successful in promoting interdisciplinary technology initiatives. The interdisciplinary strengths of the DTC are helping attract funding from government agencies that builds on existing research initiatives as well as supports new efforts, such as the Bioinformatics Summer Institute (see story on page 6). The committee report, including recommendations, was presented to the University Board of Regents this fall. The majority of the committee s recommendations reinforce our current efforts and direction. We will continue to use the recommendations and information from the report as we move forward. I m also happy to report on several additional DTC success stories. The DTC soon will add a new initiative. The Consortium for Bioinformatics and Computational Biology reinforces our work in this important area (see story on page 1). The first DTC consortium, the DTC Intelligent Storage Consortium (DISC), reached self-sufficient status and welcomed ETRI as a new corporate member. DISC faculty members also have collaborated with several other industrial partners, such as Los Alamos, Cisco, and Intel. The second DTC consortium, the Digital Design Consortium (DDC), held its first open house in August (see story on page 5) and welcomed its first member, Benjamin Moore. Other organizations have indicated a strong interest in collaborations, and we anticipate additional members will join soon. The DTC and Pine Technical College received funding for two projects from the Minnesota Job Skills Partnership and the National Science Foundation. Both projects involve development and application of realistic computer renderings of automotive finishes (see page 7). The collaborations among DTC faculty members continue to attract funding for major new projects and initiatives. Richard Voyles and Osama Massoud of computer science and engineering received funding from the Department of Homeland Security for research to monitor human activities at mass transit sites. In addition, the robotics group, in partnership with the University of South Florida, earned designation as a Safety, Security, and Rescue Research Center by the National Science Foundation. The Minnesota and Florida groups will work with industry on research applications. In February, the DTC also hosted a popular special event. Honda demonstrated its ASIMO Humanoid Robot to more than 4,400 people. Those attending included interested faculty, students, staff, and industry participants, as well as the general public. The demonstration, which also included demonstrations of the University of Minnesota robots, helped showcase the interdisciplinary nature of robotics and also generated interest in the robotics work of DTC faculty and technology in general. These successes reinforce the importance of DTC collaborations among industry, faculty, students, and staff. We appreciate and value the contributions of all our supporters, and we plan to build on our successes and strengths as we move forward to an even more promising future. 4 DTC Bulletin

5 Design Transformations DDC research and tools make possible a state-of-the-art virtual design reality At the first Digital Technology Center s Digital Design Consortium (DDC) Open House in August 2004, designers from many different industries experienced firsthand the powerful tools that may revolutionize the way they design. Building on a gift from University of Minnesota alumni Ted and Linda Johnson and start-up funds and facilities of the Digital Technology Center, the DDC brings together a team of researchers from architecture and computer science to develop the technologies that make possible a state-of-the-art digital-aided design reality. The open house allowed the more than 90 participants to see the DDC technology in action and learn about collaboration opportunities available to industry and other organizations through membership in the DDC. The DDC helps us fulfill our mission of promoting interdisciplinary collaborations among researchers and industry, said Andrew Odlyzko, Digital Technology Center director. The consortium helps makes those collaborations possible. Each DDC researcher contributes to the development of the digital design tools. As part of the open house, Baoquan Chen of computer science and engineering and graduate students showed the results of their research. They capture images throughout the University and community with a laser sensor, which they then digitize and input for use as sites in virtual environments. A demonstration of the sketch recognition software under development also attracted interest. With the software, designers start a sketch with lines, and the software helps make the three-dimensional connections to create the shapes. The ability to scan real-life images and develop three-dimensional sketches sets the stage for the virtual world that uses such information to simulate a real environment. In their work, Lee Anderson of architecture and Victoria Interrante of computer science and engineering apply those images to a physical space that allows users with the aid of headset to walk through a site simulation. The DDC most recently added a Virtual Reality Window, an eight-foot by 30-foot rear projected cylindrical screen with high-resolution capabilities. Participants who wore the headset and used a hand-held control found themselves inside a building, where they were able to add or change a feature with the click of a device. As they moved, they gained a different perspective of the space. In another DDC research focus, Gary Meyer of computer science and engineering explores accurate color representation in simulations, including on complex surfaces. The open house featured examples of color simulations and a projection of color rendering onto non-planar surfaces. The research combination has produced tools that can be used by practitioners. These are not only excellent individual pieces of research, said Tom Fischer, dean of the College of Architecture and Landscape Architecture, together they form a set of tools that could transform the way designers work. Those who attended the open house recognized the value of the research package. The open house triggered interest, says D nardo Colucci, DDC laboratory manager. The DDC has begun discussions with a diverse group of organizations, including architectural firms and builders. Our consortium covers a broad scope, and as a result, our work benefits many design applications. These applications range from the ability to realistically show the design of a home or building and view design changes before construction to the ability to see the impact of a proposed highway design on a community. In addition to developing projects with industry, DDC research also is receiving support from a number of sources, such as National Science Foundation (NSF) funding for visualization. In 2004, Meyer and Pine Technical College also began a joint project with funding from the Minnesota Job Skills Partnership and also received funding from the NSF for a related project (see page 7). The equipment and tools at the DDC support research and make possible cutting-edge applications. The DDC has nearly a half million dollars of fully operational equipment available for use, and our research is helping extend the capabilities of those resources, says Colucci. We are looking forward to increasing our collaborations with the design community. For a tour of DDC facilities or for more information on joining the DDC, contact Colucci at colucci@dtc.umn.edu. The DDC is on the web at SPRING 05 5

6 Summer Experience DTC Bioinformatics Summer Institute offers undergraduates research opportunities As part of the 2004 Bioinformatics Summer Institute (BSI) at the DTC, 14 students from throughout the country experienced research in a cutting-edge arena with faculty experts as guides. From June 6 to Aug. 13, students attended workshops and worked in faculty labs on research projects. They learned firsthand about the growing fields of bioinformatics and computational biology. As one of a few such programs nationwide, the DTC received funding from the National Institutes of Health (NIH) and the National Science Foundation (NSF) to run the institute from 2003 through The NIH and NSF recognize the impact that computational biology and bioinformatics are having on biomedical research, says Yiannis Kaznessis, BSI director, assistant professor of STUDENT Ariel Abell Georgia Southern University Benjamin Anderson University of Minnesota Andrea Carlson Augsburg College Benjamin Chacko Taylor University John Chilton University of Minnesota Katayoun Jafari University of Texas, Austin Angelo Kontgas Salt Lake Community College Akash Kumar University of Minnesota Katherine Lauer Saint Mary s College Christopher Lin Stanford University Vanessa Louis Clark Atlanta University Erika Remillard-Hagen Francis Marion University Evan Ribnick University of Minnesota Lingnan Tong University of Texas at Austin PROJECT Visualization Techniques Developed for Researching Genome Structure and Evolution Investigation into the Membrane Association of Residues 1-22 of Cytolytic NK-lysin Using Molecular Dynamic Simulations A Survey of Splice Variation in Medicago truncatula Implementation of Exact Base Spacing Calculation in DNA Base Calling GAMSA A Graphical Application for Microarray Statistical Analysis Alternative Splicing Variants in Medicago Mayo Clinic University of Minnesota Collaborative Projects Antibody Engineering for Prostate Specific Antigen Stochastic Modeling of a Tetracycline-Induced Gene Network for Implementation in Gene Therapy Applications Motif Analysis of M.truncatula ESTs of Unknown Function Initial Study of Distant Residue Contact Constraints in Monte Carlo Simulation of Protein Folding Identifying Secreted Proteins Mayo Clinic University of Minnesota Collaborative Projects Antibody Engineering for Prostate Specific Antigen Retrotransposon Activity in Maize Protein-DNA Conservation Distance Relation FACULTY ADVISOR Nevin Young Yiannis Kaznessis Kevin Silverstein Christian Domnisoru University of St. Thomas Arkady Khodursky Kevin Silverstein Yiannis Kaznessis and George Vasmatzis Yiannis Kaznessis Kevin Silverstein and Kathryn VandenBosch Yiannis Kaznessis Lynda Ellis Yiannis Kaznessis and George Vasmatzis Ron Phillips Boojala Reddy 6 DTC Bulletin

7 MILESTONES The main goal of the BSI is to provide the highest possible quality education and research experiences in bioinformatics and computational biology, chemical engineering and materials science, and DTC faculty member. Through this program, they want to introduce undergraduates to the field and encourage them to consider it as a possibility for graduate study and a potential career path. The participation of 18 faculty members from areas as diverse as chemical engineering, mathematics, laboratory medicine and pathology, biochemistry, plant biology, and computer science and engineering make it possible to offer students an impressive array of research projects. Students also received a thorough overview of bioinformatics. The main goal of the BSI is to provide the highest possible quality education and research experiences in bioinformatics and computational biology, says Kaznessis. We want them to understand bioinformatics concepts, so they can apply information technology solutions to understanding biological systems. BIS also is tracking students to determine the impact of the experience on their career path. Already the signs of success are strong: Students from the first year have indicated that they are considering bioinformatics, biological engineering, and related fields for graduate studies. The 2004 class featured talented participants with majors in information technology, chemical engineering, biology, chemistry, computer science, mathematics, biomedical computation, and electrical engineering. The list at left highlights those students, their projects, and their faculty advisors. Funding awards support diverse research projects Grant support from several sources is helping DTC faculty members move research initiatives forward. Funding from the National Science Foundation (NSF) is enhancing a collaboration that began between the DTC and Pine Technical College with a grant from the Minnesota Job Skills Partnership. Both projects involve realistic computer renderings of automotive finishes and application to the virtual reality spray painting training programs for industry that take place at the Pine Technical College Johnson Center for Virtual Reality. DTC faculty member Gary Meyer of computer science and engineering leads the DTC research effort. Other recent grants include: Monitoring Human Activities at Mass Transit Sites. Osama Massoud and Richard Voyles, computer science and engineering; $1.8 million from the Department of Homeland Security Safety, Security, and Rescue Research Center. Richard Voyles, Maria Gini, Nicolas Papanikolopoulos, and S. Roumeliotis, computer science and engineering; $250,000 from NSF Development of a System for Interactive Analysis and Visualization. Paul Woodward, astronomy, David Du, computer science and engineering, David Yuen, geology, and Ernest Retzel, Academic Health Center; $300,000 from NSF Additional faculty members join DTC The DTC recently welcomed three new faculty members: Gediminas Adomavicius, information and decision sciences at the Carlson School of Management, whose research interests include personalization technologies, knowledge discovery and data mining, electronic market mechanisms, and technology evolution Abhishek Chandra, computer science and engineering, whose research interests include operating systems, the internet, and multimedia computing Antonia Zhai, computer science and engineering, whose research interests include computer optimization and computer architecture DISC welcomes new director of business development In April, Cory Devor, Ph.D., began as the director of business development for the DTC Intelligent Storage Consortium (DISC). Devor most recently served as president and CEO of NeuStream; as former head of strategic business development at Ciprico, he also launched that company s networked attached (DiMedia) storage business. Devor will work with industry, government, and other universities to advance storage technology research and to foster the growth of DISC. DISC focuses on developing the next generation of system level storage architecture and brings together University researchers and industry experts who explore cutting-edge issues. Current full consortium members include StorageTek, Veritas, Engenio, ETRI, and Sun Microystems. For information about DISC, visit ADC fellowships support students Funded by ADC Telecommunications, the ADC Fellowships support the work of talented graduate students as they advance research in wireless and advanced networking technology. Fellows for fiscal year 2006 are Mahdi Hajiaghayi from Sharif University of Technology in Iran and Yao Huang from Beijing University. continued, next page SPRING 05 7

8 MILESTONES continued from page 7 Popular Science cites DTC contributions The DTC and the University are two reasons why Minneapolis ranks as America s top tech city, according to a March 2005 Popular Science article. The magazine evaluated cities on the ability to connect community members with technology; transportation innovations; high-tech jobs; and use of technology in education, health care, and energy. Minneapolis placed in the top half of every category, ranking first in innovative transportation solutions and fourth in energy technology. Calling the University home to quite a roster of innovative thinkers, the article cites the contributions of the University-industry partnerships and DTC interdisciplinary research. DTC events attract attention The DTC recently sponsored or co-sponsored a variety of events that helped advance knowledge about aspects of digital technology. DISC hosted the third Intelligent Storage Workshop May 4-5, The workshop featured presentations by Garth Gibson of Panasas, Alain Azagury and Michael Factor of IBM, Jerry Fredin of Engenio, Fabio Maino of Cisco, Yongdae Kim of the University, and Tom Ruwart of IO Performance, as well as sessions with industry and university researchers, and poster presentations. For additional information, visit isw2005.php. The DTC participated in the U of M/IBM Day, April 18, at the University of Minnesota. University and IBM representatives spoke about career opportunities and technology trends. For additional information, visit On April 14-15, the fourth annual bioinformatics symposium, Bioinformatics: Building Bridges, featured speakers from throughout the country, as well as academic and corporate sponsors. It included tutorials, presentations, a poster session, exhibits, and demonstrations. For additional information, visit More than 50 researchers attended the Digital Technology Initiatives Forum on Feb. 28 at the DTC. The forum highlighted 11 projects that the DTC funded through its Digital Technology Initiative (DTI) Program in The event included poster presentations and panel discussions. For information on the forum and the DTI Program, visit The DTC Bulletin is published by the Digital Technology Center (DTC) at the University of Minnesota. Direct comments or questions to: Editor, The Digital Technology Center, 499 Walter Library, 117 Pleasant St. SE, Minneapolis, MN For information about the DTC, contact us at: phone (612) fax (612) info@dtc.umn.edu Walter Library 117 Pleasant St. SE Minneapolis, MN Nonprofit Org. U.S. Postage PAID Mpls., MN Permit No. 155 The University of Minnesota is an equal opportunity educator and employer Regents of the University of Minnesota Printed on recycled paper, 10% post-consumer fiber.