Our Assets: University of Missouri
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Jianlin Cheng, PhD
Dr. Cheng is an associate professor in the Computer Science Department at the University of Missouri. He is affiliated with the University of Missouri Informatics Institute, the National Center for Soybean Biotechnology, the Interdisciplinary Plant Group and the Bond Life Science Center. His research is focused on developing computational methods and tools for big biomedical data analysis. His research group has developed a number of software tools for analyzing protein structure and function, biological sequences and networks and 3-D genome structure, which are used by scientists around the world. His research has been supported by the National Institutes of Health, the National Science Foundation, the U.S. Department of Energy, the U.S. Department of Education and the University of Missouri. Cheng is a recipient of the NSF CAREER award and the MU College of Engineering’s junior faculty research award.
Ye Duan, PhD
Dr. Duan is an associate professor in the Computer Science Department at the University of Missouri. He has received research funding from the Department of Defense, the Army Research Lab, the Leonard Wood Institute, the Brain & Behavior Research Foundation, the National Geospatial-Intelligence Agency, the Thompson Center for Autism and the National Science Foundation. His area of research interests include computer graphics and visualization, computer vision and biomedical imaging, and geometric and physics-based modeling.
Trupti Joshi, PhD
Dr. Joshi is an assistant research professor in the Computer Science Department at the University of Missouri. Her interests are in the areas of bioinformatics and its application to biology and medical fields. Her research includes development of comprehensive web-based resources for multi-omics data integration, high-throughput biological data analyses and computational tools development for genomics and systems biology research.
Toni Kazik, PhD
Dr. Kazic is an associate professor in the Computer Science Department at the University of Missouri. She is currently working on methods to infer the structure of complex networks using the disease lesion mimic mutants of maize as a model system. Her work has included the development of an architecture for community query, deposit, review and curation of information on biochemical reactions, and the analysis of extant reaction networks. Kazic is a fellow of the American College of Medical Informatics and was an Invited Researcher to the Institute for New Generation Computer Technology. She served as a program director for the National Science Foundation in computational biology, and now consults for the National Institutes of Health and the National Science Foundation and is a member of several national and international scientific advisory bodies.
Dmitry Korkin, PhD
Dr. Korkin is an assistant professor in the Computer Science Department at the University of Missouri. His interests in bioinformatics are toward characterizing structure, function and evolution of protein assemblies and predicting host-pathogen interactions. A recipient of the National Science Foundation’s CAREER award, his research in machine learning involves developing a symbolic approach for inductive learning and classification and its applications. Before coming to MU, Korkin was a postdoctoral researcher at the University of California, San Francisco and Rockefeller University. His research is supported by the University of Missouri.
Yi Shang, PhD
Dr. Shang is a professor and director of graduate studies in the Computer Science Department. He has published more than 150 refereed papers in international journals and conferences, and has six U.S. patents. Shang has worked as a researcher for the University of Illinois and the Xerox Palo Alto Research Center. He has received research funding from the National Science Foundation, National Institutes of Health, the U.S. Army, DARPA, Microsoft and Raytheon. His research interest include AI, combinatorial and nonlinear optimization, NN, GA, SAT, Web search, WSN, adaptive robotic control, traffic monitoring and control, mobile computing, location aware services, recommendation systems, and protein folding.
Chi-ren Shyu, PhD
Chi-Ren Shyu is professor and chairman of the Electrical and Computer Engineering Department and director of the University of Missouri Informatics Institute, a campuswide doctoral program in bioinformatics and health informatics. His research interests include biomedical informatics, mHealth and eHealth, information retrieval, visual knowledge reasoning and data mining. Current project sponsors, in addition to the NSF, include the National Institutes of Health, the U.S. Department of Education and other for-profit and nonprofit organizations.
Gordon Springer, PhD
Dr. Springer is an associate professor in the Computer Science Department scientific director of the UM Bioinformatics Consortium. He also serves as MU’s director of Research Support Computing for the Division of Information Technology, MU’s campus computing organization. A former director of graduate studies for MU’s Computer Science Department, Springer has worked since the late 1980s with the MU Molecular Biology Program and in the Life Science Center to develop and support computer systems and software required to carry out various research projects that need computer analysis of biological data.
Dong Xu, PhD
Dr. Xu is professor and chair of the Computer Science Department, with appointments in the Christopher S. Bond Life Sciences Center and the MU Informatics Institute at the University of Missouri. His research includes protein structure prediction, high-throughput biological data analyses and in silico studies of plants, microbes and cancers. He has published more than 240 papers and is a recipient of the 2001 R&D 100 Award, 2003 Federal Laboratory Consortium’s Award of Excellence in Technology Transfer and 2010 Outstanding Achievement Award from International Society of Intelligent Biological Medicine. Xu is an editor in chief of International Journal of Functional Informatics and Personalized Medicine and associate editor in chief of IEEE/ACM Transactions on Computational Biology and Bioinformatics. He is an editorial board member of Current Protein and Peptide Science, Applied and Environmental Microbiology and International Journal of Data Mining and Bioinformatics.
Informatics Institute: MUII’s mission has three components: education, research, and outreach. To have a global impact in advancing computational research in biology and medicine, the stakeholders across the University of Missouri System believe it is critical to the mission of the university and the development of the community to offer a doctoral program in informatics, build an international-level research program, and service to scientific communities for informatics needs. For information on the Core Faculty, see: http://muii.missouri.edu/people.php MU faculty and students have developed a wide array of informatics tools and databases. Please see the listing at: http://muii.missouri.edu/resources.php
Informatics Research Core Facility: The mission of the IRCF is to facilitate research and education through the development of computational resources. Computational resource development ranges from software creation to database design to hardware configuration consulting. IRCF staff members are skilled in these activities and are available for a range of services. The IRCF is committed to serving the informatics needs of the research community. Learn more at http://ircf.RNet.missouri.edu:8000/.
Bioinformatics Consortium: The University of Missouri Bioinformatics Consortium (UMBC) maintains a high performance computing, networking and storage infrastructure to support research across the UM-System. The UMBC provides centralized, high capacity data storage and analytical tools that can be used over high-speed Internet2 connections in support of research. The UMBC coordinates the provision of high-performance computational systems to analyze massive sets of data, very large storage devices to house major data collections, high speed networking services to facilitate location independent access and collaboration among investigators, software applications supporting system-wide computation research and technical support staff. Scalable high capacity storage is available to house many widely used and specialized genomic databases and analysis tools and packages to support the analysis needs of the research community. These systems, and various specialized laboratory equipment (e.g., high throughput sequencing systems and electron microscope), are connected via the 10G research network that is accessible to all four University campuses as well as the national Internet2 network and other international networks widely used by the higher education research community. For more information, see: http://umbc.rnet.missouri.edu/
MU is acquiring additional HPC resources. A significant upgrade to the ‘general purpose’ HPC cluster has been purchased, and will be installed in the weeks ahead. In addition, a cluster to meet the high-memory requirements of MU’s genomics researchers will be purchased soon. In addition, funds have been provided to purchase additional disk storage for research computing.
MU’s current HPC system has 190 nodes that include Dell 1850/1950 dual processor/dual core with 2.8 GHz Intel Xeon EMT64 processors and 640 GB RAM. Additional HPC infrastructure access is available through the University of Missouri Bioinformatics Consortium (UMBC) system that consists of 8 nodes of IBM 3850M2 quad core compute nodes (64 processors) with 24GB RAM on 7 nodes and 48GB RAM on 1 node, and two IBM DS3400 storage nodes with 24TB data capacity connected through a GPFS parallel file system on a QDR Infiniband low latency interconnect. In late 2013, MU purchased over 500 TB of usable disk storage from EMC/Isilon and HP/3PAR, thereby bringing total research computing disk storage to more than a petabyte of usable storage. This storage environment supports current generation QDR Infiniband (up to 80 gbps bandwidth) and two IBM 3850X5 compute nodes each with 500GB RAM and an IBM 3850M3 node containing 2 Tesla M2070 GPU boards that enables MU researchers to begin testing home-built algorithms and applications using GPU technology. As a result of the upgrades made to the research CI over the past two years, the systems are positioned so further upgrades can be made without major processing disruptions. Learn more at http://umbc.RNet.missouri.edu/resources/.
- Storage Resources (connected to the computing resources via high-speed data links).
- 110 TB EMC storage array managed by the IBRIX distributed file system.
- 948 TB Isilon storage cluster.
- 24 TB IBM DS3400 storage array.
- 12 TB SGI TP9500 InfiniteStorage storage array.
- 112 TB 3PAR storage array.
Networking: MU’s research network infrastructure and connectivity enable MU researchers to leverage and participate in various national-level advanced cyberinfrastructure efforts such as InCommon Federated Identity Management Service, XSEDE for HPC/Big Data resources/expertise access, and GENI Future Internet Testbed. In fact, MU researchers are leading several GENI experiment efforts and are developing Gigabit apps using national-level testbeds involving Health Care and Advanced Manufacturing communities, as part of the US Ignite initiative supported by NSF and The White House Office of Science and Technology Policy. MOREnet also connects Rnet today at 10 Gbps network speeds (100 Gbps connectivity future option is possible with MOREnet’s current fiber and optical infrastructure) to international R&E network peering points such as StarLight in Chicago, and thus MU researchers have the ability to create and participate in international R&E testbeds with researchers worldwide.
Internet2: Internet2 is an advanced networking consortium led by the research and education community spanning US and international institutions who are leaders in the worlds of research, academia, industry and government. The Internet2 community is developing breakthrough network technologies that support the most exacting applications of today—and spark the most essential innovations of tomorrow. MU has belonged to Internet2 since its inception in 2000. Learn more at http://www.internet2.edu.
Internet2 Innovation Campus: MU is one of a select few universities designated as an Internet2 Innovation Campus. These campuses form the building blocks of a nationwide Research & Education (R&E) innovation platform, helping to create an environment for innovation at leading research universities. Leveraging the Internet2 Network and enabling services like InCommon federated identity management; Internet2 recently began offering a portfolio of services and discounts to Internet2 members, including cloud services and video services. Learn more at http://www.internet2.edu/network/ or http://internet2.edu/pubs/IS-enabling-innovation-campus.pdf
Rnet: MU was among the first US research universities to create a separate research network (RNet) in addition to the traditional campus enterprise network. Serving MU’s research community since 1999, RNet exists and is administered separately from, but is interconnected to, MU’s high-speed network. RNet has an autonomous set of virtual local area networks (VLANs) that co-reside within the internet address space of the University, but are on a separate high-speed routing and switch infrastructure. There is no charge for using RNet. Major research labs and scientific instruments at MU campus are connected to RNet with 1 – 10 gigabits per second interfaces, which can be configured and have researcher-friendly firewall policies. IPv6 routing capabilities are supported within Rnet due to the dual-stack mode setup and a separate IPv6 address space is reserved for researcher flows. Rnet is also connected to “TigerNet”, which provides high-speed Ethernet connectivity and wireless connectivity to most on-campus offices, classrooms, conference rooms, computing sites, residence halls, and some fraternities and sororities. See also: http://doit.missouri.edu/research/RNet.html.
RNet Science DMZ (Demilitarized Zone) Protection Environment: A Science DMZ environment is being developed (through 2013-14 NSF CC-NIE funds) with minimal firewall restrictions to enable “friction-free” RNet data flows internally within the campus, and externally to other regional and national network locations. Currently, Science DMZ capabilities include: 100 Gbps connectivity to Internet2 Innovation Platform, perfSONAR multi-domain measurement points to troubleshoot network bottlenecks, Bro based intrusion-detection monitoring of RNet flows, Data Transfer Nodes with RoCE/iWARP capabilities for fast data transfers over wide-area networks, and a OpenFlow switch infrastructure. Several software-defined networking research collaborations with leading industry vendors such as Cisco, Brocade and NEC as well as with remote campuses such as The Ohio State University and Clemson University are aiding in the maturation of the OpenFlow support for domain science researcher use cases on the MU campus. Shibboleth-based authentication and authorization services also enable secure access to Science DMZ resources.
Rnet External Network Connectivity: RNet enables accessibility to high performance computing (HPC) resources throughout the four-campus University of Missouri System through a core fiber-optic network and 10 Gigabit (Gb) optics operated by the Missouri Research and Education Network (MOREnet). This MOREnet connectivity enables MU researchers to connect via high-speed networks and collaboration services such as videoconferencing with Missouri’s 900 node research and education network for higher education, K-12 education, telehealth sites and public libraries, as well as state government and their affiliates. Connectivity to Internet2 from Rnet is available directly if needed, and through MOREnet and the Great Plains Network (GPN) consortium. The direct connection to Internet2 is being upgraded with 100 Gbps connectivity with built-in redundancy provided by MOREnet for route protection to avert network disruption due to faults. The following figure depicts the 100GB network connectivity. See also: http://doit.missouri.edu/research/RNet.html
Missouri Research and Education Network: MOREnet provides high-speed Internet access to the state of Missouri’s K-12 schools, colleges, universities, public libraries, state government and other affiliates. MOREnet also provides access to online reference resources, technical expertise, security education, videoconferencing, and more. Starting in the mid 1980’s MOREnet designed and the state’s telecommunications providers constructed an advanced, high-speed, high-bandwidth network throughout the state –laying the groundwork for Internet availability to thousands of rural Missourians. MOREnet was one of the first five state educational networks to receive designation as a Sponsored Educational Group Participant (SEGP) for Internet2. Learn more at www.more.net/.
Great Plains Network: Administratively housed at the University of Missouri, the Great Plains Network (GPN) was founded in 1997 to address the needs of the research and education community resulting from increasingly overwhelming use of the public Internet. GPN members include over 20 leading universities in eight states. GPN was the first regional connector to Internet2, and GPN continues to lead in support of research collaboration, education and advanced networking for member institutions. MU and the GPN have been instrumental in developing and proving scalability of Shibboleth as a security model for fine-grained authorization needs across multiple institutions and in large high-speed networks. Learn more at www.greatplains.net.