Virginia Bioinformatics Institute

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Virginia Bioinformatics Institute building, located on the Blacksburg campus of Virginia Tech

The Virginia Bioinformatics Institute at Virginia Tech is a premier bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches combining information technology, biology and medicine to interpret and apply vast amounts of biological data generated from basic research to some of today’s key challenges in the biomedical, environmental and agricultural sciences. With more than 240 highly trained multidisciplinary, multinational personnel, research at VBI involves collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology and medicine. The institute develops -omic and bioinformatic tools and databases that can be applied to the study of diseases as well as the discovery of new vaccine, drug and diagnostic targets. The institute’s -omic and computational cores work collaboratively with VBI, Virginia Tech and other international institutions using state-of-the-art technologies (deep sequencing, high-throughput microarrays, mass spectroscopy and more) to generate tremendous amounts of new data. The large amounts of data generated by this approach are analyzed and interpreted to create new knowledge that is disseminated to the world’s scientific, governmental and wider communities.

VBI’s transdisciplinary research programs have leveraged more than $120 million (as of November 30, 2009) in active extramural funding from agencies including the National Institutes of Health, National Science Foundation, U.S. Department of Defense, U.S. Department of Agriculture, and U.S. Department of Energy.

Contents

[edit] History

In 1998, a paper by Dave Sebring, VBI’s associate director of corporate and government relations, and Dr. Gary Evans, Director of the Natural Resources Institute at the United States Department of Agriculture, found its way into the hands of Virginia Governor Jim Gilmore. The paper asserted that biotechnology would become the new economic engine of growth in the 21st century. It also explicitly argued that regions supporting entrepreneurial activities arising from leading university research in this emerging field were poised to reap major benefits in the years ahead.

Convinced by the arguments about the considerable potential of biotechnology, Gilmore sent the paper to several Virginia colleges. After reading the document, Virginia Tech President Charles Steger believed that opening a bioinformatics center could contribute in a major way to Virginia Tech’s advancement of biotechnology research. Virginia Tech had already established leading colleges of agriculture and life sciences and engineering, which made the creation of a bioinformatics center a natural progression for the university. Virginia Tech began making plans to secure state funding in 1999. The Tobacco Indemnification and Community Revitalization Commission approved $12.3 million from the state to help fund the development of the Virginia Bioinformatics Institute at Virginia Tech. This was the only funding given to the institute before its opening. VBI opened its doors in July 2000 in the Virginia Tech Corporate Research Center with only five employees. In January 2005, VBI completed its two-phase move onto Virginia Tech’s campus.

[edit] Facilities and Services

VBI occupies more than 130,000 square feet on the Virginia Tech campus, including over 40,000 square feet of laboratory space, with a building and resources designed for flexibility and access to cutting-edge computing and laboratory facilities and to support innovation and future growth. The institute also occupies space in Alexandria, Virginia, as part of Virginia Tech’s National Capital Region Operations and will soon be part of Virginia Tech’s new research facility currently being constructed near Washington, D.C. The highly visible, state-of-the-art facility will further the university's mission to expand its research portfolio in a region that offers great opportunity for partnerships with corporate research entities and close proximity to government agencies and other public and private-sector organizations. VBI’s funded program portfolio has grown rapidly, necessitating an additional 8,358 square feet of space in Virginia Tech’s Corporate Research Center to accommodate its research staff.

A unique feature of VBI’s infrastructure is the integration of multi-user core facilities that integrate high-throughput data generation (Core Laboratory Facility, CLF) and data analysis (Core Computational Facility, CCF) capabilities. VBI’s Core Facilities provide researchers with access to the latest technology platforms as well as to the computational tools needed for extensive analysis of the resulting data sets.

Core Computational Facility:

  • Two data centers occupying 1,850 square feet
  • Current resources encompass more than 1.5 TB of RAM, distributed over more than 650 processor cores, and more than 160 TB of disk storage
  • Hosts a storage area network ensuring high-speed data access and reliability
  • Connectivity is achieved via gigabit Ethernet between the desktop and data centers and high-speed paths to Network Virginia and Internet2
  • Support for the development and release of biomedical applications that demand compute intensive infrastructure

Core Laboratory Facility:

  • Multi-user resource dedicated to the development and application of various high-throughput technologies to aid in the discovery of biological macromolecules
  • 6,500 square feet of laboratory space located at VBI’s main building on the Virginia Tech campus
  • Wide range of technology platforms for the study of DNA (sequencing and genotyping), RNA (gene expression analysis), and proteins (proteomics) as well as a selection of molecular biology applications
  • State-of-the-art Roche GS-FLX™ genome sequencer, allowing researchers to go from genome to sequence in record time
  • Affymetrix National Custom Array Center for custom microarray design, sample processing and analytical services

[edit] Major Research Areas

VBI has several major programmatic research and development focus areas that include Network Dynamics and Simulation Science, Cyberinfrastructure, Biosystems, and Medical Informatics and Systems. These program areas comprise a wide range of research groups that are addressing some of today’s key challenges in information technology, biology and medicine. Scientists at VBI are helping to broaden our understanding of the natural world and impact the transformation of scientific knowledge into tools, technologies, and solutions for the life sciences. A selection of the research groups active at VBI include:

Network Dynamics and Simulation Science Laboratory (NDSSL)

  • Pursuing an advanced research and development program for interaction-based modeling, simulation, and associated analysis, experimental design, and decision support tools for understanding large biological, information, social, and technological systems.
  • Received $20 million from the Defense Threat Reduction Agency for the “Comprehensive National Incident Management System” project, which involves developing a system to provide those involved in disaster management in the United States military with essential detailed operational information about the populations being affected by a possible crisis.
  • Received $1.5 million from the National Institutes of Health for the project, “Modeling Disease Dynamics on Large, Detailed, Co-Evolving Networks,” which supports ongoing work to develop high-performance computer models for the study of very large networks, which will aid policymakers in making important public health policy decisions.

The Cyberinfrastructure Group (CIG)

  • Develops methods, infrastructure, and resources to help enable scientific discoveries in infectious disease research and other research fields. The group applies the principles of cyberinfrastructure to integrate data, computational infrastructure, and people.
  • Received $30 million from the National Institutes of Health, the largest one-time federal award in the history of Virginia Tech, to support the project, “Pathosystems Resource Integration Center - Bioinformatics Resource Center for Bacterial Diseases.” The goal of the project is to support infectious disease research across the globe, namely to integrate vital information on pathogens, provide key resources and tools to scientists, and help researchers to analyze genomic, proteomic and other data arising from infectious disease research.
  • Part of the Middle-Atlantic Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research (MARCE) project, which focuses on research to enable rapid defense against bioterror and emerging infectious diseases. Fourteen universities, seven government partners, and ten corporate partners are working together to improve our nation's public health response system. Specific diseases and disease-causing agents under investigation include anthrax, West Nile Virus, smallpox, and cryptosporidiosis, among others. The team is also working on needle-free vaccinations and new diagnostic tools. VBI serves as the Bioinformatics and Genomics Research Core for the MARCE, providing data generation, analysis, storage, and training services.
  • Works with Georgetown University and Social and Scientific Systems, Inc (SSS) on the Administrative Center of the National Institute of Allergy and Infectious Diseases-funded Proteomics Research Resource Center for Biodefense Proteomics Research project. The team helps design, develop, and maintain a publicly accessible Web site containing data and technology protocols generated by each PRC, as well as a catalog that lists reagents and products developed by the sites and available for public distribution. It is anticipated that the PRCs will discover potential targets for the next generation of vaccines, therapeutics and diagnostics.

Biochemical Networks Modeling Group

  • Develops computational methods for studying biochemical networks using data from experimental observations.
  • Received $2 million from the National Institutes of Health to support the group’s continued work on COPASI (Complex Pathway Simulator), an open-source software package that allows users with limited experience in mathematics to construct models and simulations of biochemical networks. The group has been developing COPASI for nearly a decade and it is now one of the primary tools used for computational systems biology research.

Synthetic Biology Research Group

  • Develops new computer languages to represent complex phenotypes that are encoded in long DNA sequences composed of multiple functional blocks.
  • Received $1.4 million from the National Science Foundation to develop GenoCAD - a web-based Computer Assisted Design environment for synthetic biology. The GenoCAD point-and-click user interface guides the user through the process of designing new sequences. By successively clicking on icons representing structural features or functional blocks, complex DNA sequences composed of dozens of functional blocks can be designed in a matter of minutes.

Medical Informatics & Systems (MIS)

  • Develops new computer tools and databases in support of research at the clinical-basic research interface, e.g. ‘translational’ research including -omic research involving patient samples, clinician decision support systems, hypothesis generation systems for complex diseases and traits, and systems for value extraction from electronic medical records.
  • This is a major new initiative in partnership with the Virginia Tech community, especially the Virginia Tech Carilion School of Medicine and Research Institute.

[edit] Education and Outreach

VBI’s Education and Outreach group is committed to developing educational programs designed to foster interest in scientific research for students of all ages. The team builds and maintains strong relationships with the institute’s external audiences, coordinating and promoting VBI’s involvement in a wide variety of educational programs in the Virginia Tech community and beyond.

K-12 programs

  • Kids' Tech University (KTU) is an educational research program developed at VBI with one primary goal…sparking kids' interest in science, technology, engineering, and mathematics disciplines. Kids between the ages of 9-12 have the opportunity to attend four lectures over the course of a semester. The lectures are given by world-renowned scientists and will address some of the “why?” questions about the world around us. The kids also participate in exciting hands-on activities after the lectures and have access to online lab activities and an interactive kids’ forum.
  • Destination: Bioinformatics Research is a high school summer program developed to help guide students into a research career and recruit the next generation of scientists. The week-long program consists of several research activity labs, research related tours, and a discussion/lecture series. Participants get the unique opportunity to explore the world of genomics and bioinformatics with world-renowned research scientists in professional labs. The main objective of the high school program is to positively influence the students' outlook on scientific research.

Undergraduate Programs

  • VBI was awarded a $918,000 grant from the National Science Foundation (NSF) in support of the CIBRED (CI-Team Implementation for Biological Researchers, Educators and Developers) project, which is part of VBI's education and outreach program in Cyberinfrastructure - Training, Education, Advancement and Mentoring (CI-TEAM). CIBRED has allowed VBI to form collaborations with researchers from different scientific disciplines, as well as high school and college educators from several institutions nationwide, to build an educational program for the next generation of scientific researchers. VBI is collaborating with scientific researchers and high school and undergraduate educators from several institutions nationwide to build an educational program that will help prepare students for research environments where cyberinfrastructure systems, tools and services are used effectively to fuel a knowledge-based economy.
  • The Bioengineering and Bioinformatics Summer Institute (BBSI) is a summer program designed for junior or senior undergraduates who are interested in attending graduate school in biomedical engineering and/or bioinformatics. With funding from the National Science Foundation/National Institutes of Health, VBI and the Virginia Tech-Wake Forest University School of Biomedical Engineering and Science (SBES) coordinate this ten-week educational and research experience, which emphasizes four major research areas: Computational Systems Biology, Computational Bio-Imaging, Computational Physiology, and Mathematics.

Graduate Programs

  • VBI partners with Virginia Tech’s GBCB (Genomics, Bioinformatics, Computational Biology) Graduate Program, which provides an academic platform to create team-oriented researchers who may be specialists in one area but who are literate in several other disciplines. For example, researchers with expertise in the mathematical, statistical, or computer sciences also require sufficient knowledge in biology in order to develop appropriate analytical methods and computer tools. Similarly, life scientists need sufficient grounding in mathematics, statistics, and computer science to be educated users of these quantitative methods and tools, and to conceptualize new tools. Virginia Tech’s interdisciplinary program spans traditional departmental boundaries and allow students to be enrolled in a program to study with faculty from many departments and colleges.
  • The Transdisciplinary Team Science Fellowship Program for the Life Sciences was developed for students interested in joining the Virginia Tech GBCB Ph.D. program. The fellowships, which are intended to connect students with accomplished researchers working in a team science environment, cover the costs of the students' first two years in the GBCB program plus tuition and fees. Each student will complete a laboratory rotation period, which will provide an opportunity to learn more about different research areas and identify an area of interest. After completion of the first two years of study, students will be supported by a research grant from their selected mentor professor.


[edit] Future

In 2009, with the recruitment of Dr. Harold "Skip" Garner as the new Executive Director, comes a further commitment to growth in new strategic directions (human disease, -omics), to collaboration between VBI and the greater Virginia Tech and surrounding communities (especially with the new Virginia Tech Carilion School of Medicine and Research Institute) and bioinformatics/computational biology/biomedical challenges that demand next-generation High Performance Computing environments.


[edit] External links

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