Virginia Bioinformatics Institute
Encyclopedia
The Virginia Bioinformatics Institute at Virginia Tech is a 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. VBI has more than 240 highly trained multidisciplinary, multinational personnel, including ovver 50 tenured and research faculty. 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 human, animal and plant diseases as well as the discovery of new vaccine, drug and diagnostic targets.
VBI’s transdisciplinary research programs are supported by a variety of government and private 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. Since inception, VBI has received over $179 million in extramural support.
VBI's executive director is Dr. Harold "Skip" Garner, who came to Virginia Tech in 2009.
. In January 2005, VBI moved into its building on the main Virginia Tech’s campus, but retained its existing space. In 2011 VBI moved its Nationoal Capital Region office into the Virginia Tech building in Ballston, Alexandria in Washington DC.
Advanced Computing and Informatics Laboratories (ACIL)
The Cyberinfrastructure Division (CID)
Biological Systems Division
Medical Informatics & Systems (MIS) Division
Social and Decision Informatics Laboratory (SDIL) at ACDIL focuses on the use and development of analytical technology in the areas of public health policy, national and international security policy & public and social policy. SDIL will be central to the practical transition of NDSSL-developed science and technology.
The Nutritional Immunology and Molecular Medicine Laboratory (NIMML) at ACDIL is a research organization founded in 2002 with the mission of understanding fundamental mechanisms of gut enteric immunity and identifying biomarkers and therapeutic targets for inflammatory and immune-mediated diseases. The NIMML is directed by Dr. Bassaganya-Riera and has made seminal discoveries in the areas on infectious and immune mediated diseases, including discovering the mechanism of action underlying the anti-inflammatory actions of conjugated linoleic acid Conjugated linoleic acid
in inflammatory bowel disease as well as the insulin sensitizing and anti-inflammatory effects of abscisic acid (ABA)
. The laboratory has a personalized medicine
focus and has pioneered applying high-throughput immunology techniques and system biology approaches in immunology research and discovery. Especially, through the Center for Modeling Immunity to Enteric Pathogens
Program, NIMML is applying high performance computing techniques to model and simulate human immunology systems and help immunologists conduct quick in silico experiments to narrow down experimental design, validate their hypotheses and save significant time and laboratory cost. The NIMML is co-led by Drs. Bassaganya-Riera and Hontecillas and its research programs have been funded by the National Institute of Allergy and Infectious Disease at the National Institutes of Health
, the National Center for Complementary and Alternative Medicine, Bristol Myers Squibb, Lipid Nutrition, Cognis Nutrition and Health GmbH, BASF, and commodity groups with recent research funding portfolio exceeding $12 million. The NIMML is collaborating with the Center for Global Health at University of Virginia, the Department of Gastroenterology and University of North Carolina at Chapel Hill and other medical schools and leading several human clinical trials aimed at discovering and developing safer therapies for inflammatory and immune mediated diseases.
VBI’s infrastructure includes core facilities that integrate high-throughput data generation and data analysis capabilities. VBI’s core facilities provide researchers with access to the "-omics" technology platforms and computational tools needed for analysis and interpretation of contemporary biomedial research and clinical data sets.
Core Computational Facility:
Core Laboratory Facility:
Data Analysis Core:
K–12 programs
Undergraduate Programs
Graduate Programs
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
, computational biology
Computational biology
Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems...
, and systems biology
Systems biology
Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
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. VBI has more than 240 highly trained multidisciplinary, multinational personnel, including ovver 50 tenured and research faculty. 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 human, animal and plant diseases as well as the discovery of new vaccine, drug and diagnostic targets.
VBI’s transdisciplinary research programs are supported by a variety of government and private agencies including the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
, National Science Foundation
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
, U.S. Department of Defense, U.S. Department of Agriculture, and U.S. Department of Energy. Since inception, VBI has received over $179 million in extramural support.
VBI's executive director is Dr. Harold "Skip" Garner, who came to Virginia Tech in 2009.
History
VBI opened in July 2000 in space at the Virginia Tech Corporate Research CenterVirginia Tech Corporate Research Center
the Virginia Tech Corporate Research Center, known locally as the Corporate Research Center or the CRC, is a science park on the Virginia Tech campus in Blacksburg, Virginia comprising 27 completed buildings totaling on of land...
. In January 2005, VBI moved into its building on the main Virginia Tech’s campus, but retained its existing space. In 2011 VBI moved its Nationoal Capital Region office into the Virginia Tech building in Ballston, Alexandria in Washington DC.
Major Research Divisions
VBI has several programmatic research and development focus areas 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. VBI's research divisions active are:Advanced Computing and Informatics Laboratories (ACIL)
- Directed by Dr. Chris Barrett
- Composed of several groups dedicated to "Policy Informatics", the largest of which is 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.
- Receives support from the Defense Threat Reduction AgencyDefense Threat Reduction AgencyThe Defense Threat Reduction Agency is an agency within the United States Department of Defense and is the official Combat Support Agency for countering weapons of mass destruction . DTRA's main functions are threat reduction, threat control, combat support, and technology development...
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. - Receives support from the National Institutes of HealthNational Institutes of HealthThe National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
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 aids policymakers in making public health policy decisions.
The Cyberinfrastructure Division (CID)
- Directed by Dr. Bruno Sobral
- Develops methods, infrastructure, and resources to help enable scientific discoveries in infectious disease research and other research fields. The group uses cyberinfrastructure principles to integrate data, computational infrastructure, and people.
- Receives support from the National Institutes of HealthNational Institutes of HealthThe National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
to support the project, “Pathosystems Resource Integration Center - Bioinformatics Resource Center for Bacterial Diseases.” The project supports infectious disease research across the globe, namely to integrate information on pathogens, provide 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. Specific diseases and disease-causing agents under investigation include anthraxAnthraxAnthrax is an acute disease caused by the bacterium Bacillus anthracis. Most forms of the disease are lethal, and it affects both humans and other animals...
, West Nile VirusWest Nile virusWest Nile virus is a virus of the family Flaviviridae. Part of the Japanese encephalitis antigenic complex of viruses, it is found in both tropical and temperate regions. It mainly infects birds, but is known to infect humans, horses, dogs, cats, bats, chipmunks, skunks, squirrels, domestic...
, smallpoxSmallpoxSmallpox was an infectious disease unique to humans, caused by either of two virus variants, Variola major and Variola minor. The disease is also known by the Latin names Variola or Variola vera, which is a derivative of the Latin varius, meaning "spotted", or varus, meaning "pimple"...
, and cryptosporidiosisCryptosporidiosisCryptosporidiosis, also known as crypto, is a parasitic disease caused by Cryptosporidium, a protozoan parasite in the phylum Apicomplexa. It affects the intestines of mammals and is typically an acute short-term infection...
, among others. The team is also developing 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. - Teams with Georgetown UniversityGeorgetown UniversityGeorgetown University is a private, Jesuit, research university whose main campus is in the Georgetown neighborhood of Washington, D.C. Founded in 1789, it is the oldest Catholic university in the United States...
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 (PRC) 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. The mission of the PRCs is to discover potential targets for the next generation of vaccines, therapeutics and diagnostics.
Biological Systems Division
- Directed by Dr. Stan Hefta
- Develops computational methods for studying biochemical networks using data from experimental observations.
- Receives support from the National Institutes of HealthNational Institutes of HealthThe National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
to support COPASICOPASICOPASI is an open source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others...
(Complex Pathway Simulator), an open-source software package that allows users with limited experience in mathematics to construct models and simulations of biochemical networks. - Develops new computer languages to represent complex phenotypes that are encoded in long DNA sequences composed of multiple functional blocks.
- Supported by the National Science FoundationNational Science FoundationThe National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
to develop GenoCADGenoCADGenoCADis an open source web application to design DNA constructs for genetic engineering using a rule-based methodology. GenoCAD is also considered a Computer Assisted Design application for synthetic biology.-Features:...
, a web-based Computer Assisted Design environment for synthetic biologySynthetic biologySynthetic biology is a new area of biological research that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions...
. The GenoCAD point-and-click user interface guides the user through the process of designing new sequences.
Medical Informatics & Systems (MIS) Division
- Directed by Dr. Harold "Skip" Garner
- Major focus areas include human genetics and disease, especially cancer and neurological disorders
- 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 division is highly collaborative, working with Carilion Clinics, Virginia Tech Carilion School of Medicine and Research Institute, and other universities and government agencies.
Major Research Laboratories
The Network Dynamics and Simulation Science Laboratory (NDSSL) at ACDIL is pursuing an advanced computational research and development program for interaction-based modeling, simulation, and associated analysis, experimental design, and decision support tools for understanding large and complex biological, information, social, and technological systems. Extremely detailed, high-resolution, multi-scale computer simulations allow formal and experimental investigation of these systems. The need for such simulations is derived from questions posed by scientists, policy makers, and planners involved with very large complex systems. The simulation applications are underwritten by a theoretical program in discrete mathematics and theoretical computer science that is sustained by more than a decade of experience with the interplay of research and application.Social and Decision Informatics Laboratory (SDIL) at ACDIL focuses on the use and development of analytical technology in the areas of public health policy, national and international security policy & public and social policy. SDIL will be central to the practical transition of NDSSL-developed science and technology.
The Nutritional Immunology and Molecular Medicine Laboratory (NIMML) at ACDIL is a research organization founded in 2002 with the mission of understanding fundamental mechanisms of gut enteric immunity and identifying biomarkers and therapeutic targets for inflammatory and immune-mediated diseases. The NIMML is directed by Dr. Bassaganya-Riera and has made seminal discoveries in the areas on infectious and immune mediated diseases, including discovering the mechanism of action underlying the anti-inflammatory actions of conjugated linoleic acid Conjugated linoleic acid
Conjugated linoleic acid
Conjugated linoleic acids are a family of at least 28 isomers of linoleic acid found mainly in the meat and dairy products derived from ruminants. As the name implies, the double bonds of CLAs are conjugated, with only one single bond between them....
in inflammatory bowel disease as well as the insulin sensitizing and anti-inflammatory effects of abscisic acid (ABA)
Abscisic acid
Abscisic acid , also known as abscisin II and dormin, is a plant hormone. ABA functions in many plant developmental processes, including bud dormancy. It is degraded by the enzyme -abscisic acid 8'-hydroxylase.-Function:...
. The laboratory has a personalized medicine
Personalized medicine
Personalized medicine is a medical model emphasizing in general the customization of healthcare, with all decisions and practices being tailored to individual patients in whatever ways possible...
focus and has pioneered applying high-throughput immunology techniques and system biology approaches in immunology research and discovery. Especially, through the Center for Modeling Immunity to Enteric Pathogens
Center for Modeling Immunity to Enteric Pathogens
The Center for Modeling Immunity to Enteric Pathogens is a National Institute of Allergy and Infectious Diseases -funded program with an initial budget of $10.6 million directed by Dr...
Program, NIMML is applying high performance computing techniques to model and simulate human immunology systems and help immunologists conduct quick in silico experiments to narrow down experimental design, validate their hypotheses and save significant time and laboratory cost. The NIMML is co-led by Drs. Bassaganya-Riera and Hontecillas and its research programs have been funded by the National Institute of Allergy and Infectious Disease at the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
, the National Center for Complementary and Alternative Medicine, Bristol Myers Squibb, Lipid Nutrition, Cognis Nutrition and Health GmbH, BASF, and commodity groups with recent research funding portfolio exceeding $12 million. The NIMML is collaborating with the Center for Global Health at University of Virginia, the Department of Gastroenterology and University of North Carolina at Chapel Hill and other medical schools and leading several human clinical trials aimed at discovering and developing safer therapies for inflammatory and immune mediated diseases.
Core Facilities and Services
VBI occupies more than 130000 square feet (12,077.4 m²) on the Virginia Tech campus, including over 40000 square feet (3,716.1 m²) of laboratory space, designed for flexibility and to house computing and laboratory facilities. The institute occupies 5000 square feet (464.5 m²) in Alexandria, Virginia, as part of Virginia Tech’s National Capital Region Operations. The facility is used to interact and build partnerships with corporate research entities, government agencies and other public and private-sector organizations.VBI’s infrastructure includes core facilities that integrate high-throughput data generation and data analysis capabilities. VBI’s core facilities provide researchers with access to the "-omics" technology platforms and computational tools needed for analysis and interpretation of contemporary biomedial research and clinical data sets.
Core Computational Facility:
- Directed by Dr. Kevin Shinpaugh
- Three data centers occupying over 3700 square feet (343.7 m²)
- Over 250 servers with over 10.5 TB of RAM, distributed over more than 2650 processor cores
- Storage areaa network with over 1 PB of disk and 3 PB of tape, expandable to 50 PB
- 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 High Performance Computing infrastructure
Core Laboratory Facility:
- Directed by Dr. Robert Settledge
- Resource dedicated to the development and application of various high-throughput technologies to aid in the discovery of biological macromolecules 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)
- State-of-the-art Roche GS-FLX454 Life Sciences454 Life Sciences, is a biotechnology company based in Branford, Connecticut. It is a subsidiary of Roche, and specializes in high-throughput DNA sequencing.-History and Major Achievements:...
, Illumina and Ion Torent genome sequencers - AffymetrixAffymetrixAffymetrix is a company that manufactures DNA microarrays; it is based in Santa Clara, California, United States. The company was founded by Dr. Stephen Fodor in 1992. It began as a unit in Affymax N.V...
National Custom Array Center for custom microarray design, sample processing and analytical services
Data Analysis Core:
- Directed by Dr. Robert Settledge
- Turnkey service to analyze -omics and other data from raw data in to manuscript ready figures and text out
- Nexgen sequence assembly and annotation; microarray design, analysis and interpretation; mass spec data analysis; data QC; hypothesis generation; experimental design; statistical data analysis
Business Development
VBI’s scientists develop technologies are the basis for new intellectual property which results in licensing and new start up companies being formed. VBI provides and entrepreneurial incubator environment to support its investigators and their companies. The business development effort is directed by Dr. Stan Hefta.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. Over 5,000 students and parents participate in a VBI sponsored event each year. The VBI Education and Outreach group is directed by Drs. Reinhard Laubenbacher and Kristy (DiVittorio) Collins.K–12 programs
- Kids' Tech University - Kids' Tech University (KTU) is an educational research program with one primary goal - sparking kids' interest in science, technology, engineering, and mathematics disciplines.
- Climate Change Student Summit (C2S2) - This program brings climate literacy to teachers and students by sponsoring workshops and a summit.
- VBI High School Summer Internship - High school students participate in this summer program, which was developed to help guide students into a research career and recruit the next generation of scientists.
Undergraduate Programs
- Research Experiences for Undergraduates: Microbiology in the Post Genome Era - Funded through the National Science Foundation (NSF), this program introduces undergraduate students to research through a 10-week summer program.
- Research Experiences for Undergraduates: Modeling and Simulation in Systems Biology (MSSB) - Funded through the National Science Foundation (NSF), this program introduces undergraduate students to research through a 10-week summer program.
- VBI Undergraduate Scholars Program (USP) - This program is for Virginia Tech undergraduate students who are interested in interning or for credit experiences with VBI faculty and research groups.
- Global Summer Research Institute (GSRI) – Foreign and local students work on a research project.
Graduate Programs
- Genomics, Bioinformatics, Computational Biology Graduate Program GBCB- Provides an academic platform to create team-oriented researchers who may be specialists in one area but who are literate in several other disciplines. 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.
- VT Graduate school- Graduate students in various departments are welcome to do research at VBI.