Biocomplexity Institute

Template:COI 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.

History

VBI opened in July 2000 in space at the Virginia Tech Corporate Research Center. 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 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.
• Receives support 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 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 Health 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 anthrax, West Nile Virus, smallpox, and cryptosporidiosis, 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 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 (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 Health to support 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.
• 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 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.

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) 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, a Professor of Immunology at Virginia Tech, 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.

Core Facilities and Services

VBI occupies more than 130,000 square feet (12,000 m²) on the Virginia Tech campus, including over 40,000 square feet (3,700 m²) of laboratory space, designed for flexibility and to house computing and laboratory facilities. The institute occupies 5,000 square feet (460 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 3,700 square feet (340 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
• 6,500 square feet (600 m²) 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-FLX, Illumina and Ion Torent genome sequencers
• Affymetrix 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.

External links

• Virginia Bioinformatics Institute website