Biocomplexity Institute of Virginia Tech

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Biocomplexity Institute of Virginia Tech
Motto Ut Prosim (Latin)
Motto in English
That I May Serve
Established 2000
Executive Director Chris Barrett
Location Blacksburg, Arlington, in Virginia, United States
Yearly Research Portfolio $68 Million[1]
Affiliations Virginia Tech
Website bi.vt.edu

The Biocomplexity Institute of Virginia Tech (formerly the Virginia Bioinformatics Institute) is a bioinformatics, computational biology, and systems biology research facility that combines information technology, biology and medicine to interpret and apply biological data generated from basic research to practical challenges in the biomedical, environmental and agricultural sciences. The Institute has more than 250 highly trained multidisciplinary, multinational personnel, including ovver 50 tenured and research faculty. Research at the Institute 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.

The Institute'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. It has a research portfolio totaling $68 million in grants and contracts. The Institute's executive director is Chris Barrett.

History

The Institute opened in July 2000 in space at the Virginia Tech Corporate Research Center; it was hosted briefly in Building XI, then Building X, until it moved to Building XV in 2002, which was designed to host the institute.) In January 2005, the Institute moved into its building on the main Virginia Tech’s campus, but retained its existing space in VTCRC's Building XV. In 2011, the Institute moved its National Capital Region office into the Virginia Tech building in Arlington, Virginia. [2]

Major Research Divisions

The Advanced Computing and Informatics Laboratories (ACIL) is dedicated to "Policy Informatics", including the Network Dynamics and Simulation Science Laboratory (NDSSL). It pursues research and development in interaction-based modeling, simulation, and associated analysis, experimental design, and decision support tools for understanding large biological, information, social, and technological systems.It includes 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 detailed operational information about the populations being affected by a possible crisis. It also includes 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, .

The Cyberinfrastructure Division (CID) develops methods, infrastructure, and resources primarily for infectious disease research. The “Pathosystems Resource Integration Center - Bioinformatics Resource Center for Bacterial Diseases” aims 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.It is 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 The division collaborates 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 Biological Systems Division develops computational methods for studying biochemical networks using experimental data . It developed 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. It also developed GenoCAD, a web-based Computer Assisted Design environment for synthetic biology, with a point-and-click user interface.

The Medical Informatics & Systems (MIS) Division focuses on human genetics and disease, especially cancer and neurological disorders. It develops computer tools and databases in support of research at the clinical-basic research interface. It collaborates 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 was 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 center 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. The laboratory has a personalized medicine focus and has pioneered applying high-throughput immunology techniques and system biology approaches in immunology research and discovery. Its Center for Modeling Immunity to Enteric Pathogens Program 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 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. It has recently established a partnership with the Division of Gastroenterology at the Carilion Clinic to launch a joint translational research program in inflammatory bowel diseases.

Core Facilities and Services

The Institute 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 National Capital Region. The institute's infrastructure includes core facilities that integrate high-throughput data generation and data analysis capabilities.

The Core Computational Facility has 3hree data centers occupying over 3,700 square feet (340 m2), with over 250 servers totalling over 10.5 TB of RAM, distributed over more than 2650 processor cores. It has a Storage areaa network with over 1 PB of disk and 3 PB of tape, expandable to 50 PB.

The Genomics Research Laboratory: has 6,500 square feet (600 m2) of laboratory space located at the Institute's main building. It possesses a Wide range of technology platforms for the study of DNA (sequencing and genotyping), RNA (gene expression analysis), and proteins (proteomics), including state-of-the-art Roche GS-FLX, Illumina and Ion Torent genome sequencers. It includes the Affymetrix National Custom Array Center for custom microarray design, sample processing and analytical services

The Data Analysis Core: offers Turnkey service to analyze -omics and other data from raw data in to manuscript ready figures and text out. It also provides 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

The Institute's scientists develop technologies are the basis for new intellectual property which results in licensing and new start up companies being formed. The Institute provides and entrepreneurial incubator environment to support its investigators and their companies

Education and Outreach

The Institute'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 an Institute-sponsored event each year.

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.
  • 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.
  • Undergraduate Scholars Program (USP) - This program is for Virginia Tech undergraduate students who are interested in interning or for credit experiences with 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 [2]- 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 the Institute.

References

External links