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2006 Scientific Annual Report Virginia Bioinformatics Institute at Virginia Tech Scientific Annual Report 2006 Virginia Bioinformatics Institute Washington St. (0477) Blacksburg, VA 24061 ph: 540.231.2100 Fax: 540.231.2606 email: [email protected] web: www.vbi.vt.edu The following scientifi c reports are not intended as publications and should not be cited without specifi c permission by the primary author. These reports are only an overview of each research group’s activities. For more specifi c details about the groups’ work, please refer to the refereed publications at the end of each report. TTableable ooff CContentsontents Introduction Bruno W.S. Sobral, Executive and Scientifi c Director, Virginia Bioinformatics Institute ...........5 Research reports — VBI Faculty Network Dynamics and Simulation Science Laboratory ......................................................7 Christopher L. Barrett Bioinformatics inspired by a tree .................................................................................................11 Allan W. Dickerman Genetic architecture of quantitative traits ...............................................................................15 Ina Hoeschele Modeling and simulation of biochemical networks .............................................................18 Reinhard Laubenbacher Alternaria pathogenomics .............................................................................................................22 Christopher B. Lawrence Microfl uidic mass spectrometry for proteomic and biomarker applications ..............30 Iulian M. Lazar Software, models, and experiments for systems biology ...................................................35 Pedro Mendes Methanogenic archaea, tuberculosis, coalbed methane and type 2 diabetes ...........41 Biswarup Mukhopadhyay Strategies for malaria control ........................................................................................................49 Dharmendar Rathore Computational biology for mitochondrial medicine ...........................................................54 David C. Samuels Bacterial genomics and bioinformatics .....................................................................................60 João Carlos Setubal Applications of metabolomics to functional genomics ......................................................66 Vladimir Shulaev Living inside your host: lessons from the α-proteobacteria ..............................................72 Bruno W.S. Sobral Genomic and bioinformatic analysis of oomycete-host interactions ............................86 Brett Tyler Research reports — VBI Fellows Data-driven computational systems biology ..........................................................................95 T.M Murali Simulation and analysis of molecular regulatory systems in cell biology .................101 John J. Tyson IIntroductionntroduction Dear friends, The Virginia Bioinformatics Institute (VBI) has made considerable progress over the past year. It is therefore gratifying to see the diligent work of faculty, staff and collaborators represented in this our second scientifi c annual report. At VBI, one of our primary objectives is to channel scientifi c innovation into transdisciplinary research projects that emphasize the importance of team-based science. One of the goals of the scientifi c annual report is to highlight the very latest research accomplishments of the Institute that have arisen from this collaborative approach to science. Work at VBI spans many disciplines but has at its foundation the sciences of biology, mathematics and information technologies. Faculty at VBI use a wide variety of methods and tools that range, for example, from simulation and modeling of biological networks, statistical genetics and large- scale comparative genomics to computational systems biology, microfl uidic mass spectrometry and diff erent cyberinfrastructure-based resources. These tools and methods are being used to investigate plant and animal pathogens, make advances in infectious disease research and to bett er understand a wide range of biological, information, social and technological systems. In this report, readers will not only be able to see the diversity of research projects underway at VBI but also the many synergies that exist between diff erent projects and collaborators. At VBI, we benefi t greatly from collaborations with other departments on the Virginia Tech campus as well as other leading national and international universities and institutes. The projects described here show how these relationships are fl ourishing and bringing new perspectives to our scientifi c undertakings. Reports from two of VBI’s faculty fellows – Virginia Tech faculty who work closely with VBI researchers – specifi cally describe projects involving computational systems biology as well as the simulation and analysis of molecular regulatory systems in cell biology. The work described in this report refl ects our willingness to undertake team-based scientifi c initiatives directed at some of the key research challenges facing society today. It is my sincere hope that the research described here will serve as a catalyst for future work and further ground- breaking collaborations. I would like to take this opportunity to thank you for your interest in the activities of the Virginia Bioinformatics Institute. Sincerely, Bruno Sobral Executive and Scientifi c Director Virginia Bioinformatics Institute 5 • 2006 Research Reports from the Faculty at the Virginia Bioinformatics Institute VBI Faculty - Chris Barrett NNetworketwork DDynamicsynamics andand SSimulationimulation SSciencecience LLaboratoryaboratory Christopher L. Barrett, [email protected] Professor, Virginia Bioinformatics Institute & Computer Science, Virginia Tech The Network Dynamics and Simulation Science Laboratory is pursuing an advanced research and development program for interaction-based modeling, simulation, and the associated analysis, experimental design, and decision support tools for understanding large biological, information, social, and technological systems. Extremely detailed, 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 theoretical foundations of our work are rooted in the concept of interaction-based computing and discrete dynamical systems. We are currently pursuing projects in the following programmatic areas: integrated high-performance simulation and data service architectures; human population dynamics and associated social networks in urban environments and at the national scale; epidemiology and the spread of infectious diseases; computational and behavioral economics and commodity markets; next generation computing and telecommunication systems; and computational systems biology. Keywords: interaction-based computing, simulation, and modeling; infectious diseases and public health; grid computing and service-oriented architectures; activity-based models of urban regions; population dynamics; social networks; complex systems; discrete dynamical systems; computational complexity; algorithmic semantics. Scientifi c and technical progress Signifi cant progress has been made in successful development of scalable algorithms achieving important programmatic goals during for simulating epidemics and other reaction the last twelve months. Here we highlight diff usion systems. We have now generated a some of the achievements. In the reporting synthetic population consisting of 250 million period, we have developed version 1.0 of individuals endowed with daily activity Simfrastructure, a service- and grid computing- patt erns where the activities are performed oriented modeling tool for socio-technical, at real locations. In addition, the EpiSims biological, and information systems. We have (Epidemiological Simulation System) project also developed version 1.0 of Simdemics, a has progressed to represent various disease scalable high-performance computing-based outbreak interventions. The tool is being used service environment for general reaction by the National Institutes of Health (NIH) diff usion systems. Other milestones include the Models of Infectious Disease Agent Study to support pandemic preparedness. Contributors: For applications in the fi elds of commodities Karla Atkins, Richard Beckman, Keith Bisset, Jiangzhuo and energy markets, we have developed version Chen, Stephen Eubank, V. S. Anil Kumar, Achla Marathe, 1.0 of Sigma (Simulation of Generic Markets), Madhav V. Marathe, Henning Mortveit, Julia Paul, Paula a service-oriented modeling architecture Stretz for analyzing large commodity and energy markets. We have also enhanced TRANSIMS Student contributors: Kevin Allen, Deepti Chafekar, (Transportation Analysis Simulation Systems) to Abhijit Deodhar, Aseem Deshpande, Subodh Lele, Bryan support the U.S. Department of Transportation Lewis, Farid Merchant, Kashmira Phalak, Sameer Tupe sponsored transport planning study for 7 • VBI Scientifi c Annual Report the Washington DC region. In addition, we participated in a team eff ort to implement a TRANSIMS-based traffi c simulation on reconfi gurable computing hardware. Our work has also comprised advanced computer and mathematical research in the area of high-performance computing, discrete dynamical systems, and communication networks. Notable achievements in those areas include the following: • First provable multi-criteria approximation algorithms
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