SI2007 Integrative Studies: Translational Biomedical Research

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General Information

Time: 2 to 5 pm

Location:: Atkinson Hall, Room 4004


  • Tuesday, July 31, Advanced Imaging and Informatics Tools: Applications in Cardiomyopathy Research
    Instructors: Abel Lin, Masahiko Hirojima, Rajvikram Singh
    The NCMIR Multiscale Imaging Portal is used to support multiscale imaging using advanced microscopy research instrumentations in a user friendly portal environment. This environment also produces some of the key datasets for multiscale modeling activities at NBCR. The TxBR is co-developed to enhance tomographic reconstruction image resolution, and distributed computing is used to handle the computational requirement.
    Heart failure is a major cause of death, led to by a myriad of conditions such as high blood pressure, diabetes, obesity or congenital conditions. Computational modeling of heart failure may provide answers to questions difficult to answer through biological experiments, and provide predictions that may be able to be verified experimentally. High resolution mesoscale image analysis of subcellular complexes in cardiac myocytes is providing new insight into what they really look like, and poses new challenges in producing spatially realistic models for heart failure research.
    We also provide a demonstration of the use of Tiled Display Wall (TDW) technology in the visualization of high resolution images, molecular docking and volume segmentation experiments. A brief introduction to the underlying technology will be provided.
    SAGE Architecture & API
  • Wednesday, July 1, Computational Modeling of Heart Failure at the Cellular Level
    Instructors: Zeyun Yu, Anushka Mihaylova
    Starting from the high resolution images obtained from crystal strutures and/or images from NCMIR facilities, one may use imaging processing tools to enhance image resolution and extract features, develop finite element adaptive mesh representations, and generate spatially realistic subcellular and cellular models for investigations of hear failure. We'll discuss the common tools such as LBIE Mesher and a prototype 3D-Myocyte software package under development.
    Computational Modeling at the Cellular Level
    Adaptive mesh generation
    Anushka Mihaylova will demo the prototype 3D-Myocyte software package. To visualize output from this software please instal gmv on your machine before coming the the sessions. Gmv (General Mesh Viewer) is available from
  • Thursday, July 2, Running Virtual Screening Experiments on the Grid
    INstructors: Terence Martin, Robert Konecny
    Molecular dynamics studies can provide a number of snapshots of protein motions, not visible in protein crystal structures. These snapshots may be selected and for use in large scale virtual screening experiments in various computing environment.
    AutoDock has been used in the World Community Grid for the FightAids@Home project. It's also highly suitable for use in other grids such as the Open Science Grid. An introduction to the OSG computation grid is provided, and hands on tutorials are provided to introduce the users to this grid computing environment using autodock as an example.
    We'll then provide a basic introduction to the use of NAMD and VMD for molecular dynamics simulation studies, and provide the background for its application in the relaxed complex method.
    OSG Tutorial
    VMD Tutorial
    VMD tutorial files (tar.gz UNIX format)
  • Friday, July 3, Relaxed Complex Method and Virtual Screening for Avian Flu Inhibitors
    Instructor: Rommie Amaro
    Relaxed Complex Method has been successfully used in developing therapeutic interventions for the HIV patients. It has broad implications for other infectious diseases as well. We'll present an overview of the technique and its application in searching for inhibitors for the Influenza Virus neuraminidase (NA) from the H5N1 subtype, and discuss the tools and workflow software that are under development to support transparent access of computational resources and automation for such large scale molecular dynamics simulations.
    Session Presentation

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