Genome3D Project

Genome3D is a model-view framework for displaying genomic and epigenomic data within a three-dimensional physical model of the human genome. In this framework, the model of the physical genome implicitly contains all levels of structure and hierarchy, and provides an underlying platform for integrating multi-scale structural and genomic information within three dimensions. The viewer is a Microsoft Windows based software designed to display data from multiple scales and uses a hierarchical model of the relative positions of all nucleotide atoms in the cell nucleus, i.e., the physical genome. With Genome3D, multi-resolution data can be interactively explored to uncover complex and new structural relationships. Genome3D is designed with a hierarchical architecture that establishes methods for incorporating new data of varying resolutions, and allows for user-defined annotations. The viewer can also be used to display other 3D genome models as long as they are specified in Genome3D format. A platform independent, fast response, cloud ready viewer prototype has also been developed to employ game engine to visualize 3D genome structure.

Getting Started     README     Genome3D Viewer with Example Movie 1      Cannot play? Try IE or Download Movie 2      Cannot play? Try IE or Download Genome3D Models     Genome3D Model A (1.0 Gigabyte)     Genome3D Model B (1.3 Gigabyte) Additional Data     Additional_Data_README.txt     Genome3D_Model_A_xml.tar.gz (1.3 Gigabyte)     Genome3D_Model_B_xml.tar.gz (1.6 Gigabyte)     Genome3D_Model_C.tar.gz (1.6 Gigabyte)     Genome3D_Model_D.tar.gz (1.6 Gigabyte) Presentations    1) ISMB2011 Highlight Track Presentation pdf    2) VIZBI 2013, Broad Institute, Boston, MA video Fundings    1) Dr. Jijun Tang - NSF 1161586    2) Dr. W.Jim Zheng - NSF 1339470 Citations    1) Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.       Asbury TM, Mitman M, Tang J, Zheng WJ.       BMC Bioinformatics. 2010 Sep 2; 11(1):444.    2) Exploring genomes with a game engine.       Shepherd, Jeremiah J., et al. "FD 169: Exploring Genomes with a Game Engine." Faraday Discussions (2014). Contacts:    Dr. Jijun Tang    Department of Computer Science and Engineering    Swearingen Center, Room 3A57    University of South Carolina    (803) 777-8923 (office), (803) 777-3767 (fax)    jtang@cse.sc.edu    http://www.cse.sc.edu/~jtang/    Dr. W.Jim Zheng    School of Biomedical Informatics    University of Texas Health Science Center at Houston    Phone: (713) 500 3641    Wenjin.J.Zheng@uth.tmc.edu    https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm