Genome3D v1.0 README

Genome3D is a genome visualization program written for Windows-based operation systems ( XP and later ). It can be downloaded from http://genomebioinfo.musc.edu/Genome3D/Index.html.


Installing Genome3D

The file Genome3D_Viewer_with_Examples.zip contains two folders:

Genome3D_Viewer/
Genome3D_Examples/

Unzip this file to a local program directory. The executable and all support files necessary to run it are contained in the folder Genome3D_Viewer/. Open this folder, and double-click on the executable file named "Genome3D.exe". This will start the applcation.

It make by useful to create a Windows Shortcut from your Desktop to this file to faciliate startup.

Once the program is running, click on the "?" button in the application to view the documentation. The Help Documentation is located in the Genome3D_Viewer/helpDir/ folder.

A good place to start is to load the examples or tutorials - see below.


Rendering Requirements

Genome3D uses OpenGL and GLSL to implement a SSAO (Screen Space Ambient Occlusion) shader. This requires the OpenGL Frame Buffer Object(FBO) extension and on-board memory to compile the shaders. These requirements may not be present on some older graphics adapters.

The application will not run if OpenGL v2.0 is not available. OPenGL v2.0 was released in 2004. Please go here to read more and download if needed: http://www.opengl.org/.

If your graphics adapter does not support the shader, the application will still run, but will default to a simple lighting model resulting in inferior quality images. However, in many cases, the shader functionality can be obtained by loading a more recent device driver. Please consult your graphic adapter vendor's web page for more.

Additionally, there is a startup log file ("g3d.log") which is printed out in the exectuable directory everytime the probgram executes. It contains debugging information for the rendering pipeline at startup and may be useful.


Examples

Five example state files with demo models are located in the Genome3D_Examples/ folder. These files are provided to show the full range of available data that can be visualized using Genome3D.

These examples contain sample models that are not designed for in-depth examination, they are partial models which show specific regions of the genome. A full genome model is required to navigate without constraint. Full models can be downloaded separately from http://genomebioinfo.musc.edu/Genome3D/Index.html.

Details for each example is provided in the HTML Help documentation.


Tutorials


There are three tutorials which provide step-by-step procedures to load, examine and save the state of a single chromosome model. Unlike the examples, which are saved states of previously annotated Genome3D views, the tutorials work from a clean start and describe the steps to build a state than demonstrates a particular aspect of the Genome3D's viewing capablilitles.
Details for each tutorial are provided in the HTML Help Documentation.

Full Models

Two genome models are provided: Model A and B.  While both Model A and B shares the same 3D configuration of their chromosomes in space, the nucleosome position in these two models are different.  In Model A, the nucleosome positions are determined by experimental approach (courtesy of Dr. K. Zhao from NHLBI).  See Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K: Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132(5):887-898 for how the data are generated.  Model B has standard random positioning of nucleosome.  Both models are provided in binary format at the fiber and the nucleo level for small file size and fast load. 

Additional data are provided on the Genome3D web page.  These include Model_A and Model_B in xml format.  .  Two alternative models, Genome3D_Model_C and Genome3D_Model_D, are also provided in xml format.  In these two alternative models, the coordinates of nucleotides are different from model A and B as a result of random walking algorithm.


Genome Sequence File

Chromosome sequences in FASTA format are loaded as required at run-time.  All the models are built using human genome assembly build 18 (hg18), which can be downloaded through UCSC genome browser.  For example, to load the genome sequence of Chromosome 1 or Chromosome 1a to the Genome3D viewer, download chr1.fa.gz, decompress the downloaded file and point the viewer to the decompressed file.  If no chromosome sequence is provided at run-time, ACGT will be used as default instead.


Documentation

The Genome3D documentation is written in HTML and contained in helpDir/ in the Genome3D_Viewer/ folder. It is basic XML and can be viewed either from within the application by pressing the "?" button, or using a separate Web browser.


Contact Information

Please address any questions or comments to:
zhengw@musc.edu

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