Tutorial (A brief introduction to the Cell Animator With a Sample "Switch Mechanism of lambda Phage")

Cell Animator (Tutorial)

Cell Animator is developed on the basis of XML technology. Users can realize visualizations of simulation results of aimed biological phenomenon by creating XML document in which CSV files produced by GenomcObjectNet are included as basic data for simulations. After the file GON_Visual.zip is uncompressed, 5 files and 2 directories are appeared. Files GonVisTool.exe -- Executable file of Cell Animator. GonVisTool.dtd -- DTD file which defines the grammar of XML file to be created. lysogen.xml -- An example of XML file in which XML document for visualization of lysogen path of lambda phage is described. five DLL files -- libpng1.dll, vtkdll.dll, xerces-c_1_4.dll, zlib.dll, msvcp60,dll ReadMe.txt Directories data directory -- this contains CSV files produced by Cell Illustrator images directory -- this contains PNG files which are used in the visualization of lambda phage switching mechanism
	1. Launch Cell Animator by double clicking the GonVisTool.exe icon

2. Open a file from File menu and select the file you wish to open.

3. Open lysogen.xml file.

4. Three windows appears. Arrange locations of windows as you like

5. To start the simulation, press the button. If you want to change the speed of animation, use the 6. Animations in these windows are driven by values in a CSV file containing simulation results. You can observe how the proteins regulates genes and changes concentration level produced by these genes. Try to use Mouse Mode functions. These functions does not currently make sense, but these will be used in the forthcoming version in which three dimensional visualization is possible. The XML code can be edited with any text editor if necessary. It allows you to view in real-time its edits and changes.