How to do Other Things
How to Generate a Static VRML File from the Cell Model
Optionally edit userPrefs.dat
Double click on root.wrl to view it within Netscape with a VRML browser (but tends to run out of memory)
OR, start GLView and load root.wrl
How to Change the Configuration and User Preferencences Files
The user preferences file (userPrefs.dat) contains three options. The file looks like the following:
2 # number of cells incarnated by SingleCell capsule (range 1 to 10)
1 # Gaia Type 1=SingleCell 2=SimpleEcology
50 # Number of Mitochondria per Cell (range 0 to 50)
Gaia Type determines the type of model that will be generated at run time. The single cell type consists of 1 to 10 single cells, and generates a fairly small VRML file.
The simple ecology type generates a much bigger file of at least 3MB. If your simple ecology includes any number of mitochondria per cell the file size will be bigger. If you select Gaia Type = 2, you should select Number of Mitochondria = 0 to keep the file size manageable.
How to Run the 2D Cell Visualizer
Before starting work on 3D visualization, I wrote a very simple 2D visualizer using Microsoft C++ and Microsoft Foundation Classes (MFC). For one cell in the Cell Model, it uses color to show the relative amounts of about 20 small molecules, in the overall cell and in one mitochondrion in that cell. It reads the values from the MMF, and recalculates a corresponding color pattern, every second. Basically it demonstrates continuous reading of data produced in real time by the Cell Model.
Check userPrefs.dat to make sure the SingleCell Gaia Type is chosen.
You can run several instances of the 2D Cell Visualizer at the same time, limited only by the speed of your CPU and the amount of memory available. The only reason for running more than one instance at a time is to demonstrate that multiple processes can all successfully read from the MMF at the same time.
You can run the 2D Cell Visualizer at the same time as the 3D/VRML visualizer.
Debugging using the 3D Representation
It becomes obvious when looking at the details of the 3D representation of a red blood cell (erythrocyte) that it is incorrectly portrayed. Some of this is because of an error in the RRT model. The nucleaus is missing, which is correct, but several other organelles that should not exist are still visible. This is an example of an error that can be immediately seen by a knowledgable person looking at the 3D representation, where it wouldn't be as obvious observing a RRT structure monitor.