Cell Model - Interactive version

How to Run the Interactive Version of the Cell Model

This is a model of a Biological Cell, produced by Ken Webb using Rational Rose RealTime (RRT) 6.0.2 for C++.

Instructions:

1. Create a new root level directory called Cell.

2. Unzip the zip file into this new directory, keeping the same directory structure as in the zip file.

3. Double-click on StartCell8_Everything.bat. This will start two Rose RealTime executables, each in its own DOS console window. The LifeTheUniverseAndEverything.EXE window should look like:

ObjecTime Micro Run Time System
Release 6.02.C.00 (+c,+e)
Copyright (c) 1993-1999 ObjecTime Limited
objectime: observability listening not enabled

RTS debug: ->els: not enabled

4. Within the console window type "quit". This will quit from the runtime debugger, and actually start the application thread running.

5. You should see the following:

Task 0 detached
Ken Webb's Cell Model starting
Opened file: \Cell\Configuration\userPrefs.dat in r mode
NSingleCells : 2
GaiaType : 1
NMitochondriaPerCell : 50
CreateFileMapping() succeeded
MapViewOfFile() succeeded
Opened file: \Cell\Configuration\typeData.dat in r mode
Opened file: \Cell\Configuration\molTypeData.dat in r mode
Opened file: \Cell\Configuration\genomeData.dat in r mode
Opened file: \Cell\Configuration\phenomeData.dat in r mode
MmfReflector has finished writing MMF data

6. The last line, about writing MMF data, will take about 15 seconds to appear.

7. The VrmlAgent.EXE console window should look like:

ObjecTime Micro Run Time System
Release 6.02.C.00 (+c,+e)
Copyright (c) 1993-1999 ObjecTime Limited
objectime: observability listening not enabled

RTS debug: ->els: listening at tcp port 3492 [@nnn.nnn.nnn.nnn]

8. Within the console window type "quit". This will quit from the runtime debugger, and actually start the application thread running.

9. You should see the following:

Task 0 detached
OpenFileMapping() succeeded
MapViewOfFile() succeeded
OpenFileMapping() succeeded
MapViewOfFile() succeeded
Opened file: \Cell\VrmlWorlds\root.wrl in w mode
Opened file: \Cell\VrmlWorlds\RoughEr.wrl in w mode
Opened file: \Cell\VrmlWorlds\SmoothEr.wrl in w mode
OpenFileMapping() succeeded
MapViewOfFile() succeeded

10. A third DOS console window will open, and will display:










11. Within this third console window, you can optionally press any key.

12. The Vrml browser will open up within Netscape, with a Java text edit window below it.

13. After a few seconds, two cells with a bunch of internal organelles should appear in the Vrml browser.

14. Every second, one of the two cells in ObjecTime/RRT will send a message to the Java applet, asking it to change the color of the VRML Cell. It should change back and forth between various shades of red and blue, and fairly quickly settle on a dark blue color. This represents the changing levels of Glucose and Pyruvate in that cells's cytosol.

15. Moving the cursor over a cell or organelle in the Vrml world will display the name of the entity at the bottom of the Netscape window. The entity's name is a concatenation of the RRT class (capsule) name and the address of that C++ instance in memory.

16. If you click on a cell or organelle in the Vrml world, Java will detect it and send a message to the ObjecTime/RRT executable, which will respond with some debug level information that Java will display in its text window.

17. When you're ready to quit, it's best to exit the VrmlAgent.EXE DOS window first. Do this by pressing the close button (X) at the upper right corner.

18. Then exit from Netscape, and then from the other DOS window.

Notes:

· This has been tested using the following configuration:

- Windows NT 4.0, Windows 95

- Netscape 4.5 with Java

- CosmoPlayer 2.1.1 (VRML browser)

· The following cell components are visible using the VRML browser:

Cell Bilayer (bright blue, green, red patches)
Cytosol (semi-transparent layer; red or blue changing color for one cell)
Mitochondria (orange elliptical shapes)
Nucleus (blue/grey textured sphere in the center of the cell)
Rough Endoplasmic Reticulum
Smooth Endoplasmic Reticulum
Golgi Complex (greenish flying saucer)

· If you type "quit" within the VrmlAgent.EXE window first, you will see the following message continuously displayed until the LifeTheUniverseAndEverything.EXE process starts:

waiting for LifeTheUniverseAndEverythingMMF

You will then see the following additional message repeated a number of times while the LifeTheUniverseAndEverything.EXE process initializes itself and finishes writing initial data to the shared memory mapped file (MMF):

waiting for instance table to be ready

· This is an early proof-of-concept prototype. Many of the elements are the way they are to prove that some feature (especially communication between VRML, Java and ObjecTime/RRT) is working correctly. Some of the graphic elements, including the GolgiComplex were done very quickly as place-holder graphics.

· You will need TCP/IP running on the computer to allow a socket connection between the VrmlAgent executable and Java.

· You can use other vendors' VRML browsers in place of the Cosmo browser. However some things may not work. For example, the Blaxxun browser crashes netscape when instructed by Java to change the color of the cell.

· Use the VRML browser controls to zoom into and out of the VRML world, to rotate it, and otherwise navigate through it. Once inside the outer cell membrane, you will be able to touch the internal components of the cell to see their names displayed at the bottom of the Netscape window. It can be a bit tricky getting inside. You may need to go through a series of zooms and rotations before the browser will let you through.

· You might also want to look at the CellModel_RoseRealTime.gif file to see what the RRT graphic design environment looks like. You should be able to see some of the C++ classes that correspond to elements in the Vrml scene.