Features

1. An architecture that allows dynamically loading a simulation using user-defined models for
   1. Cell program
   2. Cell Model
   3. System Model
2. A sim / config file will load these into a simulation object by reading a file with contents
   system=sysmodels.simplebiology.SimpleBiology
   cell=cellmodels.simplecell.SimpleCell
   parser=parsers.CPA.CPAParser
3. Better UI to allow simultaneous viewing of several simulations (at different stages)
4. Arcitecure allows easy specification of diffferent statistics

Installing J2SDK 1.4.1, Java3D and JavaCC for Windows

1. Install J2SDK from http://java.sun.com/downloads/ [Ver 1.4.1]
2. Install Java3D also from http://java.sun.com/downloads/ filename should be java3d-1_3-windows-i586-opengl-sdk.exe for OpenGL version for the i586
3. Install JavaCC (2.1) from http://www.webgain.com/download/javacc/details.html
   Note: This is not needed for running CellSim

All 3 are also available at http://www.cs.virginia.edu/~gsg5j/download/

Running CellSim

The applet can be viewed once (1) & (2) are installed. The applet is available at http://www.cs.virginia.edu/~gsg5j/cellsim/
The stand-alone version of CellSim is available at http://www.cs.virginia.edu/~gsg5j/download/CellSim.zip

1. Extract the CellSim.zip file
2. cd CellSim
3. init_env (a batch file) u may need to set the paths correctly for your installation
4. java gui.GUI

Select File->New and then Simulation->Step. Using the menu File->New, you can run as many simulations as you like in seperate internal windows within the main window

Writing your own models for CellSim

1. The abstract classes SystemModel, Cell and Parser reside in the core/ subdirectory and form the heart of the Cell Simulator. These must be subclassed to form different models for the system, cell and the parser
2. The class Simulation dynamically loads the models specified in the SIM file for the SystemModel, Cell and Parser
3. To create your own system model, I suggest that you begin by creating a copy of the subdirectory sysmodels/simplebiology. Store it as sysmodels/MySystemModel. Rename the class-names and the package-name in sysmodels/MySystemModel/SimpleBiology.java suitably. The heart of the model is the function
   public Vector provideService(Vector args)
   It is basically a function called by the Cell to cause system-wide effects like chemical diffusion, cell diffusion etc
4. You can similarly create a new Cell model by starting with cellmodels/SimpleCell/SimpleCell.java. Again begin by modifying the provideService() function
5. Be sure to create a sim file similar to simple.sim provided in the main directory of the CellSim distribution. Also make sure that the classes for your new models are reacheable through the CLASSPATH. As long as you keep all cell models in the cellmodels/ folder, all system models in the sysmodels/ folder and all parsers in the parsers/ folder and name the packages using the pathname from the base directory, this should not be a problem

Contact Information

Please report bugs/issues or make enhancement requests to Selvin George <selvin@cs.virginia.edu>

Please contact Prof. David Evans <evans@cs.virginia.edu> regarding our research effort