Boolean Network Simulation of Biological Networks
To compile the package, you need JAVA SE 7 or higher version. Simply clone the repository and enter the src folder. You will find all source code and you can compile the module you want by using javac. In the future I will add auto-compile script and pre-compiled jar files.
To generate network description file: modify two examples I gave (Budding_Yeast_Cell_Cycle.java & C_elegans_Cytokinesis.java). The file is self-explanatory. Then compile and run the file to generate the network structure files. Some examples can be found in the data/ folder.
To do network simulation: java StatePrediction NETWORK_FILE_NAME
To do robustness test: java RobustnessTest NETWORK_FILE_NAME
- Add auto-compile script and pre-compiled jar file
- Add comprehensive comments for source codes
- May add support for other models
If you find bugs or you want some functions to be added in this software package, please raise a issue on the GitHub page of this project. I'll respond as soon as possible.