Description

RuleBender provides an easy-to-use interface for the popular rule-based modeling software package, BioNetGen. It provides an editor with context-sensitive highlighting and syntax checking along with automated model visualization, simulation, and plotting capabilities. RuleBender also provides an automatic journaling capability that keeps all model files and simulation data in a common, chronologically-ordered workspace. RuleBender is written in Java using the Eclipse Rich Client Platform. Installation packages for Windows, Mac, and Linux operating systems can be found at http://bionetgen.org along with installation instructions, documentation, and instructional videos. Below are detailed instructions for building RuleBender using Eclipse.

Build Process

Dependencies

Ubuntu

Run the following to install the JRE and JDK:

sudo apt-get update
sudo apt-get install default-jre
sudo apt-get install default-jdk

Downloading Eclipse

1. Go to https://www.eclipse.org/downloads/packages/release/neon/3.

2. Download Eclipse Neon RCP and RAP Developers for your system.

Downloading Rulebender, creating directories and building the parser

3. Go to your terminal create a directory workspace_rb_1_git and workspace_rb_1 like this:

    mkdir ~/workspace_rb_1
    mkdir ~/workspace_rb_1_git
   

4. Go to workspace_rb_1_git directory like this:

    cd ~/workspace_rb_1_git
   

5. Clone the RuleBender repository with the following command:

    git clone https://github.com/RuleWorld/rulebender.git 
   

6. Go to the rulebender directory and build the parser:

    cd ./rulebender
    ./s_build_BNGParser.sh 
   

Creating and importing an Eclipse project

7. Go to eclipse directory and run eclipse from terminal (For mac you can add eclipse as an application)

8. Set your workspace to your recently created workspace_rb_1.

9. Close the welcome screen.

10. Click File -> New -> Project

11. Select General -> Project and click Next. Give project name RuleBender. Click Finish.

For Linux

12. In the Project Explorer Window, right click on RuleBender and click Import.

13. Select General -> File System and click Next. On the next screen locate the git repository you cloned (i.e. ~/workspace_rb_1_git/rulebender). From the left panel, click the checkbox next to rulebender to import all files. Click Finish .

For MacOS

12. On a finder window, go to workspace_rb_1_git/rulebender. Select all and copy.

13. Right click RuleBender in Project Explorer

Setting the Icons

14. Double click RuleBender in Project Explorer. Then, double click rulebender.product. Near the bottom of the middle window, go to the Launching tab.

15. At the Program Launcher menu, do the following:

• Select linux and click Browse, pick Rulebender/icons/system/linux/RB-128.xpm
• Select macosx and click Browse, pick Rulebender/icons/system/osx/RB-128.icns
• Select windows and do the same for the following:
  • 16x16 (8 bit)
  • 16x16 (32 bit)
  • 32x32 (8 bit)
  • 32x32 (32 bit)
  • 48x48 (8 bit)
  • 48x48 (32 bit)

Multiplatform building

16. For linux open Window -> Preferences, for mac go Eclipse -> Preferences.

17. Go to Plug-in Development -> Target Platform. Select Running Platform (Active) and click on Edit.

18. Click Add... and choose Software Site. Click Next.

19. In Work with type: http://download.eclipse.org/eclipse/updates/4.6 (replace 4.6 with current version of eclipse) and press Enter.

20. Important: Check Eclipse RCP Target Components and Equinox Target Components

21. Uncheck Include required software

22. Check Include all environments. Click Finish, Finish, and OK.

Exporting

23. Near the bottom of the middle menu, go to Contents and click Add Required Plug-ins.

24. In Project Explorer, right click rulebender.product and choose Export

25. Select Plug-in Development -> Eclipse product. Click Next.

26. Choose destination directory which is workspace_rb_1/RuleBender and check Export for multiple platforms. Click Next.

27. Select macosx, linux(gtk/x86_64) and win64. Click Finish. If it asks you to save changes, click Yes.

Packaging

28. Download the Java SE Development Kit 8 for Linux, OSX, and 64-bit Windows.

29. Create a directory called ~/d_java and do the following:

    • Extract the linux archive to ~/d_java/java_jre_lin64/
    • Extract the osx archive to ~/d_java/java_jre_osx64/
    • Extract the win64 archive to ~/d_java/java_jre_win64/

30. Download the latest versions of BioNetGen for Linux, OSX, and Windows.

31. Create a directory called ~/BioNetGen.latest and do the following:

    • Extract the linux archive to ~/BioNetGen.latest/Linux/
    • Extract the osx archive to ~/BioNetGen.latest/OSX/
    • Extract the win64 archive to ~/BioNetGen.latest/Win64/

32. Run the s_installation_packages.sh script. This will create RuleBender distributions in ~/workspace_rb_1/RuleBender/zips.