pc-tools

A Gentle Introduction to Installing RuleBuilder and BioNetGen on a Windows Box

I installed BioNetGen as well as I could on Windows, but it doesn't seem to work right. However, you can use RuleBuilder and you are welcome to try BioNetGen -- maybe you'll have better luck. At least one of the students in the workshop was able to get it to run on a PC.

  1. Download BioNetGenPC.zip and RuleBuilder.zip.
  2. Download ActivePerl from http://www.activestate.com/activeperl/. Follow the directions on the page to install it.
  3. Installing RuleBuilder.

    1. If RuleBuilder.zip has been unzipped, so that you have a directory RuleBuilder, then RuleBuilder has been installed. If it hasn't been unzipped, you need to extract it -- you can right click and select "Extract All" from the menu.
    2. To run RuleBuilder, double click on the file RuleBuilder-beta-1.51.jar inside the directory RuleBuilder. You can now define a model or import a bngl file (using File>import in the RuleBuilder file menu).
    3. To run the model using BioNetGen, you must first install BioNetGen as described below, tell RuleBuilder how to find the program BNG2.pl, and tell RuleBuilder where to put output files. Use File>settings to set the absolute path to BNG2.pl (see discussion of absolute paths below) and to tell RuleBuilder where to put output files.
  4. Installing BioNetGen

    1. Put BioNetGenPC.zip in a convenient directory (for example, your home directory, ie, C:\Documents and Settings\<yourloginname>\ (this is your working directory when you first open a terminal window) or your desktop (C:\Users\<yourloginname>\Desktop).

      Note: When I use pointy brackets around a word or phrase, it means you should change the entire word or phrase, including the pointy brackets, to the thing I'm describing. For example, since my loginname is nancyg, I would use C:\Users\nancyg and C:\Users\nancyg\Desktop in place of the above.

      Wherever you put the file, figure out the absolute path to the directory. This is the sequence of directories, separated by "\" characters, and beginning with C:

    2. Extract all files from BioNetGenPC.zip. I suggest that when prompted for the directory to extract them to, you make the name BioNetGen; the only reason the zip file is named BioNetGenPC is to distinguish it from the Mac version.

      Inside the BioNetGen directory are a number of subdirectories -- the most interesting are Models2, which contains a collection of models including toy-jim.bngl; Perl2, which contains a number of programs, most importantly BNG2.pl; and bin, which contains some more important programs. I have already put run_network.exe and run_network_MSWin32.exe in it for you.

    3. What is the absolute pathname for BioNetGen\Perl2? If you have figured this out correctly, you can type the command
      cd "<absolutepathname>"
      and you will find yourself in the directoryBioNetGen\Perl2.

      To run BioNetGen, all you have to do is type BNG2.pl <modelfile>.bngl.

    4. Now change directory to the Models2 directory
      cd ../Models2
      and type
      ../Perl2/BNG2.pl toy-jim.bngl
      to see what happens. You should see something that looks like this (check that the last few lines are the same). If you do, you have installed BioNetGen correctly. If not, you may be having the same problem that I am.

Last modified: Oct 13, 2011