BioNetGen Distributions

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See Release Notes for more information on each release.

Contents

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Source Code

  • Current version is 2.1.5.
    • Supports compartmental BNGL (cBNGL), which is the subject of a recent tutorial. See Release Notes for other details.
    • Binaries are not included with this distribution. You must compile them yourself (easy) or select one of the precompiled binaries below.
    • Does not include RuleBuilder, which may be downloaded separately here.
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Older Distributions

  • Last distribution under 2.0 is 2.0.48.
  • Last distribution with working version of the macro package is 2.0.47ALPHA.
  • Last distribution including RuleBuilder is 2.0.46.
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Pre-compiled Binaries

Download the correct version of the run_network executable for your platform and copy it into the bin directory of your BioNetGen distribution. Make sure the executable name is run_network (run_network.exe under Windows) and has execute permission.

  • Mac OS X 10.5 Intel
  • Linux
  • Windows. Note: This zip file expands to the create the bin directory containing the executable and the cygwin.dll file. Make sure both these files are in the bin directory of your BNG distribution.
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BNGEditor

An IDE that provides an editor, network visualization, a simulation interface, and graphing tools is available in beta version for trial. BNGEditor is a java program (running under Java 5) that is distributed as a set of jar files with compiled bytecode. You will need to download the appropriate distribution for your operating system.

  • Mac Distribution Note: For mac, use "java -jar -XstartOnFirstThread BNGEditor.jar" to start the program or it will crash.

These are for 32 bit operating systems, for 64-bit systems, download the corresponding swt.jar file from the swt website and replace the one in the /lib directory. Please note that this does not appear to work for the Mac distribution.

Configuration. Once you have downloaded the zip file, unpack it in a convenient place and launch the jar file from a directory in which you have read/write access. The editor will use that directory to write work and data files, so it's best to make a separate directory for this purpose. To configure BioNetGen to run from within the editor, click 'Run->Set BNG Path' and navigate to the location of the BNG2.pl file (yes, I know that a filename is not strictly a path). You can also configure network visualization (Contact Map and Influence Diagram) by navigating to 'View->Set dot path'. dot is a component of the Graphviz graph visualization package that is freely available. The performance of Contact Map is fairly robust, but Influence Diagrams are known to be incorrect for some networks, so use caution in interpreting the output.

Yao Sun is the author of BNGEditor. His supervisors were Jim Faeder and Liz Marai from the University of Pittsburgh.

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