Rule-based modeling framework
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README.md

BioNetGen

Rule-based modeling framework Build Status Build status

Overview

BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. The BioNetGen language has recently been extended to include explicit representation of compartments. A recent review of methods for rule-based modeling is available in L. A. Chylek et al. (2013) Wiley Interdiscip. Rev. Syst. Biol. Med., 6, 13–36.

BioNetGen is presently a mixture of Perl, C++, and Python. Network generation is currently implemented in Perl, the network simulator is C++, and a new SBML-to-BNGL translator is implemented in Python. In addition, a new language parser is currently being developed in ANTLR.

Installation of Distribution

Most users should simply download BioNetGen from www.bionetgen.org and get the appropriate distribution for their OS. To install BioNetGen, unzip the BioNetGen distribution file, e.g. BioNetGen-2.3-MacOSX.tar.gz, in the directory where you would like BioNetGen installed.

Download Latest Test Builds

These builds are the from the head of master and are not guaranteed to be stable. Use at your own risk.

Compilation from Source

The distribution mentioned above comes with pre-compiled binaries (executables) for the ODE, SSA and PLA engines. However, developers can compile their own binaries assuming they have appropriate compilation tools (autoconf, etc).

First, you'll need to pull in or update the git submodules (currently NFsim and atomizer). To do this, enter the following at the terminal:

git submodule init
git submodule update

Linux and OSX

At a terminal, type the following to build NFsim and atomizer:

cd <bngpath>
make

Windows

NFsim and atomizer

Make sure you have Ninja, CMake, and Anaconda installed and that Python is in your path. For more detailed information, please see the NFsim and atomizer repos. From a PowerShell prompt, type the following:

cd <bngpath>/atomizer/SBMLparser
python.exe -m pip install --user -r ./requirements_win.txt
python.exe -m pip install --target=. python-libsbml
python.exe -m PyInstaller ./sbmlTranslator.spec
mv ./dist/sbmlTranslator.exe ../../bin
cd ../../nfsim_src
mkdir build
cd build
cmake -G "Ninja" ..
ninja

CVODE and muparser

If you have Windows, try Strawberry Perl, (see http://strawberryperl.com/). Perl is also available for Windows users within the Cygwin environment.

Make sure Cygwin used is for the appropriate Windows architecture (32/64 bit). Make sure Cygwin has developer tools installed (Select Devel when installing Cygwin). Extract folders cvode-2.6.0 and muparser_v2_2_4 to <bngpath>\Network3 from archives in <bngpath>\libsource. In the Cygwin terminal:

cd <bngpath>\Network3
autoreconf --no-recursive --install
./configure --disable-shared --prefix=<bngpath>
make
make install
make clean

Using BioNetGen from the Windows command prompt can throw Missing DLL errors. These DLLs are specific to the Cygwin version used and found in Cygwin\bin. Copy them to <bngpath>\bin to resolve these errors. The required DLLs for the 64-bit version are:

  • cygwin1.dll
  • cygstdc++-6.dll
  • cygz.dll
  • cyggcc_s-seh-1.dll.

Creating a Distribution

Developers preparing a new distribution can simply run the following command:

cd <bngpath>
make dist

This will create a tarball called '/BioNetGen-.tgz'.

Examples

Example models are provided in the Models2 folder. To run them, go to the Models2 directory, and type:

../BNG2.pl <model>.bngl

where is one of the models found in the Models2 directory.

Validation

To validate the BioNetGen installation:

  1. run the Perl script <bngpath>/Validate/validate_examples.pl.
  2. if any tests fail, look at the log files for more information.

PLEASE NOTE: Stochastic simulation tests rely on statistical validation. Occasionally a validation will fail due to outliers. The current validation script only reports stochastic validation failures if they occur TWICE in a row. Therefore, if this occurs there is a good chance that something is wrong. To confirm, we suggest rerunning the validation script at least once. Single tests may be run by passing the model basename as an argument.

BioNetGen History and Support

The BioNetGen software package was initially developed by the Cell Signaling Team at Los Alamos National Laboratory. The current development team is based in the Department of Computational and Systems Biology at the University of Pittsburgh School of Medicine, with contributions from collaborators at the Theoretical Division and Center for Nonlinear Studies at Los Alamos National Laboratory, the Departments of Biology and Computer Science at the University of New Mexico, the Center for Cell Analysis and Modeling at the University of Connecticut Health Center, and the Department of Biological Chemistry at the Johns Hopkins University School of Medicine.

BioNetGen development is currently supported under the auspices of the Center for Multiscale Modeling of Biological Systems (MMBioS), a collaboration between the University of Pittsburgh, the Pittsburgh Supercomputing Center, Carnegie Mellon University, and the Salk Institute (NIH grant P41GM103712). BioNetGen has been supported by NIH grant GM076570 and work has been performed under DOE contract DE-AC52-06NA25396. Additional support for BioNetGen has been provided by NIH grants GM085273, AI35997, and CA109552, NSF grant 0829788, the Arizona Biomedical Research Commission, and the Department of Computational Biology at the University of Pittsburgh School of Medicine.

Distributions

The latest BioNetGen distributions, release notes, installation guides, tutorials, etc. are available at http://bionetgen.org.

RuleBender, a Java-based graphical front end for BioNetGen, is available at http://rulebender.org. RuleBender is supported on Linux, Mac OS/X, and Windows platforms. A compatible version of BioNetGen is included in the RuleBender distribution. If you are not sure if your version of BNG is compatible with RuleBender, please use the version distributed with RuleBender.

Contact Us

Email the developers at bionetgen.help@gmail.com

Troubleshooting

If you see the message ABORT: Could not find executable run_network, try setting the environment variable "BNGPATH" to the root directory of your BioNetGen installation. Under bash-like shells, this is done by typing: export BNGPATH=<bngpath>, where is the root directory of BNG.