Installation Guide
From BioNetWiki
Instructions for installing BioNetGen2
Contents |
Requirements
BioNetGen2 is written in the Perl language. The simulation back end, run_network, is written in C. The RuleBuilder front end, which is optional, is written in Java.
Running BioNetGen requires
- Perl version 5.8 or above
Compiling run_network requires
- gcc and make
Pre-compiled binaries are provided for Linux, MacOSX, and Windows.
Running RuleBuilder requires
- Java 1.5.0 Runtime Environment or above
Accessing network generation and simulation capabilities from RuleBuilder also requires that BioNetGen and run_network are installed.
Install the BioNetGen source code
- Obtain the latest source distribution from the download directory. You will be prompted for a username, which is BNG2, and a password, which is rulebuilder. The source distribution file is BioNetGen_x.xx.xxx.tgz.
- Place the source distribution file in the location where your would like to install BioNetGen2.
- Unzip the source by typing 'tar xvzf <file>.tgz', where file is the name of the BioNetGen2 source file.
Install the simulation back end
There are two options - 1) Download a precompiled binary from the website for your operating system, if its available, 2) Compile the binary from source.
Downloading the pre-compiled binary
Pre-compiled versions of the simulation back end are available for downloading. Simply extract the archive file in the main BioNetGen directory (BioNetGen_2.x.xx) and proceed to testing. Click here to see platforms for which binaries are available.
Compiling from source
Prerequisites are a working gcc compiler and the make utility. These are usually found on any linux box or Mac with OS X installed, but may need to be specially installed on a Windows machine.
- cd to the root BioNetGen directory and type 'make'.
- The main Makefile and the source code for the back end is in the Network2 directory, in case you encounter any problems.
Test run
The main BioNetGen executable is the Perl script, BNG2.pl in the Perl2 directory. BNG2 can be run from the command line by typing
path-to-Perl2/BNG2.pl file.bngl
To test this, cd to the Models2 directory, and type '../Perl2/BNG2.pl toy-jim.bngl'. You should see some output like
BioNetGen version 2.0.32+ Reading from file toy-jim.bngl Read 16 parameters. Read 5 species. Adding P as allowed state of component Y of molecule K Read 8 reaction rule(s). Read 9 observable(s). WARNING: Removing old network file toy-jim.net. Iteration 0: 5 species 0 rxns 0.00e+00 CPU s Iteration 1: 8 species 3 rxns 2.00e-02 CPU s ... Running run_network on ntal.local full command: "../bin/run_network" -o "toy-jim_kinetics" -p cvode -a 1e-10 -r 1e-08 -g "toy-jim_kinetics.net" "toy-jim_kinetics.net" 1 120 Read 16 parameters Read 25 species Read 101 reaction(s) ...
If run_network is able to run, then the compilation has been successful.
Validation
To make sure that you have a properly functioning BioNetGen program, cd to the Validate directory and type 'perl validate_examples.pl'. This may take a few minutes to run. The validation suite is currently under construction, so only a limited subset of BNG features are tested.
Getting Started
A tutorial that describes the basic and some advanced features of BioNetGen2 is available in the Tutorial directory. We are working on getting this into an online wiki format, to improve the formatting and coverage.
RuleBuilder provides a graphical user interface to BioNetGen. With the Java Runtime Environment installed, it can be run either by double-clicking on the RuleBuilder-x.xx.jar file in the RuleBuilder directory, or typing
> java -jar RuleBuilder-x.xx.jar
from the command line. Additional intstructions for configuring and running RuleBuilder are provided in the INSTALL_RB.pdf and the RuleBuilder_GettingStarted.pdf files in the RuleBuilder directory.
