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 PhiBPlot plotting utility, which is included in the PhiBPlot subdirectory of the distribution, is written in Java. RuleBuilder, which is distributed separately from BioNetGen, is written in Java.
Running BioNetGen requires
- Perl version 5.8 or above. This is usually installed on Mac OS X and Linux machines and under Windows if you are running Cygwin. An alternative Perl for Windows (and other platforms) can be downoaded from here.
Compiling run_network from source (optional under Windows, Mac, and standard Linux) requires
- gcc and make
Running RuleBuilder, the graphical front end requires
- Java 1.5.0 Runtime Environment or above
Installing the BioNetGen Distribution
- Select the desired distribution from the BioNetGen Distributions page. The source distribution file is BioNetGen_x.xx.xxx.tgz. (Avoid ALPHA releases unless you have a specific reason for using one.
- 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.
- If you are using a Linux, Mac, or Windows machine, a precompiled back end is included in the distribution, and you may proceed directly to Testing.
- This distribution does not include the RuleBuilder graphical front end, which can be downloaded separately from BioNetGen Distributions.
Testing
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.
If not, you will need to compile the run_network executable from source, as described in the next section.
Known issue
On some intel-based Macs you may encounter the error
findExec: ./bin/run_network_i386-darwin not found
when you try to run a simulation. The best fix for this problem is to recompile from source. If you don't have gcc or other development tools installed, you can work around the problem by renaming the run_network_ppc-darwin file in the bin directory to run_network-i383-darwin. This should be fixed in release 2.0.49.
Compiling run_network from source
This is optional you are running on a platform other than Windows, Mac OS X, or standard linux. Prerequisites are a working gcc compiler and the make utility.
- 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.
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
See Documentation for a more comprehensive introduction to BioNetGen.
See RuleBuilder for description of how to use the graphical front end.
