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From BioNetWiki
Welcome to BioNetWiki!
This wiki serves the BioNetGen™ user community by providing information about BioNetGen™ and tools for the development, annotation, and discussion of BioNetGen™ models.
BioNetGen™ is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. A comprehensive review of rule-based modeling is available in Science's STKE. Click here for toll-free access to the online version.
The BioNetGen™ software package was initially developed by the Cell Signaling Team at Los Alamos National Laboratory. The current development team includes researchers in 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 Department of Computational Biology at the University of Pittsburgh School of Medicine, 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.
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Getting Started
There are currently two options for using BioNetGen™: (1) Download and install the software following the instructions in the Installation Guide, and/or (2) Use an online version at the Virtual Cell, which does not require software installation, by following this link and clicking on Run BioNetGen@VCell. In the latter case you will be need to register as a Virtual Cell user, which involves completing a 1-page form, after which you will be granted immediate access.
Note: To contribute to BioNetWiki or to download the BioNetGen software you obtain an account by sending email to bionetgen@lanl.gov. Feel free to suggest the username you would like - without a specific request, we will assign a username based on your email address.
News
- The upcoming release of BioNetGen will include a module to perform automated model reduction based on the domain-oriented macro approach originally described by Borisov et al.[1][2], which has been recently extended. A preprint of the paper, some examples, and instructions for using the new module can be found here.
- Tutorial on rule-based modeling using BioNetGen presented at the 2007 International Conference on Systems Biology in Long Beach, California.
- A comprehensive list of BioNetGen-related publications is now available.
- Latest version of BioNetGen has some new features, including
- Isomorphism checking using HNauty, which was developed by Nathan Lemons (see setOption).
- Define observables with specified stoichiometry.
- Use math expressions anywhere parameter references are allowed.
- Check out the new BioNetGen FAQ! Please feel free to post questions on the wiki or email us.
- The BioNetGen Language may provide a useful tool for constructing annotated models using wiki technology. For a pioneering example of how this can be done, check out Ty Thomson's Yeast Pheromone Model wiki. Ty is a member of Drew Endy's group at MIT and is part of the Alpha project headed by Roger Brent at the Molecular Sciences Institute.
- BioNetGen is now available from within the Virtual Cell in the latest beta version. Contact Professor Blinov for details.
- A comprehensive review of rule-based modeling is available in Science's STKE. Click here for toll-free access to the online version.
- Consider attending the Second q-bio Conference on Cellular Information Processing, August 6-9, 2008. The q-bio Summer School will precede the conference, as usual.
Download
Documentation
- Tutorial (see also tutorial from 2007 ICSB)
- FAQ
- Tips
- RuleBuilder
- PhiBPlot
- Known Bugs
- Wish List
- Bugs and Other Issues
- Publications
- Credits
Models and Example Applications
A list of annotated sample models is available from the BNG@VCell web site. Thanks to Michael Blinov for putting this together. In the future, we will add more examples and description to BioNetWiki.
