Quick Start
From BioNetWiki
This page describes how to get BioNetGen running in a few steps from your computer. To learn how to write, simulate, and analyze rule-based models, please see Documentation.
If you find BioNetGen useful in your research, we would love to hear about it. Just send us an email to bionetgen@lanl.gov.
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BioNetGen interfaces
- RuleBender
- RuleBender provides a full-featured integrated development environment (IDE) for rule-based modeling with BioNetGen and is can be configured to run NFsim as well. The RuleBender tool includes a complete BioNetGen source distribution and can be downloaded from rulebender.org.
- Command-line interface
- Obtain username and password by sending email to bionetgen@lanl.gov (you may suggest a preferred username in your email, or we will assign one).
- Go to the Installation Guide and follow the instructions for Mac, Linux, or PC.
- Online version at Virtual Cell
- Go to http://vcell.org/bionetgen BioNetGen@VCell web site and click on Run BioNetGen link on the right.
- Register if necessary (which involves completing a 1-page form, after which you will be granted immediate access) and click on the BioNetGen menu tab in the main Virtual Cell window.
- Export of BNG models to Virtual Cell allows spatial simulations using PDE's.
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Related Tools
In addition the following tools provide simulation capabilities for rule-based models specified in the BioNetGen Language:
