Download

From BioNetWiki

(Redirected from Quick Start)
Jump to: navigation, search

This page describes three different ways to get BioNetGen running in a few steps from your computer. To learn how to write, simulate, and analyze rule-based models, please see Tutorials and Documentation.

When publishing papers using that use any our our rule-based modeling tools, please follow our citation guidelines. If you encounter problems with installation or operation of the tools below please send an email to bionetgen.help@gmail.com.

RuleBender Stable

Full-featured integrated development environment for BioNetGen and NFsim based on Eclipse RCP. We strongly recommend you try this first.

  • Download - Obtain the current, stable RuleBender distribution by clicking on the appropriate link for your operating system below:
  • Install -- For all platforms
  • Run -- For all platforms
    • Open MacOS Finder, or Microsoft Explorer or similar filesystem browser and traverse down to the directory with many RuleBender-related files. You can run RuleBender by clicking on file RuleBender, which will have an RB icon next to it. If you are on a Mac and that fails, try this.
    • For help on installing and configuring RuleBender distributions please send email to mailto:help@rulebender.org.
    • We also highly recommend that you install the yEd Graph Editor, which can be used for interactive visualizations generated by the visualize command.
    • Legacy versions of RuleBender for all operating systems are available here.
  • Learn - We recommend that you first watch our tutorial video. To view and simulate models in RuleBender you will need to be able to
    • Select a Sample Model by doing: File->New BioNetGen Project-> OK -> Open the dropdown menu and select a model file.
    • Create a new Project by clicking OK in the file selection dialogue box.
      • If RuleBender indicates that it has not located BioNetGen on your computer, please do the following: Window->Preferences...->Simulator and browsing to the directory containing BioNetGen (e.g., /Users/shmo/RuleBender-2.0.388-osx64/BioNetGen-2.2.6).
    • To run the simulation contained in your sample file, click on Simulate, then do a single click on the file name (in the left margin) to transfer the filename to the Simulate" dialog. Then click Run.

Once you have RuleBender up and running, we recommend that you move on to our Tutorials.

Archived Versions of RuleBender

BioNetGen Command-line Interface

For users who only want the command-line interface.

  1. Download the latest source code + binary distribution from BioNetGen Distributions.
  2. Go to the Installation Guide and follow the instructions for Mac, Linux, or Windows.

BioNetGen at Virtual Cell

An excellent way to learn rule-based modeling using a lightweight client application, but currently uses an older BioNetGen distribution that lacks many current features.

  1. Go to http://vcell.org/bionetgen BioNetGen@VCell web site and click on Run BioNetGen link on the right.
  2. 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.
  3. Export of BNG models to Virtual Cell allows spatial simulations using PDE's.

For help with BioNetGen@VCell please send email to mailto:vcell_support@uchc.edu.

Related Tools

In addition the following tools provide simulation capabilities for rule-based models specified in the BioNetGen Language:

Personal tools