Main Page

From BioNetWiki

Jump to: navigation, search

Welcome to BioNetWiki!


BioNetWiki is read-only unless you obtain a username and password by sending email to bionetgen@lanl.gov. In addition, pdf files and downloads are only accessible when logged in.

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.

Contents

Getting Started

There are currently two options for using BioNetGen™:

Standalone version
  1. 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).
  2. Go to the Installation Guide and follow the instructions (works for Mac, Linux, or PC).
Online version at Virtual Cell
  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.

News

  • A comprehensive review of rule-based modeling is available in Science's STKE. Click here for toll-free access to the online version.

Download

Documentation

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.

User Pages


BioNetGen Development

Wiki Help

Personal tools