Main Page

From BioNetWiki

This wiki serves the BioNetGen user community by providing information about BioNetGen and tools for the development, annotation, and discussion of BioNetGen models.

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

Contents 1 Contact Info: 2 Notices 3 News 4 Main Menu 5 Tips 6 About BioNetGen

Contact Info:

• Help email: bionetgen.help@gmail.com
• Website: www.bionetgen.org
• User's Google group: www.groups.google.com/d/forum/bionetgen-users
• Facebook page: www.facebook.com/bionetgen
• Twitter feed: www.twitter.com/bionetgen
• Source code: www.code.google.com/p/bionetgen

Notices

• Confidentiality. Often it is necessary for us to look at a model in order to provide help. If the model has not yet been published this can cause angst on the part of the modeler. We understand this and pledge complete confidentiality to our users. Any models, or model snippets, that you send us will never be shared outside of the direct BNG developers group.

• Group registration. If you are teaching a course that requires use of BioNetGen, please feel free to send a list of the email addresses of your students to bionetgen.help@gmail.com so that we can setup wiki accounts for all of your students at the same time.

--The BNG team

News

• BioNetGen 2.2.4-stable is now available for download. See the release notes for a list of added features and bug fixes.
• Click here for materials from the MCell/BioNetGen tutorial at GLBIO 2013.
• A new paper on hybrid particle/population (HPP) simulation in BioNetGen has been submitted. A preprint is available at http://arxiv.org/abs/1301.6854.
• A full-length paper describing RuleBender, our graphical front-end for rule-based modeling, was just published in a BMC Bioinformatics Supplement Highlights of the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011).
• Join the new BioNetGen users' google group to get all of the latest updates. It's also a great forum for asking questions and starting discussions.
• You can also follow us on Facebook and Twitter.
• We've added a Quick Reference Guide to our Facebook page summarizing the most commonly-used BNG actions and associated arguments.
• Please take the BioNetGen/NFsim/RuleBender User Survey.
• RuleBender paper wins Best Paper award at BioVis 2011. See the Final Program (Warning: big file) for cover art and listing of the award on p. 12.
• A short commentary on rule-based modeling for intracellular and cellular dynamics just appeared in BMC Biology.
• Materials for the tutorial at the 2011 q-bio conference are here.
• In a HOT article, Chylek et al. have recently proposed conventions for visualizing and annotating rule-based models. See the wiki page about Extended Contact Maps or the Molecular BioSystems Blog.
• A new (for 2012) review about rule-based modeling is available here.

Access older news items here.

Main Menu

• Getting Started - Start here if you are new to BioNetGen.
• Download - Go here to download the latest BioNetGen distribution with source code.
• Documentation - Browse the BioNetGen Online Manual or get links to other published documentation.
• Tutorials
• Model Examples
• Extended Contact Maps
• Rule-Based Modeling Community
• Feature Requests
• ModelFest

Tips

• Time-varying inputs How to define a model input that varies in time. New
• Partitioned leaping: A tau-leaping variant Under construction
• Hybrid particle-population model generator for memory efficient network-free simulations.
• Mex code generator for simulating ODE network models from the MATLAB platform.
• Trajectory continuation
• Introducing delay in a BNG model
• Loading BioNetGen trajectories into MATLAB
• Built-in mathematical operators and functions

About BioNetGen

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 introduction to modeling with BioNetGen is available and is augmented by the models found in the BioNetGen distribution and in the Model Examples. The BioNetGen language has recently been extended to include explicit representation of compartments. A recent review of methods for rule-based modeling is available in Science Signaling (formerly known as Science's STKE).

The BioNetGen software package was initially developed by the Cell Signaling Team at Los Alamos National Laboratory. The current development team is based in the Department of Computational and Systems Biology at the University of Pittsburgh School of Medicine, with contributions from collaborators at 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 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.

BioNetGen is supported by NIH grant GM076570 and work has been performed under DOE contract DE-AC52-06NA25396. Additional support for BioNetGen has been provided by NIH grants GM085273, AI35997, and CA109552, NSF grant 0829788, the Arizona Biomedical Research Commission, and the Department of Computational Biology at the University of Pittsburgh School of Medicine.

Credits