Old News

From BioNetWiki

Jump to: navigation, search
  • A new paper on hybrid particle/population (HPP) simulation using BioNetGen/NFsim has been published.
  • A full-length paper describing RuleBender, our graphical front-end for rule-based modeling, was published in a BMC Bioinformatics Supplement Highlights of the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011).
  • Join the BioNetGen users' Google group to get all of the latest updates. It's also a great forum for asking questions and starting discussions.
  • 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.
  • 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.
  • You can also follow us on Facebook and Twitter.
  • The BioNetGen codebase is now maintained at GoogleCode.
  • For help, email us at bionetgen.help@gmail.com.
  • Check out the new BioNetGen Facebook page and follow us on Twitter at @bionetgen.
  • See our new Rule-Based Modeling Community for more information about this growing field. If you are already working in this area, we welcome your addition the the Community page(s).
  • See the newly-added Tips section below.
  • RuleBender is an integrated development environment for BioNetGen that provides a self-contained and easy-to-use interface for model development, simulation, and analysis. An Applications Note describing RuleBender has been accepted to Bioinformatics.
  • NFsim is a new simulator for rule-based models that supports agent-based simulation and coarse-graining of reactions, which greatly extends the range of models that can be specified and simulated in the BioNetGen language. See also a paper describing NFsim that just appeared in Nature Methods. Support for global and local functions using ODE and SSA methods will be provided starting in release 2.1.8 of BioNetGen.
  • See our new Rule-Based Modeling Primer for a gentle introduction to rule-based modeling with BioNetGen.
  • The BioNetGen to Stochastic Simulation Compiler (SSC) translator is a new feature of BioNetGen introduced in release 2.1.6. SSC is a tool for creating spatially resolved, exact stochastic simulations of biochemical reaction networks. The translator can automatically convert BioNetGen models to SSC models. Click here for more information.
Personal tools