Wsc09

From BioNetWiki

We welcome your comments on both the paper and the cBNGL language.

Contents 1 Paper 2 Example Files 3 Downloading a cBNGL-compatible version of BioNetGen 4 Additional Material

Paper

COMPARTMENTAL RULE-BASED MODELING OF BIOCHEMICAL SYSTEMS

Leonard A. Harris, Justin S. Hogg & James R. Faeder Proceedings of the 2009 Winter Simulation Conference (WSC). (invited) (pdf) (link)

Example Files

These files contain the BNGL and cBNGL code for the example system shown in Figure 1 of the paper.

• BNGL code: file | wiki page
• cBNGL code: file | wiki page

Downloading a cBNGL-compatible version of BioNetGen

Download BioNetGen version 2.1.5 or later from BioNetGen Distributions. Be sure to check Release_Notes for additional information about each release.

Additional Material

Here is an overview and tutorial of compartmental BNGL. Additional development notes for cBNGL are maintained at this page.