BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these additions, discussing how they facilitate the construction, simulation, and analysis of larger and more complex models than previously possible.
@article{arxiv.1507.03572,
title = {BioNetGen 2.2: Advances in Rule-Based Modeling},
author = {Leonard A. Harris and Justin S. Hogg and Jose-Juan Tapia and John A. P. Sekar and Sanjana A. Gupta and Ilya Korsunsky and Arshi Arora and Dipak Barua and Robert P. Sheehan and James R. Faeder},
journal= {arXiv preprint arXiv:1507.03572},
year = {2016}
}
Comments
3 pages, 1 figure, 1 supplementary text file. Supplementary text includes a brief discussion of the RK-PLA along with a performance analysis, two tables listing all new actions/arguments added in BioNetGen 2.2, and the "BioNetGen Quick Reference Guide". Accepted for publication in Bioinformatics