BioNetGen 2.2: advances in rule-based modeling

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

(2015) Goksel Misirli et al.   BIOINFORMATICS

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

(2015) Brandon R. Thomas et al.   BIOINFORMATICS

In silico model-based inference: A contemporary approach for hypothesis testing in network biology

(2014) David J. Klinke   BIOTECHNOLOGY PROGRESS

MOSBIE: a tool for comparison and analysis of rule-based biochemical models

(2014) John E et al.   BMC BIOINFORMATICS

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

(2014) Justin S. Hogg et al.   PLoS Computational Biology

Properties of cell death models calibrated and compared using Bayesian approaches

(2013) H. Eydgahi et al.   Molecular Systems Biology

Programming biological models in Python using PySB

(2013) C. F. Lopez et al.   Molecular Systems Biology

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

(2013) Lily A. Chylek et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

RuleBender: a visual interface for rule-based modeling

(2011) Wen Xu et al.   BIOINFORMATICS

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

(2010) Michael W Sneddon et al.   NATURE METHODS

Virtual Cell modelling and simulation software environment

(2008) I.I. Moraru et al.   IET Systems Biology

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING