BioNetGen 2.2: Advances in Rule-Based Modeling
arXiv:1507.03572 · doi:10.1093/bioinformatics/btw469
Abstract
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.
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
References in corpus (4)
Cited by in corpus (16)
- PEtab -- interoperable specification of parameter estimation problems in systems biology
- Emerging whole-cell modeling principles and methods
- Rare-Event Sampling of Epigenetic Landscapes and Phenotype Transitions
- Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models
- BioSimulator.jl: Stochastic simulation in Julia
- Compositionality of Rewriting Rules with Conditions
- AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models
- Rule-based epidemic models
- BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks
- Executable Biochemical Space for Specification and Analysis of Biochemical Systems
- Tracelets and Tracelet Analysis Of Compositional Rewriting Systems
- Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks
- Regulated Multiset Rewriting Systems
- Compiling Combinatorial Genetic Circuits with Semantic Inference
- Annotations for Rule-Based Models
- A Step-by-Step Guide to Using BioNetFit