Rules Railroad - visualizing rule-based models
Visualize models in BNGL format
Examples
BNGL stands for BNGL code,
RRR stands for Rules Railroad visualization,
bnglViz stands for bnglViz visualization
- 2025
- 2024
- 2023
- A model of innate immune response for nonself RNA rewiring IFN-β signaling
(Korwek et al., 2023):
BNGL,
RRR,
bnglViz.
- A plausible identifiable model of the canonical NF-κB signaling pathway
(Jaruszewicz-Blonska et al., 2023):
BNGL,
RRR,
bnglViz.
- A model of Vascular Endothelial Growth Factor pathways
(Zhang et al., 2023):
BNGL,
RRR,
bnglViz.
- Optimization of Polydisperse Chemical Mixtures using Molecular Descriptors
(Massole et al., 2023):
BNGL,
RRR,
bnglViz.
- Pharmacodynamic model of PARP1 inhibition and global sensitivity analyses
(Mertins et al., 2023):
BNGL,
RRR,
bnglViz.
- 2022
- 2021
- A model of Nephrin-Nick-NWasp interactions used to identify phase transitions
(Chattaraj et al., 2021):
BNGL,
RRR,
bnglViz.
- A model of disruption of TNF-TNFR1 signalling by small molecules
(McMillan et al., 2021):
BNGL,
RRR,
bnglViz.
- A model of junctional localization and downstream signaling of the Ang-Tie signaling pathway
(Zhang et al., 2021):
BNGL,
RRR,
bnglViz.
- A model of inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells
(Erdem et al., 2021):
BNGL,
RRR,
bnglViz.
- Some of prominent earlier models
- A model of muscarinic receptor regulating extracellular signaling
(Jung et al., 2017):
BNGL,
RRR
bnglViz.
- A compartmental model of EGFR signaling, used as a tutorial in
(Blinov et al., 2017):
BNGL,
RRR,
bnglViz.
- A compartmental model of Ran transport, used as a tutorial in
(Blinov et al., 2017):
BNGL,
RRR,
bnglViz.
- A model or recruitment of the adaptor protein Grb2 to EGFR tetramers
(Kozer et al., 2014):
BNGL,
bnglViz,
bnglViz.
- A multi-level kinetic model of mRNA delivery via transfection of lipoplexes
(Ligon et al., 2014):
BNGL,
RRR,
bnglViz.
- A model of DNA damage G2 checkpoint
(Kesseler et al., 2013):
BNGL,
RRR,
bnglViz.
- A model of spontaneous NF-κB activation by autocrine TNFα signaling
(Pekalski et al., 2013):
BNGL,
RRR,
bnglViz.
- A model of higher-order EGFR oligomerization and phosphorylation
(Kozer et al., 2013):
BNGL,
RRR,
bnglViz.
- A structure-based kinetic model of Shp2 signaling protein function
(Barua et al., 2007):
BNGL,
RRR,
bnglViz.
- A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases
(Barua at al., 2009):
BNGL,
RRR,
bnglViz.
- A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn
(Barua et al., 2012):
BNGL,
RRR,
bnglViz.
- A mechanistic model of early FcεRI signaling with lipid rafts
(Barua & Goldstein, 2012):
BNGL,
RRR,
bnglViz.
- A model of the effect of APC truncation on destruction complex function in colorectal cancer cells
(Barua & Hlavacek, 2013):
BNGL,
RRR,
bnglViz.
- A model of initial events in EGFR signaling
(Blinov et al., 2006):
BNGL,
RRR,
bnglViz.
- A model of phosphorylation site dynamics of early T-cell receptor signaling
(Chylek et al., 2014, PLOS One):
BNGL,
RRR,
bnglViz.
- An interaction library for the FcεRI Signaling Network
(Chylek et al., 2014; Front Imm):
BNGL,
RRR,
bnglViz.
- Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling
(Creamer et al., 2012):
BNGL,
RRR,
bnglViz.
- A model of ultrasensitivity in multisite phosphorylation of membrane-anchored proteins
(Dushek et al., 2011):
BNGL,
RRR,
bnglViz.
- A model of biosensor architectures for high-fidelity reporting of cellular signaling
(Dushek et al., 2014):
BNGL,
RRR,
bnglViz.
- A model of early events in FceRI signaling
(Goldstein et al., 2002;
Faeder et al., 2003):
BNGL,
RRR,
bnglViz.
- A model of bivalent ligand - bivalent receptor, used for testing of rule-based models in
Colvin et al., 2009 and
Falkenberg et al., 2013:
BNGL,
RRR,
bnglViz.
- A model of trivalent ligand - bivalent receptor, used for testing of rule-based models in
Colvin et al., 2009 and
Falkenberg et al., 2013:
BNGL,
RRR,
bnglViz.
- A model of feedbacks, bifurcations, and cell fate decision-making in the p53 System
(Hat et al., 2016):
BNGL,
RRR,
bnglViz.
- A model of the interplay of double phosphorylation and scaffolding in MAPK pathways
(Kocieniewski et al., 2012):
BNGL,
RRR,
bnglViz.
- A model of T cell receptor proximal signaling reveals emergent ultrasensitivity
(Mukhopadhyay et al., 2013):
BNGL,
RRR,
bnglViz.
- A model of aggregation of membrane proteins by cytosolic LAT-Grb2-SOS1 system
(Nag et al., 2009):
BNGL,
RRR,
bnglViz.