BioNetGenLanguage (BNGL) code visualizer

doi:10.1093/bioinformatics/btae351

Examples

* -compartmental model

• 2024
• * Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells (Lang et al., 2024): BNGL code, visualization.
• 2023
• A model of innate immune response for nonself RNA rewiring IFN-β signaling (Korwek et al., 2023): BNGL code, visualization.
• A plausible identifiable model of the canonical NF-κB signaling pathway (Jaruszewicz-Blonska et al., 2023): BNGL code, visualization.
• A model of Vascular Endothelial Growth Factor pathways (Zhang et al., 2023): BNGL code, visualization.
• Optimization of Polydisperse Chemical Mixtures using Molecular Descriptors (Massole et al., 2023): BNGL code, visualization.
• Pharmacodynamic model of PARP1 inhibition and global sensitivity analyses (Mertins et al., 2023): BNGL code, visualization.
• 2022
• * A kinetic model of phospholipase C-γ1 linking (Nosbisch et al., 2022): BNGL code, visualization.
• 2021
• A model of Nephrin-Nick-NWasp interactions used to identify phase transitions (Chattaraj et al., 2021): BNGL code, visualization.
• A model of disruption of TNF-TNFR1 signalling by small molecules (McMillan et al., 2021): BNGL code, visualization.
• A model of junctional localization and downstream signaling of the Ang-Tie signaling pathway (Zhang et al., 2021): BNGL code, visualization.
• A model of inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells (Erdem et al., 2021): BNGL code, visualization.



• Some of prominent earlier models
• * A model of muscarinic receptor regulating extracellular signaling (Jung et al., 2017): BNGL code, visualization.
• * A compartmental model of EGFR signaling, used as a tutorial in (Blinov et al., 2017): BNGL code, visualization.
• * A compartmental model of Ran transport, used as a tutorial in (Blinov et al., 2017): BNGL code, visualization.
• A model or recruitment of the adaptor protein Grb2 to EGFR tetramers (Kozer et al., 2014): BNGL code, visualization.
• A multi-level kinetic model of mRNA delivery via transfection of lipoplexes (Ligon et al., 2014): BNGL code, visualization.
• A model of DNA damage G2 checkpoint (Kesseler et al., 2013): BNGL code, visualization.
• A model of spontaneous NF-κB activation by autocrine TNFα signaling (Pekalski et al., 2013): BNGL code, visualization.
• A model of higher-order EGFR oligomerization and phosphorylation (Kozer et al., 2013): BNGL code, visualization.
• A detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning (An & Faeder, 2009): BNGL code, vizualization.
• A structure-based kinetic model of Shp2 signaling protein function (Barua et al., 2007): BNGL code, vizualization.
• A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases (Barua at al., 2009): BNGL code, vizualization.
• 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 code, vizualization.
• A mechanistic model of early FcεRI signaling with lipid rafts (Barua & Goldstein, 2012): BNGL code, vizualization.
• A model of the effect of APC truncation on destruction complex function in colorectal cancer cells (Barua & Hlavacek, 2013): BNGL code, vizualization.
• A model of initial events in EGFR signaling (Blinov et al., 2006): BNGL code, visualization.
• A model of phosphorylation site dynamics of early T-cell receptor signaling (Chylek et al., 2014, PLOS One): BNGL code, visualization.
• An interaction library for the FcεRI Signaling Network (Chylek et al., 2014; Front Imm): BNGL code, visualization.
• Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling (Creamer et al., 2012): BNGL code, visualization.
• A model of ultrasensitivity in multisite phosphorylation of membrane-anchored proteins (Dushek et al., 2011): BNGL code, visualization.
• A model of biosensor architectures for high-fidelity reporting of cellular signaling (Dushek et al., 2014): BNGL code, visualization.
• A model of early events in FceRI signaling (Goldstein et al., 2002; Faeder et al., 2003): BNGL code, visualization.
• 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 code, visualization.
• 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 code, visualization.
• A model of feedbacks, bifurcations, and cell fate decision-making in the p53 System (Hat et al., 2016): BNGL code, visualization.
• A model of the interplay of double phosphorylation and scaffolding in MAPK pathways (Kocieniewski et al., 2012): BNGL code, visualization.
• A model of T cell receptor proximal signaling reveals emergent ultrasensitivity (Mukhopadhyay et al., 2013): BNGL code, visualization.
• A model of aggregation of membrane proteins by cytosolic LAT-Grb2-SOS1 system (Nag et al., 2009): BNGL code, visualization.