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<!DOCTYPE html>
<html lang="en">
<head>
<title>BNGL Visualizer: Examples</title>
<link rel="stylesheet" type="text/css" href="public/styleblack.css"/>
</head>
<body>
<p><h1>BioNetGenLanguage (BNGL) code visualizer</h1>
<h4><a href="https://doi.org/10.1093/bioinformatics/btae351">
doi:10.1093/bioinformatics/btae351</a></h4></p>
<table cellpadding="20">
<tr>
</tr>
<tr>
<td id="canvas-text">
<a href=index.html><b>BNGL VISUALIZER</b></a>
</td>
<td id="canvas-text">
<a href=bngl.html>BNGL overview</a>
</td>
<td id="canvas-text">
<a href=viz.html>Visualization conventions</a>
</td>
<td id="canvas-text">
<a href=examples.html>Examples</a>
</td>
<td id="canvas-text">
<a href=about.html>About</a>
</td>
</tr>
</table>
<hr>
<h2>Examples</h2>
<h3>* -compartmental model</h3>
<ul>
<li><strong>2024</strong></li>
<ul>
<li> *
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells
(<a href="https://pubmed.ncbi.nlm.nih.gov/38190398/">Lang et al., 2024</a>):
<a href="models/Lang_2024.bngl">BNGL code</a>, <a href="examples/Lang_2024.html">visualization</a></a>.
</li>
</ul>
<li><strong>2023</strong></li>
<ul>
<li>A model of innate immune response for nonself RNA rewiring IFN-β signaling
(<a href="https://pubmed.ncbi.nlm.nih.gov/38085817/">Korwek et al., 2023</a>):
<a href="models/Korwek_2023.bngl">BNGL code</a>, <a href="examples/Korwek_2023.html">visualization</a></a>.
</li>
<li>A plausible identifiable model of the canonical NF-κB signaling pathway
(<a href="https://pubmed.ncbi.nlm.nih.gov/37267242/">Jaruszewicz-Blonska et al., 2023</a>):
<a href="models/Jaruszewicz-Blonska_2023.bngl">BNGL code</a>, <a href="examples/Jaruszewicz-Blonska_2023.html">visualization</a></a>.
</li>
<li>A model of Vascular Endothelial Growth Factor pathways
(<a href="https://pubs.acs.org/doi/pdf/10.1021/acsptsci.3c00008#">Zhang et al., 2023</a>):
<a href="models/Zhang_2023.bngl">BNGL code</a>, <a href="examples/Zhang_2023.html">visualization</a></a>.
</li>
<li>Optimization of Polydisperse Chemical Mixtures using Molecular Descriptors
(<a href="https://chemrxiv.org/engage/chemrxiv/article-details/653a018348dad231205e586a">Massole et al., 2023</a>):
<a href="models/Massole_2023.bngl">BNGL code</a>, <a href="examples/Massole_2023.html">visualization</a></a>.
</li>
<li>Pharmacodynamic model of PARP1 inhibition and global sensitivity analyses
(<a href="https://www.biorxiv.org/content/10.1101/2023.02.08.527527v1">Mertins et al., 2023</a>):
<a href="models/Mertins_2023.bngl">BNGL code</a>, <a href="examples/Mertins_2023.html">visualization</a></a>.
</li>
</ul>
<li><strong>2022</strong></li>
<ul>
<li> * A kinetic model of phospholipase C-γ1 linking
(<a href="https://pubmed.ncbi.nlm.nih.gov/35367415/">Nosbisch et al., 2022</a>):
<a href="models/Nosbisch_2022.bngl">BNGL code</a>, <a href="examples/Nosbisch_2022.html">visualization</a></a>.
</li>
</ul>
<li><strong>2021</strong></li>
<ul>
<li>A model of Nephrin-Nick-NWasp interactions used to identify phase transitions
(<a href="https://pubmed.ncbi.nlm.nih.gov/34236318/">Chattaraj et al., 2021</a>):
<a href="models/Chattaraj_2021.bngl">BNGL code</a>, <a href="examples/Chattaraj_2021.html">visualization</a></a>.
</li>
<li>A model of disruption of TNF-TNFR1 signalling by small molecules
(<a href="https://pubmed.ncbi.nlm.nih.gov/33495441/">McMillan et al., 2021</a>):
<a href="models/McMillan_2021.bngl">BNGL code</a>, <a href="examples/McMillan_2021.html">visualization</a></a>.
</li>
<li>A model of junctional localization and downstream signaling of the Ang-Tie signaling pathway
(<a href="https://pubmed.ncbi.nlm.nih.gov/34417472/">Zhang et al., 2021</a>):
<a href="models/Zhang_2021.bngl">BNGL code</a>, <a href="examples/Zhang_2021.html">visualization</a></a>.
</li>
<li>A model of inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells
(<a href="https://pubmed.ncbi.nlm.nih.gov/34191793/">Erdem et al., 2021</a>):
<a href="models/Erdem_2021.bngl">BNGL code</a>, <a href="examples/Erdem_2021.html">visualization</a></a>.
</li>
</ul>
<br><br>
<li><strong>Some of prominent earlier models</strong></li>
<ul>
<li> * A model of muscarinic receptor regulating extracellular signaling
(<a href="https://pubmed.ncbi.nlm.nih.gov/24324544/">Jung et al., 2017</a>):
<a href="models/Jung_2017.bngl">BNGL code</a>, <a href="examples/Jung_2017.html">visualization</a></a>.
</li>
<li> * A compartmental model of EGFR signaling, used as a tutorial in
(<a href="https://pubmed.ncbi.nlm.nih.gov/28978431/">Blinov et al., 2017</a>):
<a href="models/Blinov_egfr.bngl">BNGL code</a>, <a href="examples/Blinov_egfr.html">visualization</a></a>.
</li>
<li> * A compartmental model of Ran transport, used as a tutorial in
(<a href="https://pubmed.ncbi.nlm.nih.gov/28978431/">Blinov et al., 2017</a>):
<a href="models/Blinov_ran.bngl">BNGL code</a>, <a href="examples/Blinov_ran.html">visualization</a></a>.
</li>
<li>A model or recruitment of the adaptor protein Grb2 to EGFR tetramers
(<a href="https://pubmed.ncbi.nlm.nih.gov/24697349/">Kozer et al., 2014</a>):
<a href="models/Kozer_2014.bngl">BNGL code</a>, <a href="examples/Kozer_2014.html">visualization</a></a>.
</li>
<li>A multi-level kinetic model of mRNA delivery via transfection of lipoplexes
(<a href="https://pubmed.ncbi.nlm.nih.gov/25237886/">Ligon et al., 2014</a>):
<a href="models/Ligon_2014.bngl">BNGL code</a>, <a href="examples/Ligon_2014.html">visualization</a></a>.
</li>
<li> A model of DNA damage G2 checkpoint
(<a href="https://pubmed.ncbi.nlm.nih.gov/23266715/">Kesseler et al., 2013</a>):
<a href="models/Kesseler_2013.bngl">BNGL code</a>, <a href="examples/Kesseler_2013.html">visualization</a></a>.
</li>
<li>A model of spontaneous NF-κB activation by autocrine TNFα signaling
(<a href="https://pubmed.ncbi.nlm.nih.gov/24324544/">Pekalski et al., 2013</a>):
<a href="models/Pekalski_2013.bngl">BNGL code</a>, <a href="examples/Pekalski_2013.html">visualization</a></a>.
</li>
<li>A model of higher-order EGFR oligomerization and phosphorylation
(<a href="https://pubmed.ncbi.nlm.nih.gov/23629589/">Kozer et al., 2013</a>):
<a href="models/Kozer_2013.bngl">BNGL code</a>, <a href="examples/Kozer_2013.html">visualization</a></a>.
</li>
<li> A detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning
(<a href="https://pubmed.ncbi.nlm.nih.gov/18835283/">An & Faeder, 2009</a>):
<a href="models/An_2009.bngl">BNGL code</a>, <a href="examples/An_2009.html">vizualization</a>.
</li>
<li> A structure-based kinetic model of Shp2 signaling protein function
(<a href="https://pubmed.ncbi.nlm.nih.gov/17208977/">Barua et al., 2007</a>):
<a href="models/Barua_2007.bngl">BNGL code</a>, <a href="examples/Barua_2007.html">vizualization</a>.
</li>
<li> A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases
(<a href="https://pubmed.ncbi.nlm.nih.gov/19381268/">Barua at al., 2009</a>):
<a href="models/Barua_2009.bngl">BNGL code</a>, <a href="examples/Barua_2009.html">vizualization</a>.
</li>
<li>A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn
(<a href="https://pubmed.ncbi.nlm.nih.gov/22711887/">Barua et al., 2012</a>):
<a href="models/BaruaBCR_2012.bngl">BNGL code</a>, <a href="examples/BaruaBCR_2012.html">vizualization</a>.
</li>
<li>A mechanistic model of early FcεRI signaling with lipid rafts
(<a href="https://pubmed.ncbi.nlm.nih.gov/23284735/">Barua & Goldstein, 2012</a>):
<a href="models/BaruaFceRI_2012.bngl">BNGL code</a>, <a href="examples/BaruaFceRI_2012.html">vizualization</a>.
</li>
<li>A model of the effect of APC truncation on destruction complex function in colorectal cancer cells
(<a href="https://pubmed.ncbi.nlm.nih.gov/24086117/">Barua & Hlavacek, 2013</a>):
<a href="models/Barua_2013.bngl">BNGL code</a>, <a href="examples/Barua_2013.html">vizualization</a>.
</li>
<li> A model of initial events in EGFR signaling
(<a href="https://pubmed.ncbi.nlm.nih.gov/16233948/">Blinov et al., 2006</a>):
<a href="models/Blinov_2006.bngl">BNGL code</a>, <a href="examples/Blinov_2006.html">visualization</a>.
</li>
<li> A model of phosphorylation site dynamics of early T-cell receptor signaling
(<a href="https://pubmed.ncbi.nlm.nih.gov/25147952/">Chylek et al., 2014, PLOS One</a>):
<a href="models/ChylekTCR_2014.bngl">BNGL code</a>, <a href="examples/ChylekTCR_2014.html">visualization</a>.
</li>
<li> An interaction library for the FcεRI Signaling Network
(<a href="https://pubmed.ncbi.nlm.nih.gov/24782869/">Chylek et al., 2014; Front Imm</a>):
<a href="models/ChylekFceRI_2014.bngl">BNGL code</a>, <a href="examples/ChylekFceRI_2014.html">visualization</a>.
</li>
<li> Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling
(<a href="https://pubmed.ncbi.nlm.nih.gov/22913808/">Creamer et al., 2012</a>):
<a href="models/Creamer_2012.bngl">BNGL code</a>, <a href="examples/Creamer_2012.html">visualization</a>.
</li>
<li> A model of ultrasensitivity in multisite phosphorylation of membrane-anchored proteins
(<a href="https://pubmed.ncbi.nlm.nih.gov/21354391/">Dushek et al., 2011</a>):
<a href="models/Dushek_2011.bngl">BNGL code</a>, <a href="examples/Dushek_2011.html">visualization</a>.
</li>
<li>A model of biosensor architectures for high-fidelity reporting of cellular signaling
(<a href="https://pubmed.ncbi.nlm.nih.gov/25099816/">Dushek et al., 2014</a>):
<a href="models/Dushek_2014.bngl">BNGL code</a>, <a href="examples/Dushek_2014.html">visualization</a>.
</li>
<li>A model of early events in FceRI signaling
(<a href="https://pubmed.ncbi.nlm.nih.gov/12217386/">Goldstein et al., 2002</a>;
<a href="https://pubmed.ncbi.nlm.nih.gov/12646643/">Faeder et al., 2003</a>):
<a href="models/fceri_2003.bngl">BNGL code</a>, <a href="examples/fceri_2003.html">visualization</a>.
</li>
<li> A model of bivalent ligand - bivalent receptor, used for testing of rule-based models in
<a href="https://pubmed.ncbi.nlm.nih.gov/19213740/">Colvin et al., 2009</a> and
<a href="https://pubmed.ncbi.nlm.nih.gov/24314076/">Falkenberg et al., 2013</a>:
<a href="models/blbr.bngl">BNGL code</a>, <a href="examples/blbr.html">visualization</a></a>.
</li>
<li> A model of trivalent ligand - bivalent receptor, used for testing of rule-based models in
<a href="https://pubmed.ncbi.nlm.nih.gov/19213740/">Colvin et al., 2009</a> and
<a href="https://pubmed.ncbi.nlm.nih.gov/24314076/">Falkenberg et al., 2013</a>:
<a href="models/tlbr.bngl">BNGL code</a>, <a href="examples/tlbr.html">visualization</a></a>.
</li>
<li>A model of feedbacks, bifurcations, and cell fate decision-making in the p53 System
(<a href="https://pubmed.ncbi.nlm.nih.gov/26928575/">Hat et al., 2016</a>):
<a href="models/Hat_2016.bngl">BNGL code</a>, <a href="examples/Hat_2016.html">visualization</a></a>.
</li>
<li>A model of the interplay of double phosphorylation and scaffolding in MAPK pathways
(<a href="https://pubmed.ncbi.nlm.nih.gov/22123371/">Kocieniewski et al., 2012</a>):
<a href="models/Kocieniewski_2012.bngl">BNGL code</a>, <a href="examples/Kocieniewski_2012.html">visualization</a></a>.
</li>
<li>A model of T cell receptor proximal signaling reveals emergent ultrasensitivity
(<a href="https://pubmed.ncbi.nlm.nih.gov/23555234/">Mukhopadhyay et al., 2013</a>):
<a href="models/Mukhopadhyay_2013.bngl">BNGL code</a>, <a href="examples/Mukhopadhyay_2013.html">visualization</a></a>.
</li>
<li>A model of aggregation of membrane proteins by cytosolic LAT-Grb2-SOS1 system
(<a href="https://pubmed.ncbi.nlm.nih.gov/19348745/">Nag et al., 2009</a>):
<a href="models/Nag_2009.bngl">BNGL code</a>, <a href="examples/Nag_2009.html">visualization</a></a>.
</li>
</li>
</ul>
</ul>
</body>
</html>