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<!DOCTYPE html>
<html lang="en">
<head>
<title>BNGL Visualizer: About</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>About</h2>
<ul>
<li> The original BioNetGen software and scripting language for the description of models was designed in <b>2004</b>:
<br>Blinov, M. L., Faeder, J. R., Goldstein, B., & Hlavacek, W. S. (2004).
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.
<i>Bioinformatics</i>, 20(17), 3289-3291. <a href="https://pubmed.ncbi.nlm.nih.gov/15217809/">PMID:15217809</a>
<br>
</li>
<li> The concept of rule-based modeling as a graph rewriting was introduced in <b>2006</b>:
<br>Blinov, M. L., Yang, J., Faeder, J. R., & Hlavacek, W. S. (2006).
Graph theory for rule-based modeling of biochemical networks.
<i>Transactions on Computational Systems Biology VII</i> (pp. 89-106).
Berlin, Heidelberg: Springer Berlin Heidelberg.
<br>
</li>
<li>The most comprehensive description of rule-based modeling using BioNetGen was published in <b>2009</b>:
<br>Faeder, J. R., Blinov, M. L., & Hlavacek, W. S. (2009).
Rule-based modeling of biochemical systems with BioNetGen.
<i>Methods Mol Biol.</i> 500:113-67.
<a href="https://pubmed.ncbi.nlm.nih.gov/19399430/">PMID:19399430</a>
<br>
</li>
<li>
The advanced BioNetGen 2.0 was described in <b>2016</b>:
<br>Harris, L. A., Hogg, J. S., Tapia, J. J., Sekar, J. A., Gupta, S., Korsunsky, I., ... & Faeder, J. R. (2016).
BioNetGen 2.2: advances in rule-based modeling.
<i>Bioinformatics</i>, 32(21), 3366-3368. <a href="https://pubmed.ncbi.nlm.nih.gov/27402907/">PMID:27402907</a>
<br>
</li>
<li>
Rule-based modeling was introduced into the VCell modeling and simulation framework in <b>2016</b>:
<br>Schaff, J. C., Vasilescu, D., Moraru, I. I., Loew, L. M., & Blinov, M. L. (2016).
Rule-based modeling with Virtual Cell.
<i>Bioinformatics</i>, 32(18), 2880-2882.
<a href="https://pubmed.ncbi.nlm.nih.gov/27497444/">PMID:27497444</a>
<br>
</li>
<li>
The compartmental rule-based modeling in VCell was introduced in <b>2017</b>:
<br>Blinov, M. L., Schaff, J. C., Vasilescu, D., Moraru, I. I., Bloom, J. E., & Loew, L. M. (2017).
Compartmental and spatial rule-based modeling with virtual cell.
<i>Biophysical journal</i>, 113(7), 1365-1372.
<a href="https://pubmed.ncbi.nlm.nih.gov/28978431/">PMID:28978431</a>
<br>
</li>
<li>
The current visualizer is implemented by Noah Liguori-Bills
(<a href="https://noahlb123.github.io/">https://noahlb123.github.io/</a>),
a former UConn student, currently PhD student at NCSU.
</li>
</ul>
</body>
</html>