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<!DOCTYPE html>
<html lang="en">
<head>
<title>BNGL Visualizer</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>Visualization conventions</h2>
<table cellpadding="10" border="1">
<tr>
<td id="canvas-text">
<b>BNGL code</b>
</td>
<td id="canvas-text">
<b>bnglViz visualization</b>
</td>
</tr>
<tr>
<td id="canvas-text">
<code>begin compartments<br>
Cyt 3 1<br>
EC 3 1<br>
M 2 1 </code><br><br>
<small><b>NB:</b> The first number after the compartment name is the dimension, and the next is the size.
So, M is 2D membrane while Cyt and EC are volumetric cytosil and extracellular space.
These definitions are not compatible with cBNGL but used by VCell software only. </small>
</td>
<td id="canvas-text">
<img src="images/bngl_comp.png" width=200>
</td>
</tr>
<tr>
<td id="canvas-text">
<code>begin molecules<br>
1 EGFR(ecd,tmd,Y1~u~p,Y2~u~p) #EGF receptor</code><br><br>
<small><b>NB:</b> The first number is optional and not included in BNGL processing or visualization.
Instead of <code>begin molecules</code> the block may start with <code>begin molecular types</code>.
This block can be omitted, and BioNetGen will find molecules by processing species and reaction rules.</small>
</td>
<td id="canvas-text">
<img src="images/bngl_molec.png" width=400>
</td>
</tr>
<tr>
<td id="canvas-text">
<code>begin species<br>
1 egfr(l,r,Y1068~Y,Y1148~Y) egfr_tot #unphosphorylated receptor</code><br><br>
<small><b>NB:</b> The first number is optional and not included in BNGL processing or visualization.
Instead of <code>begin species</code> the block may start with <code>begin seed species</code>.
This block can NOT be omitted.</small>
</td>
<td id="canvas-text">
<img src="images/bngl_species.png" width=400>
</td>
</tr>
<tr>
<td id="canvas-text">
<code>begin reaction rules<br>
1 egfr(l,r,Y1068~Y,Y1148~Y) egfr_tot #unphosphorylated receptor</code><br><br>
<small><b>NB:</b> The symbols before <code>:</code> is reaction rule order - it is optional and not included in BNGL processing or visualization.
Instead of <code>begin reaction rules</code> the block may start with <code>begin rules</code> or <code>begin reactions</code>.
This block can NOT be omitted. For details of notations (<code>?</code>, <code>|</code> under site shape, grey vs color, etc)
refer to <a href="https://pubmed.ncbi.nlm.nih.gov/19399430/">Faeder et al., 2009</a>. </small>
</td>
<td id="canvas-text">
<img src="images/bngl_rule.png" width=400>
</td>
</tr>
</table>
</body>
</html>