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index.html
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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>
<td>
<button id="dark-button" onclick="htmlInterface.switchDarkMode();">Toggle Light/Dark Mode</button>
</td>
</tr>
</table>
<hr>
<h3>
Visualize BioNetGen model:
<input id="bngl-file-input" type="file" oninput="loadingText.style.display='block'; htmlInterface.visualize(fileInput.files[0]); limitsDiv.style.display='none';" onclick="inputClick();">
<button onclick="htmlInterface.clear(); inputClick(); limitsDiv.style.display='block';">Clear</button>
</h3>
<p id="loading-p">Loading...</p>
<div id="limitation-div">
<hr>
<b>Usage and limitations:</b>
<ul>
<li>Non-visual parts of BNGL code such as parameter's block and actions are omitted in visualization for clarity, but all comments for molecules, species,
rules and observables are displayed. </li>
<li>No code validation is provided: the BNGL is visualized as is. There are rare instances when we note some errors in the code and
provide guidance, but users should not rely on it. </li>
<li>cBNGL is not supported, but compartmental export from VCell is supported. In VCell, a compartment is assigned to the whole
reactant or product, while in cBNGL a compartment can be assigned to different sites of a molecule. </li>
<li>There are many extensions and undocumented/semi-documented features in BNGL. We do not guarantee that all of them are supported.
Please email <a href="mailto:[email protected]">Michael Blinov</a> and we'll try to accommodate the visualization of more features.</li>
</ul>
<hr>
</div>
<div id="canvas-container"></div>
<div id="table-container"></div>
<script src="public/model-graphics.js"></script>
<script src="public/bngl-extractor.js"></script>
<script src="public/html-interface.js"></script>
<script>
//get major elements
const canvContain = document.getElementById("canvas-container");
const tableContain = document.getElementById("table-container");
const fileInput = document.getElementById("bngl-file-input");
const body = document.body;
const limitsDiv = document.getElementById("limitation-div");
const loadingText = document.getElementById("loading-p");
//connect interface
var htmlInterface = new HTMLInterface(body, canvContain, tableContain, fileInput, loadingText);
//function to reset input element value when it is clicked
//this is needed because chrome doesn't trigger onchange if filename is same
function inputClick() {
fileInput.value = "";
}
</script>
</body>
</html>