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Computation window #7

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merged 5 commits into from
Oct 10, 2023
Merged

Computation window #7

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d033196
created computation window
Oct 9, 2023
6815cf6
divided functionality of computation, session and their tauri command…
Oct 9, 2023
63e9595
implemented menu for new windows
Oct 9, 2023
0a5690f
implemented help window
Oct 9, 2023
7aae594
UI changes + refactoring
Oct 9, 2023
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95 changes: 95 additions & 0 deletions fe/computation-window.html
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<!DOCTYPE html>

<html lang="en">
<head>
<title>Biodivine/Aeon</title>
<meta charset="utf-8">

<!-- Favicon -->
<link rel="apple-touch-icon" sizes="57x57" href="favicon/apple-icon-57x57.png">
<link rel="apple-touch-icon" sizes="60x60" href="favicon/apple-icon-60x60.png">
<link rel="apple-touch-icon" sizes="72x72" href="favicon/apple-icon-72x72.png">
<link rel="apple-touch-icon" sizes="76x76" href="favicon/apple-icon-76x76.png">
<link rel="apple-touch-icon" sizes="114x114" href="favicon/apple-icon-114x114.png">
<link rel="apple-touch-icon" sizes="120x120" href="favicon/apple-icon-120x120.png">
<link rel="apple-touch-icon" sizes="144x144" href="favicon/apple-icon-144x144.png">
<link rel="apple-touch-icon" sizes="152x152" href="favicon/apple-icon-152x152.png">
<link rel="apple-touch-icon" sizes="180x180" href="favicon/apple-icon-180x180.png">
<link rel="icon" type="image/png" sizes="192x192" href="favicon/android-icon-192x192.png">
<link rel="icon" type="image/png" sizes="32x32" href="favicon/favicon-32x32.png">
<link rel="icon" type="image/png" sizes="96x96" href="favicon/favicon-96x96.png">
<link rel="icon" type="image/png" sizes="16x16" href="favicon/favicon-16x16.png">
<meta name="msapplication-TileColor" content="#ffffff">
<meta name="msapplication-TileImage" content="favicon/ms-icon-144x144.png">
<meta name="theme-color" content="#ffffff">

<link rel="stylesheet" href="style.css" type="text/css">

<!-- TODO - remove unused scripts -->
<script src="script/dependencies/cytoscape.min.js"></script>
<script src="script/dependencies/lodash.js"></script>
<script src="script/dependencies/cytoscape-edgehandles.js"></script>
<script src="script/dependencies/hotkeys.min.js"></script>

<script src="script/const.js"></script>
<script src="script/Results.js"></script>
<script src="script/ComputeEngine.js"></script>
<script src="script/Computation.js"></script>
<script src="script/ModelEndpoints.js"></script>
<script src="script/Examples.js"></script>
<script src="script/LiveModel.js"></script>
<script src="script/UI.js"></script>
<script src="script/CytoscapeEditor.js"></script>
<script src="script/ModelEditor.js"></script>
<script src="script/main.js"></script>
<script src="script/MessageDialog.js"></script>
<script src="script/ComputationWindowEvent.js"></script>
<script src="script/Session.js"></script>
</head>

<body onload="computationWindowInit()" style="background-color: #f5f5f5;">

<div style="position: absolute;">

<div id="tab-engine" class="new-window-panel">
<h3 id="compute-engine-status" style="margin: 0 auto; font-size: 20px; text-align: center; font-family: 'FiraMono'; text-transform: uppercase;"> ● Computation</h3>
<div style="height: 20px;"></div>

<!-- Computation status -->
<div id="computation">
Computation: <span id="computation-status">(none)</span><br><span>
Progress: <span id="computation-progress">unknown</span><br>
Discovered classes: <span id="computation-classes">-</span></span>

<div style="margin-top: 25px; text-align: center;">
<button id="computation-cancel" class="image-button" onclick="Computation.cancelComputation();" style="margin-right: 4px;">Cancel job <img src="img/cancel-24px.svg" alt="cancel"></button>
<button id="computation-download" class="image-button" onclick="Results.show();" style="margin-left: 4px;">Show partial result <img src="img/cloud_download-24px.svg" alt="download"></button>
</div>
</div>

<div style="clear: both;"></div>
</div>

<div id="tab-results" class="new-window-panel gone">
<h2 style="margin: 0 auto; font-size: 20px; text-align: center;">Bifurcation Function</h2>

<div style="text-align: center; padding: 12px;">
<span id="results-expired" class="orange center gone">The computation has been overwritten. <br>These results are no longer available!</span>
</div>

<div id="results">
<div style="text-align: center; width: 350px; margin: 0 auto;">No results loaded. Run analysis to show bifurcation function overview for the currently loaded model.</div>
</div>

<div id="open-tree-explorer" class="gone" style="text-align: center; margin: 8px;">
<a class="inline-button" onclick="UI.openTreeExplorer()"> >> Explore Bifurcation Function &lt;&lt; </a>
</div>

<div id='result-legend'>
<span class='table-behavior'>D</span> disorder | <span class='table-behavior'>O</span> oscillation | <span class='table-behavior'>S</span> stability
</div>
</div>

</div>
</body>
</html>
71 changes: 71 additions & 0 deletions fe/help-window.html
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<!DOCTYPE html>

<html lang="en">
<head>
<title>Help</title>
<meta charset="utf-8">

<!-- Favicon -->
<link rel="apple-touch-icon" sizes="57x57" href="favicon/apple-icon-57x57.png">
<link rel="apple-touch-icon" sizes="60x60" href="favicon/apple-icon-60x60.png">
<link rel="apple-touch-icon" sizes="72x72" href="favicon/apple-icon-72x72.png">
<link rel="apple-touch-icon" sizes="76x76" href="favicon/apple-icon-76x76.png">
<link rel="apple-touch-icon" sizes="114x114" href="favicon/apple-icon-114x114.png">
<link rel="apple-touch-icon" sizes="120x120" href="favicon/apple-icon-120x120.png">
<link rel="apple-touch-icon" sizes="144x144" href="favicon/apple-icon-144x144.png">
<link rel="apple-touch-icon" sizes="152x152" href="favicon/apple-icon-152x152.png">
<link rel="apple-touch-icon" sizes="180x180" href="favicon/apple-icon-180x180.png">
<link rel="icon" type="image/png" sizes="192x192" href="favicon/android-icon-192x192.png">
<link rel="icon" type="image/png" sizes="32x32" href="favicon/favicon-32x32.png">
<link rel="icon" type="image/png" sizes="96x96" href="favicon/favicon-96x96.png">
<link rel="icon" type="image/png" sizes="16x16" href="favicon/favicon-16x16.png">
<meta name="msapplication-TileColor" content="#ffffff">
<meta name="msapplication-TileImage" content="favicon/ms-icon-144x144.png">
<meta name="theme-color" content="#ffffff">

<link rel="stylesheet" href="style.css" type="text/css">

</head>

<body style="background-color: #f5f5f5; overflow-y: hidden;">

<div id="help" class="new-window-panel" style="font-family: 'FiraMono';">
<h2 style="margin: 0 auto; font-size: 20px; text-align: center;">About & Help</h2>

<p>Aeon is a tool for analysing <b style="font-family: 'FiraMonoBold';">long-term behaviour of Boolean networks with parameters</b>. Use the editor to create a new network, or import your own from .sbml or .aeon. You can leave the update functions in the network blank (this will automatically consider all admissible instantiations of such function) or specify an exact update function. In the update function, you can use <b style="font-family: 'FiraMonoBold';">arbitrary uninterpreted functions as parameters</b> (see Budding Yeast-Irons example). Aeon will then automatically consider all admissible instantiations of such functions when analysing the model.</p>

<p>Once your network is ready, you can run the long-term behaviour analysis which will show you the behaviour classes of the model. The classes are separated based on <b style="font-family: 'FiraMonoBold';">stable, oscillating or disordered</b> behaviour. For each class, you can generate a <b style="font-family: 'FiraMonoBold';">witness network</b> that exihibits the specified behaviour.</p>

<h3>Manual</h3>

Full description of the functionality Aeon provides is available in the <a href="https://biodivine.fi.muni.cz/aeon/manual/v0.4.0/">tool manual</a>.


<h3>Quick Help</h3>
<b>Network editor actions:</b>
<ul>
<li>Double click to create a new variable.</li>
<li>Drag from `+` to create a new regulation.</li>
<li>Select element (click) to show the context menu.</li>
</ul>
<b>Keyboard shortcuts:</b>
<ul>
<li>(⌫) Remove selected element.</li>
<li>(N) Add new variable.</li>
<li>(E) Edit name of the selected variable.</li>
<li>(F) Edit update function of the selected variable.</li>
<li>(O) Change observability of the selected regulation.</li>
<li>(M) Change monotonicity of the selected regulation.</li>
<li>(H) Show this help message.</li>
</ul>

<h3>Attributions</h3>

<p>Compute Engine: crossbeam, rayon, rocket, json.</p>

<p>Online client: cytoscape with edgehandles, material icons, hotkeys.</p>

</div>

</body>
</html>
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