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<!DOCTYPE html>
<html>
<head>
<title>Biodivine/Aeon</title>
<meta charset="utf-8">
<!-- Favicon -->
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<script src="script/dependencies/dagre.js"></script>
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<script src="script/dependencies/lodash.js"></script>
<script src="script/dependencies/cytoscape-edgehandles.js"></script>
<script src="script/dependencies/cytoscape-dagre.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/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>
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gtag('js', new Date());
gtag('config', 'G-HTCNPH6WMB');
</script>
</head>
<body onload="init()">
<script type="module" src="script/patch-wasm.js"></script>
<!-- Hosts the interactive model editor -->
<div id="cytoscape-editor">
</div>
<h1 id='logo'>Aeon/<span id='title'>BIODIVINE</span></h1>
<!-- Do not change it here, this is a placeholder. Change it in const.js -->
<span id="version">v0.0.0</span>
<!-- A menu element that is shown for selected graph nodes in the editor. -->
<div id="node-menu" class="float-menu invisible">
<div class="button-row">
<img alt="Edit name (E)" id="node-menu-edit-name" class="button" src="img/edit-24px.svg">
<img alt="Edit update function (F)" id="node-menu-edit-function" class="button" src="img/functions-24px.svg">
<img alt="Remove (⌫)" id="node-menu-remove" class="button" src="img/delete-24px.svg">
</div>
<br>
<span class="hint invisible">Hint</span>
</div>
<!-- A menu element which is shown for selected edges in the editor. -->
<div id="edge-menu" class="float-menu invisible">
<div class="button-row">
<img alt="Toggle observability (O)" id="edge-menu-observability" class="button" src="img/visibility_off-24px.svg"
src-on="img/visibility_off-24px.svg" src-off="img/visibility_on-24px.svg"
alt-on="Observability off (O)" alt-off="Observability on (O)"
state=""
>
<img alt="Toggle monotonicity (M)" id="edge-menu-monotonicity" class="button" src="img/trending_up-24px.svg"
src-unspecified="img/trending_up-24px.svg" alt-unspecified="Make activating (M)"
src-activation="img/trending_down-24px.svg" alt-activation="Make inhibiting (M)"
src-inhibition="img/swap_vert-24px.svg" alt-inhibition="Monotonicity off (M)"
state=""
>
<img alt="Remove (⌫)" id="edge-menu-remove" class="button" src="img/delete-24px.svg">
</div>
<br>
<span class="hint invisible">Hint</span>
</div>
<div id="quick-help">
<h3 style="display: block; margin: 0 auto; float: right;">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>
<div style="width: 100%; text-align: center; font-size: 12px;">(this message disappears when you create the first variable)</div>
</div>
<div style="position: absolute;">
<div id="tab-model-editor" class="main-panel gone" style="padding-bottom: 0px;">
<div class="invisible-input full-line">
<input id="model-name" class="center" type="text" name="model-name" placeholder="(model name)" style="font-size: 20px;">
</div>
<img alt="close" src="img/close-24px.svg" class="panel-close-button" onclick="UI.closeContent()">
<div class="invisible-input full-line" id="model-description" contenteditable data-placeholder="(model description)" style="margin-top: 4px; margin-bottom: 4px;"></div>
<div style="height: 30px;">
<h3 style="font-family: 'FiraMono'; text-transform: uppercase;"> ● Overview</h3>
</div>
<table id="model-stats">
<tr class="row"> <td>Variables: </td> <td class="value">-</td> <td>Parameter space size: </td> <td class="value">-</td> </tr>
<tr class="row"> <td>Regulations: </td> <td class="value">-</td> <td>State space size: </td> <td class="value">-</td> </tr>
<tr class="row"> <td>Max. in-degree: </td> <td class="value">-</td> <td>Max. out-degree: </td> <td class="value">-</td> </tr>
<tr class="row"> <td colspan="2">Explicit parameters: </td> <td colspan="2">(none)</td> </tr>
</table>
<div style="height: 40px;">
<h3 style="float: left; font-family: 'FiraMono'; text-transform: uppercase;"> ● Variables</h3>
<button id="button-add-variable" class="image-button" onclick="let id = LiveModel.addVariable(); CytoscapeEditor.showNode(id);" style="float: right;">Add variable (N) <img src="img/add_box-24px.svg"></button>
</div>
<div style="clear: both;"></div>
<div id="model-variables" class="full-line"></div>
<div class="templates gone">
<div id="model-variable-template" class="model-variable">
<div class="invisible-input">
<input class="variable-name" type="text" name="variable-name" value="Variable name" placeholder="(variable name)" style="font-size: 18px;" spellcheck='false' autocorrect='off'>
</div>
<img alt="Remove variable" src="img/delete-24px.svg" class="model-variable-remove button">
<img alt="Show variable" src="img/search-24px.svg" class="model-variable-show button">
<br>
<h4> ● Regulators</h4>
<div class="model-variable-regulators full-line"></div>
<h4> ● Update Function</h4>
<div class="invisible-input full-line variable-function" contenteditable data-placeholder="(default)" spellcheck='false' autocorrect='off' style="font-size: 16px; text-align: center;"></div>
<div class="variable-function-status"></div>
</div>
<div id="model-regulation-template" class="model-regulation">
<span class="model-regulation-regulator">Some name</span>
<span class="model-regulation-short">(->)</span>
<span class="model-regulation-observable">observable</span>
<span class="model-regulation-monotonicity">activation</span>
</div>
</div>
</div>
<div id="tab-engine" class="main-panel gone">
<img alt="close" src="img/close-24px.svg" class="panel-close-button" onclick="UI.closeContent()">
<h2 style="margin: 0 auto; font-size: 20px; text-align: center;">Compute Engine</h2>
<div class="invisible-input full-line" style="margin-top: 4px; margin-bottom: 4px; font-size: 16px;">
<input id="engine-address" class="center" type="text" name="engine-address" value="http://localhost:8000" placeholder="(engine address)">
</div>
<div style="height: 40px;">
<h3 id="compute-engine-status" style="float: left; font-family: 'FiraMono'; text-transform: uppercase;"> ● Disconnected</h3>
<button id="button-connect" class="image-button" onclick="ComputeEngine.toggleConnection((e,r) => { if (e !== undefined) alert(e); });" style="float: right;">Connect <img src="img/cloud-24px.svg"></button>
</div>
<div style="clear: both;"></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: 16px; text-align: center;">
<button id="computation-cancel" class="image-button" onclick="ComputeEngine.cancelComputation();" style="margin-right: 4px;">Cancel job <img src="img/cancel-24px.svg"></button>
<button id="computation-download" class="image-button" onclick="Results.download();" style="margin-left: 4px;">Show result <img src="img/cloud_download-24px.svg"></button>
</div>
</div>
<div style="clear: both;"></div>
<div style="text-align: center; margin-top: 48px;">
<h3 style="margin: 0 auto; font-size: 14px; text-align: center; margin-bottom: 4px;">No engine running? Download binary:</h3>
<a href="https://github.com/sybila/biodivine-aeon-server/releases/download/VERSION/aeon-compute-engine-windows.zip" id="engine-link-windows" target="blank"><button id="download-windows" class="image-button" style="display: inline-block; margin: 4px;">Windows <img src="img/windows-24px.svg"></button></a>
<a href="https://github.com/sybila/biodivine-aeon-server/releases/download/VERSION/aeon-compute-engine-macos.zip" id="engine-link-macos" target="blank"><button id="download-mac" class="image-button" style="display: inline-block; margin: 4px;">MacOS <img src="img/macos-24px.svg"></button></a>
<a href="https://github.com/sybila/biodivine-aeon-server/releases/download/VERSION/aeon-compute-engine-linux.zip" id="engine-link-linux" target="blank"><button id="download-linux" class="image-button" style="display: inline-block; margin: 4px;">Linux <img src="img/linux-24px.svg"></button></a>
</div>
</div>
<div id="tab-import-export" class="main-panel gone">
<img alt="close" src="img/close-24px.svg" class="panel-close-button" onclick="UI.closeContent()">
<h2 style="margin: 0 auto; font-size: 20px; text-align: center; margin-bottom: 8px;">Model File</h2>
<table style="text-align: center; margin-left: -4px;">
<tr>
<td style="padding: 4px;">
<h3 style="display: block; margin: 0 auto; text-align: center;">Import</h3>
</td>
<td style="padding: 4px;">
<h3 style="display: block; margin: 0 auto; text-align: center;">Export</h3>
</td>
</tr>
<tr>
<td style="padding: 4px;">
<button id="import-local" class="compound-button" onclick="LiveModel.loadFromLocalStorage();" style="width: 244px;"><span class="main">Last<br>model</span><span class="desc">Browser local storage</span></button>
</td>
<td style="padding: 4px;">
<button id="export-aeon" class="compound-button" onclick="UI.downloadAeon();" style="width: 244px;"><span class="main">.AEON</span><span class="desc">Simple text format</span></button>
</td>
</tr>
<tr>
<td style="padding: 4px;">
<label for="import-aeon-input" id="import-aeon" class="compound-button"><span class="main">.AEON</span><span class="desc">Simple text format</span></label>
<input onchange='UI.importAeon(this)' id='import-aeon-input' style='display:none' type='file'>
</td>
<td style="padding: 4px;">
<button id="export-sbml" class="compound-button" onclick="UI.downloadSBML();"><span class="main">.SBML<br><small>(parametrized)</small></span><span class="desc">Parametrized model</span></button>
</td>
</tr>
<tr>
<td style="padding: 4px;">
<label for="import-sbml-input" id="import-sbml" class="compound-button"><span class="main">.SBML</span><span class="desc">Standard<br>SBML L3</span></label>
<input onchange='UI.importSBML(this)' id='import-sbml-input' style='display:none' type='file'>
</td>
<td style="padding: 4px;">
<button id="export-sbml" class="compound-button" onclick="UI.downloadSBMLInstantiated();"><span class="main">.SBML<br><small>(instantiated)</small></span><span class="desc">Witness<br>model</span></button>
</td>
</tr>
<tr>
<td style="padding: 4px;">
<label for="import-bnet-input" id="import-bnet" class="compound-button"><span class="main">.BNET</span><span class="desc">Boolnet text format</span></label>
<input onchange='UI.importBnet(this)' id='import-bnet-input' style='display:none' type='file'>
</td>
<td style="padding: 4px;">
<button id="export-bnet" class="compound-button" onclick="UI.downloadBnet();"><span class="main">.BNET</span><span class="desc">Boolnet text format</span></button>
</td>
</tr>
</table>
<h3 style="display: block; margin: 0 auto; text-align: center; margin-top: 8px; margin-bottom: 8px;">Example Models</h3>
<table style="text-align: center; margin-left: -4px;">
<tr>
<td style="padding: 4px;">
<button id="example-1" class="compound-button" onclick="LiveModel.importAeon(Examples.g2a);"><span class="main">G2A</span><span class="desc">Cell<br>Division</span></button>
</td>
<td style="padding: 4px;">
<button id="example-3" class="compound-button" onclick="LiveModel.importAeon(Examples.buddingYeastOrlando);"><span class="main">Orlando</span><span class="desc">Budding<br>Yeast</span></button>
</td>
</tr>
<tr>
<td style="padding: 4px;">
<button id="example-2" class="compound-button" onclick="LiveModel.importAeon(Examples.g2b);"><span class="main">G2B</span><span class="desc">Cell<br>Division</span></button>
</td>
<td style="padding: 4px;">
<button id="example-4" class="compound-button" onclick="LiveModel.importAeon(Examples.buddingYeastIrons);"><span class="main">Irons</span><span class="desc">Budding<br>Yeast</span></button>
</td>
</tr>
</table>
</div>
<div id="tab-results" class="main-panel gone">
<img alt="close" src="img/close-24px.svg" class="panel-close-button" onclick="UI.closeContent()">
<h2 style="margin: 0 auto; font-size: 20px; text-align: center; margin-bottom: 8px;">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 << </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 id="tab-help" class="main-panel gone" style="font-family: 'FiraMono';">
<img alt="close" src="img/close-24px.svg" class="panel-close-button" onclick="UI.closeContent()">
<h2 style="margin: 0 auto; font-size: 20px; text-align: center; margin-bottom: 8px;">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>
<div id="side-menu">
<div class="button-group-fake">
<img alt="Compute Bifurcation" id="side-menu-compute" src="img/play_circle_filled-48px.svg"
onclick="ComputeEngine.startComputation(LiveModel.exportAeon());" class="button-fake">
<span class="hint invisible">Start Analysis</span>
</div>
<div class="button-group">
<img alt="Engine" id="side-menu-engine" src="img/engine-48px.svg" class="button" tab-id="tab-engine">
<span id="engine-dot">●</span>
<span class="hint invisible">Compute Engine</span>
</div>
<div class="button-group">
<img alt="Import/Export" id="side-menu-import-export" src="img/file_copy-48px.svg" class="button" tab-id="tab-import-export">
<span class="hint invisible">Import/Export</span>
</div>
<div class="button-group">
<img alt="Model" id="side-menu-model" src="img/model-48px.svg" class="button" tab-id="tab-model-editor">
<span class="hint invisible">Model Editor</span>
</div>
<div style="position: relative; height: 96px; margin-bottom: 12px;">
<span class="label"><span>DAGRE</span></span>
<div class="button-group-fake" style="position: relative; top: 24px">
<img alt="Auto Layout" id="side-menu-layout" src="img/view_quilt-48px.svg"
onclick="CytoscapeEditor.layoutDagre();" class="button-fake">
<span class="hint invisible">Hierarchical layout</span>
</div>
</div>
<div style="position: relative; height: 96px; margin-bottom: 12px;">
<span class="label"><span>COSE</span></span>
<div class="button-group-fake" style="position: relative; top: 24px">
<img alt="Auto Layout" id="side-menu-layout" src="img/view_quilt-48px.svg"
onclick="CytoscapeEditor.layoutCose();" class="button-fake">
<span class="hint invisible">Organic layout</span>
</div>
</div>
<div class="button-group">
<img alt="Model" id="side-menu-results" src="img/call_split-48px.svg" class="button" tab-id="tab-results">
<span class="hint invisible">Results</span>
</div>
<div class="button-group">
<img alt="Help" id="side-menu-help" src="img/help-48px.svg" class="button" tab-id="tab-help">
<span class="hint invisible">About and Help</span>
</div>
</div>
<div id="loading-indicator" class="invisible"><img src="img/progress.gif"/><br><br>Waiting for server...</div>
</div>
</body>
</html>