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index.html
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index.html
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<!DOCTYPE html>
<html lang="en" xmlns="http://www.w3.org/1999/html">
<head>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-109049087-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-109049087-1');
</script>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=Edge">
<title>Newt Editor</title>
<link rel="icon" href="app/img/newt-icon.png" type="image/png">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="node_modules/bootstrap/dist/css/bootstrap.css" rel="stylesheet">
<link href="node_modules/intro.js/introjs.css" rel="stylesheet" type="text/css" />
<!--cytoscape.js plugins -->
<link href="node_modules/cytoscape-panzoom/cytoscape.js-panzoom.css" rel="stylesheet" type="text/css" />
<link href="node_modules/cytoscape-panzoom/font-awesome-4.0.3/css/font-awesome.css" rel="stylesheet" type="text/css" />
<!-- <link href="node_modules/qtip2/dist/jquery.qtip.css" rel="stylesheet" type="text/css" /> -->
<link href="node_modules/cytoscape-context-menus/cytoscape-context-menus.css" rel="stylesheet" type="text/css" />
<!-- app's style -->
<link href="app/css/chise.css" rel="stylesheet">
<script src="app/bundle.js"></script>
<!-- libraries -->
<!-- <script src="node_modules/qtip2/dist/jquery.qtip.js"></script> -->
</head>
<body>
<div class="read-mode-off">
<div class="nav-menu sbgn-nav-menu">
<nav class="navbar navbar-default sbgn-nav-bar" role="navigation">
<div>
<ul class="nav navbar-nav navbar-left">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
File
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<input id="file-input" type="file" style="display:none" />
<li><a href="#" type="file" id="new-file">New</a></li>
<li><a href="#" type="file" id="load-file">Load...</a></li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Samples
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a class="title"><i>PD</i></a></li>
<li class="divider" style="margin-top: 0"></li>
<li><a href="#" id="load-sample1">Neuronal muscle signaling</a></li>
<li><a href="#" id="load-sample2">CaM-CaMK dependent signaling to nucleus</a></li>
<li><a href="#" id="load-sample3">ATM mediated phosphorylation of repair proteins</a></li>
<li><a href="#" id="load-sample4">Activated STAT1alpha induction of the IRF1 gene</a></li>
<li><a href="#" id="load-sample5">Vitamins B6 activation to pyridoxal phosphate</a></li>
<li><a href="#" id="load-sample6">Insulin-like growth factor (IGF) signaling</a></li>
<li><a href="#" id="load-sample7">PolyQ proteins interference</a></li>
<li><a href="#" id="load-sample8">Glycolysis</a></li>
<li><a href="#" id="load-sample9">MAPK cascade</a></li>
<li><a href="#" id="load-sample10">Drosophila cell cycle</a></li>
<li><a href="#" id="load-sample11">Mammalian cholesterol biosynthesis</a></li>
<li><a href="#" id="load-sample12">Two gene system behavior</a></li>
<li><a href="#" id="load-sample19">PD Learner's Reference Card</a></li>
<li class="divider" style="margin-bottom: 0"></li>
<li><a class="title"><i>AF</i></a></li>
<li class="divider" style="margin-top: 0"></li>
<li><a href="#" id="load-sample13">Transforming growth factor beta (TGFB) signaling</a></li>
<li><a href="#" id="load-sample14">Repressilator</a></li>
<li><a href="#" id="load-sample15">Epidermal growth factor receptor</a></li>
<li><a href="#" id="load-sample16">Regulation of TGF-beta induced metastasis</a></li>
<li><a href="#" id="load-sample20">AF Learner's Reference Card</a></li>
<li class="divider" style="margin-bottom: 0"></li>
<li><a class="title"><i>SIF</i></a></li>
<li class="divider" style="margin-top: 0"></li>
<li><a href="#" id="load-sample17">RTN4 controllers and binding proteins</a></li>
<li><a href="#" id="load-sample18">Signaling downstream of AKT2/3</a></li>
</ul>
</li>
<li><a href="#" id="save-as-nwt">Save...</a></li>
<li><a href="#" type="file" id="close-file">Close</a></li>
<li class="divider"></li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Import
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</a>
<ul class="dropdown-menu">
<input id="simple-af-file-input" type="file" style="display:none" />
<input id="sif-file-input" type="file" style="display:none" />
<input id="sif-style-input" type="file" style="display:none" />
<input id="sif-layout-input" type="file" style="display:none" />
<input id="sbml-file" type="file" style="display:none" />
<input id="celldesigner-file-input" type="file" style="display:none" />
<input id="gpml-file-input" type="file" style="display:none" />
<li><a href="#" id="import-simple-af-file">Simple AF</a></li>
<li><a href="#" id="import-sif-file">SIF</a></li>
<li><a href="#" id="import-sif-style">SIF Style</a></li>
<li><a href="#" id="import-sif-layout">SIF Layout</a></li>
<li><a href="#" id="import-SBML-file">SBML</a></li>
<li><a href="#" id="import-celldesigner-file">CellDesigner</a></li>
<li><a href="#" id="import-GPML-file">GPML</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Export
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="export-as-sbgnml-plain-file">SBGN-ML Plain</a></li>
<li><a href="#" id="export-as-sbgnml3-plain-file">SBGN-ML Plain 0.3</a></li>
<li><a href="#" id="export-as-nwt3-file">NWT 0.3</a></li>
<li><a href="#" id="export-to-plain-sif">SIF</a></li>
<li><a href="#" id="export-to-sif-layout">SIF Layout</a></li>
<li><a href="#" id="export-as-sbml">SBML</a></li>
<li><a href="#" id="export-as-celldesigner-file">CellDesigner</a></li>
<li><a href="#" id="export-as-gpml">GPML</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Export as Image
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="save-as-png">PNG</a></li>
<li><a href="#" id="save-as-jpg">JPG</a></li>
<li><a href="#" id="save-as-svg">SVG</a></li>
</ul>
</li>
<li class="divider"></li>
<input id="user-preferences-file-input" type="file" style="display:none" />
<li><a href="#" id="load-user-preferences">Load Preferences...</a></li>
<li><a href="#" id="save-user-preferences">Save Preferences...</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Edit
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="add-complex-for-selected" >Add Complex for Selected</a></li>
<li><a href="#" id="add-compartment-for-selected" >Add Compartment for Selected</a></li>
<li><a href="#" id="add-submap-for-selected" >Add Submap for Selected</a></li>
<li><a href="#" id="create-reaction-template" >Add from Template...</a></li>
<li><a href="#" id="clone-selected" >Clone Selected</a></li>
<li class="divider"></li>
<li><a href="#" id="delete-selected-simple">Delete Selected Simple</a></li>
<li><a href="#" id="delete-selected-smart">Delete Selected Smart</a></li>
<li class="divider"></li>
<li><a href="#" id="resize-nodes-to-content">Resize Nodes To Content</a></li>
<li><a href="#" id="highlight-errors-of-validation"> Validate Map...</a></li>
<li class="divider"></li>
<li class="disabled"><a href="#" id="undo-last-action" >Undo</a></li>
<li class="disabled"><a href="#" id="redo-last-action" >Redo</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
View
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</a>
<ul class="dropdown-menu">
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Select
</a>
<ul class="dropdown-menu">
<li><a href="#" id="select-all">All Nodes and Edges</a></li>
<li><a href="#" id="select-all-nodes">All Nodes</a></li>
<li><a href="#" id="select-all-edges">All Edges</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Zoom
</a>
<ul class="dropdown-menu">
<li><a href="#" id="zoom-to-selected">Zoom to Selected</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Hide/Show
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="hide-selected">Hide Selected</a></li>
<li><a href="#" id="show-selected">Show Selected</a></li>
<li><a href="#" id="show-hidden-neighbors-of-selected">Show Hidden Neighbors of Selected</a></li>
<li><a href="#" id="show-all">Show All</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Collapse/Expand
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="collapse-selected">Collapse Selected</a></li>
<li><a href="#" id="expand-selected">Expand Selected</a></li>
<li><a href="#" id="collapse-complexes">Collapse Complexes</a></li>
<li><a href="#" id="expand-complexes">Expand Complexes</a></li>
<li><a href="#" id="collapse-all">Collapse All</a></li>
<li><a href="#" id="expand-all">Expand All</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" id="add-node-menu-option" class="dropdown-toggle" data-toggle="dropdown">
Align
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu" id="add-node-submenu">
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Horizontal
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="align-horizontal-top">Top</a></li>
<li><a href="#" id="align-horizontal-middle">Middle</a></li>
<li><a href="#" id="align-horizontal-bottom">Bottom</a></li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Vertical
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</a>
<ul class="dropdown-menu">
<li><a href="#" id="align-vertical-left">Left</a></li>
<li><a href="#" id="align-vertical-center">Center</a></li>
<li><a href="#" id="align-vertical-right">Right</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#" id="grid-properties" style="padding-right: 30px;">Grid and Guidelines...</a></li>
<li><a href="#" id="general-properties">Map Properties...</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Highlight
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="highlight-search-menu-item">Search...</a></li>
<li><a href="#" id="highlight-selected">Selected</a></li>
<li><a href="#" id="highlight-neighbors-of-selected">Neighbors of Selected</a></li>
<li><a href="#" id="highlight-processes-of-selected">Processes of Selected</a></li>
<li><a href="#" id="remove-highlights">Remove Highlights</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Experiment
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="import-experimental-data">Load...</a></li>
<input id="overlay-data" type="file" style="display:none" />
<li><a href="#" id="sample-experiment-data">Load Sample</a></li>
<li class="divider"></li>
<li><a href="#" value="true" id="experiment-data-hide-all">Hide/Show All</a></li>
<li><a href="#" id="experiment-data-remove-all">Remove All</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Layout
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="perform-layout">Perform Layout</a></li>
<li><a href="#" id="perform-static-layout">Perform Static Layout</a></li>
<li><a href="#" id="layout-properties">Layout Properties...</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Query
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li class="dropdown-submenu">
<a href="#" id="query-pathwaycommons" class="dropdown-toggle" data-toggle="dropdown">
Pathway Commons
<!--<b class="right-caret"></b>-->
</a>
<ul class="dropdown-menu">
<li><a href="#" id="query-pathsbetween">Paths Between...</a></li>
<li><a href="#" id="query-pathsfromto">Paths From To...</a></li>
<li><a href="#" id="query-commonstream">Common Stream...</a></li>
<li><a href="#" id="query-neighborhood">Neighborhood...</a></li>
<li><a href="#" id="query-pathsbyURI">By URI...</a></li>
</ul>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Legend
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="PD-legend">Process Description</a></li>
<li><a href="#" id="AF-legend">Activity Flow</a></li>
<li><a href="#" id="SIF-legend">SIF</a></li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
Help
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#" id="quick-help">Quick Help</a></li>
<li><a href="#" id="quick-tutorial">Quick Tutorial</a></li>
<li><a href="#" id="ui-guide">UI Guide</a></li>
<li><a href="#" id="about">About</a></li>
</ul>
</li>
</ul>
<a href="http://newteditor.org" target="_blank"><img class="newt-logo" height="25" width="auto" src="app/img/newt-logo.png"/></a>
<span class="input-file" id="displayed-file-name"></span>
<span class="input-file" id="file-name"></span>
</div>
</nav>
</div>
<div id="sbgn-toolbar" class="read-mode-off">
<div class="inside-menu">
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="new-file-icon" src="app/img/toolbar/new.svg" title="New: Create a blank map">
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="load-file-icon" src="app/img/toolbar/load.svg" title="Load: Load a map from a Newt file">
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="save-icon" src="app/img/toolbar/save.svg" title="Save: Save current map to a Newt file">
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px;" class="sbgn-toolbar-element"><img id="select-mode-icon" src="app/img/toolbar/select.svg" title="Select / Edit" ></div>
<div style="padding: 1px;" class="sbgn-toolbar-element"><img id="add-node-mode-icon" src="app/img/nodes/unspecified-entity.svg" title="Create a new Unspecified Entity" ></div>
<div style="padding: 1px;" class="sbgn-toolbar-element"><img id="add-edge-mode-icon" src="app/img/edges/consumption.svg" title="Create a new Consumption" ></div>
<div style="padding: 1px;" class="sbgn-toolbar-element"><img id="marquee-zoom-mode-icon" src="app/img/toolbar/marquee.svg" title="Marquee Zoom: Zoom to area specified by Shift + left click and drag" ></div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="delete-selected-simple-icon" src="app/img/toolbar/delete-simple.svg" title="Delete Selected Simple: Delete selected nodes and edges" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="delete-selected-smart-icon" src="app/img/toolbar/delete-smart.svg" title="Delete Selected Smart: Delete selected nodes and any processes they are involved in" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="highlight-errors-of-validation-icon" src="app/img/toolbar/check.svg" title="Validate Map: Validate SBGN PD map and fix problems" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="undo-icon" src="app/img/toolbar/undo.svg" title="Undo: Undo the last operation" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="redo-icon" src="app/img/toolbar/redo.svg" title="Redo: Redo the last undone operation" >
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="hide-selected-icon" src="app/img/toolbar/hide-selected.svg" title="Hide Selected: Hide selected nodes and any processes they are involved in" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="show-selected-icon" src="app/img/toolbar/show-all.svg" title="Show Selected: Show selected nodes and any processes they are involved in, hiding the remaining nodes and their edges" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="collapse-selected-icon" src="app/img/toolbar/collapse-selected.svg" title="Collapse Selected: Collapse selected compound node to hide its members" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="expand-selected-icon" src="app/img/toolbar/expand-selected.svg" title="Expand Selected: Expand selected collapsed node to show its members" >
</div>
<div class="btn-group sbgn-toolbar-element sbgn-dd-list" role="group" id="align-list">
<button id="align-button" style="padding:3px" title="Align to First Selected: Align positions of selected nodes based on the first (if any) selected node" type="button" class="btn" aria-haspopup="true" aria-expanded="false">
<div style="height: 16px;">
<img style="height: 16px; width: auto;" id="sbgn-align-img" src="app/img/align/align.svg"/>
<!--<span style="float: right;" class="caret"></span>-->
</div>
</button>
<button id="align-dd-button" style="padding:3px; padding-top:4px;" type="button" class="btn dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<div style="height: 16px;">
<span class="caret"></span>
<span class="sr-only"></span>
</div>
</button>
<ul id="align-menu" class="dropdown-menu" >
<li><a class="dd-list-href" href="#" id="align-horizontal-top-icon"> <img src="app/img/align/align-horizontal-top.svg"/>  Align Horizontal Top</a></li>
<li><a class="dd-list-href" href="#" id="align-horizontal-middle-icon"> <img src="app/img/align/align-horizontal-middle.svg"/>  Align Horizontal Middle</a></li>
<li><a class="dd-list-href" href="#" id="align-horizontal-bottom-icon"> <img src="app/img/align/align-horizontal-bottom.svg"/>  Align Horizontal Bottom</a></li>
<li><a class="dd-list-href" href="#" id="align-vertical-left-icon"> <img src="app/img/align/align-vertical-left.svg"/>  Align Vertical Left</a></li>
<li><a class="dd-list-href" href="#" id="align-vertical-center-icon"> <img src="app/img/align/align-vertical-center.svg"/>  Align Vertical Center</a></li>
<li><a class="dd-list-href" href="#" id="align-vertical-right-icon"> <img src="app/img/align/align-vertical-right.svg"/>  Align Vertical Right</a></li>
</ul>
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="toggle-grid-snapping-icon" src="app/img/toolbar/grid.svg" title="Enable Grid: Show and snap to grid during drag" >
</div>
<img id="toggle-guidelines-snapping-icon" class="sbgn-toolbar-element" src="app/img/toolbar/guidelines.svg" title="Enable Guidelines: Enable and snap to alignment guidelines during drag" >
<img id="properties-icon" class="sbgn-toolbar-element" src="app/img/toolbar/settings.svg" title="Map Properties: Modify general properties of current SBGN map" >
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="search-by-label-icon" src="app/img/toolbar/search.svg" title="Search: Search (case insensitive) and highlight all nodes with specified label text" >
</div>
<input id="search-by-label-text-box" class="sbgn-toolbar-element" type="label">
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="highlight-selected-icon" src="app/img/toolbar/highlight-selected.svg" title="Highlight Selected: Highlight selected nodes and edges" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="remove-highlights-icon" src="app/img/toolbar/remove-highlights.svg" title="Remove Highlights: Remove any highlights" >
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="perform-layout-icon" src="app/img/toolbar/layout-cose.svg" title="Perform Layout: Perform a force-directed layout of current map, maintaining compound structures" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="perform-static-layout-icon" src="app/img/toolbar/layout-static.svg" title="Perform Static Layout: Re-calculate layout of current map from scratch, ignoring current positions and maintaining compound structures" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="layout-properties-icon" src="app/img/toolbar/layout-properties.svg" title="Layout Properties: Modify parameters used during layout" >
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="query-pathsbetween-icon" src="app/img/toolbar/PC-logo.svg" title="Perform PC Query: Perform a PathwayCommons query to get a map of interest between specified genes" >
</div>
</div>
<div class="menu-break-large sbgn-toolbar-element"> </div>
<div class="inside-menu">
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="quick-help-icon" src="app/img/toolbar/quick-help.svg" title="Quick Help" >
</div>
<div style="padding: 1px;" class="sbgn-toolbar-element">
<img id="about-icon" src="app/img/toolbar/about.svg" title="About" >
</div>
</div>
</div>
</div>
<table id="sbgn-inspector-and-canvas">
<tbody>
<tr>
<td>
<div id="network-panels-container" class="tab-content read-mode-off">
</div>
</td>
<td>
<div id="sbgn-inspector">
<ul class="nav nav-tabs">
<li id='inspector-style-tab' class="chise-tab validation-mode-tab"><a data-toggle="tab" href="#sbgn-inspector-style"><img width="18px" height="18px" src="app/img/tabs/properties.svg"/> Object</a></li>
<li id='inspector-map-tab' class="chise-tab validation-mode-tab"><a data-toggle="tab" href="#sbgn-inspector-map"><img width="18px" height="18px" src="app/img/toolbar/settings.svg"/> Map</a></li>
<li id='inspector-palette-tab' class="chise-tab active validation-mode-tab"><a data-toggle="tab" href="#sbgn-inspector-palette"><img width="18px" height="18px" src="app/img/tabs/palette.svg"/> Palette</a></li>
<li id='inspector-console-tab' class="chise-tab validation-mode-tab" style="display:none;"> <a data-toggle="tab" href="#sbgn-inspector-console"><img width="18px" height="18px" src="app/img/tabs/console.svg" /> Console</a></li>
</ul>
<div class="tab-content">
<div id="sbgn-inspector-style" class="tab-pane fade">
<div id="sbgn-inspector-style-panel-group" class="panel-group">
</div>
</div>
<div id="sbgn-inspector-map" class="tab-pane fade">
<div class="panel-group">
<div class="panel">
<div class="panel-heading" data-toggle="collapse" data-target="#sbgn-inspector-map-properties-general">
<p class="panel-title accordion-toggle">General</p>
</div>
<div id="sbgn-inspector-map-properties-general" class="panel-collapse collapse in">
<div id="map-tab-general-container" >
</div>
</div>
</div>
<div class="panel">
<div class="panel-heading collapsed" data-toggle="collapse" data-target="#sbgn-inspector-map-properties-label">
<p class="panel-title accordion-toggle">Labels</p>
</div>
<div id="sbgn-inspector-map-properties-label" class="panel-collapse collapse">
<div id="map-tab-label-container" >
</div>
</div>
</div>
<div class="panel">
<div class="panel-heading collapsed" data-toggle="collapse" data-target="#sbgn-inspector-map-properties-rearrangement">
<p class="panel-title accordion-toggle">Arrangement</p>
</div>
<div id="sbgn-inspector-map-properties-rearrangement" class="panel-collapse collapse">
<div id="map-tab-rearrangement-container" >
</div>
</div>
</div>
<div class="panel">
<div id ="sbgn-inspector-map-properties-experiment-heading"class="panel-heading collapsed" data-toggle="collapse" data-target="#sbgn-inspector-map-properties-experiment">
<p class="panel-title accordion-toggle">Experiment</p>
</div>
<div id="sbgn-inspector-map-properties-experiment" class="panel-collapse collapse">
<div id="map-tab-experiment-container" >
</div>
</div>
</div>
<div class="panel">
<div class="panel-heading collapsed" data-toggle="collapse" data-target="#sbgn-inspector-map-color-scheme">
<p class="panel-title accordion-toggle">Color Scheme</p>
</div>
<div id="sbgn-inspector-map-color-scheme" class="panel-collapse collapse">
<div id="color-scheme-template-container" >
</div>
</div>
</div>
</div>
</div>
<div id="sbgn-inspector-palette" class="tab-pane fade in active">
<div class="panel-group">
<div class="panel">
<div id="PD-palette-heading" class="panel-heading" data-toggle="collapse" data-target="#expand-collapse-pd-nodes-palette">
<p class="panel-title accordion-toggle">
Process Description
</p>
</div>
<div id="expand-collapse-pd-nodes-palette" class="panel-collapse collapse in">
<div class="panel-body">
<div id="pd-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol"><img src="app/img/nodes/macromolecule.svg" language="PD" value="macromolecule" title="Macromolecule"/></div>
<div class="paletteCol"><img src="app/img/nodes/complex.svg" language="PD" value="complex" title="Complex"/></div>
<div class="paletteCol"><img src="app/img/nodes/simple-chemical.svg" language="PD" value="simple-chemical" title="Simple Chemical"/></div>
<div class="paletteCol"><img src="app/img/nodes/unspecified-entity.svg" language="PD" value="unspecified-entity" title="Unspecified Entity"/></div>
<div class="paletteCol"><img src="app/img/nodes/nucleic-acid-feature.svg" language="PD" value="nucleic-acid-feature" title="Nucleic Acid Feature"/></div>
<div class="paletteCol"><img src="app/img/nodes/perturbing-agent.svg" language="PD" value="perturbing-agent" title="Perturbing Agent"/></div>
<div class="paletteCol"><img src="app/img/nodes/source-and-sink.svg" language="PD" value="source-and-sink" title="Source and Sink"/></div>
<div class="paletteCol"><img src="app/img/nodes/phenotype.svg" language="PD" value="phenotype" title="Phenotype"/></div>
<div class="paletteCol"><img src="app/img/nodes/process.svg" language="PD" value="process" title="Process"/></div>
<div class="paletteCol"><img src="app/img/nodes/omitted-process.svg" language="PD" value="omitted-process" title="Omitted Process"/></div>
<div class="paletteCol"><img src="app/img/nodes/uncertain-process.svg" language="PD" value="uncertain-process" title="Uncertain Process"/></div>
<div class="paletteCol"><img src="app/img/nodes/association.svg" language="PD" value="association" title="Association"/></div>
<div class="paletteCol"><img src="app/img/nodes/dissociation.svg" language="PD" value="dissociation" title="Dissociation"/></div>
<div class="paletteCol"><img src="app/img/nodes/tag.svg" language="PD" value="tag" title="Tag"/></div>
<div class="paletteCol"><img src="app/img/nodes/compartment.svg" language="PD" value="compartment" title="Compartment"/></div>
<div class="paletteCol"><img src="app/img/nodes/submap.svg" language="PD" value="submap" title="Submap"/></div>
<div class="paletteCol"><img src="app/img/nodes/and.svg" language="PD" value="and" title="AND"/></div>
<div class="paletteCol"><img src="app/img/nodes/or.svg" language="PD" value="or" title="OR"/></div>
<div class="paletteCol"><img src="app/img/nodes/not.svg" language="PD" value="not" title="NOT"/></div>
</div>
</div>
</div>
<div class="panel-body" style="padding-bottom: 0px;">
<div id="pd-edge-palette" class="element-palette edge-palette">
<div class="paletteWrapper">
<div class="paletteCol"><img src="app/img/edges/consumption.svg" language="PD" value="consumption" title="Consumption"/></div>
<div class="paletteCol"><img src="app/img/edges/production.svg" language="PD" value="production" title="Production"/></div>
<div class="paletteCol"><img src="app/img/edges/modulation.svg" language="PD" value="modulation" title="Modulation"/></div>
<div class="paletteCol"><img src="app/img/edges/stimulation.svg" language="PD" value="stimulation" title="Stimulation"/></div>
<div class="paletteCol"><img src="app/img/edges/catalysis.svg" language="PD" value="catalysis" title="Catalysis"/></div>
<div class="paletteCol"><img src="app/img/edges/inhibition.svg" language="PD" value="inhibition" title="Inhibition"/></div>
<div class="paletteCol"><img src="app/img/edges/necessary-stimulation.svg" language="PD" value="necessary stimulation" title="Necessary Stimulation"/></div>
<div class="paletteCol"><img src="app/img/edges/consumption.svg" language="PD" value="logic arc" title="Logic Arc"/></div>
<div class="paletteCol"><img src="app/img/edges/consumption.svg" language="PD" value="equivalence arc" title="Equivalence Arc"/></div>
</div>
</div>
</div>
</div>
</div>
<!-- AF Nodes Panel -->
<div class="panel">
<div id="AF-palette-heading" class="panel-heading collapsed" data-toggle="collapse" data-target="#expand-collapse-af-nodes-palette">
<p class="panel-title accordion-toggle">
Activity Flow
</p>
</div>
<div id="expand-collapse-af-nodes-palette" class="panel-collapse collapse">
<div class="panel-body">
<div id="af-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol"><img src="app/img/nodes/BA-plain.svg" language="AF" value="BA-plain" title="Biological Activity"/></div>
<div class="paletteCol"><img src="app/img/nodes/BA-macromolecule.svg" language="AF" value="BA-macromolecule" title="Macromolecule"/></div>
<div class="paletteCol"><img src="app/img/nodes/BA-complex.svg" language="AF" value="BA-complex" title="Complex"/></div>
<div class="paletteCol"><img src="app/img/nodes/BA-simple-chemical.svg" language="AF" value="BA-simple-chemical" title="Simple Chemical"/></div>
<div class="paletteCol"><img src="app/img/nodes/BA-unspecified-entity.svg" language="AF" value="BA-unspecified-entity" title="Unspecified Entity"/></div>
<div class="paletteCol"><img src="app/img/nodes/BA-nucleic-acid-feature.svg" language="AF" value="BA-nucleic-acid-feature" title="Nucleic Acid Feature"/></div>
<div class="paletteCol"><img src="app/img/nodes/BA-perturbing-agent.svg" language="AF" value="BA-perturbing-agent" title="Perturbing Agent"/></div>
<div class="paletteCol"><img src="app/img/nodes/phenotype.svg" language="AF" value="phenotype" title="Phenotype"/></div>
<div class="paletteCol"><img src="app/img/nodes/compartment.svg" language="AF" value="compartment" title="Compartment"/></div>
<div class="paletteCol"><img src="app/img/nodes/submap.svg" language="AF" value="submap" title="Submap"/></div>
<div class="paletteCol"><img src="app/img/nodes/tag.svg" language="AF" value="tag" title="Tag"/></div>
<div class="paletteCol"><img src="app/img/nodes/and.svg" language="AF" value="and" title="AND"/></div>
<div class="paletteCol"><img src="app/img/nodes/or.svg" language="AF" value="or" title="OR"/></div>
<div class="paletteCol"><img src="app/img/nodes/not.svg" language="AF" value="not" title="NOT"/></div>
<div class="paletteCol"><img src="app/img/nodes/delay.svg" language="AF" value="delay" title="Delay"/></div>
</div>
</div>
</div>
<!-- AF Edges Panel -->
<div class="panel-body" style="padding-bottom: 0px;">
<div id="af-edge-palette" class="element-palette edge-palette">
<div class="paletteWrapper">
<div class="paletteCol"><img src="app/img/edges/stimulation.svg" language="AF" value="positive influence" title="Positive Influence"/></div>
<div class="paletteCol"><img src="app/img/edges/inhibition.svg" language="AF" value="negative influence" title="Negative Influence"/></div>
<div class="paletteCol"><img src="app/img/edges/modulation.svg" language="AF" value="unknown influence" title="Unknown Influence"/></div>
<div class="paletteCol"><img src="app/img/edges/necessary-stimulation.svg" language="AF" value="necessary stimulation" title="Necessary Stimulation"/></div>
<div class="paletteCol"><img src="app/img/edges/consumption.svg" language="AF" value="logic arc" title="Logic Arc"/></div>
<div class="paletteCol"><img src="app/img/edges/consumption.svg" language="AF" value="equivalence arc" title="Equivalence Arc"/></div>
</div>
</div>
</div>
</div>
</div>
<!-- AF Edges End -->
<!-- SIF Start -->
<div class="panel">
<div id="SIF-palette-heading" class="panel-heading collapsed" data-toggle="collapse" data-target="#expand-collapse-sif-nodes-palette">
<p class="panel-title accordion-toggle">
SIF
</p>
</div>
<div id="expand-collapse-sif-nodes-palette" class="panel-collapse collapse">
<div class="panel-body">
<div id="sif-node-palette" class="element-palette node-palette">
<div class="paletteWrapper">
<div class="paletteCol"><img src="app/img/nodes/macromolecule.svg" language="SIF" value="SIF-macromolecule" title="Macromolecule"/></div>
<div class="paletteCol"><img src="app/img/nodes/simple-chemical.svg" language="SIF" value="SIF-simple-chemical" title="Simple Chemical"/></div>
</div>
</div>
</div>
<div class="panel-body" style="padding-bottom: 0px;">
<div id="sif-edge-palette" class="element-palette edge-palette">
<div class="paletteWrapper">
<div class="paletteCol"><img src="app/img/edges/controls-state-change-of.svg" language="SIF" value="controls-state-change-of" title="Controls State Change of"/></div>
<div class="paletteCol"><img src="app/img/edges/controls-transport-of.svg" language="SIF" value="controls-transport-of" title="Controls Transport of"/></div>
<div class="paletteCol"><img src="app/img/edges/controls-phosphorylation-of.svg" language="SIF" value="controls-phosphorylation-of" title="Controls Phosphorylation of"/></div>
<div class="paletteCol"><img src="app/img/edges/controls-expression-of.svg" language="SIF" value="controls-expression-of" title="Controls Expression of"/></div>
<div class="paletteCol"><img src="app/img/edges/catalysis-precedes.svg" language="SIF" value="catalysis-precedes" title="Catalysis Precedes"/></div>
<div class="paletteCol"><img src="app/img/edges/in-complex-with.svg" language="SIF" value="in-complex-with" title="In Complex With"/></div>
<div class="paletteCol"><img src="app/img/edges/interacts-with.svg" language="SIF" value="interacts-with" title="Interacts With"/></div>
<div class="paletteCol"><img src="app/img/edges/neighbor-of.svg" language="SIF" value="neighbor-of" title="Neighbor of"/></div>
<div class="paletteCol"><img src="app/img/edges/consumption-controled-by.svg" language="SIF" value="consumption-controled-by" title="Consumption Controled By"/></div>
<div class="paletteCol"><img src="app/img/edges/controls-production-of.svg" language="SIF" value="controls-production-of" title="Controls Production of"/></div>
<div class="paletteCol"><img src="app/img/edges/controls-transport-of-chemical.svg" language="SIF" value="controls-transport-of-chemical" title="Controls Transport of Chemical"/></div>
<div class="paletteCol"><img src="app/img/edges/chemical-affects.svg" language="SIF" value="chemical-affects" title="Chemical Affects"/></div>
<div class="paletteCol"><img src="app/img/edges/reacts-with.svg" language="SIF" value="reacts-with" title="Reacts With"/></div>
<div class="paletteCol"><img src="app/img/edges/used-to-produce.svg" language="SIF" value="used-to-produce" title="Used to Produce"/></div>
<div class="paletteCol"><img src="app/img/edges/activates.svg" language="SIF" value="activates" title="Activates"/></div>
<div class="paletteCol"><img src="app/img/edges/inhibits.svg" language="SIF" value="inhibits" title="Inhibits"/></div>
<div class="paletteCol"><img src="app/img/edges/phosphorylates.svg" language="SIF" value="phosphorylates" title="Phosphorylates"/></div>
<div class="paletteCol"><img src="app/img/edges/dephosphorylates.svg" language="SIF" value="dephosphorylates" title="Dephosphorylates"/></div>
<div class="paletteCol"><img src="app/img/edges/upregulates-expression.svg" language="SIF" value="upregulates-expression" title="Upregulates Expression"/></div>
<div class="paletteCol"><img src="app/img/edges/downregulates-expression.svg" language="SIF" value="downregulates-expression" title="Downregulates Expression"/></div>
</div>
</div>
</div>
</div>
</div>
<!-- SIF End -->
</div>
</div>
<div id="sbgn-inspector-console" class="tab-pane fade">
<div class="panel-group">
<div class="panel">
<div class="panel-heading" data-toggle="collapse" data-target="#sbgn-inspector-console-panel-group">
<p class="panel-title accordion-toggle">Validation Results</p>
</div>
<div id="sbgn-inspector-console-panel-group" class="panel-collapse collapse in">
<div id="sbgn-inspector-tab-validation-container" >
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</td>
</tr>
</tbody>
</table>
<div id="network-tabs-list-container" class="read-mode-off">
<ul id="network-tabs-list" class="nav nav-tabs">
</ul>
</div>
<div id="layout-properties-table" tabindex="-1" class="modal fade" role="dialog">
<!-- sbgn layout table will be shown here -->
</div>
<div id="biogene-container" style="display: none">
</div>
<div id="chemical-container" style="display: none">
</div>
<div id="query-neighborhood-table" tabindex="-1" class="modal fade" role="dialog">
<!-- neighborhood query table will be shown here-->
</div>
<div id="query-pathsbetween-table" tabindex="-1" class="modal fade" role="dialog">
<!-- paths between query table will be shown here-->
</div>
<div id="query-pathsfromto-table" tabindex="-1" class="modal fade" role="dialog">
<!-- paths from to query table will be shown here-->
</div>
<div id="query-commonstream-table" tabindex="-1" class="modal fade" role="dialog">
<!-- common stream query table will be shown here-->
</div>
<div id="query-pathsbyURI-table" tabindex="-1" class="modal fade" role="dialog">
<!-- paths by URI query table will be shown here-->
</div>
<div id="prompt-save-table" tabindex="-1" class="modal fade" role="dialog">
<!-- sbgn properties table will be shown here-->
</div>
<div id="file-save-table" tabindex="-1" class="modal fade" role="dialog">
<!-- save dialog will be shown here-->
</div>
<div id="user-preferences-save-table" tabindex="-1" class="modal fade" role="dialog">
<!-- save dialog will be shown here-->
</div>
<div id="user-preferences-load-table" tabindex="-1" class="modal fade" role="dialog">
<!-- load dialog will be shown here-->
</div>
<div id="prompt-confirmation-table" tabindex="-1" class="modal fade" role="dialog">
<!-- confirmation dialog will be shown here-->
</div>
<div id="prompt-mapType-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-invalidQuery-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-invalidLengthLimit-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-invalidURI-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-invalidFile-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-fileConversionError-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-sbmlConversionError-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-invalidURL-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-invalidImage-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="prompt-invalidEdge-table" tabindex="-1" class="modal fade" role="dialog">
<!-- map type change confirmation dialog will be shown here-->
</div>
<div id="reaction-template-table" tabindex="-1" class="modal fade" role="dialog">
<!-- reaction templatequery table will be shown here -->
</div>
<div id="grid-properties-table" tabindex="-1" class="modal fade" role="dialog">
<!-- grid properties table will be shown here -->
</div>
<div id="font-properties-table" tabindex="-1" class="modal fade" role="dialog">
<!-- sbgn properties table will be shown here -->
</div>
<div id="prompt-invalidSchematronFile-table" tabindex="-1" class="modal fade" role="dialog">
<!-- sbgn schematron validation message dialog will be shown here -->
</div>
<div id="infobox-properties-table" tabindex="-1" class="modal fade" role="dialog">
<!-- infobox properties table will be shown here -->
</div>
<div id="box">
</div>
<textarea id="node-label-textbox" rows="1"></textarea>
<!-- templates -->
<div id='PD_legend_modal' class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog sbgn-modal-dialog" style="width: 540px;">
<div class="modal-content">
<div class="modal-body">
<div class="sbgn-frame" style="text-align:center;">
<h2 class="sbgn-text">Process Description</h2>
<img src="app/img/pd-legend.svg" alt="" class="centered img-responsive sbgn-legend">
<p class="address-text" style="margin-top: 20px;margin-bottom: 10px;"><a href="https://sbgn.github.io/referencecards" target="_blank" rel="nofollow">Reference Card</a> - <a href="https://sbgn.github.io/specifications" target="_blank" rel="nofollow">Specifications</a></p>
</div>
</div>
</div>
</div>
</div>
<div id='AF_legend_modal' class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog sbgn-modal-dialog" style="width: 600px;">
<div class="modal-content">
<div class="modal-body">
<div class="sbgn-frame" style="text-align: center;">
<h2 class="sbgn-text">Activity Flow</h2>
<img src="app/img/af-legend.svg" alt="" class="centered img-responsive sbgn-legend">
<p class="address-text" style="margin-top: 20px; margin-bottom: 10px;"><a href="https://sbgn.github.io/referencecards" target="_blank" rel="nofollow">Reference Card</a> - <a href="https://sbgn.github.io/specifications" target="_blank" rel="nofollow">Specifications</a></p>
</div>
</div>
</div>
</div>
</div>
<div id='SIF_legend_modal' class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog sbgn-modal-dialog" style="width: 750px;">
<div class="modal-content">
<div class="modal-body" style="text-align: center;">
<div class="sbgn-frame">
<h2 class="sbgn-text">Simple Interaction Format</h2>
<img src="app/img/sif-legend.svg" alt="" class="centered img-responsive sbgn-legend">
<p class="address-text" style="margin-top: 20px; margin-bottom: 10px"><a href="http://www.pathwaycommons.org/pc2/formats#sif_relations" target="_blank" rel="nofollow">SIF Relations</a></p>
</div>
</div>
</div>
</div>
</div>
<div id='about_modal' class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog sbgn-modal-dialog" style="width: 360px;">
<div class="modal-content">
<div class="modal-body">
<div class="sbgn-frame">
<h2 class="sbgn-text">About</h2>
<table width="100%" height="100%" align="center" valign="center">
<tbody>
<tr><td>
<p id="about-newt-version" class="sbgn-text">Newt Editor version 3.1.1</p>
</td></tr>
<tr><td>
<img src="app/img/newt-logo.png" alt="" class="centered img-responsive" style="margin-bottom: 10px;">
</td></tr>
<tr><td>
<p class="address-text">i-Vis Information Visualization Research Lab, Ankara, Turkey</p>
</td></tr>
<tr><td>
<p class="address-text">
Please cite: Balci et al. <a href="https://doi.org/10.1093/bioinformatics/btaa850" target="_blank">Newt: a comprehensive web-based tool <br>for viewing, constructing, and analyzing biological maps</a>, Bioinf., 37(10), pp.1475-1477, 2021.
</p>
</td></tr>
<tr><td>
<p class="address-text">
See <a href="https://github.com/iVis-at-Bilkent/newt#credits" target="_blank">here</a> for third-party libraries used
</p>
</td></tr>
<tr><td>
<p class="address-text marg">
<a href="mailto:ivis@cs.bilkent.edu.tr" target="_top">ivis@cs.bilkent.edu.tr</a>
</p>
<p class="address-text">
<a href="http://newteditor.org/" target="_blank">http://newteditor.org/</a>
</p>
</td></tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
</div>
<div id='quick_help_modal' class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog sbgn-modal-dialog" style="width: 520px">
<div class="modal-content">
<div class="modal-body">
<div class="sbgn-frame quick-help">
<h2 class="sbgn-text">Quick Help</h2>
<div class="quick-help-content">
<table align="center" valign="center">
<tbody>
<tr>
<td><b>SBGN notation:</b>:
<a href="https://sbgn.github.io/learning" target="_blank" rel="nofollow">Learning SBGN</a> - <a href="https://sbgn.github.io/learnerscards" target="_blank" rel="nofollow">Learner's Cards</a></td>
</tr>
<tr>
<td><b>SIF notation:</b>:
<a href="http://www.pathwaycommons.org/pc2/formats#sif_relations" target="_blank" rel="nofollow">SIF Relations</a> </td>
</tr>
<tr>
<td><b>File > Samples</b>:
Load a sample model</td>
</tr>
<tr>
<td><b>Double-click on node</b>:
Edit label</td>
</tr>
<tr>
<td><b>Right-click</b>:
Context menu for associated object</td>
</tr>
<tr>
<td><b>Click + drag on selected edge</b>:
Add and place a bend point</td>
</tr>
<tr>
<td><b>Ctrl/Cmd + drag on a node</b>:
Transfer a node in and out of a complex/compartment/submap</td>
</tr>
<tr>
<td><b>Shift + drag</b>:
Box selection (select touched nodes and included edges)</td>