DynamicInfluenceNetworks/index.html at master · CreativeCodingLab/DynamicInfluenceNetworks · GitHub

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<!DOCTYPE html>
<html>
    <head>
        <meta name="viewport" content="width=device-width, initial-scale=1">
        <meta charset="utf-8">
        <title>Dynamic Influence Networks</title>

        <!-- CSS Libs-->
        <link href="https://fonts.googleapis.com/css?family=Istok+Web" rel="stylesheet">

        <!-- JS Libs-->
        <script src="./lib/d3.v4.js" charset="utf-8"></script>
        <script src="./lib/WebContent/zip.js"></script>
        <script src="./lib/WebContent/zip-fs.js"></script>
        <script src="./lib/lodash.js" charset="utf-8"></script>

        <!-- CSS Src -->
        <link rel="stylesheet" href="./src/css/main.css" />
        <link rel="stylesheet" href="./src/css/toolbar.css" />

        <!-- JS Src -->
        <!-- Main Script -->
        <script src="./src/js/main.js" charset="utf-8"></script>

        <!-- Individual Visualization Scripts -->
        <script src="./src/js/focusSlider.js" charset="utf-8"></script>
        <script src="./src/js/phenotype.js" charset="utf-8"></script>
        <script src="./src/js/forceDirected.js" charset="utf-8"></script>
        <script src="./src/js/lineGraph.js"></script>
        <script src="./src/js/forceDirectedUI.js"></script>
        <script src="./src/js/sliderUI.js"></script>
        <script src="./src/js/animation.js" charset="utf-8"></script>
        <script src="./src/js/paintingManager.js" charset="utf-8"></script>

    </head>

    <body onload="App.init()" onresize="App.resize()">
        <div class="mainCol" id="forceDirectedDiv">
            <div id="toolbar" class="control">
                <div id="toolbar-nav-left"></div>
                <div id="toolbar-nav-right"></div>
                <span class="ui ui-data loading">
                    <h4>Dataset</h4>
                    <div>
                        <form id="form">
                            <input id="input" type="file" accept="application/zip,application/json" style="display:none;">
                        </form>
                        <div id="filename"></div>
                        <button id="changeFile">Upload</button>
                        <hr>
                        Examples:<br>
                        <a href="./?flux_0.json">EGFR Simulation</a><br>
                        <a href="./?PreyPred/flux_0.json">Predator Prey (Simple)</a><br>
                        <a href="./?MiniKaiRun/flux_0.json">Kai C (Complex)</a>
                    </div>
                </span>
                <span class="ui ui-clusters">
                  <h4>Clustering</h4>
                  <div>
                    <div class="center">Threshold</div>
                    <input type="text" id="set-threshold">
                    <div class="center">Mode</div>
                    <div class="left-align">
                        <div>
                          <input name="mode" type="radio" id="timestep-mode" checked>
                          <label for="timestep-mode">Timestep</label>
                        </div>
                        <div>
                          <input name="mode" type="radio" id="global-mode">
                          <label for="global-mode">Global</label>
                        </div>
                        <div>
                            <input name="mode" type="radio" id="window-mode">
                            <label for="window-mode">Windowed</label>
                        </div>
                        <div>
                          Time +/-
                          <input type="text" id="set-timewindow" value="5">
                        </div>
                    </div>
                  </div>
                </span>
                <span class="ui ui-labels">
                    <h4>Appearance</h4>
                    <div>
                        <div class="center">Labels</div>
                        <input type="checkbox" id="show-labels">
                        <label for="show-labels"></label>
                        <input type="range" value="50" id="label-size-slider">
                    </div>
                    <div>
                        <div class="center">Numbers</div>
                        <input type="checkbox" id="sci">
                        <label for="sci">
                            Sci. notation
                        </label>
                    </div>
                </span>
                <span class="ui ui-mark">
                    <h4>Layout<span></span></h4>
                    <div>
                        <button id="unpin">Unpin</button>
                        <button id="pin">Pin</button>
                    </div>
                    <div>
                        <div class="center">
                            Mark
                        </div>
                        <input type="checkbox" id="paint-start">
                        <label for="paint-start">
                        </label>
                        <button id="paint-reset"></button>
                        <div id="palette">
                            <div id="palette-1">
                                <button class="cs cs20"></button>
                                <button class="cs cs0"></button>
                                <button class="cs cs1"></button>
                                <button class="cs cs2"></button>
                                <button class="cs cs4"></button>
                                <button class="cs cs5"></button>
                                <button class="cs cs6"></button>
                                <button class="cs cs7"></button>
                            </div>
                            <div id="palette-2">
                                <button class="cs cs8"></button>
                                <button class="cs cs9"></button>
                                <button class="cs cs12"></button>
                                <button class="cs cs13"></button>
                                <button class="cs cs16"></button>
                                <button class="cs cs17"></button>
                                <button class="cs cs18"></button>
                                <button class="cs cs19"></button>
                            </div>
                        </div>
                    </div>
                </span>
                <span class="ui ui-legend">
                    <h4>Legend</h4>
                    <div class="legend-type hits">
                        Num. hits
                        <div></div>
                        <div></div>
                        <div></div>
                        <div></div>
                    </div>
                    <div class="legend-type inf">
                        Amt. influence
                        <div></div>
                        <div></div>
                        <div></div>
                        <div></div>
                    </div>
                    <div class="legend-type theme">
                        <div class="center">Links</div>
                        <input type="checkbox" id="hide-positive" checked>
                        <label for="hide-positive">
                        </label>
                            Positive
                        <div class="theme-color neg"></div>
                        <br/>
                        <input type="checkbox" id="hide-negative" checked>
                        <label for="hide-negative">
                        </label>
                            Negative
                        <div class="theme-color pos"></div>
                        <br/>
                        <input type="checkbox" id="theme">
                        <label for="theme">
                            Color safe
                        </label>
                    </div>
                </span>
            </div>
            <div class="animationControls">
              <div class="animationSpeedDiv">
                <p class="animationSpeed">1x</p>
              </div>


              <i class="animationIcon frIcon"></i>
              <i class="animationIcon sbIcon"></i>
              <i class="animationIcon ppIcon"></i>
              <i class="animationIcon sfIcon"></i>
              <i class="animationIcon ffIcon"></i>

            </div>
        </div>
        <div class="sideCol">
            <div id="help">
                <h4></h4>
                <div>
                    <p>
                        DYNAMIC INFLUENCE NETWORKS, a visual analytics tool for representing protein interaction networks, based on KaSim, an open source stochastic simulator of rule-based models.
                    </p>
                    <p>
                        LEFT: A network layout of KaSim data. <em>Rules</em> are represented as circles; <em>influences</em> on other rules are represented with lines.
                    </p>
                    <p>
                        If the magnitude of influence of one rule on another is higher than a user-given threshold (defined by the influence slider), they are clustered together (represented by colored circles).
                    </p>
                    <p>
                        Click and drag a rule or cluster to pin it in place; click again to unpin it. Use the LAYOUT tab to pin nodes in place or to manually mark nodes into different clusters.
                    </p>
                    <p>
                        RIGHT, TOP: A phenotype graph representing the overall activity of the network over the entire time window.
                    </p>
                    <p>
                        RIGHT, MIDDLE AND BOTTOM: Right-click any rule in the network layout to display its fluxes over time as a line graph.
                    </p>
                    <p>
                        DATASET: Drag and drop a zipped folder of json files generated by KaSim onto the page. They must be named in consecutive order: e.g., flux_0.json, flux_1.json, flux_2.json.
                    </p>
                </div>
            </div>
            <div class="row phenograph" id="phenoVis">
            </div>
            <div class="row linegraph" id="topVis">
            </div>
            <div class="row linegraph" id="bottomVis">
            </div>
            <div class="row focusslider" id="focusSlider">
            </div>
            <div id="linegraph-help">
                Tip: select a rule with right-click to bring up more in-depth information over time
            </div>
        </div>
    </body>
</html>