User:Jessica Perez/CloningWorkflow: Difference between revisions

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==Source of DNA==
==Source of DNA==
{ "class": "go.TreeModel",
function init() {
  "nodeDataArray": [
    if (window.goSamples) goSamples();  // init for these samples -- you don't need to call this
{"key":"1", "name":"Corrado 'Junior' Soprano", "title":"The Boss"},
 
{"key":"2", "parent":"1", "name":"Tony Soprano", "title":"Underboss"},
    // Note that we do not use $ here as an alias for go.GraphObject.make because we are using $ for jQuery
{"key":"3", "parent":"1", "name":"Herman 'Hesh' Rabkin", "title":"Advisor"},
    var GO = go.GraphObject.make;  // for conciseness in defining templates
{"key":"4", "parent":"2", "name":"Paulie Walnuts", "title":"Capo"},
 
{"key":"5", "parent":"2", "name":"Ralph Cifaretto", "title":"Capo MIA"},
    myDiagram = new go.Diagram("myDiagram");  // must name or refer to the DIV HTML element
{"key":"6", "parent":"2", "name":"Silvio Dante", "title":"Consigliere"},
 
{"key":"7", "parent":"2", "name":"Bobby Baccilien", "title":"Capo"},
    // define several shared Brushes
{"key":"8", "parent":"4", "name":"Sal Bonpensiero", "title":"MIA"},
    var grad1 = GO(go.Brush, go.Brush.Linear, { 0: "rgb(115,220,241)", 0.5: "rgb(105,210,231)", 1: "rgb(75,180,201)" });
{"key":"9", "parent":"4", "name":"Christopher Moltisanti", "title":"Made Man"},
    var brush1 = "rgb(65,180,181)";
{"key":"10", "parent":"4", "name":"Furio Giunta", "title":"Muscle"},
 
{"key":"11", "parent":"4", "name":"Patsy Parisi", "title":"Accountant"}
    var grad2 = GO(go.Brush, go.Brush.Linear, { 0: "rgb(177,229,226)", 0.5: "rgb(167,219,216)", 1: "rgb(137,189,186)" });
]
    var brush2 = "rgb(127,179,176)";
}
 
    var grad3 = GO(go.Brush, go.Brush.Linear, { 0: "rgb(234,238,214)", 0.5: "rgb(224,228,204)", 1: "rgb(194,198,174)" });
    var brush3 = "rgb(184,188,164)";
 
    var grad4 = GO(go.Brush, go.Brush.Linear, { 0: "rgb(253,164,58)", 0.5: "rgb(243,134,48)", 1: "rgb(213,104,18)" });
    var brush4 = "rgb(203,84,08)";
 
    myDiagram.nodeTemplateMap.add("", // default
      GO(go.Node, go.Panel.Auto,
        { locationSpot: go.Spot.Center },
        new go.Binding("location", "loc", go.Point.parse).makeTwoWay(go.Point.stringify),
        GO(go.Shape, "Ellipse",
          { strokeWidth: 2, fill: grad1, name: "SHAPE" },
          new go.Binding("figure", "figure"),
          new go.Binding("fill", "fill"),
          new go.Binding("stroke", "stroke")
          ),
        GO(go.TextBlock,
          { margin: 5,
            maxSize: new go.Size(200, NaN),
            wrap: go.TextBlock.WrapFit,
            textAlign: "center",
            editable: true,
            font: "bold 9pt Helvetica, Arial, sans-serif",
            name: "TEXT" },
          new go.Binding("text", "text").makeTwoWay())));
 
    myDiagram.allowDrop = true;  // must be true to accept drops from the Palette
 
    // initialize the Palette that is in a floating, draggable HTML container
    myPalette = new go.Palette("myPalette");  // must name or refer to the DIV HTML element
    myPalette.nodeTemplateMap = myDiagram.nodeTemplateMap;
    myPalette.model = new go.GraphLinksModel([
      { text: "Lake", fill: grad1, stroke: brush1, figure: "Hexagon" },
      { text: "Ocean", fill: grad2, stroke: brush2, figure: "Rectangle" },
      { text: "Sand", fill: grad3, stroke: brush3, figure: "Diamond" },
      { text: "Goldfish", fill: grad4, stroke: brush4, figure: "Octagon" }
    ]);
 
    myPalette.addDiagramListener("InitialLayoutCompleted", function(diagramEvent) {
      var pdrag = document.getElementById("paletteDraggable");
      var palette = diagramEvent.diagram;
      var paddingHorizontal = palette.padding.left + palette.padding.right;
      var paddingVertical = palette.padding.top + palette.padding.bottom;
      pdrag.style.width = palette.documentBounds.width + 20  + "px";
      pdrag.style.height = palette.documentBounds.height + 30 + "px";
    });
 
    var info = document.getElementById("myInfo");
    myDiagram.addChangedListener(function (e) {
      var sel = e.diagram.selection;
      var str = "";
      if (sel.count === 0) {
        str = "Selecting nodes in the main Diagram will display information here.";
        info.innerHTML = str;
        return;
      } else if (sel.count > 1) {
        str = sel.count + " objects selected.";
        info.innerHTML = str;
        return;
      }
      // One object selected, display some information
      var elem = sel.first();
      var shape = elem.findObject("SHAPE");
      var txtblock = elem.findObject("TEXT");
      str += "
Selected Node:
 
";
      str += "
Figure: "
 
+ shape.figure + "
 
";
      str += "
Text: "
 
+ txtblock.text + "
 
";
      var strokeColor = shape.stroke;
      str += 'Color: ';
      info.innerHTML = str;
 
      // Initialize color picker
      $("#custom").spectrum({
          color: strokeColor,
 
          // Change colors by constructing a gradient
          change: function(color) {
            var c = color.toRgb();
            var r,g,b;
            var grad1 = new go.Brush(go.Brush.Linear);
            r = Math.min(c.r + 10, 255);
            g = Math.min(c.g + 10, 255);
            b = Math.min(c.b + 10, 255);
            grad1.addColorStop(0, "rgb(" + r +","+ g +","+ b + ")");
            grad1.addColorStop(0.5, color.toRgbString());
            r = Math.max(c.r - 30, 0);
            g = Math.max(c.g - 30, 0);
            b = Math.max(c.b - 30, 0);
            grad1.addColorStop(1, "rgb(" + r +","+ g +","+ b+  ")");
            shape.fill = grad1;
            shape.stroke = "rgb(" + r +","+ g +","+ b+  ")";
 
            txtblock.stroke = (r < 100 && g < 100 && b < 100) ? "white" : "black";
          }
      });
    });
 
 
    $(function() {
        $("#paletteDraggable").draggable({handle: "#paletteDraggableHandle"}).resizable({
          // After resizing, perform another layout to fit everything in the palette's viewport
          stop: function(){ myPalette.layoutDiagram(true); }
          });
        $("#infoDraggable").draggable({handle: "#infoDraggableHandle"});
    });
 
  }

Revision as of 14:21, 3 August 2013

Planning

Before you start any cloning in the lab you first do the following:

  1. Decide what parts you need
  2. Design primers
  3. Draw up your expected plasmid. This can be done in Word or freely avalible DNA editor software such as <html>

<body> <a href="http://biologylabs.utah.edu/jorgensen/wayned/ape/"> APE</a> </body> </html>.

Source of DNA

function init() { 

   if (window.goSamples) goSamples();  // init for these samples -- you don't need to call this

   // Note that we do not use $ here as an alias for go.GraphObject.make because we are using $ for jQuery
   var GO = go.GraphObject.make;  // for conciseness in defining templates

   myDiagram = new go.Diagram("myDiagram");  // must name or refer to the DIV HTML element

   // define several shared Brushes
   var grad1 = GO(go.Brush, go.Brush.Linear, { 0: "rgb(115,220,241)", 0.5: "rgb(105,210,231)", 1: "rgb(75,180,201)" });
   var brush1 = "rgb(65,180,181)";

   var grad2 = GO(go.Brush, go.Brush.Linear, { 0: "rgb(177,229,226)", 0.5: "rgb(167,219,216)", 1: "rgb(137,189,186)" });
   var brush2 = "rgb(127,179,176)";

   var grad3 = GO(go.Brush, go.Brush.Linear, { 0: "rgb(234,238,214)", 0.5: "rgb(224,228,204)", 1: "rgb(194,198,174)" });
   var brush3 = "rgb(184,188,164)";

   var grad4 = GO(go.Brush, go.Brush.Linear, { 0: "rgb(253,164,58)", 0.5: "rgb(243,134,48)", 1: "rgb(213,104,18)" });
   var brush4 = "rgb(203,84,08)";

   myDiagram.nodeTemplateMap.add("", // default
     GO(go.Node, go.Panel.Auto,
       { locationSpot: go.Spot.Center },
       new go.Binding("location", "loc", go.Point.parse).makeTwoWay(go.Point.stringify),
       GO(go.Shape, "Ellipse",
         { strokeWidth: 2, fill: grad1, name: "SHAPE" },
         new go.Binding("figure", "figure"),
         new go.Binding("fill", "fill"),
         new go.Binding("stroke", "stroke")
         ),
       GO(go.TextBlock,
         { margin: 5,
           maxSize: new go.Size(200, NaN),
           wrap: go.TextBlock.WrapFit,
           textAlign: "center",
           editable: true,
           font: "bold 9pt Helvetica, Arial, sans-serif",
           name: "TEXT" },
         new go.Binding("text", "text").makeTwoWay())));

   myDiagram.allowDrop = true;  // must be true to accept drops from the Palette

   // initialize the Palette that is in a floating, draggable HTML container
   myPalette = new go.Palette("myPalette");  // must name or refer to the DIV HTML element
   myPalette.nodeTemplateMap = myDiagram.nodeTemplateMap;
   myPalette.model = new go.GraphLinksModel([
     { text: "Lake", fill: grad1, stroke: brush1, figure: "Hexagon" },
     { text: "Ocean", fill: grad2, stroke: brush2, figure: "Rectangle" },
     { text: "Sand", fill: grad3, stroke: brush3, figure: "Diamond" },
     { text: "Goldfish", fill: grad4, stroke: brush4, figure: "Octagon" }
   ]);

   myPalette.addDiagramListener("InitialLayoutCompleted", function(diagramEvent) {
     var pdrag = document.getElementById("paletteDraggable");
     var palette = diagramEvent.diagram;
     var paddingHorizontal = palette.padding.left + palette.padding.right;
     var paddingVertical = palette.padding.top + palette.padding.bottom;
     pdrag.style.width = palette.documentBounds.width + 20  + "px";
     pdrag.style.height = palette.documentBounds.height + 30 + "px";
   });

   var info = document.getElementById("myInfo");
   myDiagram.addChangedListener(function (e) {
     var sel = e.diagram.selection;
     var str = "";
     if (sel.count === 0) {
       str = "Selecting nodes in the main Diagram will display information here.";
       info.innerHTML = str;
       return;
     } else if (sel.count > 1) {
       str = sel.count + " objects selected.";
       info.innerHTML = str;
       return;
     }
     // One object selected, display some information
     var elem = sel.first();
     var shape = elem.findObject("SHAPE");
     var txtblock = elem.findObject("TEXT");
     str += "

Selected Node:

"; 

     str += "

Figure: " 

+ shape.figure + "

"; 

     str += "

Text: " 

+ txtblock.text + "

"; 

     var strokeColor = shape.stroke;
     str += 'Color: ';
     info.innerHTML = str;

     // Initialize color picker
     $("#custom").spectrum({
         color: strokeColor,

         // Change colors by constructing a gradient
         change: function(color) {
           var c = color.toRgb();
           var r,g,b;
           var grad1 = new go.Brush(go.Brush.Linear);
           r = Math.min(c.r + 10, 255);
           g = Math.min(c.g + 10, 255);
           b = Math.min(c.b + 10, 255);
           grad1.addColorStop(0, "rgb(" + r +","+ g +","+ b + ")");
           grad1.addColorStop(0.5, color.toRgbString());
           r = Math.max(c.r - 30, 0);
           g = Math.max(c.g - 30, 0);
           b = Math.max(c.b - 30, 0);
           grad1.addColorStop(1, "rgb(" + r +","+ g +","+ b+  ")");
           shape.fill = grad1;
           shape.stroke = "rgb(" + r +","+ g +","+ b+  ")";

           txtblock.stroke = (r < 100 && g < 100 && b < 100) ? "white" : "black";
         }
     });
   });



   $(function() {
       $("#paletteDraggable").draggable({handle: "#paletteDraggableHandle"}).resizable({
         // After resizing, perform another layout to fit everything in the palette's viewport
         stop: function(){ myPalette.layoutDiagram(true); }
         });
       $("#infoDraggable").draggable({handle: "#infoDraggableHandle"});
   });

 }
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