Difference between revisions of "Team:Fudan-TSI/Notebook"

(LC after)
m
 
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−
{{Fudan-TSI}}
+
{{Fudan-TSI}}<!-- jquery loaded by HQ 1.12.4 -->
 
<html></p></div></div></div><meta name="viewport" content="width=device-width, initial-scale=1"><meta charset="UTF-8">
 
<html></p></div></div></div><meta name="viewport" content="width=device-width, initial-scale=1"><meta charset="UTF-8">
 
   <link rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/materialize.css&action=raw&ctype=text/css">
 
   <link rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/materialize.css&action=raw&ctype=text/css">
Line 115: Line 115:
 
</div><!-- #pageCover -->
 
</div><!-- #pageCover -->
 
<script src="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/bkg&action=raw&ctype=text/javascript"></script>
 
<script src="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/bkg&action=raw&ctype=text/javascript"></script>
−
<script>function bkgFunction(e){if(e){var t=new Stats;t.domElement.style.position="absolute",t.domElement.style.left="0",t.domElement.style.top="0",document.body.appendChild(t.domElement),requestAnimationFrame(function e(){t.update(),requestAnimationFrame(e)})}var n=document.getElementById("demo");tesselation.setup(n),gradients.setup();var o,r=1e4,a=3e3;window.requestAnimationFrame(function e(t){(!o||r<t-o)&&(o=t,tesselation.next(a),gradients.next(a)),window.requestAnimationFrame(e)})}var calcDelaunayTriangulation=function(){var E=1/1048576;function p(e,t,n,o){var r,a,i,l,c,u,s,d,h,f,p=e[t][0],m=e[t][1],g=e[n][0],y=e[n][1],w=e[o][0],I=e[o][1],b=Math.abs(m-y),v=Math.abs(y-I);if(b<E&&v<E)throw new Error("Can't get circumcircle since all 3 points are y-aligned");return i=-(g-p)/(y-m),l=-(w-g)/(I-y),c=(p+g)/2,u=(g+w)/2,s=(m+y)/2,d=(y+I)/2,{i:t,j:n,k:o,x:r=b<E?c:v<E?u:(i*c-l*u+d-s)/(i-l),y:a=v<b?i*(r-c)+s:l*(r-u)+d,r:(h=g-r)*h+(f=y-a)*f}}function m(e){var t,n,o,r,a,i;for(n=e.length;n;)for(r=e[--n],o=e[--n],t=n;t;){if(i=e[--t],o===(a=e[--t])&&r===i){e.splice(n,2),e.splice(t,2);break}if(o===i&&r===a){e.splice(n,2),e.splice(t,2);break}}}return function(n){var e,t,o,r,a,i,l,c,u,s,d,h,f=n.length;if(f<3||2e3<f)return[];for(n=n.slice(0),o=new Array(f),e=f;e--;)o[e]=e;for(o.sort(function(e,t){return n[t][0]-n[e][0]}),r=function(e){var t,n,o,r,a,i,l=Number.POSITIVE_INFINITY,c=Number.POSITIVE_INFINITY,u=Number.NEGATIVE_INFINITY,s=Number.NEGATIVE_INFINITY;for(t=e.length;t--;)e[t][0]<l&&(l=e[t][0]),e[t][0]>u&&(u=e[t][0]),e[t][1]<c&&(c=e[t][1]),e[t][1]>s&&(s=e[t][1]);return o=s-c,[[(a=l+.5*(n=u-l))-20*(r=Math.max(n,o)),(i=c+.5*o)-r],[a,i+20*r],[a+20*r,i-r]]}(n),n.push(r[0],r[1],r[2]),a=[p(n,f+0,f+1,f+2)],i=[],l=[],e=o.length;e--;l.length=0){for(h=o[e],t=a.length;t--;)0<(c=n[h][0]-a[t].x)&&c*c>a[t].r?(i.push(a[t]),a.splice(t,1)):c*c+(u=n[h][1]-a[t].y)*u-a[t].r>E||(l.push(a[t].i,a[t].j,a[t].j,a[t].k,a[t].k,a[t].i),a.splice(t,1));for(m(l),t=l.length;t;)d=l[--t],s=l[--t],a.push(p(n,s,d,h))}for(e=a.length;e--;)i.push(a[e]);for(a.length=0,e=i.length;e--;)i[e].i<f&&i[e].j<f&&i[e].k<f&&a.push(i[e].i,i[e].j,i[e].k);return a}}(),tesselation=function(){var a,h,f,i;return{setup:function(e){var t=(a=e).getAttribute("viewBox").split(/\D/g);h=t[2],f=t[3]},next:function(e){var t,n,o;if(e/=1e3,i&&i.children&&i.children.length){for(n=o=(t=i).children.length;n--;)TweenMax.to(t.children[n],.4*e,{opacity:0,delay:e*(.3*n/o)});TweenMax.delayedCall(.75*e,function(e){a.removeChild(e)},[t],this)}var r=function(){var e,t,n,o,r=window.innerWidth,a=window.innerHeight,i=[],l=h%(e=h/f<r/a?250*h/r:250*f/a)/2,c=f%e/2;for(n=Math.floor(h/e)+1;-1<=n;n--)for(o=Math.floor(f/e)+1;-1<=o;o--)i.push([l+e*(n+.75*(Math.random()-.5)),c+e*(o+.75*(Math.random()-.5))]);var u,s=calcDelaunayTriangulation(i),d=document.createElementNS("http://www.w3.org/2000/svg","g");for(t=s.length;t;)(u=document.createElementNS("http://www.w3.org/2000/svg","polygon")).setAttribute("points",i[s[--t]][0]+","+i[s[t]][1]+" "+i[s[--t]][0]+","+i[s[t]][1]+" "+i[s[--t]][0]+","+i[s[t]][1]),d.appendChild(u);return d}();for(n=o=r.children.length;n--;)TweenMax.fromTo(r.children[n],.4*e,{opacity:0},{opacity:.3+.25*Math.random(),delay:e*(.3*n/o+.3),ease:Back.easeOut});a.appendChild(r),i=r}}}(),gradients=function(){var o,r,a,i=["#3c6df0","#12a3b4","#00a78f","#00aa5e","#81b532","#e3bc13","#ffb000","#fe8500","#fe6100","#e62325","#dc267f","#c22dd5","#9753e1","#5a3ec8"];return{setup:function(){a=!1,o={stopA:document.getElementById("stop1a"),stopB:document.getElementById("stop1b"),rect:document.getElementById("rect1")},r={stopA:document.getElementById("stop2a"),stopB:document.getElementById("stop2b"),rect:document.getElementById("rect2")},o.rect.style.opacity=0,r.rect.style.opacity=0},next:function(e){var t,n;e/=1e3,t=a?(n=o,r):(n=r,o),a=!a,TweenMax.to(n.rect,.55*e,{opacity:0,delay:.2*e,ease:Sine.easeOut}),function(e){var t=Math.floor(i.length*Math.random()),n=Math.floor(3*Math.random())+3;n=(t+n*(Math.random()<.5?-1:1)+i.length)%i.length,e.stopA.setAttribute("stop-color",i[t]),e.stopB.setAttribute("stop-color",i[n])}(t),TweenMax.to(t.rect,.65*e,{opacity:1,ease:Sine.easeIn})}}}();bkgFunction();
+
        <script>
−
</script>
+
      //////////////////////////////
 +
      // Demo Functions
 +
      //////////////////////////////
 +
      function bkgFunction(showStats) {
 +
        // stats
 +
        if (showStats) {
 +
        var stats = new Stats();
 +
        stats.domElement.style.position = 'absolute';
 +
        stats.domElement.style.left = '0';
 +
        stats.domElement.style.top = '0';
 +
        document.body.appendChild(stats.domElement);
 +
        requestAnimationFrame(function updateStats(){
 +
          stats.update();
 +
          requestAnimationFrame(updateStats);
 +
        });
 +
        }
 +
        // init
 +
        var svg = document.getElementById('demo');
 +
        tesselation.setup(svg);
 +
        gradients.setup();
 +
        var lastTransitionAt, transitionDelay = 10000, transitionDuration = 3000;
 +
        function playNextTransition() {
 +
        tesselation.next(transitionDuration);
 +
        gradients.next(transitionDuration);
 +
        };
 +
        function tick(time) {
 +
        if (!lastTransitionAt || time - lastTransitionAt > transitionDelay) {
 +
          lastTransitionAt = time;
 +
          playNextTransition();
 +
        }
 +
        window.requestAnimationFrame(tick);
 +
        }
 +
        window.requestAnimationFrame(tick);
 +
      }
 +
      //////////////////////////////
 +
      // Delaunay Triangulation
 +
      //////////////////////////////
 +
      var calcDelaunayTriangulation = (function() {
 +
        var EPSILON = 1.0 / 1048576.0;
 +
        function getSuperT(vertices) {
 +
        var xMin = Number.POSITIVE_INFINITY, yMin = Number.POSITIVE_INFINITY,
 +
          xMax = Number.NEGATIVE_INFINITY, yMax = Number.NEGATIVE_INFINITY,
 +
          i, xDiff, yDiff, maxDiff, xCenter, yCenter;
 +
        for(i = vertices.length; i--; ) {
 +
          if(vertices[i][0] < xMin) xMin = vertices[i][0];
 +
          if(vertices[i][0] > xMax) xMax = vertices[i][0];
 +
          if(vertices[i][1] < yMin) yMin = vertices[i][1];
 +
          if(vertices[i][1] > yMax) yMax = vertices[i][1];
 +
        }
 +
        xDiff = xMax - xMin;
 +
        yDiff = yMax - yMin;
 +
        maxDiff = Math.max(xDiff, yDiff);
 +
        xCenter = xMin + xDiff * 0.5;
 +
        yCenter = yMin + yDiff * 0.5;
 +
        return [
 +
          [xCenter - 20 * maxDiff, yCenter - maxDiff],
 +
          [xCenter, yCenter + 20 * maxDiff],
 +
          [xCenter + 20 * maxDiff, yCenter - maxDiff]
 +
        ];
 +
        }
 +
        function circumcircle(vertices, i, j, k) {
 +
        var xI = vertices[i][0], yI = vertices[i][1],
 +
          xJ = vertices[j][0], yJ = vertices[j][1],
 +
          xK = vertices[k][0], yK = vertices[k][1],
 +
          yDiffIJ = Math.abs(yI - yJ), yDiffJK = Math.abs(yJ - yK),
 +
          xCenter, yCenter, m1, m2, xMidIJ, xMidJK, yMidIJ, yMidJK, xDiff, yDiff;
 +
        // bail condition
 +
        if(yDiffIJ < EPSILON){
 +
          if (yDiffJK < EPSILON){
 +
            throw new Error("Can't get circumcircle since all 3 points are y-aligned");
 +
          }
 +
        }
 +
 
 +
 
 +
        // calc circumcircle center x/y, radius
 +
        m1  = -((xJ - xI) / (yJ - yI));
 +
        m2  = -((xK - xJ) / (yK - yJ));
 +
        xMidIJ = (xI + xJ) / 2.0;
 +
        xMidJK = (xJ + xK) / 2.0;
 +
        yMidIJ = (yI + yJ) / 2.0;
 +
        yMidJK = (yJ + yK) / 2.0;
 +
        xCenter = (yDiffIJ < EPSILON) ? xMidIJ :
 +
          (yDiffJK < EPSILON) ? xMidJK :
 +
          (m1 * xMidIJ - m2 * xMidJK + yMidJK - yMidIJ) / (m1 - m2);
 +
        yCenter  = (yDiffIJ > yDiffJK) ?
 +
          m1 * (xCenter - xMidIJ) + yMidIJ :
 +
          m2 * (xCenter - xMidJK) + yMidJK;
 +
        xDiff = xJ - xCenter;
 +
        yDiff = yJ - yCenter;
 +
        // return
 +
        return {i: i, j: j, k: k, x: xCenter, y: yCenter, r: xDiff * xDiff + yDiff * yDiff};
 +
        }
 +
        function dedupeEdges(edges) {
 +
        var i, j, a, b, m, n;
 +
        for(j = edges.length; j; ) {
 +
          b = edges[--j]; a = edges[--j];
 +
          for(i = j; i; ) {
 +
          n = edges[--i]; m = edges[--i];
 +
          if(a === m){
 +
            if (b===n){
 +
              edges.splice(j, 2); edges.splice(i, 2);
 +
              break;
 +
            }
 +
          }
 +
          if(a === n){
 +
            if (b===m){
 +
              edges.splice(j, 2); edges.splice(i, 2);
 +
              break;
 +
            }
 +
          }
 +
          }
 +
        }
 +
        }
 +
        return function(vertices) {
 +
        var n = vertices.length,
 +
          i, j, indices, st, candidates, locked, edges, dx, dy, a, b, c;
 +
        // bail if too few / too many verts
 +
        if(n < 3 || n > 2000)
 +
          return [];
 +
        // copy verts and sort indices by x-position
 +
        vertices = vertices.slice(0);
 +
        indices = new Array(n);
 +
        for(i = n; i--; )
 +
          indices[i] = i;
 +
        indices.sort(function(i, j) {
 +
          return vertices[j][0] - vertices[i][0];
 +
        });
 +
        // supertriangle
 +
        st = getSuperT(vertices);
 +
        vertices.push(st[0], st[1], st[2]);
 +
        // init candidates/locked tris list
 +
        candidates = [circumcircle(vertices, n + 0, n + 1, n + 2)];
 +
        locked = [];
 +
        edges = [];
 +
        // scan left to right
 +
        for(i = indices.length; i--; edges.length = 0) {
 +
          c = indices[i];
 +
          // check candidates tris against point
 +
          for(j = candidates.length; j--; ) {
 +
          // lock tri if point to right of circumcirc
 +
          dx = vertices[c][0] - candidates[j].x;
 +
          if (dx > 0.0){
 +
            if(dx * dx > candidates[j].r){
 +
              locked.push(candidates[j]);
 +
            candidates.splice(j, 1);
 +
            continue;
 +
            }
 +
          }
 +
 
 +
 
 +
          // point outside circumcirc = leave candidates
 +
          dy = vertices[c][1] - candidates[j].y;
 +
          if(dx * dx + dy * dy - candidates[j].r > EPSILON)
 +
            continue;
 +
          // point inside circumcirc = break apart, save edges
 +
          edges.push(
 +
            candidates[j].i, candidates[j].j,
 +
            candidates[j].j, candidates[j].k,
 +
            candidates[j].k, candidates[j].i
 +
          );
 +
          candidates.splice(j, 1);
 +
          }
 +
          // new candidates from broken edges
 +
          dedupeEdges(edges);
 +
          for(j = edges.length; j; ) {
 +
          b = edges[--j];
 +
          a = edges[--j];
 +
          candidates.push(circumcircle(vertices, a, b, c));
 +
          }
 +
        }
 +
        // close candidates tris, remove tris touching supertri verts
 +
        for(i = candidates.length; i--; )
 +
          locked.push(candidates[i]);
 +
        candidates.length = 0;
 +
        for(i = locked.length; i--; )
 +
          if(locked[i].i < n){
 +
            if(locked[i].j < n){
 +
              if(locked[i].k < n){
 +
                candidates.push(locked[i].i, locked[i].j, locked[i].k);
 +
              }
 +
            }
 +
          }
 +
 
 +
 
 +
        // done
 +
        return candidates;
 +
        };
 +
      })();
 +
      var tesselation = (function() {
 +
        var svg, svgW, svgH, prevGroup;
 +
        function createRandomTesselation() {
 +
        var wW = window.innerWidth;
 +
        var wH = window.innerHeight;
 +
        var gridSpacing = 250, scatterAmount = 0.75;
 +
        var gridSize, i, x, y;
 +
        if (wW / wH > svgW / svgH) { // window wider than svg = use width for gridSize
 +
          gridSize = gridSpacing * svgW / wW;
 +
        } else { // window taller than svg = use height for gridSize
 +
          gridSize = gridSpacing * svgH / wH;
 +
        }
 +
        var vertices = [];
 +
        var xOffset = (svgW % gridSize) / 2, yOffset = (svgH % gridSize) / 2;
 +
        for (x = Math.floor(svgW/gridSize) + 1; x >= -1; x--) {
 +
          for (y = Math.floor(svgH/gridSize) + 1; y >= -1; y--) {
 +
          vertices.push(
 +
            [
 +
            xOffset + gridSize * (x + scatterAmount * (Math.random() - 0.5)),
 +
            yOffset + gridSize * (y + scatterAmount * (Math.random() - 0.5))
 +
            ]
 +
          );
 +
          }
 +
        }
 +
        var triangles = calcDelaunayTriangulation(vertices);
 +
        var group = document.createElementNS('http://www.w3.org/2000/svg','g');
 +
        var polygon;
 +
        for(i = triangles.length; i; ) {
 +
          polygon = document.createElementNS('http://www.w3.org/2000/svg','polygon');
 +
          polygon.setAttribute('points',
 +
          vertices[triangles[--i]][0] + ',' + vertices[triangles[i]][1] + ' ' +
 +
          vertices[triangles[--i]][0] + ',' + vertices[triangles[i]][1] + ' ' +
 +
          vertices[triangles[--i]][0] + ',' + vertices[triangles[i]][1]
 +
          );
 +
          group.appendChild(polygon);
 +
        }
 +
        return group;
 +
        }
 +
        return {
 +
        setup: function(svgElement) {
 +
          svg = svgElement;
 +
          var vb = svg.getAttribute('viewBox').split(/\D/g);
 +
          svgW = vb[2];
 +
          svgH = vb[3];
 +
        },
 +
        next: function(t) {
 +
          var toRemove, i, n;
 +
          t /= 1000;
 +
          if(prevGroup){
 +
            if(prevGroup.children){
 +
              if(prevGroup.children.length){
 +
                toRemove = prevGroup;
 +
                n = toRemove.children.length;
 +
                for (i = n; i--; ) {
 +
                  TweenMax.to(toRemove.children[i], t*0.4, {opacity: 0, delay: t*(0.3*i/n)});
 +
                }
 +
                TweenMax.delayedCall(t * (0.7 + 0.05), function(group) { svg.removeChild(group); }, [toRemove], this);
 +
              }
 +
            }
 +
          }
 +
 
 +
          var g = createRandomTesselation();
 +
          n = g.children.length;
 +
          for (i = n; i--; ) {
 +
          TweenMax.fromTo(g.children[i], t*0.4, {opacity: 0}, {opacity: 0.3 + 0.25 * Math.random(), delay: t*(0.3*i/n + 0.3), ease: Back.easeOut});
 +
          }
 +
          svg.appendChild(g);
 +
          prevGroup = g;
 +
        }
 +
        }
 +
      })();
 +
      //////////////////////////////
 +
      // Gradients
 +
      //////////////////////////////
 +
      var gradients = (function() {
 +
        var grad1, grad2, showingGrad1;
 +
        // using colors from IBM Design Colors this time
 +
        var colors = [ // 14 colors - use 3-5 span
 +
        '#3c6df0', // ultramarine50
 +
        '#12a3b4', // aqua40
 +
        '#00a78f', // teal40
 +
        '#00aa5e', // green40
 +
        '#81b532', // lime30
 +
        '#e3bc13', // yellow20
 +
        '#ffb000', // gold20
 +
        '#fe8500', // orange30
 +
        '#fe6100', // peach40
 +
        '#e62325', // red50
 +
        '#dc267f', // magenta50
 +
        '#c22dd5', // purple50
 +
        '#9753e1', // violet50
 +
        '#5a3ec8'  // indigo60
 +
        ];
 +
        function assignRandomColors(gradObj) {
 +
        var rA = Math.floor(colors.length * Math.random());
 +
        var rB = Math.floor(Math.random() * 3) + 3; // [3 - 5]
 +
        rB = (rA + (rB * (Math.random() < 0.5 ? -1 : 1)) + colors.length) % colors.length;
 +
        gradObj.stopA.setAttribute('stop-color', colors[rA]);
 +
        gradObj.stopB.setAttribute('stop-color', colors[rB]);
 +
        }
 +
        return {
 +
        setup: function() {
 +
          showingGrad1 = false;
 +
          grad1 = {
 +
          stopA: document.getElementById('stop1a'),
 +
          stopB: document.getElementById('stop1b'),
 +
          rect: document.getElementById('rect1')
 +
          };
 +
          grad2 = {
 +
          stopA: document.getElementById('stop2a'),
 +
          stopB: document.getElementById('stop2b'),
 +
          rect: document.getElementById('rect2')
 +
          };
 +
          grad1.rect.style.opacity = 0;
 +
          grad2.rect.style.opacity = 0;
 +
        },
 +
        next: function(t) {
 +
          t /= 1000;
 +
          var show, hide;
 +
          if (showingGrad1) {
 +
          hide = grad1;
 +
          show = grad2;
 +
          } else {
 +
          hide = grad2;
 +
          show = grad1;
 +
          }
 +
          showingGrad1 = !showingGrad1;
 +
          TweenMax.to(hide.rect, 0.55*t, {opacity: 0, delay: 0.2*t, ease: Sine.easeOut});
 +
          assignRandomColors(show);
 +
          TweenMax.to(show.rect, 0.65*t, {opacity: 1, ease: Sine.easeIn});
 +
        }
 +
        };
 +
      })();
 +
      //////////////////////////////
 +
      // Start
 +
      //////////////////////////////
 +
      bkgFunction();
 +
    </script>
 
               <div style="position:absolute;top:100px;left:9%"><center><img style="height:120px;width:auto" alt="cover notebook" src="https://static.igem.org/mediawiki/2019/4/4b/T--Fudan-TSI--coverNotebook.gif" /></center></div>
 
               <div style="position:absolute;top:100px;left:9%"><center><img style="height:120px;width:auto" alt="cover notebook" src="https://static.igem.org/mediawiki/2019/4/4b/T--Fudan-TSI--coverNotebook.gif" /></center></div>
 
           </div>
 
           </div>

Latest revision as of 05:51, 16 November 2019

Notebook | 2019 iGEM Team:Fudan-TSI


Notebook

We hereby present a toolbox for in vivo continuous mutation library construction. Our toolbox is orthogonal and provides a wide range of applications among various species.

cover notebook

Here is the link to download the file above.