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

(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 109: Line 109:
 
</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 not completely uploaded @@@@" src="https://static.igem.org/mediawiki/2019/f/f3/T--Fudan-TSI--coverExperiment.gif" /></center></div>
 
               <div style="position:absolute;top:100px;left:9%"><center><img style="height:120px;width:auto" alt="cover not completely uploaded @@@@" src="https://static.igem.org/mediawiki/2019/f/f3/T--Fudan-TSI--coverExperiment.gif" /></center></div>
 
           </div>
 
           </div>

Latest revision as of 05:56, 16 November 2019

Experiments | 2019 iGEM Team:Fudan-TSI


Experiments

We showed that our toolbox is orthogonal and provided a wide range of applications among various species. R-Evolution could mutate coding sequences and regulatory sequences, which enables the evolution of individual proteins or multiple targets at a time.

cover not completely uploaded @@@@

2019 Team Fudan-TSI works at the laboratory of Prof. Liang Cai in the School of Life Sciences of Fudan University. We mainly use the experimental devices and protocols within the laboratory, which are performed and optimized through years of practice.

Particularly, the fluorescence intensity and OD600 measurement and calibration protocols we use are from iGEM official measurement protocols.

Here is the link to download the file above.