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

(LC after)
m
 
Line 1: Line 1:
−
{{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 108: Line 108:
 
</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 parts" src="https://static.igem.org/mediawiki/2019/c/cf/T--Fudan-TSI--coverParts.gif" /></center></div>
 
               <div style="position:absolute;top:100px;left:9%"><center><img style="height:120px;width:auto" alt="cover parts" src="https://static.igem.org/mediawiki/2019/c/cf/T--Fudan-TSI--coverParts.gif" /></center></div>
 
           </div>
 
           </div>

Latest revision as of 05:55, 16 November 2019

Parts | 2019 iGEM Team:Fudan-TSI


Parts

cover parts

This year Team Fudan-TSI presents you with a toolbox for our in vivo sequence-specific continuous mutagenesis system. This toolbox includes promoters, RBSs, terminators, CDSs and other regulatory parts which undergo careful design and optimization. The Moloney Murine Leukemia Virus Reverse Transcriptase (MMLV-RT), which is new to the registry. Cre recombinase are the most important components of our system for which we have put emphasis on the construction and characterization. Also, our improved Lac repressor protein is fully equipped for regulating protein expression.

Specifically, the parts that we are presenting this year include but are not limited to these following features:
1) We attached Cre with different degradation tags, which could be used according to user’s interest to achieve optimal recombination efficiency.
2) We placed MMLV-RT under different IPTG-inducible promoters, which provides a range of different steady-state expression levels for various experimental purposes.
3) We included additional regulatory sequences (e.g. native primer binding site and poly-purine tract) required for the initiation and completion of reverse transcription.
4) To eliminate self-excision of Cre and promote recombination efficiency, we included a set of incompatible loxP sites.
5) We provide testing plasmids for system verification and optimization.

Bronze Requirement BBa_K1021005
BBa_E0040
Silver Requirement BBa_K3257071
BBa_K3257072
BBa_K3257073
Gold Requirement BBa_C0012 → BBa_K3257045
Our Best Basic Part BBa_K3257042
Our Best Composite Part BBa_K3257101
Our Part Collection  

In summary, our part collection provides a complete set for assembly, test, and optimization of continuous mutagenesis in different prokaryotic hosts.