Team:Groningen/Graphs/GlpFTransport

From 2009.igem.org

(Difference between revisions)

Latest revision as of 08:45, 17 October 2009

{ script: "var Vcells=getInput('Vcells'),\

            Vtotal=getInput('Vtotal');\
        var Vsolution = Vtotal - Vcells;\
        var c = arsenicModelConstants();\
        c.Vc = Vcells*1e-3;\
        c.Vs = Vsolution*1e-3;\
        c.AsT = c.Vs*getInput('As3exInitial')*1e-6;\
        c.v5 = getInput('v5')*1e-6;\
        c.K5 = getInput('K5')*1e-6;\
        c.ars2T = 0;\
        c.pro = 0;\
        c.beta4 = 0;\
        var data = simulate(arsenicModelInitialization(c),3600,function(t,x){return arsenicModelGradient(c,x);});\
        var d=[{title:'As(III)_exT',data:[],args:{plot:'outer',stroke: { color: '#8B2500' }}},\
               {title:'As(III)_inT',data:[],args:{plot:'inner',stroke: { color: '#FF4500' }}}];\
        var t = Number.NEGATIVE_INFINITY;\
        for(var i=0; i<data.time.length; i++) {\
          var f=data.time[i]/60;\
          if (f>=t+0.1) {\
            t = t+0.1;\
            d[0].data.push({x:f,y:data.AsexT[i]*1e6});\
            d[1].data.push({x:f,y:data.AsinT[i]*1e6});\
          }\
        }\
        d.push({title:'As(III)_exT Meng2004',\
                data:[{x:1,y:8.47076050151002}, {x:10,y:6.51596961654617}, {x:20,y:4.3195753637778},\
                      {x:40,y:1.72783014551112}, {x:60,y:0.9371282145145}],\
                args:{plot: 'outer', stroke: { color: '#8B2500' }}});\
        d.push({title:'As(III)_inT Meng2004',\
                data:[{x:1,y:101.917808219178}, {x:10,y:394.520547945205}, {x:20,y:723.287671232877},\
                      {x:40,y:1111.23287671233}, {x:60,y:1229.58904109589}],\
                args:{plot: 'inner', stroke: { color: '#FF4500' }}});\
        for(j=2; j<d.length; j++) d[j].args.stroke.style = 'Dash';\
        d;",

width: '10cm', height: '8cm', axes: {x: {title: "time (min)", minorLabels: false}, innery: {title: "concentration in cell (µM)", vertical: true, min: 0}, outery: {title: "concentration in solution (µM)", vertical: true, leftBottom: false, min: 0} }, plots: { 'inner': {type: 'Lines', vAxis: 'innery'}, 'outer': {type: 'Lines', vAxis: 'outery'} } }

@@ Line 1: / Line 1: @@
 {
-script: "var data=[Number(document.getElementById('As3exInitial').value)*1e-6,0],\
+script: "var Vcells=getInput('Vcells'),\
-              Vcells=Number(document.getElementById('Vcells').value)*1e-6,\
+              Vtotal=getInput('Vtotal');\
-             Vmedium=Number(document.getElementById('Vmedium').value)*1e-6,\
+         var Vsolution = Vtotal - Vcells;\
-             Vmax=Number(document.getElementById('Vmax').value),\
+         var c = arsenicModelConstants();\
-             K=Number(document.getElementById('KGlpF').value)*1e-6;\
+         c.Vc = Vcells*1e-3;\
-          var ddata=new Array(data.length);\
+         c.Vs = Vsolution*1e-3;\
-          var d=[{title:'As(III)<sub>ex</sub>',data:[],args:{plot:'outer'}},\
+         c.AsT = c.Vs*getInput('As3exInitial')*1e-6;\
-                 {title:'As(III)',data:[],args:{plot:'inner',marker:'m0,0'}}];\
+         c.v5 = getInput('v5')*1e-6;\
-          for(var j in data) d[j].data.push({x:0,y:data[j]*1e6});\
+         c.K5 = getInput('K5')*1e-6;\
-          for(var i=1; i<=3600; i++) {\
+         c.ars2T = 0;\
-            var f=i/60;\
+         c.pro = 0;\
-            ddata[0] = -Vmax*Vcells*data[0]/(K+data[0]);\
+         c.beta4 = 0;\
-           ddata[1] = -ddata[0]*(Vmedium/Vcells);\
+          var data = simulate(arsenicModelInitialization(c),3600,function(t,x){return arsenicModelGradient(c,x);});\
-           for(var j in data) data[j] += ddata[j];\
+          var d=[{title:'As(III)<sub>ex</sub>T',data:[],args:{plot:'outer',{{:Team:Groningen/Styles/As(III)ex}}}},\
-           for(var j in data) d[j].data.push({x:f,y:data[j]*1e6});\
+                 {title:'As(III)<sub>in</sub>T',data:[],args:{plot:'inner',{{:Team:Groningen/Styles/As(III)}}}}];\
+          var t = Number.NEGATIVE_INFINITY;\
+          for(var i=0; i<data.time.length; i++) {\
+            var f=data.time[i]/60;\
+            if (f>=t+0.1) {\
+             t = t+0.1;\
+             d[0].data.push({x:f,y:data.AsexT[i]*1e6});\
+             d[1].data.push({x:f,y:data.AsinT[i]*1e6});\
+           }\
           }\
-          d.push({title:'As(III) Meng2004',\
+          d.push({title:'As(III)<sub>ex</sub>T Meng2004',\
-                  data:[{x:1,y:93},{x:10,y:360},{x:20,y:660},{x:40,y:1014},{x:60,y:1122}],\
+                  data:[{x:1,y:8.47076050151002}, {x:10,y:6.51596961654617}, {x:20,y:4.3195753637778},\
-                  args:{plot: 'inner', stroke: {opacity:0}, marker: 'm-3,0 c0,-4 6,-4 6,0 m-6,0 c0,4 6,4 6,0'}});\
+                       {x:40,y:1.72783014551112}, {x:60,y:0.9371282145145}],\
+                  args:{plot: 'outer', {{:Team:Groningen/Styles/As(III)ex}}}});\
+         d.push({title:'As(III)<sub>in</sub>T Meng2004',\
+                 data:[{x:1,y:101.917808219178}, {x:10,y:394.520547945205}, {x:20,y:723.287671232877},\
+                       {x:40,y:1111.23287671233}, {x:60,y:1229.58904109589}],\
+                 args:{plot: 'inner', {{:Team:Groningen/Styles/As(III)}}}});\
+         for(j=2; j<d.length; j++) d[j].args.stroke.style = 'Dash';\
           d;",
 width: '10cm',
 height: '8cm',
-axes: {x: {title: "time (min)", minorLabels: false}, innery: {title: "concentration in cell (µM)", vertical: true}, outery: {title: "concentration in solution (µM)", vertical: true, leftBottom: false} },
+axes: {x: {title: "time (min)", minorLabels: false}, innery: {title: "concentration in cell (µM)", vertical: true, min: 0}, outery: {title: "concentration in solution (µM)", vertical: true, leftBottom: false, min: 0} },
-plots: { 'inner': {type: 'Lines', vAxis: 'innery', markers: true}, 'outer': {type: 'Lines', vAxis: 'outery'} }
+plots: { 'inner': {type: 'Lines', vAxis: 'innery'}, 'outer': {type: 'Lines', vAxis: 'outery'} }
 }