Team:Amsterdam/maarten/

From 2012.igem.org

(Difference between revisions)
Line 3: Line 3:
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.8.0/jquery.min.js"></script>
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.8.0/jquery.min.js"></script>
<script type='text/javascript'>
<script type='text/javascript'>
 +
 +
(function() {
 +
  var ua = navigator.userAgent,
 +
      iStuff = ua.match(/iPhone/i) || ua.match(/iPad/i),
 +
      typeOfCanvas = typeof HTMLCanvasElement,
 +
      nativeCanvasSupport = (typeOfCanvas == 'object' || typeOfCanvas == 'function'),
 +
      textSupport = nativeCanvasSupport
 +
        && (typeof document.createElement('canvas').getContext('2d').fillText == 'function');
 +
  //I'm setting this based on the fact that ExCanvas provides text support for IE
 +
  //and that as of today iPhone/iPad current text support is lame
 +
  labelType = (!nativeCanvasSupport || (textSupport && !iStuff))? 'Native' : 'HTML';
 +
  nativeTextSupport = labelType == 'Native';
 +
  useGradients = nativeCanvasSupport;
 +
  animate = !(iStuff || !nativeCanvasSupport);
 +
})();
 +
 +
var Log = {
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  elem: false,
 +
  write: function(text){
 +
    if (!this.elem)
 +
      this.elem = document.getElementById('log');
 +
    this.elem.innerHTML = text;
 +
    this.elem.style.left = (500 - this.elem.offsetWidth / 2) + 'px';
 +
  }
 +
};
 +
 +
function visualization(number){
 +
$('#infovis').empty()
 +
json = JSON.parse(unescape($(':input[name=json'+number+']').val()))
 +
    //init data
 +
    //init Sunburst
 +
    var sb = new $jit.Sunburst({
 +
        //id container for the visualization
 +
        injectInto: 'infovis',
 +
        //Distance between levels
 +
        levelDistance: 90,
 +
        //Change node and edge styles such as
 +
        //color, width and dimensions.
 +
        Node: {
 +
          overridable: true,
 +
          type: useGradients? 'gradient-multipie' : 'multipie'
 +
        },
 +
        //Select canvas labels
 +
        //'HTML', 'SVG' and 'Native' are possible options
 +
        Label: {
 +
          type: labelType
 +
        },
 +
        //Change styles when hovering and clicking nodes
 +
        NodeStyles: {
 +
          enable: true,
 +
          type: 'Native',
 +
          stylesClick: {
 +
            'color': '#000000'
 +
          },
 +
        },
 +
        //Add tooltips
 +
        Tips: {
 +
          enable: true,
 +
          onShow: function(tip, node) {
 +
            var html = "<div class=\"tip-title\">" + node.data.description + "</div>";
 +
            var data = node.data;
 +
            if("length" in data) {
 +
              html += "<b>Length of feature:</b> " + data.length + "bp";
 +
            }
 +
if("type" in data){
 +
html += "<br\><b>Type of feature:</b> " + data.type;
 +
}
 +
            tip.innerHTML = html;
 +
          }
 +
        },
 +
        //implement event handlers
 +
        Events: {
 +
          enable: true,
 +
          onClick: function(node) {
 +
            if(!node) return;
 +
            //Build detailed information about the file/folder
 +
            //and place it in the right column.
 +
            var html = "<h4>" + node.name + "</h4>", data = node.data;
 +
            if("dna" in data) {
 +
              html += "<br /><br /><b>Sequence:</b><br /><pre>" + data.dna + "</pre>";
 +
            }
 +
            $jit.id('inner-details').innerHTML = html;
 +
            //hide tip
 +
            sb.tips.hide();
 +
            //rotate
 +
            //sb.rotate(node, animate? 'animate' : 'replot', {
 +
              //duration: 1000,
 +
              //transition: $jit.Trans.Quart.easeInOut
 +
            //});
 +
          }
 +
        },
 +
        // Only used when Label type is 'HTML' or 'SVG'
 +
        // Add text to the labels.
 +
        // This method is only triggered on label creation
 +
        onCreateLabel: function(domElement, node){
 +
          var labels = sb.config.Label.type,
 +
              aw = node.getData('length');
 +
          if (labels === 'HTML' && (node._depth < 2 || aw > 2000)) {
 +
            domElement.innerHTML = node.name;
 +
          } else if (labels === 'SVG' && (node._depth < 2 || aw > 2000)) {
 +
            domElement.firstChild.appendChild(document.createTextNode(node.name));
 +
          }
 +
        },
 +
        // Only used when Label type is 'HTML' or 'SVG'
 +
        // Change node styles when labels are placed
 +
        // or moved.
 +
        onPlaceLabel: function(domElement, node){
 +
          var labels = sb.config.Label.type;
 +
          if (labels === 'SVG') {
 +
            var fch = domElement.firstChild;
 +
            var style = fch.style;
 +
            style.display = '';
 +
            style.cursor = 'pointer';
 +
            style.fontSize = "0.8em";
 +
            fch.setAttribute('fill', "#fff");
 +
          } else if (labels === 'HTML') {
 +
            var style = domElement.style;
 +
            style.display = '';
 +
            style.cursor = 'pointer';
 +
            style.fontSize = "0.8em";
 +
            style.color = "#ddd";
 +
            var left = parseInt(style.left);
 +
            var w = domElement.offsetWidth;
 +
            style.left = (left - w / 2) + 'px';
 +
          }
 +
        }
 +
  });
 +
    //load JSON data.
 +
    sb.loadJSON(json);
 +
    //compute positions and plot.
 +
    sb.refresh();
 +
 +
    //end
 +
}
 +
 +
function addForbiddenSequences(){
 +
forbiddenSequences.addSite('Forbidden-EcoRI','GAATTC')
 +
forbiddenSequences.addSite('Forbidden-XbaI','GAATTC')
 +
forbiddenSequences.addSite('Forbidden-SpeI','ACTAGT')
 +
forbiddenSequences.addSite('Forbidden-PstI','CTGCAG')
 +
forbiddenSequences.addSite('Forbidden-NotI','GCGGCCGC')
 +
}
 +
 +
var forbiddenSequences = {
 +
    forbiddenSequencesArray : {},
 +
addSite : function(name,sequence){
 +
forbiddenSequences.forbiddenSequencesArray[name] = sequence
 +
},
 +
}
 +
 +
function checkOccurrence(target,sequence){
 +
if (sequence.length > target.length){
 +
        if (sequence.indexOf(target) == -1){
 +
            return false
 +
        } else{
 +
            return true
 +
        }
 +
} else{
 +
if (target.indexOf(sequence) == -1){
 +
            return false
 +
        } else{
 +
            return true
 +
        }
 +
}
 +
}
 +
 +
function randomDNA(length){
 +
chars = 'atgc'
 +
inForbiddenSite = true
 +
while (inForbiddenSite === true){
 +
sequence = ''
 +
inForbiddenSite = false
 +
for (k=0; k<length; k++) {
 +
rnum = Math.floor(Math.random() * chars.length);
 +
sequence += chars.substring(rnum,rnum+1);
 +
}
 +
for (item in forbiddenSequences.forbiddenSequencesArray){
 +
if (checkOccurrence(sequence,forbiddenSequences.forbiddenSequencesArray[item].toLowerCase()) === false){
 +
continue
 +
} else{
 +
inForbiddenSite = true
 +
break
 +
}
 +
}
 +
}
 +
return sequence
 +
}
 +
 +
function getMethyltransferases(){
 +
    methyltransferases = new Array()
 +
    sca1 = new Object()
 +
    sca1.target = "AGTACT"
 +
    sca1.sequence = "tccgggcgggactttggatatgtgatacagtcgtccgctgcactatggaatcgactctctacattctcacagagaggaaaagccttggacaccaggcttgcagacatcaagaaggccctggggaagccgtactacgaaacctcggatgtccttctttaccacggcgacagtcttgagctgctcaagtcaatgcctcagcagattttcgaccttaccgtaactagcccaccttacaatattggcaaagagtacgagggtgtactgtcgatcgaggaatacatttcctggtgcgagacatggatgtcgcgcgttcatagggcgaccagcgcaggcggcgcattttggctcaatgttgggtacgtccctgtcccgaaccaaggaaaagcagtcccgattccttacctcttgtgggacaagagtccgttctacatgatccaggaagttgtctggaattacggggcgggagtggcgtctcgaaaatcgttttccccgcgcaatgaaaagtttctctggtatgtgcgcgacccgctgaattattacttcgacctcgattcggtgcgcgacccaaatgtgaaataccccaaccagaaaaagaatgggaagctcaaatgcaacccgttggggaaaaatcccactgacgtttggcagttccccaaggttacgtcgggcgcgaagagatcaagcgtggagcgcaccgcccatccggcacaattcccgtctgctgtcattgaacgggtcatcaaggcgtgcagcccttccgacggcgtcatcctggacccattcctcggttccggaacgacctcgctgaccgccagaaagcaaggccggtgcagcgtcggtatcgaaatccgcgaagactacctcgacatcgcggtgggacgcctggaggcggaggcgcaatccctcttctag"
 +
    sca1.description = "M.Sca1"
 +
sca2 = new Object()
 +
sca2.target = "AGTACC"
 +
sca2.sequence = "tccgggcgggactttggatatgtgatacagtcgtccgctgcactatggaatcgactctctacattctcacagagaggaaaagccttggacaccaggcttgcagacatcaagaaggccctggggaagccgtactacgaaacctcggatgtccttctttaccacggcgacagtcttgagctgctcaagtcaatgcctcagcagattttcgaccttaccgtaactagcccaccttacaatattggcaaagagtacgagggtgtactgtcgatcgaggaatacatttcctggtgcgagacatggatgtcgcgcgttcatagggcgaccagcgcaggcggcgcattttggctcaatgttgggtacgtccctgtcccgaaccaaggaaaagcagtcccgattccttacctcttgtgggacaagagtccgttctacatgatccaggaagttgtctggaattacggggcgggagtggcgtctcgaaaatcgttttccccgcgcaatgaaaagtttctctggtatgtgcgcgacccgctgaattattacttcgacctcgattcggtgcgcgacccaaatgtgaaataccccaaccagaaaaagaatgggaagctcaaatgcaacccgttggggaaaaatcccactgacgtttggcagttccccaaggttacgtcgggcgcgaagagatcaagcgtggagcgcaccgcccatccggcacaattcccgtctgctgtcattgaacgggtcatcaaggcgtgcagcccttccgacggcgtcatcctggacccattcctcggttccggaacgacctcgctgaccgccagaaagcaaggccggtgcagcgtcggtatcgaaatccgcgaagactacctcgacatcgcggtgggacgcctggaggcggaggcgcaatccctcttctagg"
 +
    sca2.description = "M.Sca2"
 +
methyltransferases[0] = sca1
 +
methyltransferases[1] = sca2
 +
addForbiddenSequence(methyltransferases,'hasTarget')
 +
    return methyltransferases
 +
}
 +
 +
function getZincFingers(){
 +
    zincFingers = new Array()
 +
    rawData = document.plasmidForm.zf.value
 +
    rawData = rawData.split('>')
 +
    rawData.reverse().pop()
 +
    rawData.reverse()
 +
    for (zf in rawData){
 +
        zfFormatted = rawData[zf].split('\n')
 +
        zfDescription = zfFormatted[0]
 +
        zfTarget = zfDescription.split('|')[5]
 +
        zfSequence = ''
 +
        for (i=1;i<zfFormatted.length;i++){
 +
            zfSequence+=zfFormatted[i]
 +
        }
 +
        zfObject = new Object()
 +
        zfObject.target = zfTarget
 +
        zfObject.sequence = zfSequence
 +
        zfObject.description = zfDescription
 +
        zincFingers[zf] = zfObject
 +
    }
 +
    addForbiddenSequence(zincFingers,'hasTarget')
 +
    return zincFingers
 +
}
 +
 +
function getLinkers(){
 +
    linkers = new Array()
 +
    linker1 = new Object()
 +
    linker1.sequence = "gcacccggc"
 +
    linker1.description = "Linker 1"
 +
linker2 = new Object()
 +
linker2.sequence = "gcaccccgccc"
 +
linker2.description = "Linker 2"
 +
    linkers[0] = linker1
 +
linkers[1] = linker2
 +
addForbiddenSequence(linkers,'noTarget')
 +
    return linkers
 +
}
 +
 +
function getMycTags(){
 +
    mycTags = new Array()
 +
    mycTag1 = new Object()
 +
    mycTag1.sequence = "gaacagaaactcatctctgaagaggatctg"
 +
    mycTag1.description = "Myc Tag 1"
 +
mycTag2 = new Object()
 +
mycTag2.sequence = "gaacagaaactcatctctgaagagaatctgaagactgagtcagt"
 +
mycTag2.description = "Myc Tag 2"
 +
    mycTags[0] = mycTag1
 +
mycTags[1] = mycTag2
 +
addForbiddenSequence(mycTags,'noTarget')
 +
    return mycTags
 +
}
 +
 +
function getTerminators(){
 +
    terminators = new Array()
 +
    terminator1 = new Object()
 +
    terminator1.sequence = "tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattt"
 +
    terminator1.description = "B0014 containing BOO12 and BOO11 terminators"
 +
terminator2 = new Object()
 +
terminator2.sequence = "tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattatttt"
 +
    terminator2.description = "Terminator 2"
 +
terminators[0] = terminator1
 +
terminators[1] = terminator2
 +
addForbiddenSequence(terminators,'noTarget')
 +
    return terminators
 +
}
 +
 +
function getRBS(){
 +
    rbs = new Array()
 +
    rbs1 = new Object()
 +
    rbs1.sequence = "tcacacaggaaag"
 +
    rbs1.description = "BBa_B0032"
 +
    rbs2 = new Object()
 +
    rbs2.sequence = "aaaaaaaaaaaccccaa"
 +
    rbs2.description = "RBS2"
 +
    rbs[0] = rbs1
 +
    rbs[1] = rbs2
 +
addForbiddenSequence(rbs,'noTarget')
 +
    return rbs
 +
}
 +
 +
function addForbiddenSequence(array,type){
 +
if (type == 'hasTarget'){
 +
for (item in array){
 +
forbiddenSequences.addSite(array[item].description,array[item].target)
 +
}
 +
} else{
 +
for (item in array){
 +
forbiddenSequences.addSite(array[item].description,array[item].sequence)
 +
}
 +
}
 +
 +
}
 +
 +
function getDate(){
 +
    today = new Date()
 +
    dd = today.getDate()
 +
    mm = today.getMonth()+1
 +
    yyyy = today.getFullYear()
 +
    if(dd<10){
 +
        dd='0'+dd
 +
    }
 +
    if(mm<10){
 +
        mm='0'+mm
 +
    }
 +
    today = dd+'-'+mm.substring(0,2)+'-'+yyyy;
 +
    return today
 +
}
 +
 +
function generateWhiteSpace(amount){
 +
        output = ''
 +
        for (i=0;i<amount;i++){
 +
            output += '&nbsp;'
 +
        }
 +
        return output
 +
}
 +
 +
function staticGenbank(name){
 +
output = 'LOCUS'
 +
        output += generateWhiteSpace(16)
 +
        output += name
 +
        output += generateWhiteSpace(8)
 +
        output += memoryPlasmid.dna.length+' bp DNA '
 +
        output += generateWhiteSpace(3)
 +
        output += 'linear'
 +
        output += generateWhiteSpace(7)
 +
        output += getDate()+'<br>'
 +
        output += 'DEFINITION<br>'
 +
        output += 'ACCESSION<br>'
 +
        output += 'VERSION<br>'
 +
        output += 'SOURCE<br>'
 +
        output += ' &nbsp;ORGANISM<br>'
 +
        output += 'COMMENT<br>'
 +
        output += 'FEATURES'
 +
        output += generateWhiteSpace(13)
 +
        output += 'Location/Qualifiers<br>'
 +
return output
 +
}
 +
 +
function genbankRestriction(targetSites){
 +
restrictionPlasmidOutput = staticGenbank('restriction_plasmid')
 +
restrictionOrigin = memoryPlasmid.features[1].sequence
 +
for (key in targetSites){
 +
    restrictionOrigin += randomDNA(10)
 +
    restrictionPlasmidOutput += generateWhiteSpace(5)
 +
restrictionPlasmidOutput += 'misc_feature'
 +
restrictionPlasmidOutput += generateWhiteSpace(5)
 +
restrictionPlasmidOutput += restrictionOrigin.length+1+'...'
 +
    restrictionOrigin += targetSites[key].zincFinger
 +
restrictionPlasmidOutput += restrictionOrigin.length+'<br>'
 +
restrictionOrigin += randomDNA(10)
 +
restrictionPlasmidOutput += generateWhiteSpace(5)
 +
restrictionPlasmidOutput += 'misc_feature'
 +
restrictionPlasmidOutput += generateWhiteSpace(5)
 +
restrictionPlasmidOutput += restrictionOrigin.length+1+'...'
 +
    restrictionOrigin += targetSites[key].methyltransferase
 +
restrictionPlasmidOutput += restrictionOrigin.length+'<br>'
 +
restrictionOrigin += targetSites[key].methyltransferase
 +
}
 +
restrictionOrigin = restrictionOrigin.toLowerCase()
 +
        restrictionOrigin = restrictionOrigin.replace(/[atgc]{10}/g,'$& ').replace(/amp;/g,'').split(' ')
 +
        pos = 1
 +
        newString = ''
 +
        restrictionPlasmidOutput += 'ORIGIN<br>'
 +
        for (i=0;i<restrictionOrigin.length;i++){
 +
            newString = newString+' '+restrictionOrigin[i]
 +
            if ((i+1)%6===0){
 +
                whiteSpace = ''
 +
                for (j=0;j<9-pos.toString().length;j++){
 +
                    whiteSpace+= '&nbsp;'
 +
                }
 +
                newString = whiteSpace+pos + ' ' + newString
 +
                restrictionPlasmidOutput+=newString+'<br>'
 +
                newString = ''
 +
            } else if ((i+1)%6==1){
 +
                  if (i!=0){
 +
                      pos+=60
 +
                  }
 +
              }
 +
        }
 +
        if (restrictionOrigin.length%6 != 0){
 +
            newString = ''
 +
            whiteSpace = ''
 +
            for (j=0;j<9-pos.toString().length;j++){
 +
                whiteSpace+= '&nbsp;'
 +
            }
 +
            newString+=whiteSpace+pos
 +
            for (i=0;i<(restrictionOrigin.length%6);i++){
 +
                newString+=' '+restrictionOrigin[restrictionOrigin.length-restrictionOrigin.length%6+i]
 +
            }
 +
            restrictionPlasmidOutput+=newString+'<br>'
 +
        }
 +
restrictionSiteWindow = window.open()
 +
restrictionSiteWindow.document.write(restrictionPlasmidOutput)
 +
restrictionSiteWindow.focus()
 +
}
 +
function genbankMemory(){
 +
        memoryPlasmidOutput = staticGenbank('memory_plasmid')
 +
        for (item in memoryPlasmid.memoryObjects){
 +
    for (key in memoryPlasmid.memoryObjects[item]){
 +
memoryPlasmidOutput += generateWhiteSpace(5)
 +
memoryPlasmidOutput += 'misc_feature'
 +
memoryPlasmidOutput += generateWhiteSpace(5)
 +
memoryPlasmidOutput += memoryPlasmid.memoryObjects[item][key].start+'...'+memoryPlasmid.memoryObjects[item][key].end+'<br>'
 +
memoryPlasmidOutput += generateWhiteSpace(10)
 +
memoryPlasmidOutput += '/label='+memoryPlasmid.memoryObjects[item][key].description+'<br>'
 +
}
 +
           
 +
        }
 +
        origin = memoryPlasmid.dna
 +
        origin = origin.replace(/[atgc]{10}/g,'$& ').replace(/amp;/g,'').split(' ')
 +
        pos = 1
 +
        newString = ''
 +
        memoryPlasmidOutput += 'ORIGIN<br>'
 +
        for (i=0;i<origin.length;i++){
 +
            newString = newString+' '+origin[i]
 +
            if ((i+1)%6===0){
 +
                whiteSpace = ''
 +
                for (j=0;j<9-pos.toString().length;j++){
 +
                    whiteSpace+= '&nbsp;'
 +
                }
 +
                newString = whiteSpace+pos + ' ' + newString
 +
                memoryPlasmidOutput+=newString+'<br>'
 +
                newString = ''
 +
            } else if ((i+1)%6==1){
 +
                  if (i!=0){
 +
                      pos+=60
 +
                  }
 +
              }
 +
        }
 +
        if (origin.length%6 != 0){
 +
            newString = ''
 +
            whiteSpace = ''
 +
            for (j=0;j<9-pos.toString().length;j++){
 +
                whiteSpace+= '&nbsp;'
 +
            }
 +
            newString+=whiteSpace+pos
 +
            for (i=0;i<(origin.length%6);i++){
 +
                newString+=' '+origin[origin.length-origin.length%6+i]
 +
            }
 +
            memoryPlasmidOutput+=newString+'<br>'
 +
        }
 +
 +
        myWindow=window.open()
 +
        myWindow.document.write(memoryPlasmidOutput)
 +
        myWindow.focus()
 +
 +
}
 +
 +
function formatPlasmidInput(backbone){
 +
        backbone = backbone.split('\n')
 +
        originBoolean = false
 +
        backboneName = ''
 +
        sequence = ''
 +
        if (backbone[0].toLowerCase().indexOf('locus') != -1){
 +
            for (i=0;i<backbone.length;i++){
 +
                if (originBoolean === true){
 +
                    if (backbone[i].indexOf('//') == -1){
 +
                      appendThis = backbone[i].replace(/[0-9]|\s|\n|\t/g,'')
 +
                      sequence = sequence+appendThis
 +
                    } else{
 +
                        originalBoolean = false
 +
                    }
 +
                }
 +
                if (backbone[i].indexOf('locus') != -1){
 +
                    backboneName = backbone[i].split(/\s+|\t+/g)[1]
 +
                }
 +
                if (backbone[i].indexOf('origin') != -1){
 +
                    originBoolean = true
 +
                }
 +
            }
 +
        } else if (backbone[0][0] == '>'){
 +
                for (i=0;i<backbone.length;i++){
 +
                    if (backbone[i][0] != '>'){
 +
                        appendThis = backbone[i].replace(/[0-9]|\s|\n|\t/g,'')
 +
                        sequence = sequence+appendThis
 +
                    } else{
 +
                        backboneName = backbone[i].replace('>','')
 +
                    }
 +
                }
 +
        }
 +
        memoryPlasmid.addFeature(1,sequence.length,'Backbone',sequence,backboneName,'')
 +
        return sequence
 +
}
 +
 +
function feature(start,end,type,sequence,description,featureObject){
 +
this.start = start;
 +
this.end = end;
 +
this.type = type;
 +
    this.sequence = sequence;
 +
    this.description = description;
 +
this.featureObject = featureObject
 +
}
 +
 +
var restrictionPlasmid = {
 +
backboneName : '',
 +
dna : '',
 +
features : {},
 +
    setBackboneName : function(backboneName){
 +
        restrictionlasmid.backboneName = backboneName
 +
    },
 +
setDNA : function(dna){
 +
restrictionPlasmid.dna = dna
 +
},
 +
addFeature : function(start,end,type,sequence,description){
 +
restrictionPlasmid.features[start] = new feature(start,end,type,sequence,description)
 +
},
 +
addRecognitionAreaObject : function(zfTarget,mtaseTarget){
 +
 +
recognitionPlasmid.zfTarget = zfTarget
 +
recognitionPlasmid.mtaseTarget = mtaseTarget
 +
}
 +
}
 +
 +
var memoryPlasmid = {
 +
    backboneName : '',
 +
dna : '',
 +
features : {},
 +
memoryObjects : {},
 +
    setBackboneName : function(backboneName){
 +
        memoryPlasmid.backboneName = backboneName
 +
    },
 +
setDNA : function(dna){
 +
memoryPlasmid.dna = dna
 +
},
 +
addMemoryObject : function(sensor,rbs,zincFinger,linker,mycTag,methyltransferase,terminator){
 +
memoryObject = new Object()
 +
memoryObject.sensor = sensor
 +
memoryObject.rbs = rbs
 +
memoryObject.zincFinger = zincFinger
 +
memoryObject.linker = linker
 +
memoryObject.mycTag = mycTag
 +
memoryObject.methyltransferase = methyltransferase
 +
memoryObject.terminator = terminator
 +
    memoryPlasmid.memoryObjects[sensor.start] = memoryObject
 +
},
 +
addFeature : function(start,end,type,sequence,description){
 +
memoryPlasmid.features[start] = new feature(start,end,type,sequence,description)
 +
}
 +
}
 +
 +
function sensorObject(name,sequence){
 +
        this.name = name
 +
        this.sequence = sequence
 +
 +
}
 +
     
 +
function formatSensors(sensors){
 +
        sensorArray = new Array()
 +
        if (sensors.indexOf('LOCUS') != -1){
 +
            sensors = sensors.split('LOCUS')
 +
            sensors.reverse().pop()
 +
            for (i=0;i<sensors.length;i++){
 +
                originBoolean = false
 +
                sensorName = ''
 +
                sequence = ''
 +
                sensor = sensors[i].split('\n')
 +
                for (j=0;j<sensor.length;j++){
 +
                    if (j===0){
 +
                        sensorName = sensor[j]
 +
                    }
 +
                    if (originBoolean === true){
 +
                        if (sensor[j].indexOf('//') == -1){
 +
                            appendThis = sensor[j].replace(/[0-9]|\s|\n|\t/g,'')
 +
                            sequence += appendThis
 +
                        } else {
 +
                            originBoolean = false
 +
                        }
 +
                    }
 +
                    if (sensor[j].indexOf('ORIGIN') != -1){
 +
                        originBoolean = true
 +
                    }
 +
                }
 +
                sensorArray[i] = new sensorObject(sensorName,sequence)
 +
            }
 +
        } else if (sensors[0] == '>'){
 +
            sensors = sensors.split('//')
 +
            sensors.pop()
 +
            sensorName = ''
 +
            for (i=0;i<sensors.length;i++){
 +
                sensor = sensors[i].split('\n')
 +
                sequence = ''
 +
                for (j=0;j<sensor.length;j++){
 +
                    if (sensor[j][0] != '>'){
 +
                        appendThis = sensor[j].replace(/[0-9]|\s|\n|\t/g,'')
 +
                        sequence = sequence+appendThis
 +
                    } else if (sensor[j][0] == '>'){
 +
                        sensorName = sensor[j].replace('>','')
 +
                    } 
 +
                }
 +
                sensorArray[i] = new sensorObject(sensorName,sequence)
 +
            }
 +
        }
 +
        return sensorArray
 +
}
 +
 +
function formatPartsregistryPromoters(){
 +
        promoters = new Array()
 +
        $("input:checkbox[name=promoter]:checked").each(function(){
 +
            promoter = $(this).val().split(':')
 +
            promoters.push(new sensorObject(promoter[0],promoter[2]))
 +
        })
 +
        return promoters
 +
}
 +
 +
function configuratePlasmid(sensorArray,number){
 +
memoryPlasmid.features = {}
 +
memoryPlasmid.memoryObjects = {}
 +
        backbone = document.plasmidForm.plasmid.value.toLowerCase()
 +
        methyltransferases = getMethyltransferases()
 +
        zincFingers = getZincFingers()
 +
        linkers = getLinkers()
 +
        mycTags = getMycTags()
 +
        rbs = getRBS()
 +
        terminators = getTerminators()
 +
        plasmidSequence = formatPlasmidInput(backbone)
 +
        memoryPlasmid.setDNA(plasmidSequence)
 +
        for (i=0;i<sensorArray.length;i++){
 +
    featureArray = new Array()
 +
featureArray[0] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+sensorArray[i].sequence.length,'Sensor',sensorArray[i].sequence,sensorArray[i].name,sensorArray[i])
 +
            memoryPlasmid.setDNA(memoryPlasmid.dna+sensorArray[i].sequence)
 +
            j = Math.floor((Math.random()*rbs.length))
 +
            featureArray[1] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+rbs[j].sequence.length,'RBS',rbs[j].sequence,rbs[j].description,rbs[j])
 +
            memoryPlasmid.setDNA(memoryPlasmid.dna+rbs[j].sequence+randomDNA(3))
 +
            memoryPlasmid.setDNA(memoryPlasmid.dna+'atg'+randomDNA(10))
 +
            for (j=0;j<zincFingers.length;j++){
 +
                if (checkOccurrence(zincFingers[j].target.toLowerCase(),memoryPlasmid.dna) === true || checkOccurrence(zincFingers[j].sequence.toLowerCase(),memoryPlasmid.dna) === true){
 +
                    continue
 +
                } else{
 +
                    featureArray[2] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+zincFingers[j].sequence.length,'Zinc Finger',zincFingers[j].sequence,'Zinc Finger '+zincFingers[j].description.split('|')[0],zincFingers[j])
 +
                    memoryPlasmid.setDNA(memoryPlasmid.dna+zincFingers[j].sequence)
 +
                    break
 +
                }
 +
            }
 +
            j = Math.floor((Math.random()*linkers.length))
 +
            featureArray[3] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+linkers[j].sequence.length,'Linker',linkers[j].sequence,linkers[j].description,linkers[j])
 +
    memoryPlasmid.setDNA(memoryPlasmid.dna+linkers[j].sequence)
 +
            j = Math.floor((Math.random()*mycTags.length))
 +
            featureArray[4] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+mycTags[j].sequence.length,'Myc Tag',mycTags[j].sequence,mycTags[j].description,mycTags[j])
 +
    memoryPlasmid.setDNA(memoryPlasmid.dna+mycTags[j].sequence)
 +
            j = Math.floor((Math.random()*methyltransferases.length))
 +
    featureArray[5] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+methyltransferases[j].sequence.length,'Methyltransferase',methyltransferases[j].sequence,methyltransferases[j].description,methyltransferases[j])
 +
            memoryPlasmid.setDNA(memoryPlasmid.dna+methyltransferases[j].sequence)
 +
            j = Math.floor((Math.random()*terminators.length))
 +
            featureArray[6] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+terminators[j].sequence.length,'Terminator',terminators[j].sequence,terminators[j].description,terminators[j])
 +
    memoryPlasmid.setDNA(memoryPlasmid.dna+terminators[j].sequence+randomDNA(10))
 +
            memoryPlasmid.addMemoryObject(featureArray[0],featureArray[1],featureArray[2],featureArray[3],featureArray[4],featureArray[5],featureArray[6])
 +
}
 +
restrictionPlasmid.setDNA(memoryPlasmid.features[1].sequence)
 +
for (item in memoryPlasmid.memoryObjects){
 +
featureArray = new Array()
 +
mtaseStart = restrictionPlasmid.dna.length+1
 +
mtaseEnd = restrictionPlasmid.dna.length+memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target.length
 +
mtaseType = 'Restriction Site'
 +
mtaseTarget = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target.toLowerCase()
 +
mtaseDescription = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.description+' restriction site'
 +
featureArray[0] = new feature(mtaseStart,mtaseEnd,mtaseType,mtaseTarget,mtaseDescription)
 +
restrictionPlasmid.setDNA(restrictionPlasmid.dna+mtaseTarget)
 +
zfStart = restrictionPlasmid.dna.length+1
 +
zfEnd = restrictionPlasmid.dna.length+memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target.length
 +
zfType = 'Restriction Site'
 +
zfTarget = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target
 +
zfDescription = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.description+' restriction site'
 +
featureArray[1] = new feature(zfStart,zfEnd,zfType,zfTarget,zfDescription)
 +
restrictionPlasmid.setDNA(restrictionPlasmid.dna+mtaseTarget)
 +
restrictionPlasmid.mtaseTarget = featureArray[0]
 +
restrictionPlasmid.zfTarget = featureArray[1]
 +
}
 +
json = createJSONMemory(number)
 +
//genbankMemory()
 +
$('#visualizationButtons').append('<input type="hidden" name="json'+number+'" value="'+escape(JSON.stringify(json))+'"/><input class="submit" type="submit" value="Memory Plasmid '+(number+1)+'" onclick="visualization('+number+');return false"/>');
 +
}
 +
function setup(){
function setup(){
-
                document.write('check')
 
$('#visualizationButtons').empty()
$('#visualizationButtons').empty()
$('#infovis').empty()
$('#infovis').empty()
Line 11: Line 686:
sensors = document.plasmidForm.sensors.value.toLowerCase()
sensors = document.plasmidForm.sensors.value.toLowerCase()
sensorArray = formatSensors(sensors)
sensorArray = formatSensors(sensors)
-
                promoters = formatPartsregistryPromoters()
+
        promoters = formatPartsregistryPromoters()
         sensorArray = promoters.concat(sensorArray)
         sensorArray = promoters.concat(sensorArray)
tempArray = new Array()
tempArray = new Array()
Line 21: Line 696:
j++
j++
if (j%5 === 0){
if (j%5 === 0){
-
    if (j !== 0){
+
    if ( j !== 0){
configuratePlasmid(tempArray,number)
configuratePlasmid(tempArray,number)
number++
number++
Line 59: Line 734:
$('#visualizationButtons').append('<input type="hidden" name="json-1" value="'+escape(JSON.stringify(json))+'"/><input class="submit" type="submit" value="Restriction Plasmid" onclick="visualization(-1);return false"/>');
$('#visualizationButtons').append('<input type="hidden" name="json-1" value="'+escape(JSON.stringify(json))+'"/><input class="submit" type="submit" value="Restriction Plasmid" onclick="visualization(-1);return false"/>');
$('#readout').append('<input type="textfield" name="readout" value=""/><input class="submit" type="submit" value="Submit" onClick="getReadout();return false"/>');
$('#readout').append('<input type="textfield" name="readout" value=""/><input class="submit" type="submit" value="Submit" onClick="getReadout();return false"/>');
 +
}
 +
 +
function getReadout(){
 +
inputArray = new Array()
 +
json = JSON.parse(unescape($(':input[name=json-1]').val()))
 +
inputs = $(':input[name=readout]').val()
 +
inputArray = inputs.split(',')
 +
totalLength = json.children[0].data.length
 +
uncutArray = new Array()
 +
i = 0
 +
for (child in json.children){
 +
totalLength+=json.children[child].data.length
 +
if (json.children[child].data.description.indexOf('Methyltransferase') != -1){
 +
uncutArray[i] = [json.children[child].id,totalLength]
 +
i++
 +
}
 +
}
 +
bandsArray = new Array ()
 +
j = 0
 +
for (item in uncutArray){
 +
i = 0
 +
tempBandArray = new Array()
 +
tempBandArray[i] = [uncutArray[item][1],uncutArray[item][0]]
 +
i++
 +
for (bandArray in bandsArray){
 +
for (band in bandsArray[bandArray]){
 +
tempBandArray[i] = [uncutArray[item][1] - bandsArray[bandArray][band][0],uncutArray[item][0]]
 +
i++
 +
}
 +
}
 +
bandsArray[j] = tempBandArray
 +
j++
 +
}
 +
matchingBands = new Array()
 +
i = 0
 +
for (input in inputArray){
 +
difference = 100000000000
 +
bandSize = inputArray[input]
 +
for (bandArray in bandsArray){
 +
for (band in bandsArray[bandArray]){
 +
if (bandSize > bandsArray[bandArray][band][0]){
 +
tempDifference = bandSize - bandsArray[bandArray][band][0]
 +
} else{
 +
tempDifference = bandsArray[bandArray][band][0] - bandSize
 +
}
 +
if (tempDifference < difference){
 +
matchingBand = bandsArray[bandArray][band][1]
 +
difference = tempDifference
 +
}
 +
}
 +
}
 +
matchingBands[i] = matchingBand
 +
i++
 +
}
 +
i = 0
 +
sensedSignals = new Array()
 +
for (matchingBand in matchingBands){
 +
for (child in json.children){
 +
if (json.children[child].id == matchingBands[matchingBand]){
 +
sensedSignals[i] = json.children[child].data.sensor
 +
i++
 +
}
 +
}
 +
}
 +
for (signal in sensedSignals){
 +
$('#readout').append('<br>'+sensedSignals[signal])
 +
}
 +
}
 +
 +
function createJSONRestriction(targetSites){
 +
json = {
 +
      "children": [],
 +
      "data": {
 +
        "$type": "none",
 +
      },
 +
      "id": "Source",
 +
      "name": "Restriction Plasmid"
 +
    };
 +
 +
json.children[0] = {}
 +
json.children[0].data = {}
 +
json.children[0].data.description = memoryPlasmid.features[1].description
 +
json.children[0].data.$color = '#B2ABF4'
 +
json.children[0].data.length = memoryPlasmid.features[1].end - memoryPlasmid.features[1].start
 +
json.children[0].data.$angularWidth = 1000
 +
json.children[0].data.type = memoryPlasmid.features[1].type
 +
json.children[0].data.dna = memoryPlasmid.dna
 +
json.children[0].children = []
 +
json.children[0].name = memoryPlasmid.features[1].description
 +
json.children[0].id = memoryPlasmid.features[1].description
 +
totalLength = memoryPlasmid.dna.length
 +
i = 1
 +
for (item in targetSites){
 +
site = targetSites[item]
 +
json.children[i] = {}
 +
json.children[i].data = {}
 +
json.children[i].children = []
 +
json.children[i].data.description = '120bp random DNA'
 +
json.children[i].data.$color = '#FFFF00'
 +
json.children[i].data.length = 120
 +
json.children[i].data.$angularWidth = 1000
 +
json.children[i].data.dna = randomDNA(120+i*10)
 +
json.children[i].name = '120bp DNA'
 +
json.children[i].id = i
 +
i++
 +
json.children[i] = {}
 +
json.children[i].data = {}
 +
json.children[i].children = []
 +
json.children[i].data.description = site.zincFingerDescription
 +
json.children[i].data.$color = '#FF0000'
 +
json.children[i].data.length = site.zincFingerLength
 +
json.children[i].data.$angularWidth = 1000
 +
json.children[i].data.dna = site.zincFinger
 +
json.children[i].name = site.zincFingerDescription.split('|')[0]+'|'+site.zincFingerDescription.split('|')[1]
 +
json.children[i].id = i
 +
i++
 +
json.children[i] = {}
 +
json.children[i].data = {}
 +
json.children[i].children = []
 +
json.children[i].data.description = '120bp random DNA'
 +
json.children[i].data.$color = '#FFFF00'
 +
json.children[i].data.length = 120
 +
json.children[i].data.$angularWidth = 1000
 +
json.children[i].data.dna = randomDNA(120)
 +
json.children[i].name = '120bp DNA'
 +
json.children[i].id = i
 +
i++
 +
json.children[i] = {}
 +
json.children[i].data = {}
 +
json.children[i].children = []
 +
json.children[i].data.description = 'Methyltransferase: '+site.methyltransferaseDescription
 +
json.children[i].data.$color = '#0000CD'
 +
json.children[i].data.length = site.methyltransferaseLength
 +
json.children[i].data.$angularWidth = 1000
 +
json.children[i].data.dna = site.methyltransferase
 +
json.children[i].data.sensor = site.sensor
 +
json.children[i].name = site.methyltransferaseDescription.split('|')[0]
 +
json.children[i].id = i
 +
i++
 +
json.children[i] = {}
 +
json.children[i].data = {}
 +
json.children[i].children = []
 +
json.children[i].data.description = '120bp random DNA'
 +
json.children[i].data.$color = '#FFFF00'
 +
json.children[i].data.length = 120
 +
json.children[i].data.$angularWidth = 1000
 +
json.children[i].data.dna = randomDNA(120)
 +
json.children[i].name = '120bp DNA'
 +
json.children[i].id = i
 +
i++
 +
json.children[i] = {}
 +
json.children[i].data = {}
 +
json.children[i].children = []
 +
json.children[i].data.description = site.zincFingerDescription
 +
json.children[i].data.$color = '#FF0000'
 +
json.children[i].data.length = site.zincFingerLength
 +
json.children[i].data.$angularWidth = 1000
 +
json.children[i].data.dna = site.zincFinger
 +
json.children[i].name = site.zincFingerDescription.split('|')[0]+'|'+site.zincFingerDescription.split('|')[1]
 +
json.children[i].id = i
 +
i++
 +
}
 +
return json
 +
}
 +
 +
function createJSONMemory(number){
 +
var json = {}
 +
json = {
 +
      "children": [],
 +
      "data": {
 +
        "$type": "none",
 +
      },
 +
      "id": "Source",
 +
      "name": "Memory Plasmid"
 +
    };
 +
 +
json.children[0] = {}
 +
json.children[0].data = {}
 +
json.children[0].data.description = memoryPlasmid.features[1].description
 +
json.children[0].data.$color = '#B2ABF4'
 +
json.children[0].data.length = memoryPlasmid.features[1].end - memoryPlasmid.features[1].start
 +
json.children[0].data.$angularWidth = 1000
 +
json.children[0].data.type = memoryPlasmid.features[1].type
 +
json.children[0].data.dna = memoryPlasmid.dna
 +
json.children[0].children = []
 +
json.children[0].name = memoryPlasmid.features[1].description
 +
json.children[0].id = memoryPlasmid.features[1].description
 +
    i = 1
 +
    for (memoryObject in memoryPlasmid.memoryObjects){
 +
for (item in memoryPlasmid.memoryObjects[memoryObject]){
 +
json.children[i] = {}
 +
json.children[i].children = []
 +
json.children[i].data = {}
 +
json.children[i].data.description = memoryPlasmid.memoryObjects[memoryObject][item].description
 +
type = memoryPlasmid.memoryObjects[memoryObject][item].type
 +
if (type == 'Sensor'){
 +
color = '#00FFFF'
 +
} else if (type == 'RBS'){
 +
color = '#FFFF00'
 +
} else if (type == 'Zinc Finger'){
 +
color = '#800080'
 +
} else if (type == 'Linker'){
 +
color = '#00FF00'
 +
} else if (type == 'Myc Tag'){
 +
color = '#FF00FF'
 +
} else if (type == 'Methyltransferase'){
 +
color = '#FFA500'
 +
} else if (type == 'Terminator'){
 +
color = '#FF0000'
 +
} else{
 +
color = '#B2ABF4'
 +
}
 +
json.children[i].data.$color = color
 +
json.children[i].data.length = memoryPlasmid.memoryObjects[memoryObject][item].end - memoryPlasmid.memoryObjects[memoryObject][item].start
 +
json.children[i].data.$angularWidth = 1000
 +
json.children[i].data.type = type
 +
json.children[i].data.dna = memoryPlasmid.memoryObjects[memoryObject][item].sequence
 +
json.children[i].id = i
 +
if (memoryPlasmid.memoryObjects[memoryObject][item].description.length > 14){
 +
json.children[i].name = memoryPlasmid.memoryObjects[memoryObject][item].description.substring(0,14)
 +
} else{
 +
json.children[i].name = memoryPlasmid.memoryObjects[memoryObject][item].description
 +
}
 +
i++
 +
}
 +
}
 +
return json
 +
 
 +
    //end
}
}
</script>
</script>

Revision as of 19:45, 3 September 2012

Enter your plasmid in fasta or genbank format


Enter your sensors in fasta or genbank format























Retrieved from "http://2012.igem.org/Team:Amsterdam/maarten/"