Difference between revisions of "Team:Lethbridge/Software"

 
(15 intermediate revisions by 3 users not shown)
Line 4: Line 4:
 
{{Template:Lethbridge/mini-template-css}}
 
{{Template:Lethbridge/mini-template-css}}
 
<html>
 
<html>
−
<head>
 
−
    <link rel="stylesheet" type="text/css" href="default.css">
 
−
 
−
    <!-- fonts below are also referred to as a redundancy in the css file -->
 
−
    <link href="https://fonts.googleapis.com/css?family=Cabin" rel="stylesheet">
 
−
    <link href="https://fonts.googleapis.com/css?family=Lato" rel="stylesheet">
 
−
    <link href="https://fonts.googleapis.com/css?family=Signika" rel="stylesheet">
 
−
    <link href="https://fonts.googleapis.com/css?family=Alegreya+Sans" rel="stylesheet">
 
−
    <link href="https://fonts.googleapis.com/css?family=Raleway" rel="stylesheet">
 
−
</head>
 
 
<body>
 
<body>
 +
<br><br>
 +
<img src="https://static.igem.org/mediawiki/2018/5/58/T--Lethbridge--banner_Software.png" width=100% alt="Software Banner Image">
 +
<div class="content"> <!--everything added for content goes after this line CHRISISAAC-->
 +
<br><br>
 +
 +
 +
<div class="container"><div class="row"><div class="col-sm">
 +
<p class="f12">The purpose of this tool is to facilitate a match between molecular cargo and cellular target and provide a protein nanocompartment recommendation as a starting point for the design of your own VINCEnT! The tool accepts user input to specify the cellular target, molecular cargo, and approximate size of the protein nanocompartment. After submitting, a recommendation will be generated and will provide a link to a datasheet with information on the PNC.<br><br></p>
 +
    </div></div></div>
 +
 +
<div style="height: 25px;"></div>
 +
    <div class="container">
 +
  <h1>Protein Nanocompartment Designer</h1>
 +
    </div>
 +
 +
    <form> <!-- BEGIN USER INPUTS -->
 +
      <div class="container">
 +
        <div class="row">
 +
          <div class="col-sm"> <!-- Target -->
 +
            <div class="form-group">
 +
              <label for="target">Target</label>
 +
              <select class="form-control" id="target">
 +
                <option value=1>Mammal</option>
 +
                <option value=2>Bacteria</option>
 +
                <option value=3>Plant</option>
 +
              </select>
 +
            </div>
 +
        </div>
 +
          <div class="col-sm"> <!-- Size Range -->
 +
              <div class="form-group">
 +
                <label for="cargo">Size Range</label>
 +
                <select class="form-control" id="size">
 +
                  <option value="1">15-30nm</option>
 +
                  <option value="2">30-60nm</option>
 +
                  <option value="3">>60nm</option>
 +
                </select>
 +
              </div>
 +
          </div>
 +
        </div>
 +
        <div class="row">
 +
          <div class="col-sm"> <!-- Cargo Sequence -->
 +
            <div class="form-group">
 +
                <label for="sequence">Cargo Sequence</label>
 +
                <input type="text" class="form-control" id="sequence" placeholder="Sequence in FASTA format">
 +
            </div>
 +
          </div>
 +
        </div>
 +
        <!-- Submit button activates the JS -->
 +
        <button onclick="submitData()" type="button" class="btn btn-primary">Submit</button>
 +
        <script>
 +
        function submitData() { //MAIN FUNCTION CALLS ALL
 +
          data = getValues(); //Extract from the HTML forms
 +
          code = pickPNC(data.sequenceType, data.targetType, data.sizeType); //What PNC suits the user needs?
 +
          showhide();
 +
          writeProtocols(code);
 +
        }
 +
 +
        function showhide() {
 +
            var x = document.getElementById("recommend");
 +
            if (x.style.display === "none") {
 +
                x.style.display = "block";
 +
            } else {
 +
                x.style.display = "block";
 +
            }
 +
        }
 +
 +
        function getValues() { //Extract Values from the Form
 +
            var target = document.getElementById('target').value;
 +
            var size = document.getElementById('size').value;
 +
            var sequence = sequenceCheck(document.getElementById('sequence').value);
 +
            var userInput = {
 +
              targetType:target,
 +
              sizeType:size,
 +
              sequenceType:sequence
 +
            };
 +
            return userInput
 +
        }
 +
 +
        function pickPNC(a, b, c) { // CargoSeq - Target - Size
 +
          const PNC = {
 +
            1: { //Protein
 +
              1: { // Mammal
 +
                1: "NONE", // S  111
 +
                2: "NONE", // M  112
 +
                3: "NONE"  // L  113
 +
              },
 +
              2: { // Bacteria
 +
                1: "MS2", // S  121
 +
                2: "NONE", // M  122
 +
                3: "P22"  // L  123
 +
              },
 +
              3: { // Plant
 +
                1: "BMV", // S  131
 +
                2: "NONE", // M  132
 +
                3: "NONE"  // L  133
 +
              }
 +
            },
 +
 +
            2: { //DNA
 +
              1: { // Mammal
 +
                1: "NONE", // S  211
 +
                2: "JCV", // M  212
 +
                3: "NONE"  // L  213
 +
              },
 +
              2: { // Bacteria
 +
                1: "VP8", // S  221
 +
                2: "NONE", // M  222
 +
                3: "P22"  // L  223
 +
              },
 +
              3: { // Plant
 +
                1: "NONE", // S  231
 +
                2: "NONE", // M  232
 +
                3: "NONE"  // L  233
 +
              }
 +
            },
 +
 +
            3: { //RNA
 +
              1: { // Mammal
 +
                1: "NONE", // S  311
 +
                2: "ARC", // M  312
 +
                3: "NONE"  // L  313
 +
              },
 +
              2: { // Bacteria
 +
                1: "PDE2", // S  321
 +
                2: "NONE", // M  322
 +
                3: "NONE"  // L  323
 +
              },
 +
              3: { // Plant
 +
                1: "CCMV", // S  331
 +
                2: "NONE", // M  332
 +
                3: "NONE"  // L  333
 +
              }
 +
            }
 +
          };
 +
          return PNC[a][b][c] //Returns the PNC Code
 +
        }
 +
 +
        function sequenceCheck(sequence) { //REGEX for Type
 +
          var PRO = /^[GALMFWKQESPVICYHRNDT]+$/gmi //Code 1
 +
          var DNA = /^[ATCG]+$/gmi //Code 2
 +
          var RNA = /^[AUCG]+$/gmi //Code 3
 +
          //Testing
 +
          if (RNA.test(sequence)) {
 +
            result = 3;
 +
          } else if (DNA.test(sequence)) {
 +
            result = 2;
 +
          } else if (PRO.test(sequence)) {
 +
            result = 1;
 +
          } else {
 +
            result = 1;
 +
          }
 +
          //Return result
 +
          return result
 +
        }
 +
 +
        function writeProtocols(code) {
 +
          const dataSheet = {
 +
            MS2: {
 +
              name: "MS2",
 +
              full: "Bacteriophage MS2 Capsid",
 +
              sequence: "MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY",
 +
              pdb: "1MSC",
 +
              radius: "Outer: 27nm Inner: 15nm",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/f/f2/T--Lethbridge--MS2_VLP_datasheet.pdf"
 +
            },
 +
            FF: {
 +
              name: "FF",
 +
              full: "E.coli Filementus Phage Capsid",
 +
              sequence: "MKKLLFAIPLVVPFYSHSAETVESCLAKPHTENSFTNVWKDDKTLDRYANYEGCLWNATGVVVCTGDETQCYGTWVPIGLAIPENEGGGSEGGGSEGGGSEGGGTKPPEYGDTPIPGYTYINPLDGTYPPGTEQNPANPNPSLEESQPLNTFMFQNNRFRNRQGALTVYTGTVTQGTDPVKTYYQYTPVSSKAMYDAYWNGKFRDCAFHSGFNEDPFVCEYQGQSSDLPQPPVNAGGGSGGGSGGGSEGGGSEGGGSEGGGSEGGGSGGGSGSGDFDYEKMANANKGAMTENADENALQSDAKGKLDSVATDYGAAIDGFIGDVSGLANGNGATGDFAGSNSQMAQVGDGDNSPLMNNFRQYLPSLPQSVECRPYVFGAGKPYEFSIDCDKINLFRGVFAFLLYVATFMYVFSTFANILRNKES",
 +
              pdb: "P03661",
 +
              radius: "So many nm",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/c/ce/T--Lethbridge--Ff_phage_datasheet.pdf"
 +
            },
 +
            P22: {
 +
              name: "P22",
 +
              full: "Bacteriophage P22 Capsid",
 +
              sequence: "atggctttgaacgaaggtcaaattgttacactggcggtagatgaaatcatcgaaaccatctccgcaatcactccaatggcgcagaaagccaagaaatacaccccgcctgctgcttctatgcagcgctccagcaataccatctggatgcctgtagagcaagagtcacccactcaggagggctgggatttaactgataaagcgacagggttactggaacttaacgtcgcggtaaacatgggagagccggataacgacttcttccagttgcgtgctgatgacttgcgagacgaaactgcgtatcgtcgccgcatccagtctgccgctcgcaagctggcgaacaacgttgagttgaaagtcgcaaacatggccgccgagatgggttcgctggttatcacctcccctgatgccatcggcactaataccgcagacgcctggaactttgtggccgacgcagaagaaatcatgttctcccgcgaacttaacccgacatggggacatcgtacttcttcaaccctcaggactacaaaaaagcgggttacgacctgaccaagcgtgacatcttcgggcgtattcctgaagaagcataccgagatggcaccattcagcgtcaggtcgctggcttcgatgatgtcctgcgctctccgaaacttcctgtgctgaccaaatccaccgcaactggcatcactgtatccggtgcgcagtccttcaagcctgtcgcatggcaactggataacgatggcaacaaagttaacgttgataaccgttttgctaccgtcaccctgtctgcaactaccggcatgaaacgcggcgacaaaatttcgtttgctggcgttaagttccttggtcagatggctaagaacgtactggctcaggatgcgactttctccgtagtccgcgttgttgacggtactcatgttgaaatcacgccgaagccggtagcgctggatgatgtttccctgtctccggagcgcgtgcctacgccaacgttaacacctcgctggctgatgcaatggcagtgaacattctgaacgttaaagacgctcgcactaatgtgttctgggctgacgatgctattcgtatcgtgtctcagccgattccggctaaccatgaactttttgcaggtatgaaaactacctcattcagcatccctgatgttggcctgaacggtatcttcgctacgcagggtgatatttccaccctgtccggcctgtgccgtattgcgctgtggtacggcgtaaacgcgacacgaccggaggcaatcggtgttggcctgcctggtcagactgcg",
 +
              pdb: "",
 +
              radius: "60nm",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/b/b2/T--Lethbridge--P22_VLP_datasheet.pdf"
 +
            },
 +
            CCMV: {
 +
              name: "CCMV",
 +
              full: "Cowpea Chlorotic Mottle Virus Capsid",
 +
              sequence: "MSTVGTGKLTRAQRRAAARKNKRNTRVVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY",
 +
              pdb: "P03601",
 +
              radius: "Outer: 24nm, Inner: 18nm",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/d/df/T--Lethbridge--CCMV_data_datasheet.pdf"
 +
            },
 +
            BMV: {
 +
              name: "BMV",
 +
              full: "Brome Mosaic Virus Capsid",
 +
              sequence: "MSTSGTGKMTRAQRRAAARRNRWTARVQPVIVEPLAAGQGKAIKAIAGYSISKWEASSDAITAKATNAMSITLPHELSSEKNKELKVGRVLLWLGLLPSVAGRIKACVAEKQAQAEAAFQVALAVADSSKEVVAAMYTDAFRGATLGDLLNLQIYLYASEAVPAKAVVVHLEVEHVRPTFDDFFTPVYR",
 +
              pdb: "P03602",
 +
              radius: "30nm",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/5/5e/T--Lethbridge--BMV_VLP_datasheet.pdf"
 +
            },
 +
            VP8: {
 +
              name: "VP1/VP8",
 +
              full: "Murine Polyomarius Capsid",
 +
              sequence: "APKRKAGVSKCETKCTKACPRPAPVPKLLIKGGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVKNPYPMASLISSLFNNMLPQVQGQPMEGENTQVEEVRVYDGTEPVPGDPDMTRYVDRFGKTKTVFPGN",
 +
              pdb: "P11196",
 +
              radius: "",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/b/b6/T--Lethbridge--VP1-VP8_VLP_datasheet.pdf"
 +
            },
 +
            JCV: {
 +
              name: "JCV",
 +
              full: "John Cunningham Virus (Similar to SV40)",
 +
              sequence: "MAPTKRKGERKDPVQVPKLLIRGGVEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQWRGLSRYFKVQLRKRRVKNPYPISFLLTDLINRRTPRVDGQPMYGMDAQVEEVRVFEGTEELPGDPDMMRYVDKYGQLQTKML",
 +
              pdb: "",
 +
              radius: "45nm",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/b/b7/T--Lethbridge--JCV_VLP_datasheet.pdf"
 +
            },
 +
            PDE2: {
 +
              name: "PDE2",
 +
              full: "Pyruvate Dehydrogenase Complex",
 +
              sequence: "MAFEFKLPDIGEGIHEGEIVKWFVKPGDEVNEDDVLCEVQNDKAVVEIPSPVKGKVLEILVPEGTVATVGQTLITLDAPGYENMTFKGQEQEEAKKEEKTETVSKEEKVDAVAPNAPAAEAEAGPNRRVIAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDAFLAGGAKPAPAAAEEKAAPAAAKPATTEGEFPETREKMSGIRRAIAKAMVHSKHTAPHVTLMDEADVTKLVAHRKKFKAIAAEKGIKLTFLPYVVKALVSALREYPVLNTSIDDETEEIIQKHYYNIGIAADTDRGLLVPVIKHADRKPIFALAQEINELAEKARDGKLTPGEMKGASCTITNIGSAGGQWFTPVINHPEVAILGIGRIAEKPIVRDGEIVAAPMLALSLSFDHRMIDGATAQKALNHIKRLLSDPELLLMEA",
 +
              pdb: "P11961",
 +
              radius: "24nm",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/1/1f/T--Lethbridge--PDE2_VLP_datasheet.pdf"
 +
            },
 +
            ARC: {
 +
              name: "Arc-Gag",
 +
              full: "Arc-Gag",
 +
              sequence: "AUG",
 +
              pdb: "P12497",
 +
              radius: "30nm",
 +
              error: "able",
 +
              protocol: "https://static.igem.org/mediawiki/2018/e/e2/T--Lethbridge--Arc-Gag_VLP_datasheet.pdf"
 +
            },
 +
            NONE: {
 +
              name: "None",
 +
              full: "a protein nanocompartment",
 +
              sequence: "CCTGGTGTGGATACACAGATCTTCGAGGACCCACGGGAGTTCCTGAGCCACCTGGAAGAGTACCTGCGGCAGGTGGGTGGCTCTGAAGAATATTGGCTGTCCCAGATCCAGAACCACATGAATGGGCCAGCCAAGAAGTGGTGGGAGTTCAAGCAGGGCTCGGTGAAGAACTGGGTGGAGTTCAAGAAGGAGTTTCTGCAATACAGTGAGGGTACACTCTCCCGTGAAGCCATTCAGCGGGAGCTGGAGCTGCCGCAGAAGCAGGGTGAACCACTCGACCAGTTCCTCTGGCGCAAGCGGGACCTGTACCAGACACTGTATGTGGACGCTGAGGAGGAGGAGATCATTCAGTATGTGGTGGGCACCCTGCAGCCCAAACTCAAGCGCTTTCTGCGCCACCCACTCCCCAAGACCCTGGAGCAGCTTATCCAGAGGGGTATGGAAGTGCAGGACGGCCTGGAGCAGGCAGCTGAGCCTTCTGGCACCCCACTG",
 +
              pdb: "",
 +
              radius: "",
 +
              error: "unable",
 +
              protocol: ""
 +
            }
 +
          }
 +
          //Change the HTML Content
 +
          document.getElementById('pnc_code').innerHTML = "Result: " + dataSheet[code].name;
 +
          document.getElementById('pnc_error').innerHTML = dataSheet[code].error;
 +
          document.getElementById('pnc_full').innerHTML = dataSheet[code].full;
 +
          document.getElementById("pnc_download").href= dataSheet[code].protocol;
 +
          document.getElementById("pnc_download").download= dataSheet[code].name + "_datasheet.pdf";
 +
          //
 +
          //
 +
          //
 +
        }
 +
 +
        </script>
 +
      </div>
 +
    </form>
 +
 +
    <!-- Spacing for the Results -->
 +
    <div style="height: 25px;"></div>
 +
    <hr />
 +
    <div style="height: 25px;"></div>
  
 +
    <!-- RESULTS RETURNED -->
 +
    <div class="container" id="recommend" style="display: none;">
 +
      <div class="row">
 +
        <div class="col-sm">
 +
          <h2 id="pnc_code"></h2>
 +
          <p class="f12">Based on your input we were
 +
            <a id="pnc_error"></a> to recommend
 +
            <a id="pnc_full"></a>
 +
            for your application.
 +
          </p>
 +
          <p class="f11">
 +
            Remember, biology is a cooperative endeavour. When people aren't careful with the biology they do, it can have long lasting effects on everyone else. Accordingly, you should be very careful about encapsulating nucleic acids that are able to self-replicate or integrate into a genome. Ideally, a PNC should be used to carry single-use cargo. For instance, encapsulating a gene drive or other heritable element is strongly discouraged.
 +
          </p>
 +
        </div>
 +
      </div>
 +
      <div class="row">
 +
        <div class="col-sm">
 +
          <a href="" download="" id="pnc_download">
 +
            <button type="button" class="btn btn-primary">Download</button>
 +
          </a>
 +
        </div>
 +
      </div>
 +
    </div>
  
 +
</div> <!--this closes off the content div CHRISISAAC-->
 
</body>
 
</body>
 
</html>
 
</html>

Latest revision as of 02:44, 18 October 2018



Software Banner Image


The purpose of this tool is to facilitate a match between molecular cargo and cellular target and provide a protein nanocompartment recommendation as a starting point for the design of your own VINCEnT! The tool accepts user input to specify the cellular target, molecular cargo, and approximate size of the protein nanocompartment. After submitting, a recommendation will be generated and will provide a link to a datasheet with information on the PNC.

Protein Nanocompartment Designer