E. coli genotypes/Exhibit: Difference between revisions

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This is a demo of [http://simile.mit.edu/exhibit/ Exhibit]. It only includes some of the data from [[E. coli genotypes]].
<exhibit>
  <source id="ecoligenotypes"
          columns="label,description,genotype,parent,requires,resistance,purpose,inducible,lambda"
          type="Strain" label="Strain" pluralLabel="Strains"
          />
  <facet facetClass="TextSearch" facetLabel="Search"/>
  <facet expression=".genotype" />
  <facet expression=".purpose" />
  <facet expression=".resistance" />
  <facet expression=".requires" />
  <view viewClass="Tabular"
        label="Table"
        columns=".label, .genotype, .parent, .purpose"
        sortColumn="0"
        />
</exhibit>
{|id="ecoligenotypes" border=1
|-
!Strain
!Description
!Genotype
!Parent
!Requires
!Resistance
!Purpose
!Inducible
!Lambda
|-
|AG1
|
|endA1;recA1;gyrA96;thi-1;relA1;glnV44;hsdR17(rK- mK+)
|
|thiamine
|nalidixic acid
|cloning
|-
|BL21(DE3)
|
|F-;ompT;gal;dcm;lon;hsdSB(rB- mB-);lacIq;lambda;lacUV5-T7 gene 1;ind1;sam7;nin5
|B834
|
|
|protein expression
|T7 RNA polymerase
|prophage
|-
|BL21(DE3) pLysS
|The pLysS plasmid (with chloramphenicol resistance) encodes T7 phage lysozyme, an inhibitor for T7 polymerase which reduces and almost eliminates expression from transformed T7 promoter containing plasmids when not induced.
|F-;ompT;gal;dcm;lon;hsdSB(rB- mB-);lacIq;lambda;lacUV5-T7 gene 1;ind1;sam7;nin5;pLysS(cmR)
|BL21(DE3)
|
|chloramphenicol
|protein expression
|T7 RNA polymerase
|prophage
|}
<html>
<html>
  <table width="100%">
      <tr valign="top">
          <td>
              <div id="exhibit-control-panel"></div>
              <div id="exhibit-view-panel"></div>
          </td>
          <td width="25%">
            <div id="exhibit-browse-panel" ex:facets=".purpose, .resistance, .requires, .lactose, .arabinose, .stopcodons, .Fplasmid, .lambda, .genotypetest"></div>
          </td>
      </tr>
  </table>
<script type="text/javascript">
<script type="text/javascript">
/*
var data = {
var data = {
    items : [
      [
        {
            label : "AG1",
            purpose : "cloning",
            resistance : "nalidixic acid",
            requires : "thiamine",
            stopcodons : "amber stop suppressed with glutamine",
            genotypetest : ["endA1", "recA1", "gyrA96", "thi-1", "relA1", "glnV44", "hsdR17(rK- mK+)"]
        },
        {
            label : "BL21(DE3)",
            purpose : "protein expression",
            Fplasmid : "F-",
            lactose : "lacIq",
            inducible : "T7 RNA polymerase",
            lambda : "prophage",
            parent : "B834",
            genotype : "F- ompT gal dcm lon hsdSB(rB- mB-) lambda(DE3 [lacI lacUV5-T7 gene 1 ind1 sam7 nin5])"
        },
        {
            label : "BL21(DE3) pLysS",
            description : "The pLysS plasmid (with chloramphenicol resistance) encodes T7 phage lysozyme, an inhibitor for T7 polymerase which reduces and almost eliminates expression from transformed T7 promoter containing plasmids when not induced.",
            purpose : "protein expression",
            Fplasmid : "F-",
            lactose : "lacIq",
            resistance : "chloramphenicol",
            inducible : "T7 RNA polymerase",
            lambda : "prophage",
            parent : "BL21(DE3)",
            genotype : "F- ompT gal dcm lon hsdSB(rB- mB-) lambda(DE3) pLysS(cmR)"
        },
         {
         {
             label : "BNN93",
             label : "BNN93",
            Fplasmid : "F-",
             lambda : "no",
             lambda : "no",
             lactose : "lac permease deletion",
             requires : ["thiamine", "threonine", "leucine"],
            requires : "thiamine threonine leucine",
             genotype : ["F-", "tonA21", "thi-1", "thr-1", "leuB6", "lacY1", "glnV44", "rfbC1", "fhuA1", "mcrB", "e14-(mcrA-)", "hsdR(rKmK)", "lambda-"]
            stopcodons : "amber stop suppressed with glutamine",
             genotype : "F- tonA21 thi-1 thr-1 leuB6 lacY1 glnV44 rfbC1 fhuA1 mcrB e14-(mcrA-) hsdR(rKmK) lambda-"
         },
         },
         {
         {
Line 57: Line 74:
             lambda : "no",
             lambda : "no",
             resistance : "kanamycin",
             resistance : "kanamycin",
            lactose : "operon deleted",
             genotype : ["D(araD-araB)567", "D(lacA-lacZ)514(::kan)", "lacIp-4000(lacIq)", "lambda-", "rpoS396(Am)?", "rph-1", "D(rhaD-rhaB)568", "hsdR514"]
            arabinose : "deletion",
             genotype : "D(araD-araB)567, D(lacA-lacZ)514(::kan), lacIp-4000(lacIq), lambda-, rpoS396(Am)?, rph-1, D(rhaD-rhaB)568, hsdR514"
         },
         },
         {
         {
             label : "C600",
             label : "C600",
            Fplasmid : "F-",
             purpose : "general purpose",
             purpose : "general purpose",
             lambda : "no",
             lambda : "no",
             lactose : "lac permease deletion",
             requires : ["thiamine", "threonine", "leucine"],
            requires : "thiamine threonine leucine",
             genotype : ["F-", "tonA21", "thi-1", "thr-1", "leuB6", "lacY1", "glnV44", "rfbC1", "fhuA1", "lambda-"]
            stopcodons : "amber stop suppressed with glutamine",
             genotype : "F- tonA21 thi-1 thr-1 leuB6 lacY1 glnV44 rfbC1 fhuA1 lambda-"
         },
         },
         {
         {
             label : "C600 hflA150 (Y1073, BNN102)",
             label : "C600 hflA150 (Y1073, BNN102)",
             parent : "C600",
             parent : "C600",
            Fplasmid : "F-",
             purpose : "cDNA libraries",
             purpose : "cDNA libraries",
             lambda : "no",
             lambda : "no",
             resistance : "tetracycline",
             resistance : "tetracycline",
             lactose : "lac permease deletion",
             requires : ["thiamine", "threonine", "leucine"],
            requires : "thiamine threonine leucine",
             genotype : ["F-", "thi-1", "thr-1", "leuB6", "lacY1", "tonA21", "glnV44", "lambda-", "hflA150(chr::Tn10)"]
            stopcodons : "amber stop suppressed with glutamine",
        },
             genotype : "F- thi-1 thr-1 leuB6 lacY1 tonA21 glnV44 lambda- hflA150(chr::Tn10)"
        {
            label : "D1210",
            parent : "HB101",
            genotype : ["lacIq", "lacY+"]
        },
        {
            label : "DB3.1",
            purpose : "propagating plasmids with ccdB",
            resistance : "streptomycin",
            parent : "HB101",
            genotype : ["F-", "gyrA462", "endA1", "glnV44", "D(sr1-recA)", "mcrB", "mrr", "hsdS20(rB-, mB-)", "ara14", "galK2", "lacY1", "proA2", "rpsL20(Smr)", "xyl5", "D(leu)", "mtl1"]
        },
        {
            label : "DH1",
            purpose : "cloning",
            resistance : "nalidixic acid",
            parent : "Hoffman-Berling 1100 strain derivative",
            genotype : ["endA1", "recA1", "gyrA96", "thi-1", "glnV44", "relA1", "hsdR17(rK- mK+)", "lambda-"]
        },
        {
            label : "DH5a",
            purpose : "cloning",
            resistance : "nalidixic acid",
            parent : "DH1",
            genotype : ["F-", "endA1", "glnV44", "thi-1", "recA1", "relA1", "gyrA96", "deoR", "nupG", "phi80dlacZD(M15)", "D(lacZYA-argF)U169", "hsdR17(rK- mK+)", "lambda-"]
         },
         },
     ]
     ]
};
};
      var SimileAjax_urlPrefix = "http://static.simile.mit.edu/ajax/api/";
      var Exhibit_urlPrefix = "http://simile.mit.edu/repository/exhibit/trunk/src/webapp/api/";
      var SimileAjax_onLoad = null;
     
      /*
        *  You can optionally specify parameters:
        */
      var Exhibit_parameters = [
/*
          {  name:  "views",
              value: "timeline"
          }
*/
*/
      ];
     
      window.setTimeout(function() {
          var head = document.getElementsByTagName("head")[0];
         
          var includeScript = function(url) {
              var script = document.createElement("script");
              script.type = "text/javascript";
              script.language = "JavaScript";
              script.src = url;
              head.appendChild(script);
          }
          var includeCSS = function(url) {
              var link = document.createElement("link");
              link.setAttribute("rel", "stylesheet");
              link.setAttribute("type", "text/css");
              link.setAttribute("href", url);
              head.appendChild(link);
          }
         
          Exhibit_onLoad = function() {
              /*
                *  Include your own styles here.
                */
              // includeCSS("my-styles.css");
              SimileAjax.History.enabled = false;
              Exhibit.create(data,
                  null // the type of item to show, if there are several types in your data
              );
              /*
                *  Code that you normally put in the onLoad handler for
                *  instantiating the exhibit and loading data.
                */
          };
         
          SimileAjax_onLoad = function() {
              SimileAjax_onLoad = Exhibit_onLoad;
              includeScript(Exhibit_urlPrefix + "exhibit-api.js?bundle=false");
          };
          includeScript(SimileAjax_urlPrefix + "simile-ajax-api.js");
      }, 100);
   </script>   
   </script>   
</html>
</html>

Latest revision as of 14:49, 24 September 2007

This is a demo of Exhibit. It only includes some of the data from E. coli genotypes.

<exhibit> 

 <source id="ecoligenotypes" 
         columns="label,description,genotype,parent,requires,resistance,purpose,inducible,lambda" 
         type="Strain" label="Strain" pluralLabel="Strains" 
         />
 <facet facetClass="TextSearch" facetLabel="Search"/>
 <facet expression=".genotype" />
 <facet expression=".purpose" />
 <facet expression=".resistance" />
 <facet expression=".requires" />
 <view viewClass="Tabular"
       label="Table"
       columns=".label, .genotype, .parent, .purpose"
       sortColumn="0"
       />

</exhibit>

Strain Description Genotype Parent Requires Resistance Purpose Inducible Lambda
AG1 endA1;recA1;gyrA96;thi-1;relA1;glnV44;hsdR17(rK- mK+) thiamine nalidixic acid cloning
BL21(DE3) F-;ompT;gal;dcm;lon;hsdSB(rB- mB-);lacIq;lambda;lacUV5-T7 gene 1;ind1;sam7;nin5 B834 protein expression T7 RNA polymerase prophage
BL21(DE3) pLysS The pLysS plasmid (with chloramphenicol resistance) encodes T7 phage lysozyme, an inhibitor for T7 polymerase which reduces and almost eliminates expression from transformed T7 promoter containing plasmids when not induced. F-;ompT;gal;dcm;lon;hsdSB(rB- mB-);lacIq;lambda;lacUV5-T7 gene 1;ind1;sam7;nin5;pLysS(cmR) BL21(DE3) chloramphenicol protein expression T7 RNA polymerase prophage

<html> <script type="text/javascript"> /* var data = { 

      [
       {
           label : "BNN93",
           lambda : "no",
           requires : ["thiamine", "threonine", "leucine"],
           genotype : ["F-", "tonA21", "thi-1", "thr-1", "leuB6", "lacY1", "glnV44", "rfbC1", "fhuA1", "mcrB", "e14-(mcrA-)", "hsdR(rKmK)", "lambda-"]
       },
       {
           label : "BW26434 CGSC Strain #7658",
           lambda : "no",
           resistance : "kanamycin",
           genotype : ["D(araD-araB)567", "D(lacA-lacZ)514(::kan)", "lacIp-4000(lacIq)", "lambda-", "rpoS396(Am)?", "rph-1", "D(rhaD-rhaB)568", "hsdR514"]
       },
       {
           label : "C600",
           purpose : "general purpose",
           lambda : "no",
           requires : ["thiamine", "threonine", "leucine"],
           genotype : ["F-", "tonA21", "thi-1", "thr-1", "leuB6", "lacY1", "glnV44", "rfbC1", "fhuA1", "lambda-"]
       },
       {
           label : "C600 hflA150 (Y1073, BNN102)",
           parent : "C600",
           purpose : "cDNA libraries",
           lambda : "no",
           resistance : "tetracycline",
           requires : ["thiamine", "threonine", "leucine"],
           genotype : ["F-", "thi-1", "thr-1", "leuB6", "lacY1", "tonA21", "glnV44", "lambda-", "hflA150(chr::Tn10)"]
       },
       {
           label : "D1210",
           parent : "HB101",
           genotype : ["lacIq", "lacY+"]
       },
       {
           label : "DB3.1",
           purpose : "propagating plasmids with ccdB",
           resistance : "streptomycin",
           parent : "HB101",
           genotype : ["F-", "gyrA462", "endA1", "glnV44", "D(sr1-recA)", "mcrB", "mrr", "hsdS20(rB-, mB-)", "ara14", "galK2", "lacY1", "proA2", "rpsL20(Smr)", "xyl5", "D(leu)", "mtl1"]
       },
       {
           label : "DH1",
           purpose : "cloning",
           resistance : "nalidixic acid",
           parent : "Hoffman-Berling 1100 strain derivative",
           genotype : ["endA1", "recA1", "gyrA96", "thi-1", "glnV44", "relA1", "hsdR17(rK- mK+)", "lambda-"]
       },
       {
           label : "DH5a",
           purpose : "cloning",
           resistance : "nalidixic acid",
           parent : "DH1",
           genotype : ["F-", "endA1", "glnV44", "thi-1", "recA1", "relA1", "gyrA96", "deoR", "nupG", "phi80dlacZD(M15)", "D(lacZYA-argF)U169", "hsdR17(rK- mK+)", "lambda-"]
       },
   ]

};

  • /
  </script>

</html>

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