Difference between revisions of "Team:HebrewU/InterLab"

Line 1: Line 1:
−
<html lang="en">
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
−
<head>
+
<html xmlns="http://www.w3.org/1999/xhtml">
−
<title>HebrewU HujiGEM 2018</title>
+
−
<meta charset="utf-8">
+
−
<meta name="viewport" content="width=device-width, initial-scale=1">
+
  
−
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+
−
     
+
−
  <script>
+
 +
<!--- Chart script --->
 +
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
 +
<script>
 
google.charts.load('current', {'packages':['corechart', 'line']});
 
google.charts.load('current', {'packages':['corechart', 'line']});
−
     google.charts.setOnLoadCallback(drawChart);
+
     google.charts.setOnLoadCallback(drawChart1);
 +
google.charts.setOnLoadCallback(drawChart2);
 +
 
 +
<!--- Graph 1 --->
  
−
     function drawChart() {
+
     function drawChart1() {
  
 
       var data = new google.visualization.DataTable();
 
       var data = new google.visualization.DataTable();
−
       data.addColumn('date', 'Date');
+
       data.addColumn('number', 'Pcounts');
−
       data.addColumn('number', 'Population');
+
       data.addColumn('number', 'Abs');
  
 
       data.addRows([
 
       data.addRows([
−
        [new Date(1400, 1, 1),  374],
+
          [ 2.35E+08, 0.977],
−
        [new Date(1500, 1, 1), 460],
+
          [ 1.18E+08, 0.568],
−
        [new Date(1600, 1, 1),  579],
+
          [ 5.88E+07, 0.305],
−
        [new Date(1700, 1, 1),  679],
+
          [ 2.94E+07, 0.195],
−
        [new Date(1750, 1, 1),  770],
+
          [ 1.47E+07, 0.139],
−
        [new Date(1800, 1, 1), 954],
+
          [ 7.35E+06, 0.113],
−
        [new Date(1850, 1, 1),  1241],
+
          [ 3.68E+06, 0.098],
−
        [new Date(1900, 1, 1), 1633],
+
          [ 1.84E+06, 0.092],
−
        [new Date(1910, 1, 1),  1750],
+
          [ 9.19E+05, 0.086],
−
        [new Date(1920, 1, 1), 1860],
+
          [ 4.60E+05, 0.087],
−
        [new Date(1930, 1, 1),  2070],
+
          [ 2.30E+05, 0.086],
−
        [new Date(1940, 1, 1),  2300],
+
−
        [new Date(1950, 1, 1),  2558],
+
−
        [new Date(1951, 1, 1),  2595],
+
−
        [new Date(1952, 1, 1),  2637],
+
−
        [new Date(1953, 1, 1),  2682],
+
−
        [new Date(1954, 1, 1),  2730],
+
−
        [new Date(1955, 1, 1),  2782],
+
−
        [new Date(1956, 1, 1),  2835],
+
−
        [new Date(1957, 1, 1),  2891],
+
−
        [new Date(1958, 1, 1),  2948],
+
−
        [new Date(1959, 1, 1),  3001],
+
−
        [new Date(1960, 1, 1),  3043],
+
−
        [new Date(1961, 1, 1),  3084],
+
−
        [new Date(1962, 1, 1),  3140],
+
−
        [new Date(1963, 1, 1),  3210],
+
−
        [new Date(1964, 1, 1),  3281],
+
−
        [new Date(1965, 1, 1),  3350],
+
−
        [new Date(1966, 1, 1),  3421],
+
−
        [new Date(1967, 1, 1),  3490],
+
−
        [new Date(1968, 1, 1),  3562],
+
−
        [new Date(1969, 1, 1),  3637],
+
−
        [new Date(1970, 1, 1),  3713],
+
−
        [new Date(1971, 1, 1),  3790],
+
−
        [new Date(1972, 1, 1),  3867],
+
−
        [new Date(1973, 1, 1),  3942],
+
−
        [new Date(1974, 1, 1),  4017],
+
−
        [new Date(1975, 1, 1),  4089],
+
−
        [new Date(1976, 1, 1),  4160],
+
−
        [new Date(1977, 1, 1),  4232],
+
−
        [new Date(1978, 1, 1),  4304],
+
−
        [new Date(1979, 1, 1),  4379],
+
−
        [new Date(1980, 1, 1),  4451],
+
−
        [new Date(1981, 1, 1),  4534],
+
−
        [new Date(1982, 1, 1),  4615],
+
−
        [new Date(1983, 1, 1),  4696],
+
−
        [new Date(1984, 1, 1),  4775],
+
−
        [new Date(1985, 1, 1),  4856],
+
−
        [new Date(1986, 1, 1),  4941],
+
−
        [new Date(1987, 1, 1),  5027],
+
−
        [new Date(1988, 1, 1),  5115],
+
−
        [new Date(1989, 1, 1),  5201],
+
−
        [new Date(1990, 1, 1),  5289],
+
−
        [new Date(1991, 1, 1),  5372],
+
−
        [new Date(1992, 1, 1),  5456],
+
−
        [new Date(1993, 1, 1),  5538],
+
−
        [new Date(1994, 1, 1),  5619],
+
−
        [new Date(1995, 1, 1),  5699],
+
−
        [new Date(1996, 1, 1),  5779],
+
−
        [new Date(1997, 1, 1),  5858],
+
−
        [new Date(1998, 1, 1),  5935],
+
−
        [new Date(1999, 1, 1),  6012],
+
−
        [new Date(2000, 1, 1),  6089],
+
−
        [new Date(2001, 1, 1),  6165],
+
−
        [new Date(2002, 1, 1),  6242],
+
−
        [new Date(2003, 1, 1),  6319],
+
−
        [new Date(2004, 1, 1),  6396],
+
−
        [new Date(2005, 1, 1),  6473],
+
−
        [new Date(2006, 1, 1),  6551],
+
−
        [new Date(2007, 1, 1),  6630],
+
−
        [new Date(2008, 1, 1),  6709],
+
−
        [new Date(2009, 1, 1),  6788]
+
 
       ]);
 
       ]);
  
 
       var linearOptions = {
 
       var linearOptions = {
−
         title: 'World Population Since 1400 A.D. in Linear Scale',
+
         title: 'Particle Standard Curve (Linear Scale)',
 
         legend: 'none',
 
         legend: 'none',
−
         width: 450,
+
      showR2: true,
−
         height: 500,
+
 
 +
         width: 350,
 +
         height: 300,
 +
pointSize: 12,
 +
        dataOpacity: 0.3,
 +
        colors: ['black'],
 +
        backgroundColor: '#edeadc',
 
         hAxis: {
 
         hAxis: {
−
           title: 'Date'
+
           title: 'Particle Count / 100 uL',
 +
  format: 'scientific'
 +
 
 
         },
 
         },
 
         vAxis: {
 
         vAxis: {
−
           title: 'Population (millions)',
+
           title: 'Abs 600',
−
           ticks: [0, 1000, 2000, 4000, 6000]
+
           ticks: [0, 0.2, 0.4, 0.6, 0.8, 1, 1.2]
 
         }
 
         }
 +
 
       };
 
       };
  
 
       var logOptions = {
 
       var logOptions = {
−
         title: 'World Population Since 1400 A.D. in Log Scale',
+
         title: 'Particle Standard Curve (Log Scale)',
 
         legend: 'none',
 
         legend: 'none',
−
         width: 450,
+
         width: 350,
−
         height: 500,
+
         height: 300,
 +
pointSize: 12,
 +
        dataOpacity: 0.3,
 +
        colors: ['black'],
 +
        backgroundColor: '#edeadc',
 
         hAxis: {
 
         hAxis: {
−
           title: 'Date'
+
           title: 'Particle Count / 100 uL',
 +
  format: 'scientific',
 +
          ticks: [1E5, 1E6, 1E7, 1E8]
 +
 
 
         },
 
         },
 
         vAxis: {
 
         vAxis: {
−
           title: 'Population (millions)',
+
           title: 'Abs 600',
 
           scaleType: 'log',
 
           scaleType: 'log',
−
           ticks: [0, 1000, 2000, 4000, 6000]
+
           ticks: [0.01, 0.1, 1]
 
         }
 
         }
 +
 
       };
 
       };
  
Line 127: Line 86:
 
       logChart.draw(data, logOptions);
 
       logChart.draw(data, logOptions);
 
     }
 
     }
−
   
+
−
   
+
<!--- Graph 2 information--->
−
   
+
−
    </script>  
+
  
 +
function drawChart2() {
  
 +
      var data = new google.visualization.DataTable();
 +
      data.addColumn('number', 'Pcounts');
 +
      data.addColumn('number', 'Abs');
  
−
 
+
       data.addRows([
−
  <script type="text/javascript">
+
           [10.00, 6.461E+06],
−
  //particle standart curve
+
           [5.00, 3.551E+06],
−
  google.charts.load('current', {'packages':['corechart']});
+
           [ 2.5, 1.900E+06],
−
       google.charts.setOnLoadCallback(drawChart);
+
           [ 1.25, 9.253E+05],
−
      function drawChart() {
+
           [ 0.625, 4.844E+05],
−
        var data = google.visualization.arrayToDataTable([
+
           [ 0.313, 2.420E+05],
−
           ['Abs 600', 'Particle Count/ 100uL'],
+
           [ 0.156, 1.162E+05],
−
          [ 2.35E+08, 0.977],
+
           [ 0.078, 5.755E+04],
−
          [ 1.18E+08, 0.568],
+
           [ 0.039, 3.016E+04],
−
           [ 5.88E+07, 0.305],
+
           [ 0.0195,1.527E+04],
−
           [ 2.94E+07, 0.195],
+
           [ 0.0098,7.731E+03],
−
           [ 1.47E+07, 0.139],
+
      ]);
−
           [ 7.35E+06, 0.113],
+
−
           [ 3.68E+06, 0.098],
+
−
           [ 1.84E+06, 0.092],
+
−
           [ 9.19E+05, 0.086],
+
−
           [ 4.60E+05, 0.087],
+
−
           [ 2.30E+05, 0.086],
+
−
           [ 0, 0.086]
+
−
         
+
−
        ]);
+
  
 +
 +
 +
 +
 +
      var linearOptions2 = {
 +
        title: 'Particle Standard Curve (Linear Scale)',
 +
        legend: 'none',
 +
        width: 350,
 +
        height: 300,
 +
pointSize: 12,
 +
        dataOpacity: 0.3,
 +
        colors: ['black'],
 +
        backgroundColor: '#edeadc',
 +
        hAxis: {
 +
          title: 'Fluorescein Concentration (uM)',
 +
  ticks: [0,2,4,6,8,10]
  
 +
        },
 +
        vAxis: {
 +
          title: 'Fluorescence',
 +
  ticks: [1E5, 2E6, 3E7, 4E8, 5E8, 6E8, 7E8, 8E8]
  
−
var options = {
+
        }
 +
 +
      };
  
−
         };
+
      var logOptions2 = {
 +
         title: 'Particle Standard Curve (Log Scale)',
 +
        legend: 'none',
 +
        width: 350,
 +
        height: 300,
 +
pointSize: 12,
 +
        dataOpacity: 0.3,
 +
        colors: ['black'],
 +
        backgroundColor: '#edeadc',
 +
        hAxis: {
 +
        title: 'Fluorescein Concentration (uM)',
 +
ticks: [0.00, 0.01, 0.1, 1, 10]
  
−
        var options = {
 
−
          pointSize: 12,
 
−
          dataOpacity: 0.3,
 
−
          colors: ['black'],
 
−
          backgroundColor: '#edeadc',
 
−
          hAxis: {minValue: 0, maxValue: 10},
 
−
          vAxis: {minValue: 0, maxValue: 1},
 
−
          hAxis: {title: 'Particle Count/ 100uL'},         
 
−
          vAxis: {title: 'Abs 600'},
 
−
         
 
−
          chartArea: {width:'60%'},
 
−
          trendlines: {
 
−
            0: {
 
−
           
 
−
              color: '#262d2e',
 
−
              type: 'linear',
 
−
              showR2: true,
 
−
              visibleInLegend: true
 
  
−
            }
+
        },
 +
        vAxis: {
 +
          title: 'Fluorescence',
 +
          scaleType: 'log',
 +
  format: 'scientific',
 +
  ticks: [1E5, 2E6, 3E7, 4E8, 5E8, 6E8, 7E8, 8E8]
  
−
          }
+
        }
 +
 +
      };
  
−
        };
+
      var linearChart2 = new google.visualization.LineChart(document.getElementById('linear_div2'));
 +
      linearChart2.draw(data, linearOptions2);
  
−
        var chartLinear = new google.visualization.ScatterChart(document.getElementById('chartLinear'));
+
      var logChart2 = new google.visualization.LineChart(document.getElementById('log_div2'));
−
        chartLinear.draw(data, options);
+
      logChart2.draw(data, logOptions2);
 +
    }
 +
 +
 +
 +
</script>
  
−
      }
+
<head>
−
      </script>
+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 +
<title>Untitled Document</title>
 +
</head>
 +
 
 +
  
 
<script>  
 
<script>  
Line 383: Line 367:
 
     width: 10%;
 
     width: 10%;
 
text-align: center;
 
text-align: center;
−
}
 
−
 
−
#tablevalues_hujigem {
 
−
    font-family: "Trebuchet MS", Arial, Helvetica, sans-serif;
 
−
    border-collapse: collapse;
 
−
    width:80%;
 
−
}
 
−
 
−
#tablevalues_hujigem td, #tablevalues_hujigem th {
 
−
    border: 1px solid #ddd;
 
−
    padding: 3px;
 
−
}
 
−
 
−
#tablevalues_hujigem tr:nth-child(even){background-color: white;}
 
−
 
−
#tablevalues_hujigem tr:hover {background-color: #edeadc;}
 
−
 
−
#tablevalues_hujigem th {
 
−
    padding-top: 12px;
 
−
    padding-bottom: 12px;
 
−
    text-align: center;
 
−
    background-color: #262d2e;
 
−
    color: white;
 
 
}
 
}
  
Line 437: Line 398:
 
}
 
}
  
−
#hujigem_showdata1{
+
#hujigem_showdata1,#hujigem_showdata2 {
 
display:none;
 
display:none;
 
}
 
}
  
−
#hujigem_showdata2{
+
table_huji {
−
display:none;
+
    border-collapse: collapse;
 +
text-align: center;
 +
font-size-adjust:inherit;
 +
font-family:Calibri
 +
 
 
}
 
}
 +
 +
th_huji, td_huji {
 +
    text-align: center;
 +
border: 1px solid #829c8c;
 +
    padding: 2px;
 +
    font-size-adjust:inherit;
 +
font-family:Calibri;
 +
 +
}
 +
 +
#tablevalues_hujigem {
 +
background-color:white;
 +
font-family:Calibri;
 +
    text-align: center;
 +
border: 1px solid #829c8c;
 +
 +
 +
 +
}
 +
  
 
</style>
 
</style>
Line 523: Line 508:
 
   <div align="center">
 
   <div align="center">
  
−
<div id="chartLinear" style="height: 80%; width: 80%;">  
+
<div style="overflow-x:auto;">
−
</div>
+
    <table class="columns">
 +
    <tr>
 +
      <td><div id="linear_div"></div></td>
 +
      <td><div id="log_div"></div></td>
 +
    </tr>
 +
  </table>
 +
</div>
  
−
<br> </br>
 
 
<button onclick="myFunction()" class="hujigem_showdata_button">Raw data 1</button>
 
<button onclick="myFunction()" class="hujigem_showdata_button">Raw data 1</button>
  
−
<div id="hujigem_showdata1">
+
<div id="hujigem_showdata1" style="overflow-x:auto;">
−
 
+
−
 
+
−
<b>
+
−
</b>
+
 
<table id="tablevalues_hujigem">
 
<table id="tablevalues_hujigem">
  
 
   <tr>
 
   <tr>
 
     <th>N. of Particles</th>
 
     <th>N. of Particles</th>
−
     <td>2.35E+08</td>
+
     <td>2.35E8</td>
−
     <td>1.18E+08</td>
+
     <td>1.18E8</td>
−
     <td>5.88E+07</td>
+
     <td>5.88E7</td>
−
     <td>2.94E+07</td>
+
     <td>2.94E7</td>
−
     <td>1.47E+07</td>
+
     <td>1.47E7</td>
−
     <td>7.35E+06</td>
+
     <td>7.35E6</td>
−
     <td>3.68E+06</td>
+
     <td>3.68E6</td>
−
     <td>1.84E+06</td>
+
     <td>1.84E6</td>
−
     <td>9.19E+05</td>
+
     <td>9.19E5</td>
−
     <td>4.60E+05</td>
+
     <td>4.60E5</td>
−
     <td>2.30E+05</td>
+
     <td>2.30E5</td>
  
  
Line 576: Line 562:
 
</div>
 
</div>
  
 +
  <br />
 +
<br />
 +
 
   
 
   
 
<script>
 
<script>
Line 590: Line 579:
  
  
−
<button onclick="myFunction2()" class="hujigem_showdata_button">Raw data 2</button>
 
  
−
<div id="hujigem_showdata2">
+
 
 +
<script>
 +
function myFunction2() {
 +
    var x = document.getElementById("hujigem_showdata2");
 +
    if (x.style.display === "block") {
 +
        x.style.display = "none";
 +
    } else {
 +
        x.style.display = "block";
 +
    }
 +
}
 +
</script>
 +
<div style="overflow-x:auto;">
 +
    <table class="columns">
 +
    <tr>
 +
      <td><div id="linear_div2"></div></td>
 +
      <td><div id="log_div2"></div></td>
 +
    </tr>
 +
  </table>
 +
</div>
 +
 
 +
 +
<button onclick="myFunction2()" class="hujigem_showdata_button">Raw data 2</button>
 +
 
 +
<div id="hujigem_showdata2" style="overflow-x:auto;">
  
  
Line 615: Line 626:
 
   <tr>
 
   <tr>
 
     <th>Abs mean</th>
 
     <th>Abs mean</th>
−
     <td>6.461E+06</td>
+
     <td>6.461E6</td>
−
     <td>3.551E+06</td>
+
     <td>3.551E6</td>
−
     <td>1.900E+06</td>
+
     <td>1.900E6</td>
−
     <td>9.253E+05</td>
+
     <td>9.253E5</td>
−
     <td>4.844E+05</td>
+
     <td>4.844E5</td>
−
     <td>2.420E+05</td>
+
     <td>2.420E5</td>
−
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Revision as of 20:19, 6 September 2018

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> Untitled Document



Inter-Lab

Universal and Standardized units are important in all disciplines of science, and especially in engineering. One important issue biology, and specifically genetic engineering faces today is a lack of standardized units. In synthetic biology we often employ marker proteins to assist in both real time assessment and in depth result interpretation. For these results to be consistent both between experiments, and between labs it is of paramount importance to create a standardized unit for said markers. Such a unit would also allow for the comparison of results from different labs and machines.

The InterLab Study utilizes the wide access that iGEM has to biology teams all over the world. Taking advantage of this rare opportunity, the InterLab aims to improve the measurement tools available to both the iGEM community and the synthetic biology community as a whole. By measuring the fluorescence on a wide range of machines, in a wide range of labs, and regulating the results to a single control group, we hope to gather enough data to create this standard unit. As GFP is one of the most used markers today, this has been the focus of the InterLab studies over the past 5 years.

Our team too believes in the need for a standardization of units with in the world of biology. We want to help make progress towards quantitative measurements between labs, and not be constrained to relative compassions. As such, were excited to take part in such a project and hope are data will support the progress of synthetic biology and genetic engineering.

N. of Particles 2.35E8 1.18E8 5.88E7 2.94E7 1.47E7 7.35E6 3.68E6 1.84E6 9.19E5 4.60E5 2.30E5
Abs mean 0.977 0.568 0.305 0.195 0.139 0.113 0.098 0.092 0.087 0.086 0.086


Fluorescein (uM) 10.00 5.00 2.5 1.25 0.625 0.313 0.156 0.078 0.039 0.0195 0.0098
Abs mean 6.461E6 3.551E6 1.900E6 9.253E5 4.844E5 2.420E5 1.162E5 5.755E4 3.016E4 1.527E4 7.731E3