Difference between revisions of "Team:Valencia UPV/Hardware"

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<html>
 
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<style>
  
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#home_logo, #sideMenu { display:none; }
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#sideMenu, #top_title, .patrollink  {display:none;}
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#content { margin-left:0px; margin-top:-30px; padding:0px; width:100%;}
  
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<div class="column full_size judges-will-not-evaluate">
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<h3>★  ALERT! </h3>
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  <meta charset="utf-8">
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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  <title>Stack Multipurpose HTML Template</title>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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  <meta name="viewport" content="width=device-width, initial-scale=1.0">
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  <meta name="description" content="Site Description Here">
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  <link href="https://fonts.googleapis.com/css?family=Open+Sans:200,300,400,400i,500,600,700%7CMerriweather:300,300i" rel="stylesheet">
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  <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
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  <link href="https://fonts.googleapis.com/css?family=Lato:400,700,900" rel="stylesheet">
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  <link href="https://2018.igem.org/Template:Valencia_UPV/fontAwesome?action=raw&ctype=text/css" rel="stylesheet" type="text/css">
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</head>
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<body class="" style="background-color:#353535;">
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<!-------------------------------IMAGEN PRINCIPAL------------------------------------------------>
  
  
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<section style="
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; ; background-size: 100%;height: 44.2em;margin-top: 0em;padding-top: 1.1em;" class="height-90 parallax">
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<div class="main-container" style="
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height: 100%;">
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<center style="
 +
height: 100%;">
 +
<div class="col-md-10" style="
 +
  height: 100%;margin-top: 4em;">
 +
  <div id="logoPrinteria" class="item" style="
 +
    background-image: url(https://static.igem.org/mediawiki/2018/3/3b/T--Valencia_UPV--laboratorioAdrianUPV2018.jpeg);
 +
    height: 100%;
 +
    width: 100%;background-attachment: fixed;background-size: cover;">
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    <div style="/* position: absolute; *//* top: 81%; *//* padding-left: 31em; */">
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      <a class="btn down inner-link active" href="#story" style="font-size: 82%;right: 50%;/* position: fixed; *//* bottom: 7%; */top: 85.2%;z-index: 99;background-color: white;position: absolute;border-radius: 80%;width: 3.8em;height: 3.8em;padding: 0;padding-top: 14px;">
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        <i class="stack-interface stack-down-open-big"></i>
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      </a>
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    </div>
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  </div>
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</div>
  
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<div class="column full_size">
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</center>
  
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<h1>Hardware</h1>
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</div><div class="all-page-modals"></div><div class="all-page-modals"></div>
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<div class="all-page-modals"></div>
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</section></div>
  
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</div>
 
  
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<div class="column two_thirds_size">
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<!----------------------EMPIEZA LA SECCIÓN DE DEBAJO DE LA IMAGEN ----------------------------->
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<h3>Best Hardware Special Prize</h3>
+
−
<p>iGEM is about making teams of students making synthetic biology projects. We encourage teams to work with parts and build biological devices in the lab. But we are inclusive and want all teams to work on many other types of problems in synbio. Robotic assembly, microfluidics, low cost equipment and measurement hardware are all areas ripe for innovation in synbio. </p>
+
  
−
<p>
 
−
Teams who are interested in working with hardware as a side project are encouraged to apply for the hardware award.
 
  
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<br><br>
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<section id="story" class="feature-large" style="padding-top: 6em; padding-bottom: 50px; outline: none;" data-scroll-id="story" tabindex="-1">
−
To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Hardware prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>.
+
<div class="container">
−
<br><br>
+
  <div class="row">
−
You must also delete the message box on the top of this page to be eligible for this prize.
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    <div class="col-md-3" style="
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</p>
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      margin-left: 0em;
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</p>
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      padding-right: 0px;
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</div>
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      padding-left: 0.2em;
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      ">
 +
     
 +
      <!------------ÍNDICE LATERAL------------------>
  
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<div class="column third_size">
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      <div class="tabs-container tabs--vertical page-navigator" style="position: -webkit-sticky;position: sticky;padding-bottom: 0px;margin-top: 11.4em;">
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<div class="highlight decoration_A_full">
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        <h4 style="
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<h3>Inspiration</h3>
+
        padding-left: 1em;
−
<p>You can look at what other teams did to get some inspiration! <br />
+
        ">Index</h4>
−
Here are a few examples:</p>
+
        <ul class="lateral">
−
<ul>
+
          <li class="lateral" style="margin-bottom: 0px;padding-bottom: 1em;padding-top: initial;padding-left: 1em;/* color: #353535; */">
−
<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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            <div class="tab__title" style="
−
<li><a href="https://2016.igem.org/Team:Aachen">2016 Aachen </a></li>
+
              line-height: 1.3em;
−
<li><a href="https://2015.igem.org/Team:TU_Delft">2015 TU Delft  </a></li>
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              /* padding-left: 0.5em; */
−
<li><a href="https://2015.igem.org/Team:TU_Darmstadt">2015 TU Darmstadt</a></li>
+
              ">
 +
              <a href="#Intro" class="lateral inner-link" style="
 +
                /* color: #ffffff; */
 +
                opacity: 1;
 +
                list-style-type: circle;
 +
              ">Introduction</a>
 +
            </div>
 +
           
 +
          </li>
 +
          <li class="lateral">
 +
            <div class="tab__title" style="
 +
              line-height: 1.3em;
 +
              ">
 +
              <a href="#Struc" class="lateral inner-link" style="
 +
                color: #353535;
 +
                opacity: 1;
 +
              ">Structure</a>
 +
            </div>
 +
           
 +
          </li>
 +
          <li class="lateral">
 +
            <div class="tab__title" style="
 +
              line-height: 1.3em;
 +
              ">
 +
              <a href="#Entry" class="lateral inner-link" style="
 +
                color: #353535;
 +
                opacity: 1;
 +
              ">Entry of consumables</a>
 +
            </div>
 +
           
 +
          </li>
 +
          <li class="lateral">
 +
            <div class="tab__title" style="
 +
              line-height: 1.3em;
 +
              ">
 +
              <a href="#Reaction" class="lateral inner-link" style="
 +
                color: #353535;
 +
                opacity: 1;
 +
              ">Reaction zone</a>
 +
            </div>
 +
           
 +
          </li>
 +
          <li class="lateral">
 +
            <div class="tab__title" style="
 +
              line-height: 1.3em;
 +
              ">
 +
              <a href="#Measurement" class="lateral inner-link" style="
 +
                color: #353535;
 +
                opacity: 1;
 +
              ">Measurement zone</a>
 +
            </div>
 +
           
 +
          </li>
 +
          <li class="lateral">
 +
            <div class="tab__title" style="
 +
              line-height: 1.3em;
 +
              ">
 +
              <a href="#Disinfection" class="lateral inner-link" style="
 +
                color: #353535;
 +
                opacity: 1;
 +
              ">Disinfection and sterility</a>
 +
            </div>
 +
           
 +
          </li>
 +
          </li>
 +
          <li class="lateral">
 +
            <div class="tab__title" style="
 +
              line-height: 1.3em;
 +
              ">
 +
              <a href="#Simultaneous" class="lateral inner-link" style="
 +
                color: #353535;
 +
                opacity: 1;
 +
              ">Future of Printeria</a>
 +
            </div>
 +
           
 +
          </li>
 +
          </li>
 +
          <li class="lateral">
 +
            <div class="tab__title" style="
 +
              line-height: 1.3em;
 +
              ">
 +
              <a href="#Results" class="lateral inner-link" style="
 +
                color: #353535;
 +
                opacity: 1;
 +
              ">Results</a>
 +
            </div>
 +
 
 +
            </li>
 +
          </li>
 +
          <li class="lateral">
 +
            <div class="tab__title" style="
 +
              line-height: 1.3em;
 +
              ">
 +
              <a href="#Replicability" class="lateral inner-link" style="
 +
                color: #353535;
 +
                opacity: 1;
 +
              ">Replicability</a>
 +
            </div>
 +
 
 +
            </li>
 +
          </li>
 +
        </ul><ul class="tabs-content"></ul>
 +
       
 +
       
 +
      </div>
 +
    </div>
 +
 
 +
 
 +
<!--------------------------------------------TEXTO------------------------------------------------>
 +
 
 +
 
 +
    <div class="col-md-9" style="
 +
      /* margin-left: 0px; */
 +
      padding-left: 6em;
 +
      padding-right: 2em;
 +
      ">
 +
      <div id="#Intro">
 +
        <h3>HARDWARE</h3>
 +
        <a class="anchorOffset" id="Intro"></a>
 +
        <h4>INTRODUCTION</h4>
 +
     
 +
 
 +
        <p>To address the lack of accessibility to synthetic biology due to the high costs and the level of knowledge required among others, our team has designed Printeria, a fully-equipped bioengineering device capable of automating the process of printing genetic circuits in bacteria.
 +
        </p>
 +
 
 +
        <p> To ensure a functional, economical and easy-to-use design, collaboration between the hardware and the wet lab teams has been necessary throughout the development process. After several drafts we have achieved a unique design that can be easily transported and replicated at a cost not exceeding xxx € (xxx $).</p>
 +
 
 +
        <p> Printeria is divided into three main parts dependent on each other:</p>
 +
 
 +
        <div>
 +
        <ul>
 +
          <li>
 +
            <p> <b><u>Entry of consumables</u></b>: components that allow the entry of consumables into the reaction zone.</p>
 +
          </li>
 +
          <li>
 +
            <p> <b><u>Reaction zone</u></b>: space where the process of printing genetic circuits in bacteria occurs thanks to digital microfluidic technology.</p>
 +
          </li>
 +
          <li>
 +
            <p> <b><u>Measurement zone</u></b>: the bacteria are kept in conditions that allow for growth and expression while OD and fluorescence measurements are taken.</p>
 +
          </li>
 +
        </ul>
 +
      </div>
 +
 
 +
        <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://static.igem.org/mediawiki/2018/3/3c/T--Valencia_UPV--ConjuntoUPV2018.png" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>PRINTERIA</h6>
 +
              </div>
 +
              </div>
 +
 
 +
        <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://static.igem.org/mediawiki/2018/thumb/f/fe/T--Valencia_UPV--Conjunto2UPV2018.png/800px-T--Valencia_UPV--Conjunto2UPV2018.png" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Assembly Sketch</h6>
 +
              </div>
 +
              </div>
 +
 
 +
      <ul class="accordion accordion-1">
 +
  <li>
 +
      <div class="accordion__title">
 +
          <span class="h5">Overall budget</span>
 +
      </div>
 +
      <div class="accordion__content">
 +
        <div class="divTabla">
 +
<table class="border--round table--alternate-row tableBetty" style="width:100%;">
 +
          <thead><tr>
 +
            <th class="thHec">Part</th>
 +
            <th class="thHec">Quantity</th>
 +
            <th class="thHec">Cost per unit</th>
 +
            <th class="thHec">Cost</th>
 +
          </tr>
 +
        </thead><tbody><tr>
 +
        <td class="tdHec">Structure</td>
 +
        <td class="tdHec">1</td>
 +
        <td class="tdHec">381,91 €</td>
 +
        <td class="tdHec">381,91 €</td>
 +
      </tr>
 +
      <tr>
 +
        <td class="tdHec">Entry system</td>
 +
        <td class="tdHec">1</td>
 +
        <td class="tdHec">49,02 €</td>
 +
        <td class="tdHec">49,02 €</td>
 +
      </tr>
 +
      <tr>
 +
        <td class="tdHec">Reaction zone</td>
 +
        <td class="tdHec">----</td>
 +
        <td class="tdHec">----</td>
 +
        <td class="tdHec">----</td>
 +
      </tr>
 +
      <tr>
 +
        <td class="tdHec">Measurement zone</td>
 +
        <td class="tdHec">----</td>
 +
        <td class="tdHec">----</td>
 +
        <td class="tdHec">----</td>
 +
      </tr>
 +
      <tr>
 +
        <td class="tdHec" style="background-color: #909090;color: #fff; font-weight: bold;" colspan="3">Total</td>
 +
        <td class="tdHec">----</td>
 +
      </tr>
 +
    </tbody></table>      </div>
 +
  </li>
 +
  <li>
 +
      <div class="accordion__title">
 +
          <span class="h5">Downloads</span>
 +
      </div>
 +
      <div class="accordion__content">
 +
        <div>
 +
        <ul>
 +
          <li>
 +
            <p> Assembly drawings</p>
 +
          </li>
 +
          <li>
 +
            <p> Printeria's CAD 3D model</p>
 +
          </li>
 +
        </ul>
 +
      </div>
 +
      </div>
 +
  </li>
 +
 
 
</ul>
 
</ul>
 +
 +
  </div>
 +
 +
 +
 +
 
 +
        <div>
 +
        <a class="anchorOffset" id="Struc"></a>
 +
        <h5>STRUCTURE</h5>
 +
        </div>
 +
 +
        <h5 style="padding-left: 1em;">Frame</h5>
 +
        <div style="padding-left: 1em;">
 +
            <p>First of all, it is necessary to design a structure that confines all the elements necessary for the operation of the device inside it and also allows the creation of a sterile atmosphere to carry out the biological reactions.</p>
 +
 +
            <p> In order to facilitate its transport, aluminum has been chosen for the frame, which in addition to its low weight, has other great qualities such as great resistance to corrosion and low cost.</p>
 +
 +
            <p> It has been used 15x15x1mm square tube profiles joined by plastic corner connectors obtaining as a result a 415x360x280mm chassis. Thanks to the generated blueprints we have been able to contact a company specializing in cutting and handling aluminum that has provided us with all the parts as we required. As it was not possible for us to find plastic connectors that fit our needs, we have decided to design these parts ourselves and then print them on a 3D printer. </p>
 +
 +
            <div>
 +
              <div class="row" style="
 +
                margin: 0;
 +
                ">
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-right: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-left: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div style="
 +
                  width: 100%;
 +
                  padding-left: 19em;
 +
                  padding-right: 1em;
 +
                  "><h6>Aluminum frame</h6>
 +
                </div>
 +
              </div>
 +
            </div>
 +
        </div>
 +
 +
            <h5 style="padding-left: 1em;">Methacrylate</h5>
 +
 +
            <div style="padding-left: 1em;">
 +
              <p> To complete the structure, it is necessary to create walls that are attached to this frame and contribute to its stability.  We have opted for the use of methacrylate due to its attractive appearance, durability and scratch resistance. </p>
 +
 +
              <p> As well as the aluminum profiles, the blueprints created were used for ordering the custom-made parts to a company.</p>
 +
 +
              <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://via.placeholder.com/800x400" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Methacrylate cladding</h6>
 +
              </div>
 +
              </div>
 +
 +
              <p> Finally, 4mm diameter countersunk head screws DIN 7991 (M4 L25) and nuts DIN 934 (M4), both made of galvanized steel, were used for joining the methacrylate plates to the frame. </p>
 +
 +
              <p> Thanks to the use of plastic connectors and bolted joints, the entire structure can be disassembled and reassembled as often as required, making it much easier to transport and store. </p>
 +
 +
              <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://static.igem.org/mediawiki/2018/thumb/7/74/T--Valencia_UPV--Metacrilato1UPV2018.png/800px-T--Valencia_UPV--Metacrilato1UPV2018.png" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Assembly sketch of the methacrylate cladding</h6>
 +
              </div>
 +
              </div>
 +
 +
            </div>
 +
 +
            <h5 style="padding-left: 1em;">Leveling system</h5>
 +
 +
            <div style="padding-left: 1em;">
 +
              <p> Given the great importance of keeping the reaction zone perfectly horizontal, it is necessary to use levelling feet. In addition, for checking the horizontal position, a bull’s eye level has been installed next to the reaction zone. </p>
 +
 +
                <div style="
 +
                  padding-bottom: 0.8em;
 +
                  text-align: right;
 +
                 
 +
                  ">
 +
                  <div class="row" style="margin: 0;">
 +
                      <div class="col-md-6" style="
 +
                        padding: 0;
 +
                        padding-right: 0.3em;
 +
                        ">
 +
                        <img src="https://via.placeholder.com/800x400" alt="" style="
 +
                        margin-top: 0.5em;
 +
                        margin-bottom: 0.8em;
 +
                        border-radius: 0.3em;
 +
                        ">
 +
                      </div>
 +
                      <div class="col-md-6" style="
 +
                        padding: 0;
 +
                        padding-left: 0.3em;
 +
                        ">
 +
                        <img src="https://via.placeholder.com/800x400" alt="" style="
 +
                        margin-top: 0.5em;
 +
                        margin-bottom: 0.8em;
 +
                        border-radius: 0.3em;
 +
                        ">
 +
                      </div>
 +
                      <div style="
 +
                        width: 100%;
 +
                        padding-left: 19em;
 +
                        padding-right: 1em;
 +
                        "><h6>Levelling system</h6>
 +
                      </div>
 +
                  </div>
 +
                </div>
 +
            </div>
 +
       
 +
<ul class="accordion accordion-1">
 +
  <li>
 +
      <div class="accordion__title">
 +
          <span class="h5">Structure's budget</span>
 +
      </div>
 +
      <div class="accordion__content">
 +
              <div class="divTabla">
 +
        <table class="border--round table--alternate-row tableBetty" style="width:100%;">
 +
                  <thead><tr>
 +
                    <th class="thHec">Part</th>
 +
                    <th class="thHec">Quantity</th>
 +
                    <th class="thHec">Cost per unit</th>
 +
                    <th class="thHec">Cost</th>
 +
                  </tr>
 +
                </thead><tbody><tr>
 +
                <td class="tdHec">Aluminum profiles</td>
 +
                <td class="tdHec">6 m</td>
 +
                <td class="tdHec">6,99 €/m</td>
 +
                <td class="tdHec">41,94 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Profiles' cutting and drilling</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">70 €</td>
 +
                <td class="tdHec">70 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Custom-made methacrylate</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">250 €</td>
 +
                <td class="tdHec">250 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Screws DIN 7991</td>
 +
                <td class="tdHec">60</td>
 +
                <td class="tdHec"> 0,07 €</td>
 +
                <td class="tdHec">4,2 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Nuts DIN 934</td>
 +
                <td class="tdHec">60</td>
 +
                <td class="tdHec">0,03 €</td>
 +
                <td class="tdHec">1,8 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Kg of PLA for the connectors</td>
 +
                <td class="tdHec">0,155 Kg</td>
 +
                <td class="tdHec">20 €/Kg</td>
 +
                <td class="tdHec">3,1 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Leeveling feet</td>
 +
                <td class="tdHec">4</td>
 +
                <td class="tdHec">0,97 €</td>
 +
                <td class="tdHec">3,88 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Bull's eye level</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">6,99 €</td>
 +
                <td class="tdHec">6,99 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec" style="background-color: #909090;color: #fff; font-weight: bold;" colspan="3">Total</td>
 +
                <td class="tdHec">381,91 €</td>
 +
              </tr>
 +
            </tbody></table> 
 +
 +
        </div>
 +
  </li>
 +
  <li>
 +
      <div class="accordion__title">
 +
          <span class="h5">Downloads</span>
 +
      </div>
 +
      <div class="accordion__content">
 +
        <div>
 +
        <ul>
 +
          <li>
 +
            <p> Aluminium frame drawings</p>
 +
          </li>
 +
          <li>
 +
            <p> Methacrylate cladding drawings</p>
 +
          </li>
 +
          <li>
 +
            <p> Corner connectors' CAD 3D models</p>
 +
          </li>
 +
          <li>
 +
            <p> Structure CAD 3D model</p>
 +
          </li>
 +
        </ul>
 +
      </div>
 +
      </div>
 +
  </li>
 +
 
 +
</ul>
 +
 +
 +
 +
       
 +
        <div>
 +
        <a class="anchorOffset" id="Entry"></a>
 +
        <h5>ENTRY OF CONSUMABLES</h5>
 +
        </div>
 +
 +
                <p>In order to carry out the reactions it is necessary to introduce the consumables into the PCB. Therefore, a carousel-based system has been designed in which pipette tips with the parts necessary for the reaction are placed. The user should place these pipette tips before the experiments in the positions indicated. </p>
 +
 +
        <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://via.placeholder.com/800x400" alt="" style="
 +
              margin-top: 0.3em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Foto de todo el sistema de entrada</h6>
 +
              </div>
 +
              </div>
 +
 +
        <p> Once the tips have been inserted and the machine is ready to operate, the carousel is rotated with the help of a stepper motor until each of the tips is placed in the blowing position. In this position a needle connected to a peristaltic pump lowers vertically and injects air, thus producing the fall of the genetic material on the PCB. </p>
 +
 +
        <p> The vertically moving needle is made possible by the use of a solenoid, a device that converts electrical energy into mechanical energy which, in turns, raises or lowers the needle. Once the needle is in its low position and inserted into the pipette tip, the pump is activated and air is injected. </p>
 +
 +
        <div>
 +
              <div class="row" style="
 +
                margin: 0;
 +
                ">
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-right: 0.3em;
 +
                  ">
 +
                  <img src="https://static.igem.org/mediawiki/2018/9/94/T--Valencia_UPV--Entrada2UPV2018.png">
 +
                </div>
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-left: 0.3em;
 +
                  ">
 +
                  <img src="https://static.igem.org/mediawiki/2018/8/86/T--Valencia_UPV--Entrada1UPV2018.png">
 +
                </div>
 +
                <div style="
 +
                  width: 100%;
 +
                  padding-left: 19em;
 +
                  padding-right: 1em;
 +
                  "><h6>Needle in its high and low position</h6>
 +
                </div>
 +
              </div>
 +
            </div>
 +
 +
        <p> All the necessary parts have been designed using a 3D modeling software and then printed on our 3D printer, which means that we have been able to implement this system at a very low cost. </p>
 +
 +
        <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://via.placeholder.com/800x400" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Video de la prueba de concepto</h6>
 +
              </div>
 +
              </div>
 +
 +
<ul class="accordion accordion-1">
 +
  <li>
 +
      <div class="accordion__title">
 +
          <span class="h5">Entry of consumables system's budget</span>
 +
      </div>
 +
      <div class="accordion__content">
 +
              <div class="divTabla">
 +
        <table class="border--round table--alternate-row tableBetty" style="width:100%;">
 +
                  <thead><tr>
 +
                    <th class="thHec">Part</th>
 +
                    <th class="thHec">Quantity</th>
 +
                    <th class="thHec">Cost per unit</th>
 +
                    <th class="thHec">Cost</th>
 +
                  </tr>
 +
                </thead><tbody><tr>
 +
                <td class="tdHec">Kg of PLA for the 3D printed elements</td>
 +
                <td class="tdHec">0,115 Kg</td>
 +
                <td class="tdHec">20 €/Kg</td>
 +
                <td class="tdHec">2,3 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Bearing</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">2 €</td>
 +
                <td class="tdHec">2 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Needle</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">0,3 €</td>
 +
                <td class="tdHec">0,3 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Stepper motor</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">26,43 €</td>
 +
                <td class="tdHec">26,43 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Solenoid</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">5 €</td>
 +
                <td class="tdHec">5 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Peristaltic pump</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">11,99 €</td>
 +
                <td class="tdHec">11,99 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Air filter</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">1 €</td>
 +
                <td class="tdHec">1 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec" style="background-color: #909090;color: #fff; font-weight: bold;" colspan="3">Total</td>
 +
                <td class="tdHec">49,02 € </td>
 +
              </tr>
 +
            </tbody></table> 
 +
 +
        </div>
 +
  </li>
 +
        <li>
 +
            <div class="accordion__title">
 +
                <span class="h5">Downloads</span>
 +
            </div>
 +
                <div class="accordion__content">
 +
                  <div>
 +
                  <ul>
 +
                    <li>
 +
                      <p> Entry of consumables system drawings</p>
 +
                    </li>
 +
                  <li>
 +
                      <p> All-part's CAD 3D models</p>
 +
                    </li>
 +
                  </ul>
 +
                </div>
 +
                </div>
 +
        </li>
 +
 
 +
</ul>
 +
 +
        <div>
 +
        <a class="anchorOffset" id="Reaction"></a>
 +
        <h5>REACTION ZONE</h5>
 +
        </div>
 +
 +
            <h5 style="padding-left: 1em;">Digital Microfluidics Movement</h5>
 +
            <div style="padding-left: 1em;">
 +
 +
            <p>For the main part of the device we needed to be able to reliably and precisely control the movement of liquids involved in the reaction. This ensures that the components mix was intended and then follow every procedure accurately. For this we have decided to use a technology called digital microfluidics, which is based on applying electromagnetic fields to a special surface so that it changes its properties. More precisely we can change the hydrophobicity of the surface as to attract droplets and repel them, ensuring in this way that they follow an established route.</p>
 +
 +
            <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://via.placeholder.com/800x400" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>DMF technology (vídeo o esquema explicativo)</h6>
 +
              </div>
 +
              </div>
 +
           
 +
          </div>
 +
          <div style="padding-left: 1em;">
 +
          <p>To take advantage of this we have designed the PCB under the surface with small pads on which we can apply a high voltage to cause this effect on the coating of our surface.</p>
 +
          </div>
 +
 +
          <div style="padding-left: 1em;">
 +
                <div class="row" style="
 +
                margin: 0;
 +
                ">
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-right: 0.3em;
 +
                  ">
 +
                  <img src="https://static.igem.org/mediawiki/2018/3/30/T--Valencia_UPV--PCB1UPV2018.png">
 +
                </div>
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-left: 0.3em;
 +
                  ">
 +
                  <img src="https://static.igem.org/mediawiki/2018/b/b7/T--Valencia_UPV--PCB3UPV2018.png">
 +
                </div>
 +
                <div style="
 +
                  width: 100%;
 +
                  padding-left: 19em;
 +
                  padding-right: 1em;
 +
                  "><h6>PCB render</h6>
 +
                </div>
 +
                </div>
 +
            </div>
 +
 +
          <div style="padding-left: 1em;">
 +
          <p>This surface must be very hydrophobic, therefore it is necessary to coat the PCB with a polytetrafluoroethylene (PTFE) foil (12 microns thickness) and then apply a thin layer of a very hydrophobic gel called FluoroPel. In order to keep the Teflon foil well glued to the surface of the PCB, a custom-made piece has been designed and printed. The foil will be glued to this piece and then joined to the PCB by means of screws.</p>
 +
          </div>
 +
 +
          <div style="padding-left: 1em;">
 +
                <div class="row" style="
 +
                margin: 0;
 +
                ">
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-right: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-left: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div style="
 +
                  width: 100%;
 +
                  padding-left: 19em;
 +
                  padding-right: 1em;
 +
                  "><h6>Renders y fotos reales</h6>
 +
                </div>
 +
                </div>
 +
            </div>
 +
         
 +
          <div style="padding-left: 1em;">
 +
          <p>To be able to control so many pads we are using a HV507, a special driver chip which is a high voltage serial to parallel converter. This means that it takes data one bit at a time and then it displays them all at the same time at a high voltage. This chip can handle up to 64 outputs, meaning that we can connect 64 pads to it. So we only need a total of 6 chips for our entire surface.</p>
 +
        </div>
 +
          <div <div style="padding-left: 1em;">
 +
                <div class="row" style="
 +
                margin: 0;
 +
                ">
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-right: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-left: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div style="
 +
                  width: 100%;
 +
                  padding-left: 19em;
 +
                  padding-right: 1em;
 +
                  "><h6>Foto chip y conexiones por detrás</h6>
 +
                </div>
 +
                </div>
 +
            </div>
 +
 +
          <h5 style="padding-left: 1em;">ThermoCycling by displacement of droplets</h5>
 +
 +
            <div style="padding-left: 1em;">
 +
 +
            <p>For the Golden Gate assembly reaction we needed to make the droplets with the DNA and the enzymes go through a thermocycling process, which means to change the temperature in cycles. </p>
 +
 +
            <head></head><body><div class="divTabla">
 +
              <table class="border--round table--alternate-row tableBetty" style="width:100%;">
 +
                <thead>
 +
                  <tr>
 +
                    <th class="thHec">Time</th>
 +
                    <th class="thHec">Temperature</th>
 +
                    <th class="thHec">Number of cycles</th>
 +
                  </tr>
 +
                </thead>
 +
                <tbody>
 +
                  <tr>
 +
                    <td class="tdHec">10 min</td>
 +
                    <td class="tdHec">37 ºC</td>
 +
                    <td class="tdHec">1</td>
 +
                  </tr>
 +
                  <tr>
 +
                    <td class="tdHec">3 min</td>
 +
                    <td class="tdHec">37 ºC</td>
 +
                    <td rowspan="2" class="tdHec">2</td>
 +
                  </tr>
 +
                  <tr>
 +
                    <td class="tdHec">4 min</td>
 +
                    <td class="tdHec">16 ºC</td>
 +
                  </tr>
 +
                  <tr>
 +
                    <td class="tdHec">10 min</td>
 +
                    <td class="tdHec">50 ºC</td>
 +
                    <td class="tdHec">1 </td>
 +
                  </tr>
 +
                </tbody>
 +
              </table>
 +
            </div></body>
 +
 +
            <p>To take advantage of the digital microfluidics, instead of changing the temperature of a fixed place, we have decided to have the droplet alternating between two places that are at the correct temperature. This means that the temperature of the droplet changes very quickly. And it also means that we only have to stabilize two discrete temperatures instead of changing them constantly, which translates into greater temperature accuracy.</p>
 +
           
 +
            <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://via.placeholder.com/800x400" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Esquema zonas frías y caliente</h6>
 +
              </div>
 +
              </div>
 +
 +
              <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://via.placeholder.com/800x400" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Demostración de que funciona</h6>
 +
              </div>
 +
              </div>
 +
 +
              <div>
 +
              <ul>
 +
                <li>
 +
                <p> For the hot zone we are using a power resistor attached to the PCB from below and to control the current going through it we are using PWM. This means putting shortly quickly alternating between voltage on or off to create a pseudo analog voltage that is a percentage of the applied voltage depending on the duty cycle. If the pulse is longer the analog voltage would be closer to the real voltage.</p>
 +
 +
              <li>
 +
                  <p> For the cold zone a Peltier effect device has been used. This effect consists of directly converting a difference in voltage to a difference in temperature due to the P and N semiconductors that, when carrying current, transfer the heat from one side to the other. For having a good precision and better efficiency we are using voltage control. Which means actually changing the DC voltage level to alter the temperature difference. With peltier effect devices PWM is not a suitable control method because they require constant current to properly function. </p>
 +
                </li>
 +
 +
                <div>
 +
                <div class="row" style="
 +
                margin: 0;
 +
                ">
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-right: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-left: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div style="
 +
                  width: 100%;
 +
                  padding-left: 19em;
 +
                  padding-right: 1em;
 +
                  "><h6>Resistencia (izq)  Peltier (dcha)</h6>
 +
                </div>
 +
                </div>
 +
            </div>
 +
               
 +
              </ul>
 +
              </div>
 +
 +
           
 +
            <p> At both zones we are going to keep a thermistor monitoring the temperature to complete the control feedback loop. This thermistor is calibrated by using a lab grade thermometer and then adjusted using Steinhart-Hart model coefficients based on the readings (MAY EXPAND) </p>
 +
          </div>
 +
 +
            <h5 style="padding-left: 1em;">Output electroporation</h5>
 +
 +
            <div style="padding-left: 1em;">
 +
 +
            <p>
 +
            We have chosen to do the transformation of the cells in Printeria by electroporation. The cells will enter Printeria via the entry carrousel in a pipette tip stored at -20ºC. We found that at this temperature the competent cells were transformed with sufficient efficiency for at least the first two weeks. </p>
 +
 +
          <p> From this point on until the assembly reaction is complete, the competent cells are transported to a zone at 4ºC where they will remain stored. Once the assembly is complete the competent cells are mixed with the assembled genetic material and transported to the electroporator.
 +
 +
          <p> The reason for choosing electroporation as a transformation method is that, as we have seen, it is the most efficient method outperforming heat shock and other commercial methods. Furthermore the implementation of the electroporator in Printeria was simple because the necessary electronic circuit had already been designed by the Valencia_UPV team in 2016 for the HYPE-IT project. </p>
 +
          <p> As a summary, the circuit charges a Capacitor at 1600V with step-up converters. Then a simple circuit with a transistor is able to apply the voltage to the Cuvette. This means that we can apply a voltage during a very short period of time, producing the required reaction.</p>
 +
          </div>
 +
 +
<ul class="accordion accordion-1">
 +
  <li>
 +
      <div class="accordion__title">
 +
          <span class="h5">Reaction zone's budget</span>
 +
      </div>
 +
      <div class="accordion__content">
 +
              <div class="divTabla">
 +
        <table class="border--round table--alternate-row tableBetty" style="width:100%;">
 +
                  <thead><tr>
 +
                    <th class="thHec">Part</th>
 +
                    <th class="thHec">Quantity</th>
 +
                    <th class="thHec">Cost per unit</th>
 +
                    <th class="thHec">Cost</th>
 +
                  </tr>
 +
                </thead><tbody><tr>
 +
                <td class="tdHec">----</td>
 +
                <td class="tdHec">----</td>
 +
                <td class="tdHec">----</td>
 +
                <td class="tdHec">----</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">---</td>
 +
                <td class="tdHec">---</td>
 +
                <td class="tdHec">--- €</td>
 +
                <td class="tdHec">--- €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">---</td>
 +
                <td class="tdHec">---</td>
 +
                <td class="tdHec">--- €</td>
 +
                <td class="tdHec">--- €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">---</td>
 +
                <td class="tdHec">---</td>
 +
                <td class="tdHec">--- €</td>
 +
                <td class="tdHec">--- €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec" style="background-color: #909090;color: #fff; font-weight: bold;" colspan="3">Total</td>
 +
                <td class="tdHec">----</td>
 +
              </tr>
 +
            </tbody>
 +
          </table> 
 +
 +
        </div>
 +
  </li>
 +
        <li>
 +
            <div class="accordion__title">
 +
                <span class="h5">Downloads</span>
 +
            </div>
 +
                <div class="accordion__content">
 +
                  <div>
 +
                  <ul>
 +
                    <li>
 +
                      <p> Reaction zone drawings</p>
 +
                    </li>
 +
                  <li>
 +
                      <p> All-part's CAD 3D models</p>
 +
                    </li>
 +
                  </ul>
 +
                </div>
 +
                </div>
 +
        </li>
 +
      </ul>
 +
   
 +
        <div>
 +
        <a class="anchorOffset" id="Measurement"></a>
 +
        <h5>MEASUREMENT ZONE</h5>
 +
        </div>
 +
        <p> Also known as the output system, the measurement zone consists of an area separated from the rest of the zones in which the ideal conditions for the growth of bacteria are established. These conditions are achieved thanks to an electrical resistance that maintains the temperature of the whole zone at 37º and a shaker that keeps the test tubes moving to achieve a homogeneous mixture. In addition, sensors for OD and Fluorescence measurement have been implemented to monitor the entire process.</p>
 +
 +
        <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://static.igem.org/mediawiki/2018/d/d2/T--Valencia_UPV--Agitador3UPV2018.png" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Output system 3D model</h6>
 +
              </div>
 +
              </div>
 +
 +
        <p> The shaker is achieved through the use of a stepper motor connected to a methacrylate base by means of an eccentric piece and a bearing. This eccentric piece produces the oscillating movement of the methacrylate base with the help of a spring that limits the rotating movement. </p>
 +
 +
        <div style="
 +
              padding-bottom: 1em;
 +
              text-align: right;
 +
              ">
 +
              <img src="https://static.igem.org/mediawiki/2018/thumb/5/58/T--Valencia_UPV--Agitador2UPV2018.png/800px-T--Valencia_UPV--Agitador2UPV2018.png" alt="" style="
 +
              margin-top: 0.5em;
 +
              margin-bottom: 0.8em;
 +
              border-radius: 0.3em;
 +
              ">
 +
              <div style="
 +
                width: 100%;
 +
                padding-left: 19em;
 +
                padding-right: 1em;
 +
                "><h6>Exploded view of the output system</h6>
 +
              </div>
 +
              </div>
 +
 +
        <p> To this methacrylate base will be attached the test tubes’ holders in which the bacteria are contained and to which the sensors will be connected to take the measurements of OD and Fluorescence during the whole cycle of growth of the bacteria. </p>
 +
        <p> Both the eccentric piece and the test tubes’ holders have been designed by the team and obtained thanks to our 3D printer using PLA filament. </p>
 +
 +
        <div>
 +
              <div class="row" style="
 +
                margin: 0;
 +
                ">
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-right: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div class="col-md-6" style="
 +
                  padding: 0;
 +
                  padding-left: 0.3em;
 +
                  ">
 +
                  <img src="https://via.placeholder.com/800x400">
 +
                </div>
 +
                <div style="
 +
                  width: 100%;
 +
                  padding-left: 19em;
 +
                  padding-right: 1em;
 +
                  "><h6>Pieza excentrica y soporte tubo</h6>
 +
                </div>
 +
              </div>
 +
            </div>
 +
 +
        <h5 style="padding-left: 1em;">How does it work?</h5>
 +
            <div style="padding-left: 1em;">
 +
            <p>Before putting the machine into operation, the user must insert a 14 ml tube with 700ul of SOC (antibiotic-free recovery medium) into the output. Once the reactions have taken place in the experimentation area, the genetically modified and electroporated bacteria will be introduced into the 14ml tubes by means of peristaltic pumps where they will remain for 1 hour being shaken.</p>
 +
            <p>Subsequently, by means of the peristaltic pump, 3 ml of LB medium are introduced with the antibiotic to complete the bacterium growth cycle and after 16 hours the bacteria are ready and the user can remove them.</p>
 +
            <p>It should be noted that although the number of bacteria transformed with plasmids without the correct assembly has been significantly reduced, the culture obtained will not be pure. In order to obtain a pure culture it would be necessary to always make a step by plate of the culture and to isolate a transformed colony with the correct assembly.</p>
 +
          </div>
 +
 +
        <h5 style="padding-left: 1em;">Sensors</h5>
 +
            <div style="padding-left: 1em;">
 +
              <div>
 +
              <ul>
 +
                <li>
 +
                <p> <b> OD: </b> As for measuring the resulting bacteria we need a high precision light sensor we decided to use TSL235-LF. This converts the magnitude of light received into frequency, which can be precisely measured. Our sensor compares the light from a laser of <b> XXX nm </b> that passes through the experimentation tube over time. We chose a laser for a more stable light output. Comparing the values measured to the initial values without any bacteria we can calculate the percentage of absorbance of the medium, obtaining that way a suitable measurement of the cell population.</p>
 +
                </li>
 +
              <li>
 +
                  <p> <b> FL: </b>Similarly to our OD sensor we opted for the TSL235-LF for high precision light measuring. The only difference is that in this case the bacteria are excited with a LED of wavelength <b> XXX nm </b>, since it is the most suitable to excite them and obtain a fluorescent reaction from them. In front of the sensor we have put a filter that only allows light of <b>XXX nm </b>of wavelength to pass through. That way we obtain a result on the peak of fluorescent emission from the bacteria.</p>
 +
                </li>
 +
              </ul>
 +
              </div>
 +
          </div>
 +
 +
          <div style="
 +
              padding-bottom: 1em;
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              text-align: right;
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              ">
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              <img src="https://via.placeholder.com/800x400" alt="" style="
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                padding-right: 1em;
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                "><h6>Foto sensor, led y láser</h6>
 +
              </div>
 +
              </div>
 +
 +
 +
 +
<ul class="accordion accordion-1">
 +
  <li>
 +
      <div class="accordion__title">
 +
          <span class="h5">Measurement zone's budget</span>
 +
      </div>
 +
      <div class="accordion__content">
 +
              <div class="divTabla">
 +
        <table class="border--round table--alternate-row tableBetty" style="width:100%;">
 +
                  <thead><tr>
 +
                    <th class="thHec">Part</th>
 +
                    <th class="thHec">Quantity</th>
 +
                    <th class="thHec">Cost per unit</th>
 +
                    <th class="thHec">Cost</th>
 +
                  </tr>
 +
                </thead><tbody><tr>
 +
                <td class="tdHec">Kg of PLA for the 3D printed components</td>
 +
                <td class="tdHec">0,160 Kg</td>
 +
                <td class="tdHec">20 €/Kg</td>
 +
                <td class="tdHec">3 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Methacrylate plate</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">5 €</td>
 +
                <td class="tdHec">5 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Bearing</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">2 €</td>
 +
                <td class="tdHec">2 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Stepper motor</td>
 +
                <td class="tdHec">1</td>
 +
                <td class="tdHec">26,43 €</td>
 +
                <td class="tdHec">26,43 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Peristaltic pump</td>
 +
                <td class="tdHec">3</td>
 +
                <td class="tdHec">11,99 €</td>
 +
                <td class="tdHec">35,97 €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">TSL235-LF sensor</td>
 +
                <td class="tdHec">6</td>
 +
                <td class="tdHec">--- €</td>
 +
                <td class="tdHec">--- €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Led XX nm</td>
 +
                <td class="tdHec">3</td>
 +
                <td class="tdHec">--- €</td>
 +
                <td class="tdHec">--- €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec">Láser XX nm</td>
 +
                <td class="tdHec">3</td>
 +
                <td class="tdHec">--- €</td>
 +
                <td class="tdHec">--- €</td>
 +
              </tr>
 +
              <tr>
 +
                <td class="tdHec" style="background-color: #909090;color: #fff; font-weight: bold;" colspan="3">Total</td>
 +
                <td class="tdHec">----</td>
 +
              </tr>
 +
            </tbody>
 +
          </table> 
 +
 +
        </div>
 +
  </li>
 +
        <li>
 +
            <div class="accordion__title">
 +
                <span class="h5">Downloads</span>
 +
            </div>
 +
                <div class="accordion__content">
 +
                  <div>
 +
                  <ul>
 +
                    <li>
 +
                      <p> Output system drawings</p>
 +
                    </li>
 +
                  <li>
 +
                      <p> All-part's CAD 3D models</p>
 +
                    </li>
 +
                  </ul>
 +
                </div>
 +
                </div>
 +
        </li>
 +
    </ul>
 +
 +
        <div>
 +
        <a class="anchorOffset" id="Disinfection"></a>
 +
        <h5>DISINFECTION AND STERILITY</h5>
 +
        </div>
 +
        <p> It is really important to keep a sterile atmosphere around the reaction. To ensure this we have implemented a series of measures to keep Printeria clean.</p>
 +
        <div>
 +
              <ul>
 +
                <li>
 +
                <p> UltraViolet light: We have installed UV leds under the aluminum profiles in order to sterilize the reaction surface between uses. In order to achieve disinfection, the short wavelength of ultraviolet light is required to be between 280 and 100 nm.</p>
 +
                </li>
 +
              <li>
 +
                  <p> An air filter with a 220 nm pore size on the peristaltic pump of the entrance.</p>
 +
                </li>
 +
 +
                <li>
 +
                  <p> Filtered ventilation holes.</p>
 +
                </li>
 +
 +
                <li>
 +
                  <p> Water and alcohol droplets that sweep across the surface in order to absorb any remaining of the reaction.
 +
                  </p>
 +
                </li>
 +
 +
              </ul>
 +
              </div>
 +
 +
 +
        <div>
 +
        <a class="anchorOffset" id="Simultaneous"></a>
 +
        <h5>FUTURE OF PRINTERIA</h5>
 +
        </div>
 +
        <p> One of the possible upgrades that we would do to Printeria for better usage in the future is the parallelization of experiments. This means being able to run multiple experiments at the same time in paralel. We support up to three reactions at the moment but we are limited to the design of the output zone and the input of the machine. We could alter this design to be able to do many more reactions at the same time, or one right after another to optimize the resources inside the machine.</p>
 +
        <p> In addition, one of the great advantages of Printeria is that the Output system can be independent from the rest. In this way, it is possible to introduce any culture of bacteria that has not been created in the machine to monitor its growth.</p>
 +
 +
        <div>
 +
        <a class="anchorOffset" id="Results"></a>
 +
        <h5>RESULTS</h5>
 +
      </div>
 +
      <p> proximamente...</p>
 +
 +
      <div>
 +
        <a class="anchorOffset" id="Replicability"></a>
 +
        <h5>REPLICABILITY</h5>
 +
      </div>
 +
      <p> BOM-Bill of materials, explicar que con los planos se puede pedir todo a medida y poner ls planos de conjunto en grande para que se vean.</p>
 +
     
 +
          </div>
 +
  </div>
 
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<!--------------------FIN TEXTO------------------------------>
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Revision as of 09:50, 6 October 2018

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Index

    HARDWARE

    INTRODUCTION

    To address the lack of accessibility to synthetic biology due to the high costs and the level of knowledge required among others, our team has designed Printeria, a fully-equipped bioengineering device capable of automating the process of printing genetic circuits in bacteria.

    To ensure a functional, economical and easy-to-use design, collaboration between the hardware and the wet lab teams has been necessary throughout the development process. After several drafts we have achieved a unique design that can be easily transported and replicated at a cost not exceeding xxx € (xxx $).

    Printeria is divided into three main parts dependent on each other:

    • Entry of consumables: components that allow the entry of consumables into the reaction zone.

    • Reaction zone: space where the process of printing genetic circuits in bacteria occurs thanks to digital microfluidic technology.

    • Measurement zone: the bacteria are kept in conditions that allow for growth and expression while OD and fluorescence measurements are taken.

    PRINTERIA
    Assembly Sketch
    • Overall budget
      Part Quantity Cost per unit Cost
      Structure 1 381,91 € 381,91 €
      Entry system 1 49,02 € 49,02 €
      Reaction zone ---- ---- ----
      Measurement zone ---- ---- ----
      Total ----
    • Downloads

      • Assembly drawings

      • Printeria's CAD 3D model

    STRUCTURE
    Frame

    First of all, it is necessary to design a structure that confines all the elements necessary for the operation of the device inside it and also allows the creation of a sterile atmosphere to carry out the biological reactions.

    In order to facilitate its transport, aluminum has been chosen for the frame, which in addition to its low weight, has other great qualities such as great resistance to corrosion and low cost.

    It has been used 15x15x1mm square tube profiles joined by plastic corner connectors obtaining as a result a 415x360x280mm chassis. Thanks to the generated blueprints we have been able to contact a company specializing in cutting and handling aluminum that has provided us with all the parts as we required. As it was not possible for us to find plastic connectors that fit our needs, we have decided to design these parts ourselves and then print them on a 3D printer.

    Aluminum frame
    Methacrylate

    To complete the structure, it is necessary to create walls that are attached to this frame and contribute to its stability. We have opted for the use of methacrylate due to its attractive appearance, durability and scratch resistance.

    As well as the aluminum profiles, the blueprints created were used for ordering the custom-made parts to a company.

    Methacrylate cladding

    Finally, 4mm diameter countersunk head screws DIN 7991 (M4 L25) and nuts DIN 934 (M4), both made of galvanized steel, were used for joining the methacrylate plates to the frame.

    Thanks to the use of plastic connectors and bolted joints, the entire structure can be disassembled and reassembled as often as required, making it much easier to transport and store.

    Assembly sketch of the methacrylate cladding
    Leveling system

    Given the great importance of keeping the reaction zone perfectly horizontal, it is necessary to use levelling feet. In addition, for checking the horizontal position, a bull’s eye level has been installed next to the reaction zone.

    Levelling system
    • Structure's budget
      Part Quantity Cost per unit Cost
      Aluminum profiles 6 m 6,99 €/m 41,94 €
      Profiles' cutting and drilling 1 70 € 70 €
      Custom-made methacrylate 1 250 € 250 €
      Screws DIN 7991 60 0,07 € 4,2 €
      Nuts DIN 934 60 0,03 € 1,8 €
      Kg of PLA for the connectors 0,155 Kg 20 €/Kg 3,1 €
      Leeveling feet 4 0,97 € 3,88 €
      Bull's eye level 1 6,99 € 6,99 €
      Total 381,91 €
    • Downloads

      • Aluminium frame drawings

      • Methacrylate cladding drawings

      • Corner connectors' CAD 3D models

      • Structure CAD 3D model

    ENTRY OF CONSUMABLES

    In order to carry out the reactions it is necessary to introduce the consumables into the PCB. Therefore, a carousel-based system has been designed in which pipette tips with the parts necessary for the reaction are placed. The user should place these pipette tips before the experiments in the positions indicated.

    Foto de todo el sistema de entrada

    Once the tips have been inserted and the machine is ready to operate, the carousel is rotated with the help of a stepper motor until each of the tips is placed in the blowing position. In this position a needle connected to a peristaltic pump lowers vertically and injects air, thus producing the fall of the genetic material on the PCB.

    The vertically moving needle is made possible by the use of a solenoid, a device that converts electrical energy into mechanical energy which, in turns, raises or lowers the needle. Once the needle is in its low position and inserted into the pipette tip, the pump is activated and air is injected.

    Needle in its high and low position

    All the necessary parts have been designed using a 3D modeling software and then printed on our 3D printer, which means that we have been able to implement this system at a very low cost.

    Video de la prueba de concepto
    • Entry of consumables system's budget
      Part Quantity Cost per unit Cost
      Kg of PLA for the 3D printed elements 0,115 Kg 20 €/Kg 2,3 €
      Bearing 1 2 € 2 €
      Needle 1 0,3 € 0,3 €
      Stepper motor 1 26,43 € 26,43 €
      Solenoid 1 5 € 5 €
      Peristaltic pump 1 11,99 € 11,99 €
      Air filter 1 1 € 1 €
      Total 49,02 €
    • Downloads

      • Entry of consumables system drawings

      • All-part's CAD 3D models

    REACTION ZONE
    Digital Microfluidics Movement

    For the main part of the device we needed to be able to reliably and precisely control the movement of liquids involved in the reaction. This ensures that the components mix was intended and then follow every procedure accurately. For this we have decided to use a technology called digital microfluidics, which is based on applying electromagnetic fields to a special surface so that it changes its properties. More precisely we can change the hydrophobicity of the surface as to attract droplets and repel them, ensuring in this way that they follow an established route.

    DMF technology (vídeo o esquema explicativo)

    To take advantage of this we have designed the PCB under the surface with small pads on which we can apply a high voltage to cause this effect on the coating of our surface.

    PCB render

    This surface must be very hydrophobic, therefore it is necessary to coat the PCB with a polytetrafluoroethylene (PTFE) foil (12 microns thickness) and then apply a thin layer of a very hydrophobic gel called FluoroPel. In order to keep the Teflon foil well glued to the surface of the PCB, a custom-made piece has been designed and printed. The foil will be glued to this piece and then joined to the PCB by means of screws.

    Renders y fotos reales

    To be able to control so many pads we are using a HV507, a special driver chip which is a high voltage serial to parallel converter. This means that it takes data one bit at a time and then it displays them all at the same time at a high voltage. This chip can handle up to 64 outputs, meaning that we can connect 64 pads to it. So we only need a total of 6 chips for our entire surface.

    Foto chip y conexiones por detrás
    ThermoCycling by displacement of droplets

    For the Golden Gate assembly reaction we needed to make the droplets with the DNA and the enzymes go through a thermocycling process, which means to change the temperature in cycles.

    Time Temperature Number of cycles
    10 min 37 ºC 1
    3 min 37 ºC 2
    4 min 16 ºC
    10 min 50 ºC 1

    To take advantage of the digital microfluidics, instead of changing the temperature of a fixed place, we have decided to have the droplet alternating between two places that are at the correct temperature. This means that the temperature of the droplet changes very quickly. And it also means that we only have to stabilize two discrete temperatures instead of changing them constantly, which translates into greater temperature accuracy.

    Esquema zonas frías y caliente
    Demostración de que funciona

    • For the hot zone we are using a power resistor attached to the PCB from below and to control the current going through it we are using PWM. This means putting shortly quickly alternating between voltage on or off to create a pseudo analog voltage that is a percentage of the applied voltage depending on the duty cycle. If the pulse is longer the analog voltage would be closer to the real voltage.

    • For the cold zone a Peltier effect device has been used. This effect consists of directly converting a difference in voltage to a difference in temperature due to the P and N semiconductors that, when carrying current, transfer the heat from one side to the other. For having a good precision and better efficiency we are using voltage control. Which means actually changing the DC voltage level to alter the temperature difference. With peltier effect devices PWM is not a suitable control method because they require constant current to properly function.

      • Resistencia (izq) Peltier (dcha)

    At both zones we are going to keep a thermistor monitoring the temperature to complete the control feedback loop. This thermistor is calibrated by using a lab grade thermometer and then adjusted using Steinhart-Hart model coefficients based on the readings (MAY EXPAND)

    Output electroporation

    We have chosen to do the transformation of the cells in Printeria by electroporation. The cells will enter Printeria via the entry carrousel in a pipette tip stored at -20ºC. We found that at this temperature the competent cells were transformed with sufficient efficiency for at least the first two weeks.

    From this point on until the assembly reaction is complete, the competent cells are transported to a zone at 4ºC where they will remain stored. Once the assembly is complete the competent cells are mixed with the assembled genetic material and transported to the electroporator.

    The reason for choosing electroporation as a transformation method is that, as we have seen, it is the most efficient method outperforming heat shock and other commercial methods. Furthermore the implementation of the electroporator in Printeria was simple because the necessary electronic circuit had already been designed by the Valencia_UPV team in 2016 for the HYPE-IT project.

    As a summary, the circuit charges a Capacitor at 1600V with step-up converters. Then a simple circuit with a transistor is able to apply the voltage to the Cuvette. This means that we can apply a voltage during a very short period of time, producing the required reaction.

    • Reaction zone's budget
      Part Quantity Cost per unit Cost
      ---- ---- ---- ----
      --- --- --- € --- €
      --- --- --- € --- €
      --- --- --- € --- €
      Total ----
    • Downloads

      • Reaction zone drawings

      • All-part's CAD 3D models

    MEASUREMENT ZONE

    Also known as the output system, the measurement zone consists of an area separated from the rest of the zones in which the ideal conditions for the growth of bacteria are established. These conditions are achieved thanks to an electrical resistance that maintains the temperature of the whole zone at 37º and a shaker that keeps the test tubes moving to achieve a homogeneous mixture. In addition, sensors for OD and Fluorescence measurement have been implemented to monitor the entire process.

    Output system 3D model

    The shaker is achieved through the use of a stepper motor connected to a methacrylate base by means of an eccentric piece and a bearing. This eccentric piece produces the oscillating movement of the methacrylate base with the help of a spring that limits the rotating movement.

    Exploded view of the output system

    To this methacrylate base will be attached the test tubes’ holders in which the bacteria are contained and to which the sensors will be connected to take the measurements of OD and Fluorescence during the whole cycle of growth of the bacteria.

    Both the eccentric piece and the test tubes’ holders have been designed by the team and obtained thanks to our 3D printer using PLA filament.

    Pieza excentrica y soporte tubo
    How does it work?

    Before putting the machine into operation, the user must insert a 14 ml tube with 700ul of SOC (antibiotic-free recovery medium) into the output. Once the reactions have taken place in the experimentation area, the genetically modified and electroporated bacteria will be introduced into the 14ml tubes by means of peristaltic pumps where they will remain for 1 hour being shaken.

    Subsequently, by means of the peristaltic pump, 3 ml of LB medium are introduced with the antibiotic to complete the bacterium growth cycle and after 16 hours the bacteria are ready and the user can remove them.

    It should be noted that although the number of bacteria transformed with plasmids without the correct assembly has been significantly reduced, the culture obtained will not be pure. In order to obtain a pure culture it would be necessary to always make a step by plate of the culture and to isolate a transformed colony with the correct assembly.

    Sensors

    • OD: As for measuring the resulting bacteria we need a high precision light sensor we decided to use TSL235-LF. This converts the magnitude of light received into frequency, which can be precisely measured. Our sensor compares the light from a laser of XXX nm that passes through the experimentation tube over time. We chose a laser for a more stable light output. Comparing the values measured to the initial values without any bacteria we can calculate the percentage of absorbance of the medium, obtaining that way a suitable measurement of the cell population.

    • FL: Similarly to our OD sensor we opted for the TSL235-LF for high precision light measuring. The only difference is that in this case the bacteria are excited with a LED of wavelength XXX nm , since it is the most suitable to excite them and obtain a fluorescent reaction from them. In front of the sensor we have put a filter that only allows light of XXX nm of wavelength to pass through. That way we obtain a result on the peak of fluorescent emission from the bacteria.

    Foto sensor, led y láser
    • Measurement zone's budget
      Part Quantity Cost per unit Cost
      Kg of PLA for the 3D printed components 0,160 Kg 20 €/Kg 3 €
      Methacrylate plate 1 5 € 5 €
      Bearing 1 2 € 2 €
      Stepper motor 1 26,43 € 26,43 €
      Peristaltic pump 3 11,99 € 35,97 €
      TSL235-LF sensor 6 --- € --- €
      Led XX nm 3 --- € --- €
      Láser XX nm 3 --- € --- €
      Total ----
    • Downloads

      • Output system drawings

      • All-part's CAD 3D models

    DISINFECTION AND STERILITY

    It is really important to keep a sterile atmosphere around the reaction. To ensure this we have implemented a series of measures to keep Printeria clean.

    • UltraViolet light: We have installed UV leds under the aluminum profiles in order to sterilize the reaction surface between uses. In order to achieve disinfection, the short wavelength of ultraviolet light is required to be between 280 and 100 nm.

    • An air filter with a 220 nm pore size on the peristaltic pump of the entrance.

    • Filtered ventilation holes.

    • Water and alcohol droplets that sweep across the surface in order to absorb any remaining of the reaction.

    FUTURE OF PRINTERIA

    One of the possible upgrades that we would do to Printeria for better usage in the future is the parallelization of experiments. This means being able to run multiple experiments at the same time in paralel. We support up to three reactions at the moment but we are limited to the design of the output zone and the input of the machine. We could alter this design to be able to do many more reactions at the same time, or one right after another to optimize the resources inside the machine.

    In addition, one of the great advantages of Printeria is that the Output system can be independent from the rest. In this way, it is possible to introduce any culture of bacteria that has not been created in the machine to monitor its growth.

    RESULTS

    proximamente...

    REPLICABILITY

    BOM-Bill of materials, explicar que con los planos se puede pedir todo a medida y poner ls planos de conjunto en grande para que se vean.