Difference between revisions of "Team:NTNU Trondheim/Hardware"

Line 1: Line 1:
−
{{NTNU_Trondheim}}
+
<html lang="en">
−
<html>
+
<!--
 +
    Colours used:
 +
        white: #F5F5F5 (whitesmoke)
 +
        black: #101417
 +
        grey: #808080
 +
-->
 +
<head>
 +
    <meta charset="UTF-8">
 +
    <!-- Preloaded elements which is added dynamically to the page, and as such might be needed before normally loaded -->
 +
    <link rel="preload" as="image" href="https://static.igem.org/mediawiki/2017/3/3a/T--NTNU_Trondheim--arrow_down_black.png">
 +
    <link rel="preload" as="image" href="https://static.igem.org/mediawiki/2017/8/85/T--NTNU_Trondheim--arrow_up_black.png">
 +
    <link rel="preload" as="image" href="https://static.igem.org/mediawiki/2017/d/d2/T--NTNU_Trondheim--arrow_up_grey.png">
 +
    <link rel="preload" as="image" href="https://static.igem.org/mediawiki/2017/4/4c/T--NTNU_Trondheim--IMG_8959.jpg">
 +
    <link rel="preload" as="image" href="https://static.igem.org/mediawiki/2017/e/e2/T--NTNU_Trondheim--IMG_8974.jpg">
 +
    <link rel="preload" as="image" href="https://static.igem.org/mediawiki/2017/7/75/T--NTNU_Trondheim--IMG_9887.jpg">
 +
    <!--stylesheets etc -->
 +
    <link rel="stylesheet" type="text/css"
 +
          href="https://2017.igem.org/Template:NTNU_Trondheim/CSS/global?action=raw&ctype=text/css" />
 +
    <link rel="stylesheet" type="text/css"
 +
          href="https://2017.igem.org/Template:NTNU_Trondheim/CSS/footer?action=raw&ctype=text/css" />
 +
    <link rel="stylesheet" type="text/css"
 +
          href="https://2017.igem.org/Template:NTNU_Trondheim/CSS/menu?action=raw&ctype=text/css" />
 +
    <link rel="stylesheet" type="text/css"
 +
          href="https://2017.igem.org/Template:NTNU_Trondheim/CSS/content?action=raw&ctype=text/css" />
 +
    <link rel="stylesheet" type="text/css"
 +
          href="https://2017.igem.org/Template:NTNU_Trondheim/CSS/page_picture?action=raw&ctype=text/css" />
 +
    <link rel="stylesheet" type="text/css"
 +
          href="https://2017.igem.org/Template:NTNU_Trondheim/CSS/fix_code?action=raw&ctype=text/css" />
  
 +
    <script src="http://code.jquery.com/jquery-latest.min.js" type="text/javascript"></script>
  
 +
    <script type="text/javascript" src="https://2017.igem.org/Template:NTNU_Trondheim/JS/picture_field_resize?action=raw&ctype=text/javascript"></script>
 +
    <script type="text/javascript" src="https://2017.igem.org/Template:NTNU_Trondheim/JS/slideshow?action=raw&ctype=text/javascript"></script>
 +
    <script type="text/javascript" src="https://2017.igem.org/Template:NTNU_Trondheim/JS/show_more_text?action=raw&ctype=text/javascript"></script>
 +
</head>
 +
<body>
 +
<div id="page_content_container">
 +
    <div id="menu">
 +
        <div id='cssmenu'>
 +
            <!-- Is ordered left to right! -->
 +
            <ul>
 +
                <li class='active'>
 +
                    <a href='https://2017.igem.org/Team:NTNU_Trondheim'>
 +
                        <div>
 +
  <span>
 +
    Home
 +
  </span>
 +
                        </div>
 +
                    </a>
 +
                </li>
 +
                <li>
 +
                    <a href='https://2017.igem.org/Team:NTNU_Trondheim/Safety'>
 +
                        <div>
 +
  <span>
 +
Safety
 +
  </span>
 +
                        </div>
 +
                    </a>
 +
                </li>
 +
                <li>
 +
                    <a href='https://2017.igem.org/Team:NTNU_Trondheim/Parts'>
 +
                        <div>
 +
  <span>
 +
Parts
 +
  </span>
 +
                        </div>
 +
                    </a>
 +
                </li>
 +
                <li class="has-sub">
 +
                    <div>
 +
                        <span>
 +
                            Project
 +
                        </span>
 +
                    </div>
 +
                    <ul>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Description'>
 +
                                <span>
 +
                                    Description
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Background'>
 +
                                <span>
 +
                                    Background
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Results'>
 +
                                <span>
 +
                                    Results
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Contribution'>
 +
                                <span>
 +
                                    Contribution
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Demonstrate'>
 +
                                <span>
 +
                                    Demonstrate
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Model'>
 +
                                <span>
 +
                                    Modeling
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Notebook'>
 +
                                <span>
 +
                                    Lab Journal
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Experiments'>
 +
                                <span>
 +
                                    Protocols
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                    </ul>
 +
                </li>
 +
                <li class='has-sub'>
 +
                    <div>
 +
                        <span>
 +
                            Human practices
 +
                        </span>
 +
                    </div>
 +
                    <ul>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/HP/Silver'>
 +
                                <span>
 +
                                    Human practice
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Engagement'>
 +
                                <span>
 +
                                    Public engagement
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                    </ul>
 +
                </li>
 +
                <li class='has-sub'>
 +
                    <div>
 +
                        <span>
 +
                            People
 +
                        </span>
 +
                    </div>
 +
                    <ul>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Team'>
 +
                                <span>
 +
                                    Team
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Collaborations'>
 +
                                <span>
 +
                                    Collaborations
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Attributions'>
 +
                                <span>
 +
                                    Attributions
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/People/Sponsors'>
 +
                                <span>
 +
                                    Sponsors
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                    </ul>
 +
                </li>
 +
                <li class='has-sub'>
 +
                    <div>
 +
                        <span>
 +
                            Awards
 +
                        </span>
 +
                    </div>
 +
                    <ul>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Achievements'>
 +
                                <span>
 +
                                    Achievements
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Applied_Design'>
 +
                                <span>
 +
                                    Applied Design
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href='https://2017.igem.org/Team:NTNU_Trondheim/Hardware'>
 +
                                <span>
 +
                                    Hardware
 +
                                </span>
 +
                            </a>
 +
                        </li>
 +
                    </ul>
 +
                </li>
 +
            </ul>
 +
        </div>
 +
    </div>
  
−
<div class="column half_size">
+
    <div id="picture_field">
 +
        <div id="triangle_topright">
 +
            <img src="https://static.igem.org/mediawiki/2017/e/e6/T--NTNU_Trondheim--top_right_triangle.svg">
 +
        </div>
 +
        <div id="icon">
 +
            <img src="https://static.igem.org/mediawiki/2017/8/89/T--NTNU_Trondheim--logo_wo_background.svg">
 +
        </div>
 +
        <div id="triangle_topleft">
 +
            <img src="https://static.igem.org/mediawiki/2017/7/74/T--NTNU_Trondheim--top_left_triangle.svg">
 +
        </div>
 +
        <div id="slideshow_container">
 +
            <!-- example of slideshow of 1, ie. only a picture. If you wish to make slideshow again, remember to comment
 +
            back the slideshow.js script in the head section-->
 +
            <!-- dimensions 2:1 must be honored for ALL pictures added to slideshow -->
 +
            <img src="https://static.igem.org/mediawiki/2017/a/a1/T--NTNU_Trondheim--Hardware.jpg">
 +
        </div>
 +
    </div>
  
−
<h1>Hardware</h1>
+
    <div class="content">
−
<h3>Best Hardware Special Prize</h3>
+
        <div class="break_header">
−
<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>
+
            <img src="https://static.igem.org/mediawiki/2017/4/49/T--NTNU_Trondheim--splitter_header.svg">
 +
        </div>
  
−
<p>
+
        <div class="paragraph_no_img">
−
Teams who are interested in working with hardware as a side project are encouraged to apply for the hardware award.  
+
            <h1>Hardware</h1>
 +
            <p>
 +
                Hardware has been central to our project this year. Our goal was to make a chemostat system (consisting
 +
                of three connected chemostats) that would allow us to evolve phage against phage-resistant bacteria. We
 +
                were given a set of old peristaltic pumps, a water heating/pumping unit and some tubing. We developed an
 +
                Arduino-DUE-based system, which controls five chemostats through RS232 ports, getting inputs from five
 +
                self-designed scales (we constructed them from load cells, aluminum plates and electric amplifiers) and
 +
                three self-designed 3D-printed OD600 photometers. The system controls the liquid volume within and the
 +
                flow rate through each chemostat using a PID controller. The liquid volume, flow and OD data it acquires
 +
                is transferred to a PC, logged and plotted in real time on a graphical user interface (also self-written),
 +
                with the possibility of controlling chemostat parameters from the PC itself. This made the whole of our
 +
                hardware/software system (the pumps excluded) quite user-friendly and cheaper than a single lab-scale!
 +
                Below we describe each developed piece of hardware in detail.
 +
                <br><br>
 +
                Click <a href="https://static.igem.org/mediawiki/2017/8/89/T--NTNU_Trondheim--HarwareMovie.mp4">here</a> for
 +
                video of the setup.
 +
            </p>
 +
        </div>
  
−
<br><br>
 
−
To compete for the <a href="https://2017.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://2017.igem.org/Judging/Judging_Form">judging form</a>.
 
−
<br><br>
 
−
You must also delete the message box on the top of this page to be eligible for this prize.
 
−
</p>
 
−
</p>
 
−
</div>
 
  
−
<div class="column half_size">
+
        <div class="break_2">
−
<h5>Inspiration</h5>
+
            <img src="https://static.igem.org/mediawiki/2017/5/52/T--NTNU_Trondheim--splitter_2.svg">
−
<p>You can look at what other teams did to get some inspiration! <br />
+
        </div>
−
Here are a few examples:</p>
+
−
<ul>
+
−
<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
+
−
<li><a href="https://2016.igem.org/Team:Aachen">2016 Aachen </a></li>
+
−
<li><a href="https://2015.igem.org/Team:TU_Delft">2015 TU Delft  </a></li>
+
−
<li><a href="https://2015.igem.org/Team:TU_Darmstadt">2015 TU Darmstadt</a></li>
+
−
</ul>
+
  
−
</div>
+
        <div class="paragraph_no_img">
 +
            <h1>OD reader</h1>
 +
            <p>
 +
                The OD reader was designed to allow real time measurement of OD600 in a chemostat culture. It consisted
 +
                of a core scaffold into which a flow-through cuvette, a LED module and a sensor module could be slid.
 +
                All parts where 3D-modeled from scratch and prited using a PLA-based 3D-printer.
 +
                We made our own flow-through cuvettes by gluing 3D-printed tubing connectors on each end of a
 +
                normal spectrophotometry cuvette. When everything is attached light is passed from the LED module
 +
                (we used a standard yellow 10p LED for this) through a narrow slit in the core scaffold, the cuvette,
 +
                a new slit and onto the sensor. For the light sensor we used the $7 Adafruit TSL2591 high dynamic range
 +
                sensor, in total $7.10. The sensor could yield an accuracy of about 0.05%. In order to be able to control
 +
                all three OD sensors from the only I2C port on the Arduino, we used two CD4066 bilateral switches both
 +
                on the signal and on the clock lines.
 +
            </p>
 +
        </div>
  
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/4/4f/T--NTNU_Trondheim--OD_reader_scaffold.jpg">
 +
            <p>Reader scaffold module (3D-printed).</p>
 +
        </div>
  
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/1/13/T--NTNU_Trondheim--OD_reader_cyvette.jpg">
 +
            <p>Modified cuvette attached to tubing taken out from the reader scaffold.</p>
 +
        </div>
  
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/a/af/T--NTNU_Trondheim--OD_reader_setup.jpg">
 +
            <p>Three OD readers in an array (one for each chemostat).<br><br><br><br></p>
 +
        </div>
 +
 +
 +
        <div class="break_1">
 +
            <img src="https://static.igem.org/mediawiki/2017/6/6d/T--NTNU_Trondheim--splitter_1.svg">
 +
        </div>
 +
 +
        <div class="paragraph_no_img">
 +
            <h1>Scale</h1>
 +
            <p>
 +
                To make a fully controllable chemostat setup we needed a total of five scales whose readings we could
 +
                record on an Arduino board. There were not enough available scientific scales in the lab, while common
 +
                scales (<$1000) do not come with external communication buses. So we decided to make our own cheap
 +
                alternative, consisting of a SparkFun TAL220 load cell ($7) with an HX711 load cell amplifier ($10),
 +
                two aluminium plates and screws. The production of plates amounted to about $10 per plate, giving a
 +
                total of $37 expenses per scale. The scale could measure up to 10kg of load with <0.5g accuracy. Given
 +
                that the load was dynamic due to pumping, the accuracy of the weight readings was similar to an $2000
 +
                lab scale, which we tried as an alternative! 
 +
            </p>
 +
        </div>
 +
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/7/73/T--NTNU_Trondheim--Scale.jpg">
 +
            <p>Self-designed scale overview.</p>
 +
        </div>
 +
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/d/db/T--NTNU_Trondheim--Loadingcell.jpg">
 +
            <p>Side view of scale. The load cell can be seen in the middle. The screws to the left correspond to the ones in the middle of the plate on the previous picture.<br><br><br><br></p>
 +
        </div>
 +
 +
 +
        <div class="break_2">
 +
            <img src="https://static.igem.org/mediawiki/2017/5/52/T--NTNU_Trondheim--splitter_2.svg">
 +
        </div>
 +
 +
        <div class="paragraph_no_img">
 +
            <h1>Lids</h1>
 +
            <p>
 +
                In addition to the electronic hardware, we designed and printed lids for the chemostats and medium tanks,
 +
                which made it easier to use tubing and take samples from the chemostats. We hope to be able to print whole
 +
                chemostats in the future.
 +
            </p>
 +
        </div>
 +
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/3/3d/T--NTNU_Trondheim--Lid_above.jpg">
 +
            <p>A chemostat lid from above. Holes for air intake and input/output tubes can be seen, as well as the lid
 +
                on top of an opening for taking samples of the culture.</p>
 +
        </div>
 +
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/1/1f/T--NTNU_Trondheim--Lid_below.jpg">
 +
            <p>The same lid from beneath.<br><br><br><br></p>
 +
        </div>
 +
 +
 +
        <div class="break_1">
 +
            <img src="https://static.igem.org/mediawiki/2017/6/6d/T--NTNU_Trondheim--splitter_1.svg">
 +
        </div>
 +
 +
        <div class="paragraph_no_img">
 +
            <h1>Setup</h1>
 +
            <p>
 +
                We used an Arudino Due to control the 5 scales, 5 pumps and 3 OD sensors. A set of classes was written
 +
                for calibration and simplified use of the hardware. A PID regulator was constructed and shown to be able
 +
                to stably control the flows and volumes in each chemostat over any tested period of time
 +
                (16 hours in our case). In order to make the system user friendly, a graphical C++ based interface module
 +
                was written for the computer. The interface could perform bidirectional communication with the Arduino,
 +
                visualizing ODs, chemostat weights and flows in real time, and sending back user defined targets for
 +
                flows and weights (pausing and flushing buttons were also implemented). Additionally the software logged
 +
                all the data read in from the Arduino into spreadsheet files.
 +
            </p>
 +
        </div>
 +
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/2/21/T--NTNU_Trondheim--Arduino_setup.jpg">
 +
            <p>An overview of the Arduino pinout.</p>
 +
        </div>
 +
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/e/ec/T--NTNU_Trondheim--Chemostats_setup_bench.jpg">
 +
            <p>The general setup of the three-chemostat system. Printed locks can be seen on the medium tanks to the right and left as well as on the chemostats.</p>
 +
        </div>
 +
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/a/a0/T--NTNU_Trondheim--Hardware_graph1.png">
 +
            <p>A screenshot of the self-written chemostat control GUI.</p>
 +
        </div>
 +
 +
        <div class="image" style="width: 50%;margin-top: 5em">
 +
            <!-- The width of the page the picture will occupy. The height is calculated from it to honor the source dimensions. Should NOT exceed 70%-->
 +
            <!-- margin-top and margin-bottom should be set to reach a suitable amount of whitespace, depending on the image location. 0 by default -->
 +
            <img src="https://static.igem.org/mediawiki/2017/d/d5/T--NTNU_Trondheim--Hardware_graph2.png">
 +
            <p>A plot of the OD measurements of a three chemostat system for a 13 hour experiment.<br><br><br><br></p>
 +
        </div>
 +
 +
        <div class="footer">
 +
            <img src="https://static.igem.org/mediawiki/2017/7/7c/T--NTNU_Trondheim--splitter_footer.svg">
 +
            <div class="footer_content">
 +
                <div class="sponsors">
 +
                    <a href="https://www.ntnu.edu/nv" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/e/e1/T--NTNU_Trondheim--Faculty_logo_black.png">
 +
                    </a>
 +
<a href="http://www.ntnu.edu/ibt" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/8/83/T--NTNU_Trondheim--Instituttlogo_english_white.png">
 +
                    </a>
 +
                    <a href="http://aquagen.no/en/" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/2/27/T--NTNU_Trondheim--AquaGen_forslag1_transparent.png">
 +
                    </a>
 +
                    <a href="http://www.biokjemisk.no/" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/f/f4/T--NTNU_Trondheim--NBS_forslag1_transparent.png">
 +
                    </a>
 +
                    <a href="http://www.imr.no/en" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/e/e4/T--NTNU_Trondheim--Havforskningsinstituttet_white.png">
 +
                    </a>
 +
<a href="http://www.vectronbiosolutions.com/" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/8/86/T--NTNU_Trondheim--Vectron_forslag1_transparent.png">
 +
                    </a>
 +
<a href="http://digitallifenorway.org/gb/" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/d/da/T--NTNU_Trondheim--SDL_LOGO_ENG_confirmed_version2.png">
 +
                    </a>
 +
                    <a href="https://www.skretting.com/en-us/" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/4/4d/T--NTNU_Trondheim--Skretting_logo_black.png">
 +
                    </a>
 +
</div>
 +
                <div class="sosial_media">
 +
                    <a href="mailto:igem-team@ntnu.no" >
 +
                        <img src="https://static.igem.org/mediawiki/2017/5/5a/T--NTNU_Trondheim--mail.png">
 +
                    </a>
 +
                    <a href="http://www.facebook.com/igemntnu2017/" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/8/8b/T--NTNU_Trondheim--facebook.png">
 +
                    </a>
 +
                    <a href="http://twitter.com/ntnuigem?lang=en/" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/8/8b/T--NTNU_Trondheim--twitter.png">
 +
                    </a>
 +
                    <a href="http://www.instagram.com/ntnu_igem/" target="_blank">
 +
                        <img src="https://static.igem.org/mediawiki/2017/6/64/T--NTNU_Trondheim--instagram.png">
 +
                    </a>
 +
                    <p>
 +
                        Email: igem-team@ntnu.no
 +
                    </p>
 +
                </div>
 +
            </div>
 +
        </div>
 +
    </div>
 +
 +
</div>
 +
</body>
 
</html>
 
</html>

Revision as of 18:55, 1 November 2017

Hardware

Hardware has been central to our project this year. Our goal was to make a chemostat system (consisting of three connected chemostats) that would allow us to evolve phage against phage-resistant bacteria. We were given a set of old peristaltic pumps, a water heating/pumping unit and some tubing. We developed an Arduino-DUE-based system, which controls five chemostats through RS232 ports, getting inputs from five self-designed scales (we constructed them from load cells, aluminum plates and electric amplifiers) and three self-designed 3D-printed OD600 photometers. The system controls the liquid volume within and the flow rate through each chemostat using a PID controller. The liquid volume, flow and OD data it acquires is transferred to a PC, logged and plotted in real time on a graphical user interface (also self-written), with the possibility of controlling chemostat parameters from the PC itself. This made the whole of our hardware/software system (the pumps excluded) quite user-friendly and cheaper than a single lab-scale! Below we describe each developed piece of hardware in detail.

Click here for video of the setup.

OD reader

The OD reader was designed to allow real time measurement of OD600 in a chemostat culture. It consisted of a core scaffold into which a flow-through cuvette, a LED module and a sensor module could be slid. All parts where 3D-modeled from scratch and prited using a PLA-based 3D-printer. We made our own flow-through cuvettes by gluing 3D-printed tubing connectors on each end of a normal spectrophotometry cuvette. When everything is attached light is passed from the LED module (we used a standard yellow 10p LED for this) through a narrow slit in the core scaffold, the cuvette, a new slit and onto the sensor. For the light sensor we used the $7 Adafruit TSL2591 high dynamic range sensor, in total $7.10. The sensor could yield an accuracy of about 0.05%. In order to be able to control all three OD sensors from the only I2C port on the Arduino, we used two CD4066 bilateral switches both on the signal and on the clock lines.

Reader scaffold module (3D-printed).

Modified cuvette attached to tubing taken out from the reader scaffold.

Three OD readers in an array (one for each chemostat).



Scale

To make a fully controllable chemostat setup we needed a total of five scales whose readings we could record on an Arduino board. There were not enough available scientific scales in the lab, while common scales (<$1000) do not come with external communication buses. So we decided to make our own cheap alternative, consisting of a SparkFun TAL220 load cell ($7) with an HX711 load cell amplifier ($10), two aluminium plates and screws. The production of plates amounted to about $10 per plate, giving a total of $37 expenses per scale. The scale could measure up to 10kg of load with <0.5g accuracy. Given that the load was dynamic due to pumping, the accuracy of the weight readings was similar to an $2000 lab scale, which we tried as an alternative! 

Self-designed scale overview.

Side view of scale. The load cell can be seen in the middle. The screws to the left correspond to the ones in the middle of the plate on the previous picture.



Lids

In addition to the electronic hardware, we designed and printed lids for the chemostats and medium tanks, which made it easier to use tubing and take samples from the chemostats. We hope to be able to print whole chemostats in the future.

A chemostat lid from above. Holes for air intake and input/output tubes can be seen, as well as the lid on top of an opening for taking samples of the culture.

The same lid from beneath.



Setup

We used an Arudino Due to control the 5 scales, 5 pumps and 3 OD sensors. A set of classes was written for calibration and simplified use of the hardware. A PID regulator was constructed and shown to be able to stably control the flows and volumes in each chemostat over any tested period of time (16 hours in our case). In order to make the system user friendly, a graphical C++ based interface module was written for the computer. The interface could perform bidirectional communication with the Arduino, visualizing ODs, chemostat weights and flows in real time, and sending back user defined targets for flows and weights (pausing and flushing buttons were also implemented). Additionally the software logged all the data read in from the Arduino into spreadsheet files.

An overview of the Arduino pinout.

The general setup of the three-chemostat system. Printed locks can be seen on the medium tanks to the right and left as well as on the chemostats.

A screenshot of the self-written chemostat control GUI.

A plot of the OD measurements of a three chemostat system for a 13 hour experiment.



Email: igem-team@ntnu.no