Difference between revisions of "Team:Newcastle/Software"

m
 
(34 intermediate revisions by 7 users not shown)
Line 1: Line 1:
−
{{Newcastle/navbar}}
+
{{Newcastle/navbar2}}
 
<html>
 
<html>
 
<head>
 
<head>
−
   <title>Alternative Roots/Attributions</title>
+
   <title>Alternative Roots/Software</title>
 
</head>
 
</head>
  
Line 9: Line 9:
 
     <!-- home
 
     <!-- home
 
     ================================================== -->
 
     ================================================== -->
−
     <section id="home" class="s-home target-section" data-parallax="scroll" data-image-src="https://static.igem.org/mediawiki/2018/9/96/T--Newcastle--SoftHeader.jpeg">
+
     <section id="home" class="s-home target-section" data-parallax="scroll" data-image-src="https://static.igem.org/mediawiki/2018/f/fb/T--Newcastle--SoftwareCover.png">
  
 
         <div class="overlay"></div>
 
         <div class="overlay"></div>
Line 21: Line 21:
  
 
                 <h1>
 
                 <h1>
−
                   Software
+
                   Software Overview
 
                    
 
                    
 
                    
 
                    
Line 27: Line 27:
  
 
                 <div class="home-content__buttons">
 
                 <div class="home-content__buttons">
−
                     <a href="#Attributions" class="smoothscroll btn btn--stroke">
+
                     <a onclick="location.href='https://2018.igem.org/Team:Newcastle/Software/OT'" class="smoothscroll btn btn--stroke">
−
                         Attributions
+
                         OpenTrons
 
                     </a>
 
                     </a>
−
                     <a href="#Acknowledgements" class="smoothscroll btn btn--stroke">
+
                     <a onclick="location.href='https://2018.igem.org/Team:Newcastle/Software/NH1'" class="smoothscroll btn btn--stroke">
−
                        Acknowledgements
+
                         NH-1
−
                    </a>
+
−
                    <a href="#sponsors" class="smoothscroll btn btn--stroke">
+
−
                         Sponsors
+
 
                     </a>
 
                     </a>
 
                 </div>
 
                 </div>
Line 40: Line 37:
 
             </div>
 
             </div>
  
−
            <div class="home-content__scroll">
 
−
                <a href="#Attributions" class="scroll-link smoothscroll">
 
−
                    <span>Scroll Down</span>
 
−
                </a>
 
−
            </div>
 
−
 
−
            <div class="home-content__line"></div>
 
  
 
         </div> <!-- end home-content -->
 
         </div> <!-- end home-content -->
Line 56: Line 46:
 
================================================== -->
 
================================================== -->
  
−
    <section id='code' class="s-about">
+
<section id='Opentrons' class="s-services">
  
 
         <div class="row section-header has-bottom-sep" data-aos="fade-up">
 
         <div class="row section-header has-bottom-sep" data-aos="fade-up">
−
            <div class="col-full">
+
                <div class="col-full">
−
                <h3 class="subhead subhead--dark">NH-1</h3>
+
                            <h3 class="subhead"></h3>
−
                 <h1 class="display-1 display-1--light">Software</h1>
+
                 <h1 class="display-1">Overview</h1>
 
             </div>
 
             </div>
 
         </div> <!-- end section-header -->
 
         </div> <!-- end section-header -->
  
−
        <div class="row about-desc" data-aos="fade-up">
+
            <div class="row about-desc" data-aos="fade-up">
−
            <div class="col-full">
+
−
                <p class="about-para">Adaptability was a major issue with the existing plant growth infrastructure within the University and, in fact, with many traditional growth facilities. We designed the NH-1 to combat this. The NH-1 is controlled entirely by an Arduino micro-controller. The Arduino offers a low-cost, easy-to-use solution to control and adapt the function of the LEDs. The Arduino also offers an open-source electronic prototyping platform and offers plenty of opportunities for further development of the NH-1, in terms of user interface and interaction. All the code and the IDE are freely available online and the UNO board can be purchased online from Arduino for less than £20. The Arduino language is based on C/C++ so it is incredibly easy to become familiar with, especially if you already have experience with C/C++ but if not there is a wealth of resources online that can help with this. We have designed a guide to using the IDE and included some examples of the capabilities of the NH-1. Some of the features that you can incorporate include:</p>
+
−
                <ul style="list-style-type:circle;display:grid;text-align:left;">
+
−
                    <li>Solid colours across the system</li>
+
−
                    <li>Cyclically varying colours (rainbow) in the system</li>
+
−
                    <li>Linear gradients of colours across the system</li>
+
−
                    <li>Colours can be defined by RGB, HSV values or HTML standard</li>
+
−
                    <li>Brightness can be varied, for example to simulate a day/night cycle or a gradual sunrise/sunset</li>
+
−
                </ul>
+
−
                <p class="about-para" style="margin-top:4%;">The list goes on as the possibilities with the NH-1 are incredibly varied. This makes it the ideal system for plant-based experimentation, with the added bonus that the system is completely contained and portable. The end result is a highly adaptable, semi-autonomous system that is simple to code and even easier to run.</p>
+
−
 
+
−
+
−
            </div>
+
−
        </div> <!-- end project-desc -->
+
−
 
+
−
 
+
−
        <div class="about__line"></div>
+
−
 
+
−
    </section> <!-- end s-about -->
+
−
 
+
−
 
+
−
    <!-- works
+
−
    ================================================== -->
+
−
    <section id='Acknowledgements' class="s-works">
+
−
 
+
−
        <div class="intro-wrap">
+
−
               
+
−
            <div class="row section-header has-bottom-sep light-sep" data-aos="fade-up">
+
 
                 <div class="col-full">
 
                 <div class="col-full">
−
                    <h3 class="subhead">Additional Support</h3>
 
−
                    <h1 class="display-2 display-2--light">ACKNOWLEDGEMENTS</h1>
 
−
                    <font size="4" font face="verdana" font color="white">We would like to thank these people for helping us along the way. We have been supported by people from a diverse range of disciplines in every aspect of our project. </font>
 
−
                </div>
 
−
            </div>
 
  
−
        <div class="row services-list block-1-2 block-tab-full">
 
  
−
            <div class="col-block service-item" data-aos="fade-up">
+
                     <p style="font-size:100%">A significant proportion of the Alternative Roots project was based on software, whether that was for automation of experiments via the Opentrons OT-2 or small-scale plant growth via our NH-1. Both systems were carefully programmed by our team for efficiency and reliability.</p>
−
                <div class="service-icon">
+
−
                     <i class="icon-paint-brush"></i>
+
−
                </div>
+
−
                <div class="service-text">
+
−
                    <h3 class="h2"style="color:white">Induction Talks</h3>
+
−
                    <!--<img src="">-->
+
−
                    <ul style="list-style-type:circle;overflow:visible; color:white;">
+
−
                        <li>Dr. Jem Stach</li>
+
−
                        <li>Dr. Jon Marles-Wright</li>
+
−
                        <li>Dr. Thomas Howard</li>
+
−
                        <li>Dr. Kenneth Taylor</li>
+
−
                        <li>Dr. Harold Fellermann</li>
+
−
                        <li>Dr. Martyn Dade-Robertson</li>
+
−
                        <li>Professor Rachel Armstrong</li>
+
−
                        <li>Professor Phillip Wright</li>
+
−
                        <li>Dr. Dana Ofiteru</li>
+
−
                        <li>Dr. Maxim Kapralov</li>
+
−
                        <li>Dr. Angel Goni-Moreno</li>
+
−
                        <li>Dr. Nicholas Aldred</li>
+
−
                        <li>Dr. Vasilios Andriotis</li>
+
−
                        <li>Dr. Ilke Turkmendag</li>
+
−
                    </ul>
+
−
                </div>
+
−
            </div>
+
  
−
            <div class="col-block service-item" data-aos="fade-up">
+
                     <p style="font-size:100%">Newcastle were fortunate to win an Opentrons OT-2 liquid-handling robot in 2018. The OT-2 is programmed in Python and is equipped with two pipettes capable of pipetting between 1 and 300 µL as well as a temperature module, capable of maintaining temperatures between 0-100 °C. We have created and deposited code that allows OT-2 users to automate small-scale (100 µL) heat-shock transformations of <i>E. coli</i>. The value of this code was demonstrated when it was used to perform a statistical ‘Definitive Screening Design’ screen to examine the impact that transformation buffers have on transformation efficiency. As a result, we identified a new buffer composition with 10-fold improved transformation efficiency. Perhaps more importantly, the combination of the code and the robot resulted in greater reliability than the manual protocol.</p>
−
                <div class="service-icon">
+
<br>
−
                     <i class="icon-paint-brush"></i>
+
<br>
−
                </div>
+
−
                <div class="service-text">
+
−
                    <h3 class="h2"style="color:white">Subject Specific Support</h3>
+
−
                    <!--<img src="">-->
+
−
                    <ul style="list-style-type:circle;overflow:visible; color:white;">
+
−
                        <li>Dr. Alice Banks (Chemotaxis)</li>
+
−
                        <li>Dr. Maria Del Carmen Montero-Calasanz (Endophyte Development)</li>
+
−
                        <li>Bradley Brown (Wiki Development/Community Modelling))</li>
+
−
                        <li>Josh Isaac (Biosynthesis Pathway Modelling)</li>
+
−
                        <li>Aidan Clamp (Biosynthesis Pathway Modelling)</li>
+
−
                        <li>Connor Barker (Biosynthesis Pathway Modelling)</li>
+
−
                        <li>Dr. Martyn Dade-Robertson (Human Practices)</li>
+
−
                        <li>Professor Rachel Armstrong (Human Practices)</li>
+
−
                    </ul>
+
 
                 </div>
 
                 </div>
 
             </div>
 
             </div>
  
 +
    </section> <!-- end s-services -->
  
 +
<section id='team' class="s-services">
  
  
−
            <div class="col-block service-item" data-aos="fade-up">
+
        <div class="row section-header has-bottom-sep" data-aos="fade-up">
−
                 <div class="service-icon">
+
                 <div class="col-full">
−
                    <i class="icon-paint-brush"></i>
+
                            <br>
−
                </div>
+
<br>
−
                <div class="service-text">
+
<br>
−
                    <h3 class="h2"style="color:white">Stakeholder Engagement</h3>
+
<br>
−
                    <!--<img src="">-->
+
<h3 class="subhead"></h3>
−
                    <ul style="list-style-type:circle;overflow:visible; color:white;">
+
                <h1 class="display-2">References & Attributions</h1>
−
                        <li>Professor Chris Tapsell (KWS Seeds)</li>
+
−
                        <li>Richard Ballard (Growing Underground)</li>
+
−
                        <li>Steve Dring (Growing Underground)</li>
+
−
                        <li>Tom Webster (GrowUp Urban Farms)</li>
+
−
                        <li>Nicola Cowell (Food Nation)</li>
+
−
                        <li>Paul Brown (GrowModule 365)</li>
+
−
                        <li>Clive Goodwin (Victoria Tunnels)</li>
+
−
                    </ul>
+
−
                </div>
+
 
             </div>
 
             </div>
  
−
            <div class="col-block service-item" data-aos="fade-up">
+
        </div>
−
                <div class="service-icon">
+
−
                    <i class="icon-paint-brush"></i>
+
−
                </div>
+
−
                <div class="service-text">
+
−
                    <h3 class="h2"style="color:white">Newcastle University Farms</h3>
+
−
                    <!--<img src="">-->
+
−
                    <ul style="list-style-type:circle;overflow:visible; color:white;">
+
−
                        <li>Dr. Ankush Prashar</li>
+
−
                        <li>James Standen</li>
+
−
                        <li>Rachel Chapman</li>
+
−
                    </ul>
+
−
                </div>
+
−
            </div>
+
  
−
<!-- end section-header -->
 
  
−
        </div> <!-- end intro-wrap -->
 
−
    </section> <!-- end s-works -->
 
  
  
  
−
   
 
−
    <!-- clients
 
−
    ================================================== -->
 
−
    <section id="sponsors" class="s-clients">
 
  
−
        <div class="row section-header" data-aos="fade-up">
 
−
            <div class="col-full">
 
−
                <h3 class="subhead">Our Sponsors</h3>
 
−
                <h1 class="display-2">SPONSORS</h1>
 
−
            </div>
 
−
        </div> <!-- end section-header -->
 
  
−
        <div class="row clients-outer" data-aos="fade-up">
 
−
            <div class="col-full">
 
−
                <div class="clients">
 
−
                   
 
−
                    <a href="#sponsors" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/6/65/T--Newcastle--SAgELogo.png/600px-T--Newcastle--SAgELogo.png" /></a>
 
−
                    <a href="https://bbsrc.ukri.org/" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/2/21/T--Newcastle--BBSRCSquare.png/600px-T--Newcastle--BBSRCSquare.png"></a>
 
−
                    <a href="https://wellcome.ac.uk/home" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/b/be/T--Newcastle--Wellcomelogo.png/600px-T--Newcastle--Wellcomelogo.png"/></a>
 
−
                    <a href="https://www.idtdna.com/pages" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/1/10/T--Newcastle--IDTLogo.png/600px-T--Newcastle--IDTLogo.png" /></a>
 
−
                    <a href="https://www.ncl.ac.uk/sage/" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/4/42/T--Newcastle--Ibidi.png/600px-T--Newcastle--Ibidi.png" /></a>
 
−
                    <a href="http://opentrons.com/" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/9/9a/T--Newcastle--OpenTronsLogoPNG.png/600px-T--Newcastle--OpenTronsLogoPNG.png" /></a>
 
−
                    <a href="https://seedcell.co.uk/" title="" class="clients__slide"><img src="https://static.igem.org/mediawiki/2018/thumb/8/86/T--Newcastle--SeedCellSquare2.png/600px-T--Newcastle--SeedCellSquare2.png" /></a>
 
−
                   
 
  
−
                   
 
−
                </div> <!-- end clients -->
 
−
            </div> <!-- end col-full -->
 
−
        </div> <!-- end clients-outer -->
 
  
−
        <div class="row clients-testimonials" data-aos="fade-up">
+
<button class="collapsible">Click for References & Attributions</button>
−
            <div class="col-full">
+
<div class="content">
−
                <div class="testimonials">
+
              <div class="row about-desc" data-aos="fade-up">
 +
                <div class="col-full">
  
−
                    <div class="testimonials__slide">
+
<p class="about-para"><font size="2"><strong>Attributions: Umar Farooq
 +
</strong><font></p>
  
−
                        <p>The iGEM Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition,
 
−
                        and the development of an open community and collaboration. This is done by fostering an open, cooperative community and friendly competition.</p>
 
  
−
                        <img src="https://static.igem.org/mediawiki/2018/thumb/b/bb/T--Newcastle--iGEMGrey.png/600px-T--Newcastle--iGEMGrey.png" alt="Author image" class="testimonials__avatar">
 
−
                        <div class="testimonials__info">
 
−
                            <span class="testimonials__name"></span>
 
−
                            <span class="testimonials__pos"></span>
 
−
                        </div>
 
  
−
                    </div>
 
  
−
                    <div class="testimonials__slide">
 
−
                       
 
−
                        <p>iGEMers are building a better world by solving problems with the help of synthetic biology.
 
−
                        We inspire responsible innovation through our efforts in biosafety, biosecurity and public outreach.</p>
 
  
−
                        <img src="https://static.igem.org/mediawiki/2018/thumb/b/bb/T--Newcastle--iGEMGrey.png/600px-T--Newcastle--iGEMGrey.png" alt="Author image" class="testimonials__avatar">
 
−
                        <div class="testimonials__info">
 
−
                            <span class="testimonials__name"></span>
 
−
                            <span class="testimonials__pos"></span>
 
−
                        </div>
 
  
−
                    </div>
 
  
−
                    <div class="testimonials__slide">
 
−
                       
 
−
                        <p> This global network is leading the field, taking what they learned in the competition and expanding it to continue to build a better world.</p>
 
−
 
−
                        <img src="https://static.igem.org/mediawiki/2018/thumb/b/bb/T--Newcastle--iGEMGrey.png/600px-T--Newcastle--iGEMGrey.png" alt="Author image" class="testimonials__avatar">
 
−
                        <div class="testimonials__info">
 
−
                            <span class="testimonials__name"></span>
 
−
                            <span class="testimonials__pos"></span>
 
−
                        </div>
 
−
 
−
                    </div>
 
−
 
−
                </div><!-- end testimonials -->
 
−
               
 
−
            </div> <!-- end col-full -->
 
−
        </div> <!-- end client-testimonials -->
 
−
 
−
    </section> <!-- end s-clients -->
 
  
 +
</div>
 +
</section>
  
 
      
 
      
Line 323: Line 160:
 
     <script type="text/javascript" src="https://2018.igem.org/Template:Newcastle/JSmain?
 
     <script type="text/javascript" src="https://2018.igem.org/Template:Newcastle/JSmain?
 
     action=raw&ctype=text/javascript"></script>  
 
     action=raw&ctype=text/javascript"></script>  
 +
 +
    <script>
 +
var coll = document.getElementsByClassName("collapsible");
 +
var i;
 +
 +
for (i = 0; i < coll.length; i++) {
 +
  coll[i].addEventListener("click", function() {
 +
    this.classList.toggle("active");
 +
    var content = this.nextElementSibling;
 +
    if (content.style.maxHeight){
 +
      content.style.maxHeight = null;
 +
    } else {
 +
      content.style.maxHeight = content.scrollHeight + "px";
 +
    }
 +
  });
 +
}
 +
</script>
 
</body>
 
</body>
 
</html>
 
</html>
 
{{Newcastle/footer}}
 
{{Newcastle/footer}}

Latest revision as of 23:24, 17 October 2018

Alternative Roots/Software

Alternative Roots

Software Overview

OpenTrons NH-1

Overview

A significant proportion of the Alternative Roots project was based on software, whether that was for automation of experiments via the Opentrons OT-2 or small-scale plant growth via our NH-1. Both systems were carefully programmed by our team for efficiency and reliability.

Newcastle were fortunate to win an Opentrons OT-2 liquid-handling robot in 2018. The OT-2 is programmed in Python and is equipped with two pipettes capable of pipetting between 1 and 300 µL as well as a temperature module, capable of maintaining temperatures between 0-100 °C. We have created and deposited code that allows OT-2 users to automate small-scale (100 µL) heat-shock transformations of E. coli. The value of this code was demonstrated when it was used to perform a statistical ‘Definitive Screening Design’ screen to examine the impact that transformation buffers have on transformation efficiency. As a result, we identified a new buffer composition with 10-fold improved transformation efficiency. Perhaps more importantly, the combination of the code and the robot resulted in greater reliability than the manual protocol.







References & Attributions

Attributions: Umar Farooq