Difference between revisions of "Team:Newcastle/Software"

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   <title>Alternative Roots/Attributions</title>
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   <title>Alternative Roots/Software</title>
 
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                   Software
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                   Software Overview
 
                    
 
                    
 
                    
 
                    
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                         Attributions
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                         OpenTrons
 
                     </a>
 
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                     <a onclick="location.href='https://2018.igem.org/Team:Newcastle/Software/NH1'" class="smoothscroll btn btn--stroke">
                        Acknowledgements
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                         NH-1
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                         Sponsors
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                <h3 class="subhead subhead--dark">NH-1</h3>
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                 <h1 class="display-1 display-1--light">Software</h1>
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                 <h1 class="display-1">Overview</h1>
 
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                <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>
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                <ul style="list-style-type:circle;display:grid;text-align:left;">
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                    <li>Solid colours across the system</li>
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                    <li>Cyclically varying colours (rainbow) in the system</li>
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                    <li>Linear gradients of colours across the system</li>
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                    <li>Colours can be defined by RGB, HSV values or HTML standard</li>
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                    <li>Brightness can be varied, for example to simulate a day/night cycle or a gradual sunrise/sunset</li>
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                </ul>
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                <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>
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    <!-- works
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    <section id='Acknowledgements' class="s-works">
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        <div class="intro-wrap">
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                 <div class="col-full">
 
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                    <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>
 
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                     <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">
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                </div>
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                <div class="service-text">
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                    <h3 class="h2"style="color:white">Induction Talks</h3>
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                    <ul style="list-style-type:circle;overflow:visible; color:white;">
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                        <li>Dr. Jem Stach</li>
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                        <li>Dr. Jon Marles-Wright</li>
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                        <li>Dr. Thomas Howard</li>
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                        <li>Dr. Kenneth Taylor</li>
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                        <li>Dr. Harold Fellermann</li>
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                        <li>Dr. Martyn Dade-Robertson</li>
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                        <li>Professor Rachel Armstrong</li>
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                        <li>Professor Phillip Wright</li>
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                        <li>Dr. Dana Ofiteru</li>
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                        <li>Dr. Maxim Kapralov</li>
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                        <li>Dr. Angel Goni-Moreno</li>
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                        <li>Dr. Nicholas Aldred</li>
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                        <li>Dr. Vasilios Andriotis</li>
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                        <li>Dr. Ilke Turkmendag</li>
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                    </ul>
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                </div>
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            </div>
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            <div class="col-block service-item" data-aos="fade-up">
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                     <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>
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                     <i class="icon-paint-brush"></i>
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                </div>
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                <div class="service-text">
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                    <h3 class="h2"style="color:white">Subject Specific Support</h3>
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                    <ul style="list-style-type:circle;overflow:visible; color:white;">
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                        <li>Dr. Alice Banks (Chemotaxis)</li>
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                        <li>Dr. Maria Del Carmen Montero-Calasanz (Endophyte Development)</li>
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                        <li>Bradley Brown (Wiki Development/Community Modelling))</li>
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                        <li>Josh Isaac (Biosynthesis Pathway Modelling)</li>
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                        <li>Aidan Clamp (Biosynthesis Pathway Modelling)</li>
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                        <li>Connor Barker (Biosynthesis Pathway Modelling)</li>
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                        <li>Dr. Martyn Dade-Robertson (Human Practices)</li>
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                        <li>Professor Rachel Armstrong (Human Practices)</li>
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                    </ul>
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                 </div>
 
                 </div>
 
             </div>
 
             </div>
  
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<section id='team' class="s-services">
  
  
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                </div>
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<br>
                <div class="service-text">
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<br>
                    <h3 class="h2"style="color:white">Stakeholder Engagement</h3>
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<br>
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<h3 class="subhead"></h3>
                    <ul style="list-style-type:circle;overflow:visible; color:white;">
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                <h1 class="display-2">References & Attributions</h1>
                        <li>Professor Chris Tapsell (KWS Seeds)</li>
+
                        <li>Richard Ballard (Growing Underground)</li>
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                        <li>Steve Dring (Growing Underground)</li>
+
                        <li>Tom Webster (GrowUp Urban Farms)</li>
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                        <li>Nicola Cowell (Food Nation)</li>
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                        <li>Paul Brown (GrowModule 365)</li>
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                        <li>Clive Goodwin (Victoria Tunnels)</li>
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                    </ul>
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                </div>
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             </div>
 
             </div>
  
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                    <h3 class="h2"style="color:white">Newcastle University Farms</h3>
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                    <!--<img src="">-->
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                    <ul style="list-style-type:circle;overflow:visible; color:white;">
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                        <li>Dr. Ankush Prashar</li>
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                        <li>James Standen</li>
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                        <li>Rachel Chapman</li>
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                    </ul>
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                </div>
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            </div>
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                <h3 class="subhead">Our Sponsors</h3>
 
                <h1 class="display-2">SPONSORS</h1>
 
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                    <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>
 
                   
 
  
                   
 
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                    <div class="testimonials__slide">
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<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">
 
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                        <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">
 
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                            <span class="testimonials__name"></span>
 
                            <span class="testimonials__pos"></span>
 
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                    <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">
 
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Latest revision as of 23:24, 17 October 2018

Alternative Roots/Software

Alternative Roots

Software Overview

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