Difference between revisions of "Team:Newcastle/Software"

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                         OpenTrons
 
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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 <a href="https://static.igem.org/mediawiki/2018/f/f1/T--Newcastle--SoftwareGuide.pdf" class="white">guide to using the IDE</a> 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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                    <li>Brightness can be varied, for example to simulate a day/night cycle or a gradual sunrise/sunset</li>
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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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                    <h3 class="subhead">Additional Support</h3>
 
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                    <h1 class="display-2 display-2--light">ACKNOWLEDGEMENTS</h1>
 
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                    <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>
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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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                     <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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                    <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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                    <h3 class="h2"style="color:white">Stakeholder Engagement</h3>
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                <h1 class="display-2">References & Attributions</h1>
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                        <li>Professor Chris Tapsell (KWS Seeds)</li>
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                        <li>Richard Ballard (Growing Underground)</li>
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                        <li>Steve Dring (Growing Underground)</li>
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                        <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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                    <h3 class="h2"style="color:white">Newcastle University Farms</h3>
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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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                <h3 class="subhead">Our Sponsors</h3>
 
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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>
 
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                    <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>
 
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<p class="about-para"><font size="2"><strong>Attributions: Umar Farooq
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</strong><font></p>
  
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                        <p>The iGEM Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition,
 
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                        and the development of an open community and collaboration. This is done by fostering an open, cooperative community and friendly competition.</p>
 
  
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                        <p>iGEMers are building a better world by solving problems with the help of synthetic biology.
 
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                        We inspire responsible innovation through our efforts in biosafety, biosecurity and public outreach.</p>
 
  
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                        <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> 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>
 
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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