Difference between revisions of "Team:Newcastle/Software"

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                <h3 class="subhead subhead--dark">NH-1</h3>
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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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                <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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                    <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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                    <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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                    <p style="font-size:100%">As part of our lab work a number of the team members have become familiar with the Opentrons. Which required learning python, the coding language used by the robot. This machine has been very useful in the lab as we have been able to automate the pipetting increasing the accuracy of our experiments and saving time in the labs.</p>
 
  
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                    <p style="font-size:100%">We have 3D printed custom labware which can hold a variety of beakers and tubes through a removable acrylic lid cut to specification. This equipment also doubles up as a cold deck when filled with ice, allowing us to heat shock transform <i>E.coli</i>. There has also been a number of kill curves performed on pseudomonas to identify a suitable anti-biotic which can then be used as our test to identify if our transformations have worked. Gentamycin and Streptomycin being two that were a success.</p>
 
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                    <p style="font-size:100%">The Python script and the protocol can be found here. The code has been done in a way where it can be easily adapted for alternate uses. The code and results can be found here!!!</p>
 
  
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                <p style="font-size:100%">Using the OT-2 and the Peltier thermocycler (TempDeck), a robust a <a href="https://github.com/jbird1223/Newcastle-iGEM/blob/master/OT-2%20Protocol/Transformation.py" class="green">Transformation Buffer</a>(TB) was developed that could be used to rapidly transform Escherichia coli DH5a in a microtitre plate format. This was developed as part of a Biodesign Automation (BDA) workflow that would allow us to optimise TB using a Design of Experiments (DoE) methodology. Our initial automated transformation workflow produced E. <i>coli</i> with a transformation efficiency (TrE) of 1.89 x 10<sup>4</sup> and scoping experiments determined that the 96 well plate format decreases TrE by a factor of 100 (Figure ...) </p>
 
  
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                <p style="font-size:100%">With optimisation of the TB, automated TrE was increased to 2.21 x 10<sup>6</sup>, a 100x increase on the initial workflow (Figure ...). More importantly, it appeared to be highly robust, with every aliquot producing some successful transformants and it was rapid, without need for excessive centrifugation and incubation.</p>
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<p class="about-para"><font size="2"><strong>Attributions: Umar Farooq
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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