Alternative Roots/Software

Alternative Roots

Software 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