Team:Newcastle/Software
OpenTrons
Software Overview
Opentrons
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.
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 E.coli. 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.
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!!!
Transformation Protocol
Using the OT-2 and the Peltier thermocycler (TempDeck), a robust a Transformation Buffer(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. coli with a transformation efficiency (TrE) of 1.89 x 104 and scoping experiments determined that the 96 well plate format decreases TrE by a factor of 100 (Figure ...)
With optimisation of the TB, automated TrE was increased to 2.21 x 106, 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.
Figure 1.0; Falcon tube rack.
Figure 1.1; 3D printed rack/ice holder.