Gitlab repository: https://gitlab.igem.org/2023/software-tools/unsw-australia
We have implemented a collaborative system between an xArm6 Sample Handler and an OT2 (OpenTron Robot 2) Liquid Handler. The main crux of the system is a Jupyter Notebook, coded in python, from which commands for both the OT2 and xArm6 are delivered. At a base level, using pre-prepared solutions, the OT2 repeatedly generates experimental assays at a level of precision sufficient for the scope of our experiment. Subsequently, xArm6 removes the assay plate, places it into a plate reader, or wherever necessary for subsequent photometric analysis.
Specifically, the OT2 has an associated Jupyter notebook page, with the ability to contain scripts, folders, and Jupyter notebook files. In this space, the xArm-Python-SDK API functionality code from the xArm-Python-SDK GitHub (https://github.com/xArm-Developer/xArm-Python-SDK) is stored in a folder. This provides the needed functionality to run python programs adapted to xArm6 control. Any xArm6 program can be run by uploading the file to the examples folder in the xArm master folder and running the command in the master integrator file as described in the README on github.
On this Jupyter notebook hub, a Jupyter notebook file acts as a centre for integration, where python code for controlling the OT2 and the xArm6 is combined. Our system works together with the xArm-Python-SDK API to send commands from the OT2 via a control computer to the xArm6. We utilised this system for a urease and carbonic anhydrase assay. However, thanks to its modular nature, any protocol can be configured on it.
Our system underwent testing through a run of the urease assay, wherein the reactants urease enzyme solution, urea, water and phenol red indicator were placed into reservoirs in the OT2. The assay steps were followed using the Python protocol, creating 8 replicates for three concentrations (control, low urease, high urease). The xArm6 then moved the plate to the platereader, where the resulting visual absorbance was measured.
As this assay had not yet been validated by wetlab experimentation, after running, an imprecision with the adapted protocol we chose to use was discovered and more phenol red was added after assay completion.
Figure 2: Visual results of urease test assay.
Plate reader results confirm the visual inspection, displaying higher absorbance at higher urease concentration as shown in figure 3. A student-t test on the control and high urease sample produced a significant P-value of 4.91E-06.
Figure 3: Absorbency as measured by plate reader averaged across 8 replicates.
Prior to any run with potentially hazardous materials, countless dry/water runs were performed, confirming the accuracy of the xArm6 and OT2, and confirming the steps as what is intended.